DEVELOPMENT OF HIGHLY EFFICIENT TANDEM PEROVSKITE/POLYMER SOLAR CELLS [COMPLETED]
Principal Investigators: Qiquan Qiao, Syracuse University (formerly South Dakota State University); Hamdy Mahmoud Zeyada and Nasser El-Ghamaz, University of Damietta
Overview: Multi-junction (tandem) solar cells (TSCs) consisting of sandwiching two or more different light absorbers with contrasting bandgap. TSC’s have higher potential of obtaining much higher power conversation efficiencies due to higher photo absorption characteristics. Perovskite solar cells (PSCs) are supreme light absorbers for TSCs due to their tunable band gaps, high PCE surpassing 25%, and uncomplicated fabrication techniques. PSCs with high PCEs are typically fabricated via a low temperature solution processed spin coating method, which are easy to combine with many other types of solar cells like silicon (Si), copper indium gallium selenide (CIGS), narrow band gap PSCs, dye-sensitized, organic, and quantum dot solar cells. tandem cell designs utilizing a wide bandgap “top” cell and low bandgap “bottom” cell, have been widely adopted as a matter of fact, perovskite TSCs have stimulated enormous scientific and industrial interest since their first development in 2014. Significant progress has been made on the development of perovskite TSCs both in the research laboratories and industrial companies.
In the current work we developed both wide bandgap 1.78 ev PSCs with efficiency exceeding 17%, as well as back contact low band gap Pb-Sn PSC’s with a record voltage of 0.85 V and efficiencies exceeding 19%. we expect that the findings of defects assessments and performance improvement strategies in this work can provide proper guidelines to enable high-efficiency perovskites and realize high-efficiency tandem cells.
Year 1 Project Progress Summary (Submitted June 2017)
There is increasing global interest in alternative forms of energy, and sunlight is a particularly promising clean and readily available source compared with conventional fossil fuels. Perovskite solar cell is a new entry in the line of next generation solar cells, with rapidly increasing performance getting close to those of silicon solar cells. In the last year, we have been working on improving single junction perovskite solar cell efficiencies using new materials. Use of different doped hole transport layers has been effective but possess disadvantages such as complex processing, corrosive additives, processing in ambient air for efficient hole doping.
In this work, we report a solution processed polymer as an alternative hole transport layer and achieved an efficiency of ~ 11.6% which was comparable to that obtained from other commonly used materials. Another advantages of using polymer as hole transport layer is the processing inside N2 filled glove box compared to other materials that requires processing in ambient humid air and doped with additives mixed in corrosive solvent. This can cause degradation to perovskite layer underneath. This result has been published as a joint publication between Dr. Qiao at SDSU in USA and Dr. Zeyada at Damietta University in Egypt.
Year 2 Project Progress Summary (Submitted July 2018)
We have demonstrated that the incorporation of various additives including BMImI, LiI and LiTFSI into the PbI2 precursor solution led to enhancement in stability of CH3NH3PbI3 perovskite solar cells along with higher efficiency. The new additives BMImI, LiI and LiTFSI incorporated CH3NH3PbI3 perovskite solar cells exhibited 57%, 60%, 91% decrease respectively after exposure to air for 70 days versus 93% decrease for pristine cell after only 24 days. The lithium salt additives LiI and LiTFSI led to higher stability attributed to their hygroscopic nature that enables them to serve as desiccants, thus preventing moisture degradation to perovskite. Further, higher stability in BMImI case can be attributed to the presence of active [N] heteroatom of the heterocyclic imidazolium group that enables prevention of formation of free radicals upon exposure to light and heat. In addition, incorporation of additives helped achieve high efficiency perovskite solar cells with efficiency of 18.0%, 17.01% and 15.6% for BMImI, LiI and LiTFSI respectively versus 11.3% for pristine perovskite. Adding these additives resulted in formation of perovskites with larger grain size and higher crystallinity with reduced PbI2 residue. This work is expected to open door to further investigations of other additives as stabilizers towards achieving stable perovskites as stability is the major hurdle for commercialization of this technology.
Incorporation of these additives led to formation of perovskites with larger grain size and higher crystallinity with reduced PbI2 residue as indicated by x-ray diffraction (XRD) and atomic force microscopy (AFM) results. Kelvin Probe Force Microscopy (KPFM) and current sensing (CS) - AFM are in good agreement with external quantum efficiency (EQE) measurements and proved the great enhancement in short circuit current density (Jsc) as a result of doping. Transient photovoltage measurement results exhibited longer charge carrier lifetimes for the additives incorporated perovskites than those without additives, thus improving the fill factor (FF) and open circuit voltage (Voc). In addition to the improved efficiency, the incorporation of these additives led to higher stability of the CH3NH3PbI3 perovskite solar cells. The new additives BMImI, LiI and LiTFSI incorporated CH3NH3PbI3 perovskite solar cells exhibited a reduced degradation at 57%, 60%, 91% decrease in performance respectively after exposure to air for 70 days compared to a 93% decrease for the pristine cell after only 24 days. The lithium salt additives can serve as desiccants to absorb moisture preventing perovskite degradation. Further, the BMImI additive can prevent formation of free radicals in perovskites upon exposure to light and heat.
Year 3 Project Progress Summary (Submitted May 2019)
We have developed wide and low-bandgap perovskite to fabricate all perovskite tandem devices. Four cation perovskites with a bandgap of 1.75 eV has been used for wide-bandgap perovskite devices. Whereas, perovskite with three cations having a bandgap of 1.25 eV has been developed for the low-bandgap devices. Both the structures contain unique perovskite composition to achieve better performance and stability. Highest efficiency that we achieved for wide-bandgap perovskite is 16.90%, which was attained optimizing the process conditions.
On the other hand, the highest efficiency achieved for low-bandgap perovskite is 12%. We observed that the performance of the devices is much affected by the charge transport layer. We also confirmed that this Tin (Sn) containing low-bandgap perovskite is very sensitive to glove box environment and the process conditions.
Year 4 Project Progress Summary (Submitted June 2021)
This work demonstrates an efficient strategy of combining cation management and post-growth technique to passivate GB defects in wide-bandgap PSCs to achieve excellent device performance. By introducing Rb to triple cation perovskite, a novel quadruple-cation 1.78 eV wide-bandgap perovskite layer is formed. In addition, a SG technique using GAI was applied which produces a champion device efficiency of 17.71%. In-depth analysis of GB defects correlating to device performance of the perovskite films was performed using KPFM and nanoscale charge carrier dynamics mappings to visualize the defect passivation achieved. Our findings indicate that positively charged defects (i.e., halide vacancies) have a large effect on the performance of the wide bandgap PSCs, with a severe loss in FF and Voc. Such trap assisted defects can be partially mitigated by cation management and further significantly minimized by SG treatment. In addition, SG using GAI can greatly reduce unreacted PbX2 precipitates from the surface of the film, converting them to the perovskite phase to form a more compositionally uniform and smooth film morphology. We expect that the findings of defects assessments in this work can provide proper guidelines to enable high-efficiency perovskites and realize high-efficiency tandem cells.
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DEVELOPMENT OF NEXT GENERATION ARYTHIAZOLES FOR COMBATING METHICILLIN & VANCOMYCIN-RESISTANT STAPHYLOCOCCUS AUREUS [COMPLETED]
Principal Investigators: Mohamed Seleem, Purdue University; Ashraf Bayoumi, Al Azhar University
Overview: The increasing emergence of antibiotic-resistant bacterial pathogens calls for additional urgency in the development of new antibacterial candidates. The aim of this project is to develop a second-generation antibiotic (phenylthiazole derivatives) with enhanced pharmacokinetic profiles for treatment of drug resistant pathogens.
Several compounds have been synthesized and tested and their toxicity and efficacy were evaluated. In addition, their mechanism of action was explored. The newly synthesized compounds were more potent against drug resist pathogens, including MRSA and were less toxic. In addition, we were able to improve the pharmacokinetic profiles of the new compounds.
Year 1 Project Progress Summary (Submitted June 2017)
The aim of this project is to synthesis new series of antimicrobial compounds to target drug resistant pathogens, such as methicillin-resistant and vancomycin-resistant Staphylococcus aureus (MRSA & VRSA). We successfully synthesized new potent analogs with the objectives of improving the metabolic stability of the lead compound and exploring the new analogues’ structure-activity-relationship against MRSA. The new compounds exhibit enhanced stability to hepatic metabolism compared to the parent compound. We are moving forward with the project to the next stage of optimization and animal testing in the next year.
Year 2 Project Progress Summary (Submitted July 2018)
The aim of this reporting period is to synthesis more stable and more antimicrobial compounds to target multi-drug resistant pathogens such as methicillin-resistant and vancomycin-resistant Staphylococcus aureus (MRSA & VRSA). We successfully synthesized more potent compounds with the objectives of improving metabolic stability of the lead compound that was developed last year and exploring the new analogues’ structure-activity-relationship against MRSA. The new compounds exhibit more potent activity and enhanced stability to hepatic metabolism compared to the parent compound. We are moving forward with the project to the next stage of final optimization and modification.
Year 3 Project Progress Summary (Submitted May 2019)
The aim of this reporting period is to synthesis orally available antimicrobial compounds to target multi-drug resistant pathogens. We successfully synthesized oral available compounds active against methicillin-resistant and vancomycin-resistant Staphylococcus aureus (MRSA & VRSA). The new compounds exhibit more potent activity and enhanced stability to hepatic metabolism compared to the parent compound. We are moving forward with the project to the next stage of final optimization, modification and testing in animal models.
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AN ENVIRONMENTAL FRIENDLY SYSTEMATIC STRATEGY FOR ELIMINATING RED TIDE ALGAL CELLS AND TOXINS FROM MARINE AND FRESHWATER SOURCES [COMPLETED]
Principal Investigators: Dionysious Dionysiou, University of Cincinnati; Said M. El-Sheikh, Central Metallurgical Research and Development Institute
Overview: The increase of harmful algal blooms (HABs) by cyanobacteria in estuaries and freshwater aquatic systems is a major global problem. Both United States and Egypt face environmental and public health problems associated with red tides and HABs. Egypt is coasted by the Mediterranean Sea and has many estuaries, harbors, and semi-enclosed basins, which are ideal for massive algal growth. Such geographical characteristics determine that Egypt, especially around the Alexandria coast and Nile Delta, is prone to recurrent outbreaks of red tides. Since the first massive outbreak of red tide was recorded in 1958 in Alexandria, this problem has been recurring in this area, with even increasing frequency and severance in the last decade. The growing prevalence of red tides presents an ongoing threat to human health and ecosystems, and impacts the local economy from losses to tourism, aquaculture, and fisheries. Conventional water treatment processes are not adequate for the complete removal of algal cells and related toxic compounds. It is necessary to develop more robust technologies to provide cost-effective and sustainable solutions to address the problem of harmful algal blooms. Therefore, our research focuses on developing novel coagulants to remove intact harmful algal cells in the early steps of the treatment process and a solar-driven photocatalyst to degrade cyanotoxins completely.
The outcome of the research is reflected in the following aspects:
(1) Novel composite coagulants consisting of clay, magnetic particles, and chitosan were developed and successfully applied to remove both freshwater and marine algal cells. The application of these natural and bio-friendly materials could potentially lower the life cycle impacts of current environmental remediation and water treatment processes.
(2) Bi2WO6-based and TiO2-based composite photocatalysts with novel structures were synthesized and demonstrated remarkable performance in removing cyanotoxins and other contaminants of emerging concern. The catalytic process is highly efficient and could be driven by solar light. These findings contribute to systematically addressing the HAB-related environmental issues and play a role in the development of technologies that produce better water quality for other applications.
(3) The project directly provided training opportunities to graduate students and early career scientists on a wide range of materials processing and characterization techniques, water treatment process development, analytical skills, and the development of scientific publications.
(4) The project incorporated advanced topics on drinking water quality, application of functional nanomaterials in environmental remediation, and development of sustainable water treatment technologies into undergraduate and graduate courses at the University of Cincinnati (UC).
(5) The research results, which could guide the development of new water treatment processes with renewable energy, have been presented and discussed at several national and international conferences.
(6) The scientific collaboration between UC and CMRDI of Egypt has encouraged an innovative and inclusive culture of research and practice. Several lectures about water treatment technologies for the removal of cyanotoxins and other contaminants of emerging concern from source waters were delivered at various Egyptian universities, research centers, and professional societies. Connections created with several other institutions in Egypt were very instrumental and will lead to potential collaborations on related topics in the future.
(7) Findings and experience gained from the U.S.-Egypt collaboration project have inspired the researchers at UC to further develop sustainable technologies for phosphorus removal and algae control. A new project, which builds on the current work, has been awarded from another funding source.
Year 1 Project Progress Summary (Submitted June 2017)
In this project, we aimed at the development of novel nanomaterials to systematically address the problems caused by algal cells and cyanotoxins. We expected to develop an environmental friendly coagulant to separate algal cells from water sources and a photocatalyst driven by solar light to degrade cyanotoxins. The results obtained here will facilitate the understanding and development of bismuth-based photocatalysts. They will also have large potential in designing other sustainable solar-driven technologies for the treatment of water contaminated with cyanotoxins or other emerging contaminants of concerns.
In addition, the project has made a significant impact on human resource development. It provided an opportunity for the graduate students involved in this work to be trained with advanced materials processing and characterization techniques as well as analytical skills. Special concepts and practical examples about the application of nanomaterials in environmental remediation were part of Dr. Dionysiou’s undergraduate and graduate dual level courses at the University of Cincinnati.
The project also promoted the development of related field in Egypt through our collaborative efforts. Dr. Dionysiou has organized several keynote lectures and seminars at the Egyptian institution and is also seeking opportunity to expand our work with new collaborators in Egypt.
Year 2 Project Progress Summary (Submitted July 2018)
In this project, we aimed at the development of novel nanomaterials to systematically address the problems caused by algal cells and cyanotoxins. We expected to develop an environmental friendly coagulant to separate algal cells from water sources and a photocatalyst driven by solar light to degrade cyanotoxins. The results obtained here will facilitate the understanding and development of bismuth-based photocatalysts. They will also show great potential in designing other sustainable solar-driven technologies for the treatment of water contaminated with cyanotoxins or other emerging contaminants of concerns.
In addition, the project has made a significant impact on human resource development. It provided an opportunity for the graduate students involved in this work to be trained with advanced materials processing and characterization techniques as well as analytical skills. Special concepts and practical examples about the application of nanomaterials in environmental remediation were part of Dr. Dionysiou’s undergraduate and graduate dual level courses at the University of Cincinnati.
The project also promoted the development of related field in Egypt through our collaborative efforts. Dr. Dionysiou has organized several keynote lectures and seminars at the Egyptian institution and is also seeking opportunity to expand our work with new collaborators in Egypt.
Year 3 Project Progress Summary (Submitted June 2019)
The increase of harmful algal blooms by cyanobacteria (CyanoHABs) in estuaries and freshwater aquatic systems around the world is a major global problem. The presence of high concentrations of harmful cyanotoxins in aquatic systems that could serve as sources of drinking water supply poses a significant threat to human and environmental health. Conventional water treatment process are not effective for the complete removal of these highly toxic compounds. In this research, we aimed to develop an environmental friendly coagulant to separate algal cells from water sources and a photocatalyst driven by solar light to degrade cyanotoxins.
Three specific objectives were fulfilled in the reporting period (1) Synthesize, characterize, and optimize triple component coagulants which are composed of clays, chitosan, and magnetite to remove algae cells; (2) Synthesize and characterize solar light-driven Bi2WO6-based photocatalysts for the degradation of cyanotoxins and other emerging contaminants; (3) Explore the influence of water parameters, kinetics, reaction pathways in the degradation process.
This work makes significant contribution to the field since this is one of the few studies that use nanotechnology to address the issues of HABs systemically. Novel approaches to synthesize Bi2WO6-based composite photocatalysts with different structures are being studied. The photocatalysts developed in this study are stable, cost effective, and easy to access. In addition, this technology is considered a green and sustainable alternative since the system is capable to operate under visible light or solar irradiation.
The research activities directly provided training opportunities to graduate students and junior scientists on a wide range of analytical and nanomaterials characterization techniques. The project also advanced integration of the latest topics about drinking water quality and treatment technology into undergraduate and graduate taught courses at UC. Collaborative research activities and training were also promoted between UC and CMRDI of Egypt. The knowledge obtained from these research activities were presented and discussed in national or global conferences, which served as a guide to the development of new water treatment processes using renewable energy.
Year 4 Project Progress Summary (Submitted May 2020)
Both the United States and Egypt experience environmental and public health problems associated with red tides and harmful algal blooms (HABs). These problems are encountered both in coastal areas and freshwater aquatic systems. Considering the poor removal efficiency of algae cells and toxins by conventional water treatment processes, and limited safety precaution of negative impacts on public health, it is necessary to develop more robust technologies to provide cost-effective and sustainable solutions to address the problem of harmful algal blooms. Therefore. The aims of our research focus on the development of novel physical methods to remove intact cyanobacteria in the early steps of the treatment process as well as a solar-driven photocatalyst to completely degrade cyanotoxins.
The significance of the research is reflected by the following outcomes: (1) The study of clay-based coagulants has been successfully applied to remove HAB cells. Bi2WO6-based composite photocatalysts with novel structure also showed high efficiency for removing cyanotoxins and emerging contaminants. These findings not only have great potential for systematically addressing the problem of HABs, but also play a role in the development of technologies that produce better water quality for other applications; (2) The project directly provided training opportunities to graduate students and junior scientists on a wide range of materials processing and characterization techniques, water treatment process development, analytical skills, and development of scientific publications; (3) the project incorporated advanced topics on drinking water quality, application of functional materials in environmental remediation, and development of sustainable water treatment technologies into undergraduate and graduate courses at the University of Cincinnati (UC); (4) the research results, which serve as a guide to the development of new water treatment processes with renewable energy, have been presented and discussed at both national and global conferences; 5) The scientific collaboration between UC and CMRDI of Egypt has encouraged an innovative and inclusive culture of research and practice. Many lectures about water treatment for removal of cyanotoxins and other contaminants of emerging concerns from source waters were delivered in various Egyptian universities, research centers, and professional societies. Connections created with several other institutions of Egypt were very instrumental and will lead to potential collaborations on related topics in the future.
Year 5 Project Progress Summary (Submitted June 2021)
The impacts of harmful algal blooms (HABs) on human health, tourism, fisheries, and ecosystems have increased in recent decades. Control of source water quality and optimizing treatment operations are considered equally important to mitigate the risk of cyanobacterial toxins in drinking water. Reducing external nutrient loads is fundamental to sustainably restore lakes degraded by eutrophication. White at the same time, reducing internal loads by in-lake engineering or chemical treatments is also indispensable to provide faster improvements in water bodies. Both the United States and Egypt experience environmental and public health problems associated with red tides and HABs. Optimizing existing water treatment systems or upgrading with alternative treatment processes are implemented to meet water quality goals. However, changing climate patterns have led to the frequent reoccurrence of extreme events like HABs. Besides, as future regulations become more stringent and comprehensive, the task to meet treatment goals will become more challenging and costly. It is necessary to develop more robust technologies to provide cost-effective and sustainable solutions to address the problem of HABs. Therefore, our research aimed at developing novel physical methods to remove algal cell as well as solar-driven photocatalytic processes to completely degrade cyanotoxins.
Through the project, we successfully developed clay-chitosan based coagulants to remove algal cells. Due to their natural occurrence and abundance, clays and related minerals are commonly considered as environmentally friendly and inexpensive. Chitosan is generally produced from crustacean shell waste of seafood and fishing industries. The application of these natural and biofriendly materials could potentially lower the life cycle impacts of environmental remediation and water treatment processes. In addition, we also fabricated novel metal oxide-based photocatalysts to remove cyanotoxins and emerging contaminants. The catalytic process is highly efficient and can be driven by solar light. These findings not only have great potential for systematically addressing the problem of HABs, but also play a role in the development of technologies that produce better water quality for other applications. Moreover, the project directly provided training opportunities to graduate students and junior scientists of both sides on a wide range of materials processing and characterization techniques, analytical skills, and development of scientific publications. The project also benefited the development of undergraduate and graduate courses at the University of Cincinnati. Advanced topics on drinking water quality, application of functional materials in environmental remediation, and development of sustainable water treatment technologies were discussed in the courses.
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EPIGENETIC CHARACTERIZATION OF PREDICTORS OF CISPLATIN CHEMORESISTANCE IN MUSCLE INVASIVE BLADDER CANCER [COMPLETED]
Principal Investigator: Jayoung Kim, Cedars-Sinai Medical Center
Overview: Bladder cancer often recurs following chemotherapy, resulting in poor survival rate. Clinopathological biomarkers that indicate response to chemotherapy and probable disease course would allow better assessment of treatment strategies for individual patients. The goals of this proposed study are to investigate the role of epigenetic reprogramming in aggressive bladder cancer that indicate poor chemoresponse and to assess potential mechanism for re-sensitizing the non-responsive bladder cancer to chemotherapy. Our study demonstrated a novel mechanistic link of the epigenetic perturbation of metabolism-related genes with cancer metabolism in aggressive bladder cancer. These findings suggested potential predictive biomarkers in re-sensitizing bladder cancer to chemotherapy and personalizing therapy.
Year 1 Project Progress Summary (Submitted June 2017)
In Egypt, bladder cancer (BC) is the most common cancer, and a major burden on the nation’s public health care system and economics. Owing to the prevalence of Schistosomiasis, Egypt has the highest incidence of Squamous cell carcinoma. However, novel biomarkers for early detection and prognosis of BC remain unmet needs. In this proposed study, we will determine that epigenetically regulated metabolic reprogramming associated with BC, and that expression of two specific proteins predicts the development of drug resistance of BC patients.
Our research performance over the past year has been outstanding. During this funding year, two PIs worked jointly and independently within the proposed research framework. We were able to complete regulatory documentation in order to initiate our proposed research and optimized experimental protocols and the necessary pipeline for data analysis. In this 1st year of funding period, our tissue micro-array slides were constructed and tested for protocol optimization of tissue and computational analysis. This has been a major step that has allowed us to facilitate the collaboration between two internationally prominent bladder cancer research teams, involving both Mansoura University (Mansoura, Egypt) and Cedars-Sinai Medical Center (Los Angeles, CA). Both PIs have had substantial one-on-one conversations several times per month and are in near-constant contact via email, telephone, and Skype. We also had, and will continue to have, close communication with other senior investigators within the research program through many other routes, including joint webinar series.
Year 2 Project Progress Summary (Submitted July 2018)
Alterations in DNA methylation are important epigenetic markers in bladder cancer. We believe that these epigenome modifications may be what drive the mechanisms of aggressive chemo-resistant bladder cancer. Clinicopathological biomarkers that can indicate chemotherapeutic resistance are critical for better assessing treatment strategies for individual patients. Thus, in this study, we aimed to determine whether DNA methylation of certain metabolic enzymes is significantly altered in cisplatin-resistant bladder cancer cells. In this funding period, our study was successfully able to demonstrate a novel mechanistic link of the epigenetic perturbation of certain genes with cancer metabolism in cisplatin-resistant bladder cancer cells. These exciting findings suggest potential predictive biomarkers in re-sensitizing bladder cancer to chemotherapy and personalizing therapy.
Year 3 Project Progress Summary (Submitted June 2019)
Rationale: Alterations in DNA methylation are important epigenetic markers in bladder cancer. These epigenome modifications may be what drive the mechanisms of aggressive chemo-resistant bladder cancer. Clinicopathological biomarkers that can indicate chemotherapeutic resistance are critical for better assessing treatment strategies for individual patients. Thus, in this study, we aimed to determine whether DNA methylation of certain metabolic enzymes is significantly altered in cisplatin-resistant bladder cancer (BC) cells.
Methods: To characterize the CpG methylation and nucleosome accessibility in cisplatin-resistant BC cells, the Illumina Infinium HM450 DNA methylation assay was performed. Perturbed gene expression was associated with cisplatin resistance, and the biological roles of SAT1 (spermidine/spermine N1-acetyltransferase) and ASS1 (arginosuccinnate synthase 1) were further studied by qRT-PCR analysis and various cell biology assays including western blot analysis.
Results: Genes for the amino acid and polyamine metabolism catalysts, ASS1 and SAT1, respectively, were found to be vastly hyper-methylated, resulting in greatly downregulated expression. ASS1 expression is of particular interest because prior studies have demonstrated its potential association with the stage and recurrence of BC. With regard to chemoresistance, we found that aberrant expression, or induced stimulation, of SAT1 restored cisplatin sensitivity in the cell culture system. We also found that the addition of exogenous arginine deiminase through administration of ADI-PEG 20 (pegylated arginine deiminase) increased ASS1 expression and enhanced cisplatin’s apoptotic effects.
Conclusions: Our study demonstrates a novel mechanistic link of the epigenetic perturbation of SAT1 and ASS1 with cancer metabolism in cisplatin-resistant bladder cancer cells. These findings suggest potential utility of SAT1 and ASS1 as predictive biomarkers in re-sensitizing bladder cancer to chemotherapy and personalizing therapy.
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AN INTEGRATED APPROACH FOR A BETTER UNDERSTANDING OF THE HYDROLOGIC SETTING, LONGEVITY, AND OPTIMUM UTILIZATION OF THE NUBIAN SANDSTONE AQUIFER SYSTEM IN EGYPT [COMPLETED]
Principal Investigators: Mohamed Sultan, Western Michigan University; Baher El Kalioubi, Ain Shams University
Overview: Researchers from Ain Shams University and Western Michigan University worked closely together to unravel the secrets of the fresh water underlying the vast Western Desert of Egypt. Up till now everyone believed that all of these waters came from rainfall tens and hundreds of thousands of years ago when the climate was wetter and the deserts were green and none of these waters was from precipitation at present times. Using state-of-the-art satellite data, namely the Gravity and Recovery and Climate Experiment (GRACE), the Egyptian-US team came to a different conclusion and published their findings in the Science of the Total Environment.
They concluded that in wet periods, more rain falls in neighboring Sudan and seeps into the ground or makes it to the River Nile and gets impounded in Lake Nasser. Despite the fact that Egypt remains dry over these wet periods, the country’s aquifer (Nubian Sandstone Aquifer System) receives increments of modern recharge from the south and from excess surface waters in Lake Nasser that also seeps into the ground. These waters travel very fast for hundreds of kilometers under the ground through interconnected networks of fractures, faults, and large openings in carbonate rocks (karst topography).
The last wet period was in years 2013, 2014, 2015, and 2016 where there was excess precipitation over the source areas in Sudan and Chad, and this is when Egypt received some 8 billion cubic meter of water for each of these four years. Such influx could compensate at least in part, for the losses due to the damming of the River Nile water by the Renaissance Dam.
Year 1 Project Progress Summary (Submitted June 2017)
Researchers from Western Michigan University, led by Dr. Mohamed Sultan and from Ain Shams University, led by Dr. Baher El Kalioubi, are applying an integrated approach that utilizes state-of-the-art satellite (Gravity Recovery and Climate Experiment [GRACE]) that measures temporal variations in water content, hereafter referred to as Total Water Storage (TWS), geophysical, field, and geochemical data together with hydrological modelling to develop a better understanding of the architecture, longevity, and optimum utilization of the Nubian Sandstone Aquifer System (NSAS) and its response in wet and dry periods. The aquifer underlies extensive areas of the deserts of Egypt, Sudan, Libya, and Chad.
Specifically, the research team is addressing the following questions: (1) Where are, and what is the nature of the observed temporal variations in GRACE-derived TWS over the NSAS (2) Is the NSAS being depleted If it is, which part(s) are being depleted and what are the depletion rates (3) What is the nature of the factors causing these depletions (4) For how long could the NSAS be utilized given current and/or projected rates of extraction (5) Is the NSAS receiving modern recharge If so, where is it receiving modern recharge and what is the recharge rate The research team found that during the dry period that extended from 2002 to 2012, the aquifer in Egypt endured a deficit of 4.44 ± 0.42 109 m3/yr and gained a surplus of 6.5 x 109 m3/yr during the wet period that followed (2012-2015). The aquifer in Egypt is replenished in the wet years by groundwater flow from Lake Nasser and from neighboring Libya and Sudan. The flow from Sudan is impeded by an east-west trending basement uplift (Uweinat-Aswan uplift), especially in dry periods and the groundwater flow from Libya is facilitated by a northwest-trending structure (Pelusium shear system).
Year 2 Project Progress Summary (Submitted July 2018)
Egypt is facing shortages in fresh water supplies that will be exasperated over the upcoming few years due to the construction of the Renaissance Dam on the Blue Nile in Ethiopia. During the filling of the reservoir, Egypt will be deprived of an estimated 15 billion cubic meters of Nile waters for each of the upcoming seven to 10 years. Thus, finding alternative water resources is critical to the Egyptian population. Our findings indicate that the Nubian Aquifer, previously considered as entirely formed of water that was precipitated tens to hundreds of thousands of years ago in previous wet periods is actually receiving increments of modern recharge from precipitation over neighboring Sudan in the south and from excess surface waters in Lake Nasser. These fresh water supplies travel as groundwater flow from the south and from Lake Nasser to its surroundings to feed the Nubian Aquifer. Another interesting finding is that the travel time of groundwater is very fast through interconnected networks of fractures, faults, and large openings in carbonate rocks (Karst topography). What this means is that in wet years, like those we witnessed in years 2013, 2014, and 2015, where there was excess precipitation over the source areas in Sudan and Chad, Egypt will be receiving an influx of groundwater flow from neighboring Sudan, and possibly from Libya, that could at least in part compensate for the losses due to the damming of the River Nile water by the Renaissance Dam.
Year 3 Project Progress Summary (Submitted June 2019)
Researchers from Ain Shams University and Western Michigan University worked closely together to unravel the secrets of the fresh water underlying the vast Western Desert of Egypt. Up till now everyone believed that all of these waters came from rainfall tens and hundreds of thousands of years ago when the climate was wetter and the deserts were green and none of these waters was from precipitation at present times. Using state-of-the-art satellite data, namely the Gravity and Recovery and Climate Experiment (GRACE), the Egyptian-US team came to a different conclusion and published their findings in the Science of the Total Environment. They concluded that in wet periods, more rain falls in neighboring Sudan and seeps into the ground or makes it to the River Nile and gets impounded in Lake Nasser. Despite the fact that Egypt remains dry over these wet periods, the country’s aquifer (Nubian Sandstone Aquifer System) receives increments of modern recharge from the south and from excess surface waters in Lake Nasser that also seeps into the ground. These waters travel very fast for hundreds of kilometers under the ground through interconnected networks of fractures, faults, and large openings in carbonate rocks (karst topography). The last wet period was in years 2013, 2014, 2015, and 2016 where there was excess precipitation over the source areas in Sudan and Chad, and this is when Egypt received some 8 billion cubic meter of water for each of these four years. Such influx could compensate at least in part, for the losses due to the damming of the River Nile water by the Renaissance Dam.
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INTEGRATED PROBABILISTIC AND COMPUTATIONAL FRAMEWORK FOR ANALYZING 3D/4D CONTRAST-ENHANCED MEDICAL IMAGES [COMPLETED]
Principal Investigators: Ayman El-Baz, University of Louisville; Moumen T. El-Melegy, Assiut University
Overview: Our project was targeting Chronic Kidney Disease, which is by all means a world health crisis. 10% of the world population is affected by this disease. It is 9th leading cause of death in the US. The definite therapy for this disease is kidney transplantation. But unfortunately 15% of the patents will suffer from acute kidney rejection within the first 5 years. So the early detection of acute kidney rejection is the key to increasing the lifespan of the transplanted kidney.
Our project objective was to design and develop a computer aided diagnosis system to help the doctor to check the status of the transplant kidney and to early detect any signs of rejection. Towards this objective, a novel framework for the classification of acute rejection versus non-rejection status of renal transplants from 3D (2D + time) dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) was developed. The framework consisted of three main steps. First, kidney objects were segmented from adjacent structures taking into account the kidney/background shape and intensity and spatial appearances. In the second step, a non-rigid registration approach was applied to account for local deformations caused by physiological effects and patient’s motion during data acquisition. In the third step, an AI algorithm was able to provide the final diagnosis result as rejection or non-rejection of the transplanted kidney. This theoretical approach was fully converted into a software program that the doctor can use on her/his desktop. The doctor uploads the patient’s MRI data, and few minutes later she/he will get the status of the transplanted kidney. Moreover, a cloud-based version of this software was developed, which allowed any doctor anywhere in the world to use our solution using just a browser.
Year 1 Project Progress Summary (Submitted June 2017)
A novel framework for the classification of acute rejection versus non-rejection status of renal transplants from 3D (2D + time) dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is in the development process. The framework consists of three main steps. First, kidney objects are segmented from adjacent structures with a level set deformable boundary guided by a stochastic speed function that accounts for the kidney/background shape and intensity and spatial appearances. So far, we have promising results based on a leave-one-subject-out approach, on the 50 subjects that we have, of a 98% accuracy in segmenting kidneys. More cases need to be collected to test the segmentation approach.
We plan for the next step to develop a Laplace-based nonrigid registration approach to account for local deformations caused by physiological effects. Then, as a third step, the classification process will be investigated after extracting the discriminatory features from the registered segmented kidneys.
Year 2 Project Progress Summary (Submitted July 2018)
A novel framework for the classification of acute rejection versus non-rejection status of renal transplants from 3D (2D + time) dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is in the development process. The framework consists of three main steps. First, kidney objects are segmented from adjacent structures with a level set deformable boundary guided by a stochastic speed function that accounts for the kidney/background shape and intensity and spatial appearances. So far, we have promising results based on a leave-one-subject-out approach, on the 50 subjects that we have, of a 98% accuracy in segmenting kidneys. More cases need to be collected to test the segmentation approach. Additionally, the next step has been developed, which is a Laplace-based non-rigid registration approach to account for local deformations caused by physiological effects. Moreover, the third stage has been started, which is basically developing a CAD system for early detection of acute renal rejection. We have successfully started to extract the TIPCs features after handling the local motion of the kidney, namely, initial up-slope, peak signal intensity, time-to-peak, and average of the slowly varying agent delivery.
We plan for the next step to investigate a new classification technique after we extracted the discriminatory features from the registered segmented kidneys to get the final diagnosis as rejection or non-rejection renal transplants.
Year 3 Project Progress Summary (Submitted June 2019)
A novel framework for the classification of acute rejection versus non-rejection status of renal transplants from 3D (2D + time) dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) has been developed. The framework consists of three main steps. First, kidney objects are segmented from adjacent structures with a level set deformable boundary guided by a stochastic speed function that accounts for the kidney/background shape and intensity and spatial appearances. In the second step, a Laplace-based non-rigid registration approach is applied to account for local deformations caused by physiological effects and patient’s motion during data acquisition. In the third step, a complete CAD system for early detection of acute renal rejection has been developed. The CAD system is able to provide the final diagnosis as rejection or non-rejection of the transplanted kidney.
This theoretical framework has been converted into a software program that the doctor can use on her/his desktop. The doctor uploads the patient’s MRI data and few minutes back she/he will get the status of the transplanted kidney. We are now teaming with the Cloud Computing Center at Assiut University to develop a cloud-based version of this software which will allow any doctor anywhere in the world to use our solution using just a browser. This will largely extend the benefit from the project.
Year 4 Project Progress Summary (Submitted May 2020)
Our project is targeting Chronic Kidney Disease, which is by all means a world health crisis. 10% of the world population is affected by this disease. It is 9th leading cause of death in the US. The definite therapy for this disease is kidney transplantation. But unfortunately 15% of the patents will suffer from acute kidney rejection within the first 5 years. So the early detection of acute kidney rejection is the key to increasing the lifespan of the transplanted kidney.
Our project objective is to design and develop a computer aided diagnosis system to help the doctor to check the status of the transplant kidney and to early detect any signs of rejection. Towards this objective, a novel framework for the classification of acute rejection versus non-rejection status of renal transplants from 3D (2D + time) dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) has been developed. The framework consists of three main steps. First, kidney objects are segmented from adjacent structures with a level set deformable boundary guided by a stochastic speed function that accounts for the kidney/background shape and intensity and spatial appearances. In the second step, a Laplace-based non-rigid registration approach is applied to account for local deformations caused by physiological effects and patient’s motion during data acquisition. In the third step, a complete CAD system for early detection of acute renal rejection has been developed. The CAD system is able to provide the final diagnosis as rejection or non-rejection of the transplanted kidney.
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A MEDICAL TEXTILE FOR COMPREHENSIVE WOUND CARE: A LAMINATED MULTIFUNCTIONAL ELECTROSPUN FABRIC THAT IS HEMOSTATIC, ANTI-INFLAMMATORY AND ANTI-MICROBIAL [COMPLETED]
Principal Investigators: Samuel Hudson, North Carolina State University; Nabil Yousseri Abou-Zeid, National Research Centre
Overview: A research team lead by Dr. Nabil Abou-Zeid, Dr. Ahmed Nada (Textile Research Division, National Research Centre, Cairo, Egypt) and Dr. Samuel Hudson (Wilson College of Textiles, NCSU, Raleigh, NC, USA) have developed a new laminated multifunctional wound dressing. Uncontrolled hemorrhages are the major cause of fatality during traumatic events where standard medical treatments are usually not readily available. Therefore, a comprehensive trauma care product, which is effective in all aspects of the wound healing processes and can be easily applied in the absence of trained medical personnel, is much sought after. However, none can be found in the current market that meets all the requirements including hemostatic, anti-inflammatory, anti-microbial, etc. They have fabricated a laminated multifunctional medical textile using non-toxic biomaterials. Each layer serves certain functions in the wound healing process, and out of which, the hemostatic layer is the most critical.
The first step was to create a hemostatic material, chitosan iodoacetamide (CI) which was synthesized using carbodiimide chemistry and the chemical structure was characterized. The hemostatic properties were evaluated using a Erythrocyte Sedimentation Rate (ESR) method. The active hemostatic mechanism of this material is believed to be outside of the regular blood coagulation cascade as was evidenced by the much faster ESR in the presence of CIs for citrated horse whole blood. CI was electrospun with polyethylene oxide, in order to provide a hemostatic textile layer in the wound dressing. In order to have a complete and effective hemostasis, a second hemostatic agent was incorporated into an electrospun gelatin mat and loaded with tranexamic acid (TA), a hemostatic medication.
An analgesic layer was prepared with cellulose acetate. Cellulose acetate (CA) electrospun fibers have been used in different medical applications, such as drug delivery systems to release various drugs, but show little control over the release rate of the incorporated substances. In this work, click chemistry was used to activate CA and produce a crosslinked mat to provide sustained release for topical administration. CA was activated by introducing azide functional groups on the residual hydroxyl groups of the polymer chains. Capsaicin and diclofenac sodium, as pain-relieving drugs, were encapsulated during the electrospinning of the CA. Propargylated maltose was synthesized, for first time, as a crosslinker to the Azido-CA via triazole chemistry. Prepared samples were assessed for cytotoxicity and showed an acceptable cell viability. In rat animal model, diclofenac sodium and capsaicin-loaded electrospun mats of Azido-CA showed superior closure rates over the untreated rats and those treated with commercial samples.
A series of adhesives were synthesized, to be utilized in the final assembly of the multilayer wound dressing. The preparation and characterization of adhesive sheets based on hydroxy ethyl cellulose and 2-Ethylhexyl acrylate was accomplished. Also, a set of adhesives based on carboxymethyl cellulose and methylmethacrylate and 2-Ethylhexyl acrylate was synthesized. Diclofenac sodium, an anti-inflammatory drug, was encapsulated into the adhesives and its release profile in phosphate buffer solution was recorded. Cytotoxicity of the adhesive sheets was conducted against human skin fibroblast cells, and found to be nontoxic.
This work resulted in a new type of wound dressing for the comprehensive treatment, in the field, of traumatic injuries involving hemorrhage. The materials developed could also be used in other types of wound dressings, such as for surgical applications. Industrial partners are being sought to commercialize new products based on the concepts described here.
Year 1 Project Progress Summary (Submitted June 2017)
Hemostasis is the physiological process to arrest bleeding and minimize blood loss from damaged blood vessels. Hemostasis can be accelerated by contact of the blood with foreign materials. The goal of this research is to develop and evaluate materials which could be used in hemostatic wound dressings to arrest the heavy bleeding associated with traumatic wounds. This would be accomplished by the novel approach of using a composite material to create an in situ artificial blood clot. A mesh of micron scale fibers to mimic the fibrous network formed by the self-association of fibrin, would be combined with a material or agent that would lead to the gelation of the soluble blood proteins. This would lead to the in situ formation of a blood clot, at a more rapid rate than could naturally occur by the enzymatic processes associated with natural blood clot formation.
During this research period, equipment was established in Egypt to electrospin the new fibers for this wound dressing. Preliminary experiments preparing the drug loaded fibers were begun. The first fibers prepared contained a hemostatic drug, tranexamic acid. The physical and chemical properties of the fibers were determined. Preparation for the synthesis of a new hemostatic agent, based on chitosan, was also begun. In the next phase, other fibers containing analgesic and other hemostatic agents will be prepared.
Year 2 Project Progress Summary (Submitted July 2018)
Uncontrolled hemorrhages are the major cause of fatality during traumatic events where standard medical treatments are usually not readily available. Therefore, a comprehensive trauma care product, which is effective in all aspects of the wound healing processes and can be easily applied in the absence of trained medical personnel, is much sought after. However, none can be found in the current market that meets all the requirements including hemostatic, anti-inflammatory, anti-microbial, etc. We proposed to fabricate a laminated multifunctional medical textile using non-toxic biomaterials. Each layer serves certain functions along the wound healing processes, and out of which hemostatic layer is the most critical.
New hemostatic material chitosan iodoacetamides (CI) with varying degree of substitution (DS) were synthesized using carbodiimide chemistry and were characterized in terms of their DS using 1H and 13C NMR, FITR, SEM-EDS, elemental analysis, iodine content analysis, and conductometry titration. The effects of synthetic conditions were evaluated including the choice of solvent, pH of the reaction medium, reaction time and the molecular weights of the starting chitosan materials. Their hemostatic properties were evaluated using Erythrocyte Sedimentation Rate (ESR) method and were compared with regard to their iodine content and weight loading. The active hemostatic mechanism of this material is believed to be outside of the regular blood coagulation cascade as was evidenced by the much faster ESR in the presence of CIs for citrated horse whole blood. Iodide is reactive towards several amino acid moieties, such as L-cysteine, lysine, methionine, and L-histidine, and could potentially form covalent crosslinks with proteins naturally found in blood. In order to have a complete effective hemostasis, a second mechanism can be incorporated as was exemplified by electrospun gelatin mat (prepared in Cairo) and loaded with tranexamic acid (TA), a hemostatic medication. In future work, other layers will be prepared, including adhesive and analgesic components.
Year 3 Project Progress Summary (Submitted June 2019)
Uncontrolled hemorrhages are the major cause of fatality during traumatic events where standard medical treatments are usually not readily available. Therefore, a comprehensive trauma care product, which is effective in all aspects of the wound healing processes and can be easily applied in the absence of trained medical personnel, is much sought after. However, none can be found in the current market that meets all the requirements including hemostatic, anti-inflammatory, anti-microbial, etc. properties. We proposed to fabricate a laminated multifunctional medical textile using non-toxic biomaterials. Each layer serves certain functions along the wound healing processes, and out of which the hemostatic layer is the most critical.
Earlier, in this project, a new hemostatic material, chitosan iodoacetamides (CI), with varying degree of substitution (DS) were synthesized using carbodiimide chemistry and were characterized using 1H and 13C NMR, FITR, SEM-EDS, elemental analysis, iodine content analysis, and conductometry titration. The effects of synthetic conditions were evaluated including the choice of solvent, pH of the reaction medium, reaction time and the molecular weights of the starting chitosan materials. Their hemostatic properties were evaluated using Erythrocyte Sedimentation Rate (ESR) method and were compared regarding their iodine content and weight loading. The active hemostatic mechanism of this material is believed to be outside of the regular blood coagulation cascade, as was evidenced by the much faster ESR in the presence of CIs for citrated horse whole blood. In order to have a complete effective hemostasis, a second hemostatic agent can be incorporated, as was exemplified by electrospun gelatin mat (prepared in Cairo) and loaded with tranexamic acid (TA), a hemostatic medication.
In the current work, layers containing pain-relieving drugs, were prepared and tested. Cellulose acetate (CA) electrospun fibers have been used in different medical applications for drug delivery systems. CA is usually available with a DS of 2.4-2.5, and shows little control over the release rate of the incorporated drug, due to the lack of active functional groups. In this work, click chemistry was used to activate CA and produce cross linked electrospun mat to provide sustained release for topical administration. CA was activated by introducing azide functional groups onto the residual hydroxyl groups of the cellulose with DSazide of 0.24. Azido-CA was electrospun to produce nanofiber mats wherein capsaicin and sodium diclofenac were encapsulated as pain relieving drugs.
Propargylated maltose was synthesized for the first time, as a crosslinker to the Azido-CA via triazole chemistry. Spectral analysis confirmed the chemical structure of the new derivatives and the click chemistry. Morphological analysis of the electrospun fibers of Azido-CA showed a range of diameters of 140-270 nm, with smooth surfaces. Samples incorporating Azido-CA were assessed for cytotoxicity and showed an acceptable cell viability. In a rat animal model, sodium diclofenac and capsaicin loaded mats of Azido- CA showed superior closure rates over the untreated rats and those treated with commercial samples. Rats treated with electrospun mats of CA and Azido-CA, loaded with drugs, showed normal intact histological structure of the epidermis and skin dermis.
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MOLECULAR AND ANTIGENIC EVOLUTION OF H5N1 AVIAN INFLUENZA VIRUS IN EGYPT AND DEVELOPMENT OF BROADLY EFFECTIVE VACCINE [COMPLETED]
Principal Investigator: Chang-Won Lee, The Ohio State University
Overview: Egypt is one of the few countries suffering from highly pathogenic bird flu (called the H5N1 influenza) every year since 2006. The continuing outbreaks of H5 subtype viruses have caused massive economic losses, and the disease also threatens human health. Egypt has been using vaccines to control the disease in birds. However, the flu virus continues to change and has been ahead of the game against the currently available commercial vaccine. In this project, the US-Egyptian team collaborated to help the country to deal with devastating and continuing outbreaks of highly pathogenic H5N1 flu. The team monitored the genetic and antigenic changes of H5N1 viruses from Egypt which affect the efficacy of the commercially available vaccine. Our surveillance data shows that in addition to H5 highly pathogenic viruses, low pathogenic bird flu (known as H9N2) is highly prevalent in Egyptian poultry and complicates the epidemiology and control of the H5N1 viruses. More importantly, we also isolated new highly pathogenic flu (called the H5N8) from duck and geese early 2017 in Egypt, which demonstrate introduction of this new strain into Africa most likely through migratory birds (published in journal “Avian Pathology”). During 2017/2018 season, the H5N8 virus co-circulated with H5N1 virus in waterfowl and transmitted to chickens, causing high mortalities and massive economic losses to different poultry sectors in the country. Although H5N1 and H5N8 virus share same H5 subtype, they are both genetically and antigenically different which complicated the development of the effective vaccine. Based on the accumulated epidemiologic and biological data with the H5N1 and H5N8 viruses, we established a practical approach to develop vaccines using genetic tool that can shape the most important flu virus protein, the hemagglutinin (HA) protein, for vaccine development. The team has generated cost-effective vaccine seed strains and showed improved efficacy against highly pathogenic bird flu in experimental condition. Our study highlights that targeted mutation in the HA can be effectively used as a tool to develop broadly reactive influenza vaccines to cope with the continuous antigenic evolution of influenza viruses.
Year 1 Project Progress Summary (Submitted June 2017)
Egypt is one of the few countries suffering from highly pathogenic bird flu (called the H5N1 influenza) every year since 2006. The continuing outbreaks of H5N1 have caused massive economic losses, and the disease also threatens human health. Egypt has been using vaccines to control the disease in birds. However, the flu virus continues to change and has been ahead of the game against the currently available commercial vaccine. In this project, the US-Egyptian team is collaborating to help the country deal with devastating and continuing outbreaks of highly pathogenic H5N1 avian influenza. The team has been monitoring the genetic and antigenic changes of H5N1 viruses from Egypt which affect the efficacy of the commercially available vaccine.
Our surveillance data shows that in addition to H5N1, low pathogenic bird flu (known as H9N2) is highly prevalent in Egyptian poultry and complicates the epidemiology and control of the H5N1. More importantly, we also isolated new highly pathogenic avian influenza (called the H5N8) from duck and geese early this year in Egypt, which demonstrate introduction of this new strain into Africa most likely through migratory birds. Although H5N1 and H5N8 virus share same H5 subtype, they are both genetically and antigenically different and complicate the development of the vaccine. Based on the accumulated epidemiologic and biological data with the H5N1 viruses isolated, the team established a practical approach to develop vaccines using genetic tool that can shape the most important flu virus protein, the hemagglutinin (HA) protein, for vaccine development. The team is generating cost-effective vaccine seed strains that can be used for Egyptian poultry against highly pathogenic avian influenza.
Year 2 Project Progress Summary (Submitted July 2018)
Egypt is one of the few countries suffering from highly pathogenic bird flu (called the H5N1 influenza) every year since 2006. The continuing outbreaks of H5N1 have caused massive economic losses, and the disease also threatens human health. Egypt has been using vaccines to control the disease in birds. However, the flu virus continues to change and has been ahead of the game against the currently available commercial vaccine. In this project, the US-Egyptian team is collaborating to help the country deal with devastating and continuing outbreaks of highly pathogenic H5N1 flu. The team has been monitoring the genetic and antigenic changes of H5N1 viruses from Egypt which affect the efficacy of the commercially available vaccine. Our surveillance data shows that in addition to H5N1, low pathogenic bird flu (known as H9N2) is highly prevalent in Egyptian poultry and complicates the epidemiology and control of the H5N1. More importantly, we also isolated new highly pathogenic flu (called the H5N8) from duck and geese early 2017 in Egypt, which demonstrate introduction of this new strain into Africa most likely through migratory birds (published in journal “Avian Pathology”). During 2017/2018 season the H5N8 virus co-circulated with H5N1 virus in waterfowl and transmitted to chickens, causing high mortalities and massive economic losses to different poultry sectors in the country. Although H5N1 and H5N8 virus share same H5 subtype, they are both genetically and antigenically different which complicate the development of the effective vaccine. Based on the accumulated epidemiologic and biological data with the H5N1 and H5N8 viruses, the team established a practical approach to develop vaccines using genetic tool that can shape the most important flu virus protein, the hemagglutinin (HA) protein, for vaccine development. The team is generating cost-effective vaccine seed strains that can be used for Egyptian poultry against highly pathogenic bird flu.
Year 3 Project Progress Summary (Submitted May 2019)
Egypt is one of the few countries suffering from highly pathogenic bird flu (called the H5N1 influenza) every year since 2006. The continuing outbreaks of H5N1 have caused massive economic losses, and the disease also threatens human health. Egypt has been using vaccines to control the disease in birds. However, the flu virus continues to change and has been ahead of the game against the currently available commercial vaccine. In this project, the US-Egyptian team is collaborating to help the country deal with devastating and continuing outbreaks of highly pathogenic H5N1 flu. The team has been monitoring the genetic and antigenic changes of H5N1 viruses from Egypt which affect the efficacy of the commercially available vaccine. Our surveillance data shows that in addition to H5N1, low pathogenic bird flu (known as H9N2) is highly prevalent in Egyptian poultry and complicates the epidemiology and control of the H5N1. More importantly, we also isolated new highly pathogenic flu (called the H5N8) from duck and geese early 2017 in Egypt, which demonstrate introduction of this new strain into Africa most likely through migratory birds (published in journal “Avian Pathology”). During 2017/2018 season the H5N8 virus co-circulated with H5N1 virus in waterfowl and transmitted to chickens, causing high mortalities and massive economic losses to different poultry sectors in the country. Although H5N1 and H5N8 virus share same H5 subtype, they are both genetically and antigenically different which complicate the development of the effective vaccine. Based on the accumulated epidemiologic and biological data with the H5N1 and H5N8 viruses, the team established a practical approach to develop vaccines using genetic tool that can shape the most important flu virus protein, the hemagglutinin (HA) protein, for vaccine development. The team has generated cost-effective vaccine seed strains that can be used for Egyptian poultry against highly pathogenic bird flu once validated in experimental studies.
Year 4 Project Progress Summary (Submitted June 2020)
Egypt is one of the few countries suffering from highly pathogenic bird flu (called the H5N1 influenza) every year since 2006. The continuing outbreaks of H5N1 have caused massive economic losses, and the disease also threatens human health. Egypt has been using vaccines to control the disease in birds. However, the flu virus continues to change and has been ahead of the game against the currently available commercial vaccine. In this project, the US-Egyptian team is collaborating to help the country deal with devastating and continuing outbreaks of highly pathogenic H5N1 flu. The team has been monitoring the genetic and antigenic changes of H5N1 viruses from Egypt which affect the efficacy of the commercially available vaccine. Our surveillance data shows that in addition to H5N1, low pathogenic bird flu (known as H9N2) is highly prevalent in Egyptian poultry and complicates the epidemiology and control of the H5N1. More importantly, we also isolated new highly pathogenic flu (called the H5N8) from duck and geese early 2017 in Egypt, which demonstrate introduction of this new strain into Africa most likely through migratory birds (published in journal “Avian Pathology”). During 2017/2018 season the H5N8 virus co-circulated with H5N1 virus in waterfowl and transmitted to chickens, causing high mortalities and massive economic losses to different poultry sectors in the country. Although H5N1 and H5N8 virus share same H5 subtype, they are both genetically and antigenically different which complicate the development of the effective vaccine. Based on the accumulated epidemiologic and biological data with the H5N1 and H5N8 viruses, the team established a practical approach to develop vaccines using genetic tool that can shape the most important flu virus protein, the hemagglutinin (HA) protein, for vaccine development. The team has generated cost-effective vaccine seed strains that can be used for Egyptian poultry against highly pathogenic bird flu once validated in experimental vaccine efficacy studies.
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A NEUROBIOLOGICAL APPROACH TO VECTOR CONTROL FOR INTESTINAL SCHISTOSOMIASIS [COMPLETED]
Principal Investigators: Mark Miller, University of Puerto Rico, San Juan; Mohamed R. Habib, Theodor Bilharz Research Institute
Overview: Schistosomiasis remains one of the most prevalent neglected tropical diseases, affecting populations in many parts of Africa, Asia, and South America. Recently, the World Health Organization (WHO) estimated that more than 218 million people in 78 countries required preventive chemotherapy in 2019. The WHO has established a multifaceted strategic plan for control and prevention of schistosomiasis, including large scale chemotherapy for high-risk populations, hygiene education, access to safe drinking water, and snail control.
Fresh water pulmonate snails from the genus Biomphalaria act as the obligatory intermediate host of the Schistosoma mansoni, the trematode species that causes intestinal schistosomiasis. In Egypt, where schistosomiasis dates to antiquity, Biomphalaria alexandrina is the predominant intermediate host for S. mansoni. The presence of B. alexandrina is a key factor that determines the prevalence of intestinal schistosomiasis in the country. For example, construction of Aswan High Dam in 1967 led to an expansion of S. mansoni toward Upper Egypt due to the creation of more suitable habitats for the snails.
Efforts to control snail populations, such as molluscicides or introduction of predator species, have yielded only modest results. One potential target to be considered for snail control is its central nervous system (CNS), since it regulates vital functions including cardiac activity, feeding and reproductive behavior. Funding from this collaborative project enabled Egyptian and U.S. investigators to generate a neural transcriptome with the ultimate goal of identifying signaling mechanisms involved in the response of B. alexandrina to infection by S. mansoni larvae (Mansour et al. 2017). Transcripts were used to deduce the organization of neuropeptide systems and anatomical approaches localized expression of major signaling systems in the nervous system. These findings may lead to novel and highly specific strategies for the control of snail populations.
Year 1 Project Progress Summary (Submitted June 2017)
Schistosomiasis remains one of the most prevalent neglected tropical diseases, affecting populations in many parts of Africa, Asia, and South America. Recently, the World Health Organization (WHO) estimated that more than 218 million people in 78 countries required preventive chemotherapy in 2015. The WHO has established a multifaceted strategic plan for control and prevention of schistosomiasis, including large scale chemotherapy for high-risk populations, hygiene education, access to safe drinking water, and snail control.
Fresh water pulmonate snails from the genus Biomphalaria act as the obligatory intermediate host of the Schistosoma mansoni, the trematode species that causes intestinal schistosomiasis. In Egypt, where schistosomiasis dates to antiquity, Biomphalaria alexandrina is the predominant intermediate host for S. mansoni. The presence of B. alexandrina is a key factor that determines the prevalence of intestinal schistosomiasis in the country. For example, construction of Aswan High Dam in 1967 led to an expansion of S. mansoni toward Upper Egypt due to the creation of more suitable habitats for the snails.
Efforts to control snail populations, such as molluscicides or introduction of predator species, have yielded only modest results. One potential target to be considered for snail control is its central nervous system (CNS), since it regulates vital functions including cardiac activity, feeding and reproductive behavior. During the present funding period, a neural transcriptome was generated with the ultimate goal of identifying signaling mechanisms involved in the response of B. alexandrina to infection by S. mansoni larvae. Such mechanisms may lead to novel and highly specific strategies for the control of snail populations.
Year 2 Project Progress Summary (Submitted July 2018)
Schistosomiasis remains one of the most prevalent neglected tropical diseases, affecting populations in many parts of Africa, Asia, and South America. Recently, the World Health Organization (WHO) estimated that more than 218 million people in 78 countries required preventive chemotherapy in 2015. The WHO has established a multifaceted strategic plan for control and prevention of schistosomiasis, including large scale chemotherapy for high-risk populations, hygiene education, access to safe drinking water, and snail control.
Fresh water pulmonate snails from the genus Biomphalaria act as the obligatory intermediate host of the Schistosoma mansoni, the trematode species that causes intestinal schistosomiasis. In Egypt, where schistosomiasis dates to antiquity, Biomphalaria alexandrina is the predominant intermediate host for S. mansoni. The presence of B. alexandrina is a key factor that determines the prevalence of intestinal schistosomiasis in the country. For example, construction of Aswan High Dam in 1967 led to an expansion of S. mansoni toward Upper Egypt due to the creation of more suitable habitats for the snails.
Efforts to control snail populations, such as molluscicides or introduction of predator species, have yielded only modest results. One potential target to be considered for snail control is its central nervous system (CNS), since it regulates vital functions including cardiac activity, feeding and reproductive behavior. During the present funding period, a neural transcriptome was generated with the ultimate goal of identifying signaling mechanisms involved in the response of B. alexandrina to infection by S. mansoni larvae (see Mansour et al. 2017). We also reported the distribution of a major neurotransmitter, GABA, in the nervous system of Biomphalaria snails (Vaasjo et al. 2018). Such mechanisms may lead to novel and highly specific strategies for the control of snail populations.
Year 3 Project Progress Summary (Submitted June 2019)
Schistosomiasis, or snail fever, remains one of the most prevalent neglected tropical diseases, affecting populations in many parts of Africa, Asia, and South America. Recently, the World Health Organization (WHO) estimated that more than 218 million people in 78 countries required preventive chemotherapy in 2015. The WHO has established a multifaceted strategic plan for control and prevention of schistosomiasis, including large scale chemotherapy for high-risk populations, hygiene education, access to safe drinking water, and snail control.
Freshwater pulmonate snails from the genus Biomphalaria act as the obligatory intermediate host of the Schistosoma mansoni, the trematode species that causes intestinal schistosomiasis. If these snails could be controlled, the prevalence of schistosomiasis could be greatly reduced or eliminated. During this reporting period, we undertook a study to identify neuropeptides that could be involved in regulating male and female reproductive behaviors (Acker et al. 2019). First, we examined the neural transcriptome that was constructed previously (Mansour et al. 2017) to identify neuropeptides with homology to reproductive regulators in related gastropods. Several transcripts were identified. In November 2018, three Biomphalaria alexandrina sequences (MK144534, MK 144535, and MK144536) were submitted to GenBank, the annotated open access collection of nucleotide and protein sequences maintained by the National Center for Biotechnology Information (NCBI). These sequences were released to the public domain by the NCBI on June 11, 2019. On that date, our sequences were also made available to the DNA Bank of Japan and the European Nucleotide Archive.
Antibodies raised against selected reproductive neuropeptides were used to locate neurons in the Biomphalaria nervous system where they are expressed (Acker et al. 2019). This strategy enabled us to locate peptidergic neurons that control both male and female reproductive behaviors in this hermaphroditic snail vector. This information could lead to novel and highly specific strategies for disrupting the snail life cycle and reducing the prevalence of schistosomiasis.
Year 4 Project Progress Summary (Submitted May 2020)
During the reporting period, the project produced two publications advancing our knowledge about Biomphalaria snails, intermediate hosts for intestinal schistosomiasis. In the first article, we showed that an antibody against the protein keyhole limpet hemocyanin (KLH) labeled specific neurons in the nervous system of Biomphalaria (Beach et al., 2019). This finding is important because KLH is often used as a carrier protein to produce antibodies. Its use could lead to artifacts when used on molluscan tissues. In another study, we examined biochemical and apoptotic changes in the nervous and ovotestis tissues of Biomphalaria alexandrina following infection with Schistosoma mansoni (Habib et al., 2020). In many host-parasite systems, infection reduces host reproductive activities. This study disclosed some mechanisms by which schistosomes could produce such 'parasitic castration' in snails. Most of the experimental work for this major project was conducted by the Egyptian team.
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A PET TOOL KIT FOR EGYPTIAN BIOMEDICAL RESEARCHERS [COMPLETED]
Principal Investigator: Ramsey Badawi, University of California, Davis
Overview: Two Egyptian students have been trained in the software simulation of Positron Emission Tomography (PET) scanners for biomedical use and have learned how to reconstruct the data produced by the simulations to generate images.
We have implemented an approach to radiation detector readout that is simple, compact, robust and cheap. This approach will form the basis of a PET toolkit which can easily be utilized, maintained and developed by Egyptian biomedical laboratories.
We have developed two toolkit-PET detectors; a TOF-PET detector in which the core unit is a simplified pulse-processing circuit for energy estimation and time-of-flight measurements, a PSPMT-based PET detector in which a Hamamatsu position sensitive PMT is used as a photodetector for accumulating the output light from the scintillation crystals. This makes the toolkit design more flexible and versatile for Egyptian researchers.
Year 1 Project Progress Summary (Submitted June 2017)
In the first year of our project, the primary goals of the project are:
Develop skills and expertise in Minia University in the software simulation of Positron Emission Tomography (PET) scanners for biomedical use. We have made solid progress in this area, with three students developing skills and a fourth, who recently joined the team, being trained. In addition, we have started work on building skills in image reconstruction.
At UC Davis, to develop detector modules that can be used in the re-usable PET scanner kit that we aim to deliver to Egypt. Again, solid progress has been made, with a variety of detector configurations being tested. In addition, we have made headway in developing a new, more compact method for reading out the signals from the detectors.
Year 2 Project Progress Summary (Submitted July 2018)
The primary goals of the project are:
Develop skills and expertise in Minia University in the software simulation of Positron Emission Tomography (PET) scanners for biomedical use. Students have been trained in this area and have learned how to reconstruct the data produced by the simulations to generate images.
At UC Davis, to develop detector modules that can be used in the re-usable PET scanner kit that we aim to deliver to Egypt. We have developed a series of new, more compact methods for reading out the signals from the detectors. We are currently working on optimizing these and will select the most promising one for incorporation into the toolkit.
Year 3 Project Progress Summary (Submitted June 2019)
We have implemented an approach to radiation detector readout that is simple, compact, robust and cheap. This approach will form the basis of a PET toolkit which can easily be utilized, maintained and developed by Egyptian biomedical laboratories.
Year 4 Project Progress Summary (Submitted June 2020)
We have implemented an approach to radiation detector readout that is simple, compact, robust and cheap. This approach will form the basis of a PET toolkit which can easily be utilized, maintained and developed by Egyptian biomedical laboratories.
Year 5 Project Progress Summary (Submitted June 2021)
We have developed two toolkit-PET detectors; a TOF-PET detector in which the core unit is a simplified pulse-processing circuit for energy estimation and time-of-flight measurements, a PSPMT-based PET detector in which a Hamamatsu position sensitive PMT is used as a photodetector for accumulating the output light from the scintillation crystals. This makes the toolkit design more flexible and versatile for Egyptian researchers.
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POROUS-ORGANIC POLYMERS FOR CO2 CAPTURE APPLICATIONS: STRUCTURE-PROPERTY RELATIONSHIPS THROUGH NUCLEAR MAGNETIC RESONANCE [COMPLETED]
Principal Investigators: Edwin Rivera, University of South Florida; Mohamed H. Alkordi, Zewail City of Science and Technology
Overview: This research Grant focuses on understanding an exceptional class of material known as Porous Organic Polymers or POPs. These materials are highly porous and have a high affinity towards adsorbing gases such as CO2, rendering the potential to extract CO2 from the atmosphere or prevent the gases from being transferred to the atmosphere and contaminating the air. Because these polymers are highly amorphous, in contrast to other crystalline porous materials like Metal Organic Frameworks) MOFs, it has been challenging to study these materials' structure and gas interactions at the atomic levels. There are no crystals, and the materials are insoluble in solution. We engaged in a study that uses NMR spectroscopy and solid-state techniques to seek changes in the chemical shifts [13C(carbon), 15N(nitrogen), and ultimately 1H(proton)] between no-dosed and dosed samples with isotopically labeled 13CO2. Changes in the nuclei chemical shift can pinpoint the polymer linkers or molecular domains responsible for the adsorption or desordtion potential towards the gases. With this knowledge, we could help design and fine-tune better adsorption materials in the future. It will also give us a better fundamental understanding of how these materials adsorb and desorb gases.
This research found that spectra of 13C, 15N, and 1H collected on samples spinning between 20,000Hz and 40,000Hz are dominated by line broadening contributed by the natural inhomogeneities of the polymers, which gives the POP its porosity properties or other sources inherent by the nature of the polymer. Observations of these changes in chemical shift or changes in line width are minor. Due to the resonance position of 13CO2 overlapping with resonances of the POP material, observation of the 13CO2 signal in the complex is hard. Significant broadening in the POP spectrum and the inability to cross polarize to the residence 13CO2 molecule in the POP complex are some reasons for using two distinct pulse sequences to observe the molecules separately (13CO2 and POPs) from one another. Complete synthesis and physical characterization of the samples studied in this project (Egyptian team) provides these materials with their characteristic adsorption and desorption properties of CO2.
This research concludes with several samples submitted for experiments using state-of-the-art solid-state techniques. In such studies, POP materials were spun at rotational speeds of 60,000Hz( 1.3mm O.D. diameter rotors) and in excess 100,000Hz (0.7mm O.D. rotors, ULTRA-HIGH SPINNING SPEEDS), and we reveal a new direction by which these polymers should be studied in the future. Proton NMR and heteronuclear (13C/1H, 15N/1H) NMR experiments were conducted at ultra high spinning speeds where resolution has strikingly improved. NMR spectra can be analyzed from these materials at the atomic level resolution to the degree that will yield more information relevant to the 13CO2~POP complex than those spun at lower spinning speed. Also, additional heteronuclear pulse sequences can provide more detailed characterization with the enhanced resolution obtained from the higher spinning experiments, as shown in the few examples.
Lastly, the new construction of a rotor loader cell to activate and dose solid materials with gases was submitted to the office of Transfer Technology of USF before the end date of this grant, June 2021.
Year 1 Project Progress Summary (Submitted June 2017)
The first well publicized occurrence of a CO2 capture improvised device made under emergency conditions was well known around the world in 1970 when an explosion aboard the Apollo 13 mission to the moon, left the Central Module (CM) crippled. Astronauts under the guidance of Houston command center improvised a device to capture CO2 built ups in the Lunar Module (LM) that would sustain life during the emergency return to earth. While the general public is mostly unaware of the use of porous materials in day-to-day life, they are present made filters used at home in dehumidifiers, air conditioners, facemasks and at industrial plant’s gas scrubbers, etc.
The current political climate to renew fossil fuels as the principal energy source instead of alternative sources such as solar and wind will lead to an increased release of greenhouse gasses into the atmosphere. Research in preventing the release of these gases into the air, storage and conversion of CO2 into a source of energy will be critical and must be encouraged, to be stepped-up to stop and reverse global warming. The race to produce porous materials that have high capturing efficient, reversibility, are cheap to produce to produce, easy to built and available are scientifically, environmentally, economically and of course politically significant.
Inspired by porous rocks, zeolites, and silicates, as found in nature, derivatives like porous organic polymers (POPs), metal-organic frameworks (MOF’s) and organic carbon frameworks (COF’s) are aggressively being researched to replace existing methods of gas scrubbers and subsequent conversion into energy. In this study, we target the POPs fragments.
The grant is comprised of two teams, the Egyptian team responsible for the new synthesis of the POP’s and the USA team in charge of the characterization of POPs via solid state NMR and XPS. Used extensively in polymer science solid state NMR can be utilized for the characterization of this new family of porous organic polymers as indicated in this proposal. Data in the form of spectra obtained by solid state NMR will be used to characterize the polymer structure and its interaction with gases i.e. CO2. Further analysis of the data will provide mechanisms to fine-tune the improvement of the POP’s gas adsorption and storage capacity.
The first year of the grant serves to establish collaborations at the national and international levels. The University of Torino, Italy, was responsible for constructing a 1.9mm rotor loader cell. The cell was modeled using a 4 mm rotor cell and represents the first use of a 1.9 mm cell for gas adsorption work. This cell will connect to a Schlenk (vacuum) line, currently undergoing assembly at the University of South Florida. The cell is a critical component to purge POP's of any residues left after the synthesis before loading the gas, i.e. water that may interfere with NMR signals. Finally, the University of South Carolina, with its state of the art solid state Spectrometer, was selected as the site for conducting the experiments because of its relative proximity, the readily available spectrometer time and experience working with such materials. We have visited the side twice already and have conducted some preliminary experiments in solid state NMR.
Year 2 Project Progress Summary (Submitted July 2018)
The grant is composed of two teams, the Egyptian team responsible for thesynthesis of the new material as well as some of the gas adsorbance and physical characterization, however, the structural characterization via solid-state NMR occurs in the United States.
Specifically, three distinct universities are involved one Zewail City of Science and Technology in Cairo Egypt and two in the USA South Florida (Tampa) and South Carolina (Columbia) where the analysis by Nuclear Magnetic Resonance takes place. Used extensively in polymer science solid-state NMR can be utilized for the characterization of this new family of porous organic polymers as indicated in the initial proposal. Data in the form of spectra obtained by solid-state NMR will is being used to characterize the polymer structure and its interaction with gases, i.e., 13CO2. Further analysis of the 13C and 15N NMR chemical shifts, when available, should provide mechanisms to fine-tune the synthesis by correlating the POP’s gas adsorption and storage capacity with the observed NMR shifts produced by the adsorption of 13CO2.
The first year of the grant served to establish collaborations at the national and international levels. The University of Torino, Italy, was responsible for constructing a
1.9mm rotor loader cell. The cell was modeled using a 4 mm rotor cell and represents the first use of a 1.9 mm cell for gas adsorption work. This cell connects to a Schlenk (vacuum) line, was assembled at the University of South Florida and tested. The cell is a critical component to purge the raw POP's of any residues left after the synthesis before loading the gas, i.e., water that may interfere with NMR signals. Finally, the University of South Carolina, with its state of the art solid state Spectrometer, was selected as the site for conducting the experiments because of its relative proximity and the readily available spectrometer time and experience working with such materials. During the first year of this grant, we visited the USC core facility lab under the direction of Dr. Perry Pellechia (collaborator), twice and conducted some survey 13C solid-state NMR experiments the raw POP's (untreated) solid-state NMR as reported in the first Annual Report. Through the second year, we started conducting experiments of the POPs sent from our collaborators from Egypt, treated and loaded with 13CO2 using the Torino rotor loader cell and the Schlenk (vacuum) line built during the year and a half of the grant. Control experiments were conducted to determine the integrity of the rotors. Figure 1 shows that 13CO2 can be loaded into the Bruker 1.9mm rotor using the Torino built cell. It is easily detectable in both static and spinning rotors (20 kHz) using the simple Bloch decay pulse sequence.
However, the caps on the 1.9mm rotors do not provide a tight seal and within two hours over 70% of the 13CO2 escaped from the rotor. However, the binding of 13CO2, to a rotor loaded with POPs like PyPOP and TriPOP show a slower leak from the rotor in addition to a chemical shift indicating adsorption to the material. Figure 2A and 2B clearly shows 13CO2 leaking out at a rate much slower than the 13CO2 by itself. With the POP’s the leaking rate is reflected by the decrease in intensity of the signal in intervals of about 3 hours. This is the state of the research at the moment of this report. The following results were obtained at the University of South Carolina when Edwin Rivera visited to transport the gas loading rack that was previously assembled at USF.
Year 3 Project Progress Summary (Submitted June 2019)
Our Study outlines the importance of careful design and synthesis of porous solids towards carbon dioxide capture and uptake - a subject of great importance and political controversy, involving dangerous increases in carbon dioxide (CO2) emissions and their effect on global warming for the last decade. A detailed relationship between the composition and structure of the molecular building blocks and their performance as solid sorbents for CO2 is being outlined. The use of cutting-edge characterization techniques, including state-of-the-art nuclear-magnetic resonance is helping elucidate the material's structure and binding affinity for CO2 for the more efficient CO2 sorbent materials of the future.
Year 4 Project Progress Summary (Submitted June 2020)
Our study outlines the importance of careful design and synthesis of porous solids towards carbon dioxide capture and uptake - a subject of great importance and political controversy, involving dangerous increases in carbon dioxide (CO2) emissions and their effect on global warming for the last decade. A detailed relationship between the composition and structure of the molecular building blocks and their performance as solid sorbents for CO2 is being outlined. The use of cutting-edge characterization techniques, including state-of-the-art nuclear-magnetic resonance is helping elucidate the material's structure and binding affinity for CO2 for the more efficient CO2 sorbent materials of the future.
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PREPARING AND EVALUATING IPM TACTICS FOR INCREASING STRAWBERRY AND CITRUS PRODUCTION [COMPLETED]
Principal Investigators: Larry Duncan, University of Florida; Mahfouz M. M. Abd-Elgawad, National Research Centre
Overview: Entomopathogenic nematodes (EPN) are specialized, microscopic worms that kill insects in soil. They have been introduced in some countries to re-establish control of invasive insect pests, they have been commercially formulated to inundate soil for pest management, and sometimes tactics are developed to modify soil properties in ways that enhance or conserve the biological control provided by endemic EPN. In this project we focused on two objectives. We developed a standardized approach to characterize EPN communities and identify their natural enemies. In this way we seek to find soil properties that affect the performance of EPNs as well as their predators and pathogens with an eye toward managing soil in ways that increase biological control. Here we demonstrated a simple method to process soil samples to recover EPNs and all other relevant organisms. We compared state of the art molecular tools to those currently used, producing data sets that are more sensitive with greater capacity to characterize the key components of soil food webs. Using these tools to standardize survey methods, we confirmed that Florida citrus orchards have greater likelihood to respond favorably to conservation tactics than citrus orchards in countries with Mediterranean climates such as Egypt, Greece or Portugal. We also identified potential insect and microarthropod predator and prey species of EPN in a Florida citrus orchard using these methods.
With respect to augmenting EPN in soil with commercial products, we demonstrated that the nematode Steinernema riobrave is capable of moving in pine bark beds to control root weevils in blueberry fields, but at levels inferior to its ability in citrus orchard soils. We demonstrated that EPN are challenged by natural enemies to a higher degree in pine bark than soil. A common soil fungus that was especially prevalent in pine bark mulch was shown capable of attracting EPN and fungivorous insect species by emitting identified volatile compounds, while repelling a root weevil pest that does not feed on fungi. We also validated the utility of low volume irrigation systems to deliver EPN evenly and efficiently in berry fields in Florida and Egypt. Entomopathogenic nematodes increased yield of strawberry in Egypt, whereas trials in Florida blueberry are ongoing for logistical reasons.
Year 1 Project Progress Summary (Submitted June 2017)
The importance of strawberry and citriculture to both Egypt and USA is reflected at several levels involving economics of local and export markets and the effects of horticultural practices on the society and environment. Both countries will benefit from increasing and stabilizing their fruit production and quality by methods that do not degrade the environment. Our overall objective is to enhance strawberry and citrus production through the use of improved bio-pesticides, various commonly used organic mulches, and horticultural practices that foster the conservation of naturally occurring biological organisms.
To achieve our first objective, surveys were conducted at several distant Egyptian fields of both strawberry and citrus to characterize the indigenous EPNs which may be more adapted to and pose fewer threats to the existing soil biodiversity. Three regions across Egypt were sampled: Beheira; Qalyubia, Ismailia and Sharqia regions. Ten to fifteen fields from each region (field’s selection varied in their soil type from coarse and fine soil texture, fumigated or not fumigated). Composite samples consisting of 20 soil cores were collected to a depth of 0-30 cm using a soil probe. Four samples from the same area of each field were collected using zig-zag patterns. Each sample was thoroughly mixed and divided into two subsamples (approximately 1 kg each) for nematode extraction and a third smaller (250 g) subsample for soil characterization. One subsample was baited with insect larvae to recover and identify EPN species and 250 g from the other sample soil were extracted using direct sieving decanting techniques. Nematodes and any other microorganisms recovered from each sample were concentrated in 1.5-mL micro-centrifuge tubes with 95% alcohol. All samples were kept at the room temperature for DNA extraction. Molecular primer/probe sets will be used for the first time in Egypt to better characterize EPN communities that are adapted to different edaphic habitats.
Year 2 Project Progress Summary (Submitted June 2018)
Citriculture and berries including strawberry, blueberry and blackberry are very important, have a very high cash value for the local, and export markets to both Egypt and USA. In the last decades, researchers worldwide have been looking for new safe, environmentally friendly methods to manage some of the harmful insects to such crops. Our overall objective is to enhance the production of such crops with improved bio-pesticides to avoid or lessen the use of chemical pesticides, which may cause environmental and health hazards. In addition, various commonly used organic mulches, and horticultural practices that foster the conservation of naturally occurring beneficial organisms were tested.
The application of entomopathogenic nematodes (EPNs) in blueberry in Florida is complicated by the near-universal use of pine-bark mulches or amendments to reduce soil pH. We compared the efficacy of the EPN Steinernema riobrave (30 infective juveniles/cm2 soil surface) against caged, sentinel Diaprepes abbreviates weevil larvae buried either in bare soil or in beds of pine bark, pine bark mixed with composted chicken manure, or pine bark amended soil beds covered with woven, landscape fabric. Seven days after S. riobrave application, cages were recovered, mortality assessed, and cadavers placed on White traps. Sentinel mortality did not differ significantly between the bare soil (83%), fabric-covered soil (75%), mounded pine bark with manure (60%) or mounded pine bark (48%). However, 80% of sentinels from bare soil produced S. riobrave or bactivorous nematodes that compete with S. riobrave, in contrast (P=0.05) to fabric-covered soil (35%), compost plus pine bark (25%) or pine bark (20%). Sentinels in compost plus pine bark produced cadavers (43%) infested by mites or Fusarium sp. at higher rates (P=0.05) than those in fabric covered soil (25%) or pine bark (23%). Just 2% of sentinels in bare soil produced cadavers with mites or Fusarium sp.
A field experiment with blueberry plants were designed using 2 varieties, Emerald and Kestrel. Eight plants from each variety were planted in each of twelve, 24-30 inch wide beds. The beds were composed of one of the following soil amendments, pine bark, pine bark mixed with composted chicken manure, or pine bark amended soil beds covered with woven, landscape fabric. For each blueberry variety, four plants were infested with 15 neonate larvae, and after six weeks two plants of each variety in each plot were treated with EPN (Steinernema riobrave) at 30 infective juveniles/cm2 soil surface. The four remaining plants of each variety in each plot were left as untreated controls. Prior to adding EPN a plant vigor index (0-5, five being healthiest) varied significantly for mulch (P = 0.0001) and variety (P = 0.0001) and there was an interaction between variety and Diaprepes root weevil (P = 0.006).
To maximize the application efficiency of EPN in blueberry fields, we have investigated their delivery through drip irrigation. Five million nematodes were injected into a single, 220 foot long irrigation line during 15 minutes, and EPNs were collected from individual drippers for 25 minutes. The line was then cut into segments and remaining nematodes were rinsed from each section. Relatively few nematodes remained in the line and although there was a trend of increased recovery of EPN with distance until the last section, the efficiency was nearly 100%. Based on the prior experiment we tested whether the EPN could be delivered efficiently across a field. Two billion nematodes were applied at the irrigation pump that supplies water to approximately 21 acre of blueberry. We collected EPNs in a 410 foot long irrigation line installed 1,100 feet from the injection point. Again, the efficiency was high, actually exceeding the estimated number applied by five percent, which was due to the production practice of overpacking the material somewhat to account for potential loss of viability over time.
Based on these trials, we conclude that Florida blueberry growers can efficiently applied EPN via their irrigation system. We are now focusing on the efficacy of different species in the various mulch materials to determine if EPNs can provide adequate control of Diaprepes root weevil.
Surveys were conducted for the second year at several distant Egyptian fields of both strawberry and citrus to characterize the indigenous EPN species. Two regions across 2 Egyptian governorate (Qaliobyia and Behera) were sampled in March 2018. Samples were collected as described in the previous reports. One subsample was baited with Gallaria larvae to isolate entomopathogenic nematodes (EPNs). In this survey, no EPNs were detected when soil was baited with Gallaria larvae. To recover and identify entomopathogenic nematode (EPN) species from soil, 250 g soil were extracted using sugar centrifugation techniques. Nematodes and any other microorganisms recovered from each sample were concentrated in 1.5-mL micro-centrifuge tubes with 95% alcohol. DNA from all samples will be extracted and stored at -20 C until use. Species-specific primers and probes will be used to identify EPN species. Real-time PCR or the Next Generation Sequence (NES) will be used to identify EPN species and other organisms in soil. Sixty-seven samples were also collected from citrus orchards in two surveys and baited with Galleria mellonella insect larvae to detect EPNs. We extracted forty-four isolates of EPN from eleven citrus orchards. The positive samples are being examined to identify and characterize the species of EPN. Those unknown EPN isolates were tested against the scarab beetle (Temnorhynchus baal) larvae. The test results are reported in the semi Annual report for the reporting period January 1 2018 until May 31st 2018.
Year 3 Project Progress Summary (Submitted June 2019)
In Florida
Citrus: Growers rely on a single entomopathogenic nematode (EPN) species (Steinernema riobrave) to control the citrus root weevils Diaprepes abbreviatusand Pachnaeus litus. The nematode is just once or twice annually, due to cost. However, EPN augmentation provides control for a matter of weeks leaving a large window between applications for weevil population growth. Due to the disease huanglongbing, there is a much higher than normal replanting of young citrus trees. Growers can afford to treat these young trees more frequently due to the smaller root volume. This provides an opportunity for more effective pest management by reducing the window between the EPN applications. We treated small areas of soil (0.66 M diameter) with recommended rates of S. riobrave and monitored the effects on buried sentinel weevil larvae. Results were encouraging, with 70% mortality of the insects at the time of treatment and persistence up to 6 weeks in which sentinels were killed at 2.5 times the rate of controls Further, there was significant movement of the augmented EPNs beyond the treated area for up to 6 weeks.
Assessing the EPN community structure in an ecoregion can help reveal their biological control potential against important crop pests. In order to assess the use of high throughput Illumina sequencing to characterize naturally occurring EPNs and their natural enemies we compared the approach to our standard methodology (qPCR). We compared qPCR (published data) and metabarcoding to characterize food webs using DNA from soil samples from two ecoregions in Portugal. All EPN species detected by qPCR were also detected by metabarcoding. The EPN species and nearly all free-living nematodes detected by both processes were highly correlated. Metabarcoding also detected more EPN species than did qPCR. Sample accuracy, measured by the fit of Taylor’s Power Law to data from each method, was significantly better using metabarcoding. Canonical correspondence analysis also revealed the same abiotic variables (pH, and clay content) as most related to the community variation in both data sets. Our results suggest that metabarcoding may provide the most cost-effective and accurate means of assessing soil food webs of methods currently available. We shall use this approach to evaluate EPNs and associated food webs in citrus orchards in a transect across the Mediterranean comprising the Peloponnese, Crete, and the Egyptian delta and desert regions.
Berries: Based on previous laboratory results indicating more intense competition between EPNs, fungi and mites for insect cadavers in pine bark mulch compared to soil, we buried caged, sentinel weevil larvae in field beds of blueberry and treated with S. riobrave. Examination of the insect cadavers after seven days confirmed that microarthropods present a formidable challenge to the EPNs in bedded pine bark as opposed to soil. The mites in these beds reproduce on the insect cadaver tissues and they also prey voraciously on the nematodes. The results suggest that while S. riobrave is documented to be a superior EPN species for control of weevil larvae in soil, other EPN species may kill weevils more effectively in pine bark and even compete more strongly with other organisms for the cadaver. We compared the efficacy of 3 EPN species in laboratory assays using either soil-filled or pine bark filled cartons containing buried Diaprepes root weevil larvae. Whereas S. riobrave was the most effective biocontrol agent in soil, it was the least effective in pine bark. By contrast, Steinernema carpocapsae was least effective in soil and most effective in pine bark. Therefore. A second trial comparing S. riobrave and S. carpocapsae was conducted in the field. In contrast to the laboratory trials described in our previous report this year, the performance of S. riobrave was superior to that of S. carpocapsae in bark mulch and in soil. Additional trials are required to resolve these conflicting results. An ongoing trial will compare 1) untreated control plots with 2) plots treated with S. riobrave EPNs, 3) foliar insecticides, or 4) EPNs + insecticides.
Laboratory trials were conducted to evaluate the potential use of volatile compounds to enhance biological control of weevils by naturally occurring EPNs. Using headspace solid-phase microextraction (HS-SPME) combined with gas chromatography mass spectrometry (GC-MS) analysis, two insect-attracting volatile organic compounds (VOCs) were detected from the insect-parasitic fungus Fusarium solani. Bioassays showed that both compounds attract entomopathogenic nematodes (EPNs) on a species-specific basis. Both compounds are highly attractive to fungivorous insects such as fruitflies, fungus gnats and rove beetles. EPNs may have evolved to exploit these VOCs as a means of encountering fungivorous insects. Ongoing trials are testing whether these compounds could function as baits to facilitate host finding of fungivorous arthropod pests by EPNs.
In Egypt
Surveys were conducted for the second year at several widely distant Egyptian fields of both strawberry and citrus to characterize the indigenous EPN species. Two regions across 2 Egyptian governorates (Qaliobyia and Behera) were sampled several times. Samples were collected as described in the previous reports. Samples from strawberry fields were baited with Gallaria larvae to isolate entomopathogenic nematodes (EPNs), but none were detected. To recover and identify entomopathogenic nematode (EPN) species directly from soil, 250 g soil were extracted using sugar centrifugation techniques and preserved in ethanol. DNA from all samples will be extracted and stored at -20 C until use. Real-time PCR or the Next Generation Sequencing (NES) will be used to identify EPN species and other organisms in soil.
Thirty eight EPN isolates (all identified as H. indica) obtained from citrus orchards in 2017 and maintained for several generations in the laboratory were tested for efficacy against larvae of the scarab beetle Temnorhynchus baal collected from strawberry fields. The mean corrected mortality induced by indigenous H. indica population in T. baal larvae was > 98.57% for 15 populations originally from sandy soil and 23 from loamy sand soil. Overall average of infective juveniles (IJs) produced per T. baal larva was about 41,000. The average number of emerged nematodes per larva for the 15 EPN populations in sandy soil, (46,960 IJs/grub), was significantly (P < 0.001) higher than that (36,502 IJs/grub) of 23 EPN populations in loamy sand soil.
Two ongoing field experiments were initiated in El-Behera (reclaimed area) and ElQalioubia (Nile river region) governorates. Strawberries were planted 20 days after mulching each farm with poultry manure, buffalo manure, or both together. An untreated (non-fertilizer mulching) check was left as a control. Commercial EPNs (Heterorhabditis bacteriophora; Nemasys G, BASF corporation) were applied via drip irrigation in 2018 and 2019 as bio-insecticides against strawberry scarab beetles (Temnorhynchus baal). The experiments will be conducted through 2020 to evaluate the efficacy of EPNs against scarab beetles in a variety of soil matrices.
Year 4 Project Progress Summary (Submitted June 2020)
Florida research updates for the June 1 - December 31, 2019 has been reported in the second Semi-Annual meeting submitted in January 2020.
In Egypt
Three of the Egyptian project team visited the faculty of agriculture, Zagazig university where they displayed and operated the in vivo entomopathogenic nematode mass production system (Fig. 1) at the university before handing it over to Dr. Ramadan El Ashry (who works there) to follow up such an activity. Our end in view is to solve limitations in expanding biocontrol efforts which are further aggravated by the lack of awareness of efficient implementation methods by resource-poor farmers as well as limited knowledge of these biocontrol agents by extension personnel who advise these farmers. Insecticidal nematodes have been developed globally (marketed on four continents) as alternatives to toxic and expensive chemical pesticides. In most countries, small companies produce the majority of biopesticides. Our goal is to build several technology bases (one of them at the faculty of agriculture, Zagazig university) that help to spark the development of a biopesticide industry in Egypt.
Biological control agents (BCAs) are increasingly used against various plant-parasitic nematode (PPN) pests and offer a favorable alternative to hazardous chemical nematicides (Fig. 2). Yet, their lack of efficacy, inconsistent field performance, and/or unfavorable economic factors have generally relegated them to a relatively small sector of pesticide market. Efficacy and biocontrol success can be boosted via holistic grasping of soil biological and ecological factors. Therefore, farmers and growers should consult agricultural extensions to give better directions for their use. Main points for success in using these BCAs should include improved sampling, grasping BCAs interactions with soil biota and ecology, cost-effective use of BCAs, genetic manipulation for better PPN control, grower acceptance and awareness-raising of BCA techniques, and commercial application.
Budget conscious choice of different reliability levels associated with fixed, cost-determined, sample sizes was presented. Pre-defined sample costs usually provide a basis of estimating the accuracy or reliability of nematode sampling especially in case of limited fund. Therefore, levels of sampling accuracy for the citrus nematode could be calculated which would give a primary approximation of expenditure especially when the farmer has fund shortage. For example, different levels of accuracy are estimated along with their corresponding costs for two sampling methods of the citrus nematode in infested orchards. Yet, if such an accuracy level were a cause for concern, it could be minimized by collecting, recovering, and counting more samples per plot. Higher precision than the commonly used one is recommended when the economic threshold figure for the targeted nematode species lies close to the sample mean. Recent developments in sample collection and processing may facilitate such an adoption. Such and more relevant information could be found on the following link: https://doi.org/10.1186/s42269-020-00298-9*
Various approaches to minimize pest control costs, optimize application and enhance efficacy of the management measures especially when safe bio-pesticides or biocontrol agents are used should rely on grasping the complex network of interactions among biotic and abiotic factors in intimate contact with these BCAs to maximize their gains via safe and skillful application and advanced technology. Therefore, strawberry field surveys were started in three Egyptian governorates which are most famous for strawberry cultivation. Ninety soil and root samples were collected from different strawberry cultivars (five composite samples per site and six sites per a governorate). Samples were taken in December 2019 and again in February 2020 (i.e., about two and four months after transplanting of strawberry). Results of the encountered microorganisms in the plant rhizosphere that may characterize the examined sites are detected and identified. We plan to follow up such characterization as a pre-requisite for effective biocontrol strategies.
Since entomopathogenic nematodes (EPN) can provide a substantial control, especially of the root feeding larval pests, a recent study by the project team examined beneficial traits of an indigenous EPN Heterorhabditis bacteriophora (Hb-EG strain), to identify superior biocontrol candidates for suppression of the scarab beetle Temnorhynchus baal larvae as serious pests of strawberry in Egypt. The nematodes were applied to infect the greater wax moth, Galleria mellonella cadavers, to represent natural emergence from the host in laboratory and under field conditions. Its average yield was 49604 infective juveniles (IJs) per G. mellonella larva. Overall averages of nematode-induced mortality in G. mellonella larvae were (4.63, 3.12, and 1.92) at 4, 8, and 12 weeks, respectively, after continuous weekly baiting with 5 cadavers. Nematode capability for infection and reproduction ranged from 72 to 26% one to five months, respectively, after field inoculation of the infected larvae into the strawberry rhizosphere. The number of IJs, moved to the North of the rhizosphere, was significantly (P = 0.05) less than that moved to the South or the East as reflected by the numbers of infected insects. The factors that may have a marked influence on EPN foraging behavior, persistence, and movement direction with implications for harnessing them as biological pest control agents were discussed in a paper published in year 2020.
The efficacy of beneficial bacterial strains, namely three Bacillus pumilus isolates, for controlling black root rot disease of strawberry plants was examined under laboratory and field conditions. The tested B. pumilus isolates significantly reduced the growth area of the pathogenic fungi causing the black root rot disease. The highest reduction was obtained with isolates no. 2 and 3 which reduced growth area more than 83.6, 85.2 and 89.0 % for the fungi Fusarium solani, Rhizoctonia solani, and Pythium sp. respectively. Under field conditions, all the tested bacterial isolates significantly reduced the disease. The most effective isolates were B. pumilus no. 2 and 3 which reduced the disease incidence by 64.4 and 68.9 % as well as disease severity by 65.3 and 67.3 %, respectively The fungicide Actamyl showed significant level similar to that of the best isolates. Bacillus pumilus isolates significantly increased fresh and dray weight of strawberry plants and increased strawberry yield; isolates no. 2 and 3 increased yield by 66.7 and 73.3 %, respectively.
Two ongoing field experiments are being monitered in El-Behera (reclaimed area) and El-Qalioubia (Nile river region) governorates. At each season, strawberries are planted 20 days after mulching each farm with poultry manure, buffalo manure, or both together. An untreated (non-fertilizer mulching) check was left as a control. Commercial EPNs (Heterorhabditis bacteriophora; Nemasys G, BASF corporation) are applied via drip irrigation in 2018 and 2019 as bio-insecticides against strawberry scarab beetles (Temnorhynchus baal). The experiments are being conducted through 2020 to evaluate the efficacy of EPNs against scarab beetles in a variety of soil matrices. Although the nematodes can effectively control the scarab grub, we need to investigate the best control method relative to the applied mulching.
This article is not produced by the National Academies of Sciences, Engineering, and Medicine and may not represent the views of the institution.
Year 5 Project Progress Summary (Submitted June 2021)
The overall aims of this project are to deliver environmentally safe and profitable methods of managing soil dwelling pest insects to growers of blueberry, strawberry and citrus. We focus on the use of insect killing nematodes (called EPN) that can be formulated commercially and sprayed on the soil where they migrate to find and kill the target insects. Thus, we study how to effectively use these commercial products and we also study their fate in soil after application in order to discover ways to prolong their usefulness following application. We also focus some of the research on discovery of naturally occurring species of EPN because these species are often better adapted to local conditions. Finally, we seek to understand what physical and biological properties of soil habitats regulate populations of EPNs in order to discover cultural practices that growers can employ to enhance the services of these nematodes.
In Egypt the primary pest target is a species of white grub that has become increasingly damaging as it spreads into new areas of strawberry production by movement of organic fertilizers. One of the most important results to date of our research is that application of the EPN throughout blueberry and strawberry fields can be done at no cost by injecting them into the low-volume irrigation systems. Our results, contrast with other reports in that we have demonstrated repeatedly that EPNs are delivered uniformly and very efficiently over fields larger than 30 acres. Using this application method, our results after two years of testing in Egyptian commercial strawberry fields at both Qualubiya and Behira governorates show that EPN use increased yields by at least 10%, regardless of the form of fertilizer (synthetic or manure) applied in the fields. This level of crop improvement would provide between $1500-4000 per acre of extra income to growers depending on crop prices and whether the berries are marketed locally or for export. We will continue these trials for one additional year before reporting the results.
In Florida the target pest is a root weevil that is moving from the citrus orchards into newly planted blueberry fields. There is a great deal of information about how different EPN species perform in managing this pest in citrus orchards. However, whereas citrus is grown in the soil, blueberry in Florida is planted in raised beds constructed of pine bark (to reduce the soil pH) mixed with soil and various other vegetable and manure organic materials. Our initial experiments for this project, in which EPN were applied by spraying them on the blueberry bed surfaces or on the mulch surfaces of laboratory bioassays, indicated that EPN species used in citrus can kill the insect in these mulches, albeit at a somewhat lower rate of pest mortality that in pure soil. This work also revealed much greater competition between EPN and certain soil microorganisms than documented previously in soil, forming the basis for a great deal of ongoing and previously reported research supported by this project. We also found clear evidence that an EPN species that performs poorly against the weevil pests in soil, performed better in pine bark than did the EPN species preferred for use in citrus.
We then initiated large-scale commercial field trials in which we demonstrated that, as in Egypt, the EPN can be delivered via irrigation from an injection point, through drip-tape irrigation lines, uniformly and efficiently in berry fields >30 acres. However, in two large field trials in which EPNs were delivered via drip-tape irrigation lines, neither nematode killed appreciable numbers of weevil pests. Both trials were conducted nearly simultaneously during an abnormally rainy period and it was apparent that the drainage in the blueberry beds was exceptionally poor. We are reasonably certain that the lack of efficacy was due to the saturated condition of the beds (nematodes do not swim, they move in films of water on soil surfaces), but we need to prove this. These experiments have been delayed because a USDA insectary that closed due to the pandemic in March 2020 could not provide the necessary weevil larvae to use in the trials. With the reopening of the insectary imminent, we will conduct these final trials during the next six months.
The more basic research supported by the project has demonstrated improved experimental and molecular analysis techniques for studying the soil food webs that regulate the services of naturally occurring EPN. These observations have been used to help design several cultural practices (soil pH regulation, planting hole modifications, etc.) used by growers to improve the naturally occurring biological control provided by these nematodes.
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RHIZOBACTERIAL APPLICATION TO IMPROVE WHEAT CROP AND REDUCE CHEMICAL FERTILIZER INPUTS UNDER DROUGHT STRESS [COMPLETED]
Principal Investigators: Ann Hirsch, University of California, Los Angeles; Saleh A. Saleh, Agricultural Research Center
Overview: During this project, we isolated bacterial strains from Egyptian soils that have the potential to be used as inoculants for dry-land agriculture. This funding allowed us to analyze the soil microbiomes from several sites in Egypt and then isolate, cultivate, and test bacteria that have potential for promoting plant growth, especially in arid environments. However, these microbes need additional study for their ultimate use in agriculture: More needs to be known about: 1) their efficacy in Egyptian agricultural fields, 2) their ability to compete with indigenous microbes, and 3) their biosafety. From what we have learned so far, the majority are safe to use as inoculants. Also, our works demonstrates that it is possible to increase the culturability of the bacteria strains isolated from the wheat microbiome. In general, only ca. 3% of bacteria can be cultured. This strategy (https://journals.asm.org/doi/10.1128/Spectrum.00678-21*) has the potential of increasing the percentage of bacterial species that can be developed as future inoculants for dryland agriculture.
This article is not produced by the National Academies of Sciences, Engineering, and Medicine and may not represent the views of the institution.
Year 1 Project Progress Summary (Submitted June 2017)
The Egyptian research team conducted three collection missions to collect soil samples from the rhizosphere of field-grown wheat, so that the U.S. side could start carrying out the tasks entrusted to it. The soil samples have arrived and will be subjected this summer to both cultivation-dependent and –independent analysis. The UCLA laboratory has recruited Ms. Genova Hernandez and Mr. David Younessi, two undergraduate students, who will assist Dr. Maymon in the analyses of the three different soil samples.
Year 2 Project Progress Summary (Submitted July 2018)
AR-SA">Modern agriculture depends heavily on use of high level of agrochemicals such as fertilizers and pesticides, which have repercussions for both the environment and human health. An emerging alternative to such practices is the utilization of plant microbiomes that can improve plant health and productivity. In this context, the main premise of this project is to enhance the activity of beneficial soil microorganisms for improving growth of wheat plants under drought stress-conditions and low-inputs of chemical fertilizers. We are likely to elaborate new practices by which we explore large proportion of the soil bacterial inventory in order to uncovering the hidden life of soil compared to the traditional methodologies for isolation. We also are also likely to identify bacterial isolates with plant growth promoting activities, which are of great agriculture importance in terms of improving soil fertility and crop yield.
Year 3 Project Progress Summary (Submitted June 2019)
A new movement in farming is taking place that involves restoring degraded soils that are over-fertilized and over-tilled by reducing the amount of fertilizer added and using zero- or no-tillage methods. To reduce fertilizer use, new approaches are needed to promote crop productivity, especially in arid environments that are predicted to get hotter and dryer with climate change.
Our research will develop new practices to explore a large proportion of the soil bacterial microbiome to uncover the hidden life of soil. We will accomplish this by going beyond the traditional methodologies for microbial isolation from soil. In so doing, we may identify and learn more about bacterial isolates that effectively improve the growth of wheat plants using low synthetic N inputs as well as under drought stress. These goals when achieved are of great agricultural importance in terms of improving soil fertility and wheat crop productivity under both normal and drought-stressed agro-climatic conditions.
Year 4 Project Progress Summary (Submitted June 2020)
Modern agriculture depends heavily on the use of high levels of agrochemicals such as fertilizers and pesticides, which have major repercussions for the environment and human health. An emerging alternative to such practices is the utilization of the plant’s own microbiome to improve plant health and productivity. In this context, the main premise of this project is enhancing the activity of beneficial soil microorganisms for promoting growth of wheat plants under drought stress-conditions and low-inputs of synthetic fertilizers. We believe our research will develop new practices to explore a large proportion of the soil bacterial inventory to uncover the hidden life of soil. We will accomplish this by going beyond the traditional methodologies for microbial isolation from soil. In so doing, we may identify and learn more about bacterial isolates that effectively improve the growth of wheat plants using low synthetic N inputs as well as under drought stress conditions. These goals when achieved are of great agricultural importance in terms of improving soil fertility and wheat crop productivity under both normal and drought-stressed agro-climatic conditions.
Year 5 Project Progress Summary (Submitted June 2021)
One of our original project goals was to isolate plant growth-promoting bacteria from soils in Egypt, an increasingly arid agricultural environment, for their potential use as inoculants for growing crops sustainably. Toward this end, we analyzed the soil microbial population and studied the effects of cultivatiible bacteria on plant growth. Towards this end, we have isolated several potential growth-promoting microbes that positively support plant growth and yield in increasingly arid lands. These microbes now need further study not only for their efficacy in dry environments, but also to understand their biosafety in terms of the environment and the people who farm it.
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SUSTAINABLE AGRICULTURAL DRAINAGE IN THE NILE DELTA OF EGYPT [COMPLETED]
Principal Investigators: Mohamed Youssef, North Carolina State University; Ashraf El Sayed Ismail, Drainage Research Institute
Overview: This U.S.-Egypt joint project was initiated between North Carolina State University (NCSU) and the Drainage Research Institute (DRI) of Egypt's National Water Research Center (NWRC) to develop and evaluate new design criteria for agricultural drainage in Egypt that explicitly link the design of drainage systems to crop yields, water quality, and water conservation. The project had three components: 1) regional reconnaissance survey of performance of existing subsurface drainage systems; 2) field experimental study to assess the performance of subsurface drainage systems with three different intensities; and 3) a modeling component to extrapolate the findings of the short-term experimental study over a longer time scale (e.g., 10 to 15 years).
Five sites across the Nile Delta were identified for monitoring during the one-year long regional study of the project. The salinity of irrigation water, drainage water, and groundwater varied among sites. The northern sites and the sites located farther from the freshwater irrigation canals had highest water salinity. There was a strong correlation between water and topsoil salinity for each monitored site. This demonstrates that the drainage needs vary among sites and underscores the need for effective drainage design framework to control salt buildup in the plant rootzone and maintain soil productivity.
The goal of the field experimental study of the project was to investigate the effect of drainage intensity on water quantity, water quality, and crop yield. This two-year study was carried out at an experimental field located at the Zankalon Experimental Station, which is located in the Zagazig Governorate. Three experimental treatments with different drainage intensities were implemented at the three main plots and each treatment was replicated three times at the three subplots of each main plot. Each treatment had the same drain spacing (20 m) but different drain depth (100 cm, 120 cm, and 140 cm). After the instrumentation of the field site, the experiment was carried out over three growing seasons (Corn, 2019; Wheat, 2019-2020; Corn, 2020). The field experiment faced logistical challenges during the two corn growing seasons caused by the COVID-19 pandemic and other reasons beyond the control of the research team. Therefore, the field experiment was successfully conducted only during the 2019/2020 wheat growing season. The irrigation, drainage, groundwater, soil, and crop measurements during the wheat growing season did not show any significant difference among treatments in terms of soil and water salinity and crop yield. This means that the three drainage intensities provided adequate drainage facilitating healthy environment for crop growth. The data collected from only one growing season is not enough to make conclusions about the performance of the different treatment over the long term.
The agricultural water management computer model, DRAINMOD, was used to predict the long-term effects of drainage design on soil salinity, crop productivity, and water use. The model was run using a 10-year weather record. Model parameterization was done based on the data collected during the regional survey study and the field experimental study of this project as well as previous studies. Several scenarios were simulated including drainage systems with varying lateral drain depths (90 cm to 150 cm) and spacings (20 m to 50 m) as well as two salinity levels of irrigation water. Simulated crops were corn as summer crop and wheat as winter crop.
It is planned to use the data collected from the experimental field to calibrate and validate the DRAINMOD model. Then, the calibrated model will be used to simulate different water management systems and proposing a new drainage design criteria according to the findings of the experimental study and model simulations. However, the modeling activities of the project have been delayed because of the COVID-19 pandemic. As expected, optimum crop yield can be achieved by different combinations of drain depths and spacings. Shallower lateral drains must be installed closer to achieve adequate drainage intensity and optimum crop yield. For the simulated conditions (soil type and cropping system), lateral drains that were 90 to 100 cm deep and spaced 30 to 40 m provided adequate drainage and ensured optimum or near-optimum crop yield. Model simulations indicated that salt levels in the plant root zone fluctuated during the year with higher levels during the summer and lower levels during the winter. The drainage systems with less intensity (particularly with shallow drain depths) drain less water, which keep more water in the soil profile for crop use. Therefore, the reduction in drainage intensity can conserve water, which is a scare resource. Finally, model simulations show that the optimum crop yield may not be the overall goal since the drainage intensity that is required to achieve this optimum crop yield could be more costly to install and could waste more irrigation water (higher intensity systems drain more water). Drainage systems with considerably less intensity can achieve “near-optimum” crop yield, with less irrigation water, less cost of installation, and manageable levels of salts in the plant root zone.
Year 1 Project Progress Summary (Submitted June 2017)
Agricultural drainage is essential for crop production in Egypt. Over 78% of Egypt’s agricultural land is artificially drained. Drainage, however, has negative impacts on ground and surface water quality. Drainage mobilizes salts and agricultural chemicals, which may contaminate shallow groundwater aquifers and surface water bodies. Drainage systems must be carefully designed to increase yields, reduce production costs, and minimize nutrient losses from drained farmlands to ground and surface waters. Despite the dramatic changes in farming practices and the availability of water resource, the design criteria for drainage systems in Egypt has not been updated during the last three decades. The goal of this project is to develop and evaluate new drainage design criteria that explicitly link the design of drainage systems to crop yields and profits, water quality, and water conservation. The project start has been delayed and the project is currently behind schedule. The main task of the first year of the project was to conduct a regional study across the Nile Delta to evaluate the performance of existing drainage systems. We have made significant progress in identifying the field sites that will be included in the regional study, which is expected to start in July 2017.
Additionally, a short course was organized in year one for the Junior Researchers of the Drainage Research Institute who are on the Egyptian research team of the project. Topics covered include conducting experimental research and hypothesis testing, field instrumentation to make hydrologic and water quality measurements, effects of agricultural drainage on field hydrology, the nitrogen dynamics and soil salinity, data analysis and presentation, and technical report writing.
Year 2 Project Progress Summary (Submitted July 2018)
A U.S.-Egypt joint project has been initiated between North Carolina State University (NCSU) and the Drainage Research Institute (DRI) of Egypt's National Water Research Center (NWRC) to develop and evaluate new design criteria for agricultural drainage in Egypt that explicitly link the design of drainage systems to crop yields, water quality, and water conservation. The project started in year 1 by conducting a reconnaissance survey across the Nile Delta for regional monitoring of the performance of existing drainage systems that were designed according to the current design criteria adopted by the Egyptian Public Authority for Drainage Projects (the authority in charge of the design and implementation of drainage projects in Egypt). Seven drainage collector sites were selected among a total of identified seventeen collector sites representing soil types, cropping systems, and farming practices in the Nile Delta. The seven selected sites include three sites in East Delta, two sites in Mid Delta, and two sites in West Delta. Data characterizing irrigation and drainage water quantity and quality, soil properties, crop yield and farming practices are being collected for each field site. The regional monitoring started in February 2018 and will continue for two crop growing seasons. The collected data will be used along with computer models to evaluate the current drainage design criteria in Egypt. The project team is currently communicating with farmers and land owners at each monitored field site to educate them on the potential benefits of the project, ensure cooperation and sharing information on farming practices. The project team also has engaged the leadership of the Egyptian Authority for Drainage Project to get their feedback on the ongoing research and explore opportunities for collaboration.
Year 3 Project Progress Summary (Submitted June 2019)
A U.S.-Egypt joint project has been initiated between North Carolina State University (NCSU) and the Drainage Research Institute (DRI) of Egypt's National Water Research Center (NWRC) to develop and evaluate new design criteria for agricultural drainage in Egypt that explicitly link the design of drainage systems to crop yields, water quality, and water conservation. During the last year, the regional monitoring continued till the end of the second monitored cropping season at the seven selected sites in the Nile delta of Egypt. Data characterizing irrigation and drainage water quantity and quality, soil properties, crop yield, and farming practices were collected for each field site. The collected data were analyzed to study the relationship between the drainage intensity and crop yield, drainage volumes, soil salinity, and nitrogen leaching losses.
The results of this regional analysis have been utilized during the development of the new design criteria. The drainage water management model, DRAINMOD was used to simulate the hydrology, carbon and nitrogen dynamics, salinity, and crop yield for the conditions (crop rotation, farming practices, soil type, irrigation water management, and drainage intensity) of the seven monitored sites across the Nile Delta. Several model runs were conducted to identify for each site the drain depth and spacing that will lead to the highest predicted yield, prevents water-logging, and control soil salinity with least nitrogen losses and drainage outflow.
An experimental field site (Zankalon research station – east delta) was selected for a two-years experiment to assess the newly developed drainage design criteria. The experimental field site with an area of 9 feddans “acres” was divided into 3 plots. The drainage system installed in the first plot was designed according to EPADP’s (Egyptian Public Authority for Drainage Projects) current design methods. The drainage systems installed in the other two plots were designed according to two different proposed design criteria to conduct a side-by-side comparison of the performance of the three drainage systems.
Year 4 Project Progress Summary (Submitted May 2020)
A U.S.-Egypt joint project has been initiated between North Carolina State University (NCSU) and the Drainage Research Institute (DRI) of Egypt's National Water Research Center (NWRC) to develop and evaluate new design criteria for agricultural drainage in Egypt that explicitly link the design of drainage systems to crop yields, water quality, and water conservation.
An experimental field site (Zankalon research station – east delta) was selected for a two-years experiment to assess the newly developed drainage design criteria. The experimental field site with an area of 9 feddans “acres” was divided into 3 plots. The drainage system installed in the first plot was designed according to EPADP’s (Egyptian Public Authority for Drainage Projects) current design methods. The drainage systems installed in the other two plots were designed according to two different proposed design criteria to conduct a side-by-side comparison of the performance of the three drainage systems.
During the last year, three experimental treatments (replicated three times) with different drain depths (100 cm, 120 cm, and 140 cm below soil surface) were investigated in phase 2 of the project. All treatments have the same drain spacing (20 m). The experimental field was planted with maize and wheat during the last year and we have implemented a monitoring plan with specific measurements (Irrigation and drainage amounts, groundwater table depth, groundwater quality, irrigation and drainage water quality, soil chemical and mechanical analysis, crop yield, farming activities, and collecting weather data).
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TRANSDISCIPLINARY COLLABORATIVE CENTER (TCC) FOR COLORECTAL CANCER RESEARCH [COMPLETED]
Principal Investigators: Mona Fouad, University of Alabama, Birmingham; Waleed O. Arafat, Alexandria University
Overview: The objective of this project, led collaboratively by the University of Alabama at Birmingham (UAB) and the University of Alexandria Faculty of Medicine (UAFM), is to establish a Transdisciplinary Collaborative Center for Colorectal Cancer Research (CRC) in Egypt. The Center’s long-term goal is to reduce the high rates of illness and death due to colorectal cancer in the Egyptian population.
The first aim of the project is to identify demographic and socio-cultural factors associated with using screening for the prevention and early detection of colon cancer in Egypt. To do this, we conducted seven focus groups with Egyptians with no history of colorectal cancer as well as 17 interviews with Egyptian primary care physicians and specialists. Findings from the one-on-one physician interviews examined healthcare providers’ perceptions and practices of CRC screening and identified physician-level barriers and facilitators to CRC screening. Physicians felt that there was a lack of emphasis on prevention and believed that only high-risk patients should be screened. In addition, these providers were concerned about the invasiveness of colonoscopy and how patients perceived screening and their fear of a cancer diagnosis. They reported that inadequate training among laboratory providers was problematic, as well. In addition, they felt that barriers were multilevel and required a multilevel response in order to successfully lower morbidity and mortality of CRC. Some suggestions included providing screening tests at no or low cost, making tests widely available, and creating a nationwide media campaign to educate the public regarding prevention and early detection that highlights younger-age prevalence. Focus groups were held with 7-8 participants per group. Most participants knew very little about CRC in general and were unaware of the lower-age prevalence of CRC in Egypt. Participants discussed individual-level barriers to screening, which included fear and anxiety about the procedure, high cost, lack of testing availability, and the fear being diagnosed with cancer. They felt that making screening test kits convenient, low-cost or free, and obligatory, would increase testing and save lives. Based on the results, we designed a CRC intervention that was tested in a pilot later study.
Our second aim was to identify sub-populations in Egypt at high-risk for aggressive colorectal cancer. Tissue samples were identified and sent to the University of Alabama at Birmingham for analysis to identify and validate the clinical utility of molecular markers identified in U.S. colorectal cancer tissues and tissues from Alexandrian patients. Two Egyptian research fellows have visited the University of Alabama at Birmingham have been trained to conduct the analysis. The microbiome profile of 20 Egyptian colorectal patients and 8 healthy Egyptians have been analyzed via 16S rRNA gene sequencing data from paired biopsies from colorectal patients. This analysis has revealed that young colorectal cancer patients have an absence of specific beneficial microbiota.
One third of our CRC patient population was under 50 years old at the time of diagnosis with CRC, and most were female. Healthy controls were even younger than CRC cases, and most were females. There were differences in relative abundances of bacteria between healthy controls and those with CRCs. Analysis showed a low abundance of Mitsuokella multacida, a short-chain fatty acid (SCFA)-producing bacterium, in CRC patients when compared to healthy individuals. In particular, this trend was evident for older CRC patients (= 50 years); of note, this bacterium was absent in younger patients (<50 years) (adj. p-value = 0.01). Further, there was a high abundance of Fusobacterium nucleatum in all CRC patients compared to healthy individuals (adj. p-value = 0.04). In cross-talk analysis for healthy controls, elevated abundance of M. multacida was inversely associated with macrophage abundance (global p-value =0.055). For Egyptian patients, the absence of SCFA-producing multacida in younger patients may be a reason for early onset of CRC. These findings suggest that the oncoprotective effect of Mitsuokella multacida should be further investigated.
Our third aim focused on survivorship by identifying dietary and physical activity patterns among colorectal cancer survivors in Egypt. Because of challenges recruiting survivors for Aim 3 due to the low numbers of survivors presenting for follow-up appointments in the public oncology clinic we identified for this study, we extended the eligibility criteria to survivors in active treatment. We also expanded to private oncology clinics. In Phase I of Aim 3, we assessed physical activity levels and dietary intake among current colorectal cancer patients and survivors. Assessments included the Global Physical Activity Questionnaire (GPAC) and the Godin Leisure-Time Exercise Questionnaire (GLTEQ) and 24-hour diet recalls taken at 3 time points. Participants could also wear an accelerometer for seven days. We recruited 86 participants, 29 of whom agreed to wear an accelerometer. All participants completed the questionnaires. Participants meeting the GPAC recommendations (63%) were less likely to be married and those meeting GLTEQ recommendations (14%) were more likely to be female and had cancer diagnosed in an early stage; 41% of accelerometer wearers met recommended minutes. Considering multiple sources of physical activity, beyond recreation, is important to fully understand physical activity behaviors. Implementing behavioral interventions aimed at increasing physical activity would be an important component of a treatment regimen and survivorship plan post-cancer treatment.
This aim included a qualitative Phase II in which we conducted 12 interviews with a subset of participants in Phase I. Findings indicate that although some interviewees expressed an understanding of elements of a healthy diet, most could not explain the benefits. And, most were not familiar with the associations between diet and cancer, including specific foods that could decrease cancer risk. In terms of barriers to consuming a healthy diet as a cancer survivor, participants cited cost and that healthy foods were not tolerated. Barriers to physical activity included side effects of chemotherapy and general weakness, depression, and structural issues related to the neighborhood living environment. Providing an adequate place for physical activity and having social support were mentioned as facilitators for physical activity. Although they did not seem to understand the link between physical activity and cancer, nor guidelines for physical activity, a few participants did mention that physical activity could improve the cardiovascular system, mental health and muscle and bone health. In terms of coping mechanisms, participants discussed faith, social support and optimism, with optimism mentioned the most (by half the participants) and the others mentioned by one third. Several survivors showed their readiness to help other patient go through their treatment journey, they have been doing that spontaneously before. Findings indicate that a health promotion program for cancer survivors would include education and nutrition, physical activity and coping.
Our final aim was to ensure sustainability through a structured research training program for Egyptian investigators. This was accomplished through (1) An ongoing training program in which we hosted 7 training events, and (2) in depth mentored research of 7 Egyptian trainees and 2 American trainees. We hosted trainings in Alexandria that included topics such as CRC survivorship and prevention, qualitative and quantitative research methods, data collection protocols, cancer biomarker development and validation, and clinical trials. A concluding workshop was held in June 2022 in Alexandria. Seven Egyptian junior investigators were chosen by the research team to participate in the mentored training program. They participated in the training workshops offered, but each included a research internship in the US at UAB. Two US medical school students were also chosen to participate in the program. Trainees participated in didactic lectures over zoom and in person while at UAB, and they each worked on a specific project and submitted papers and/or grants based on their project.
The significance of this project is that the Transdisciplinary Collaborative Center will serve as the basis for a fully developed cancer research program in Egypt that will continue to grow after the end of the current funding and implement independent intervention studies in the areas of basic, clinical, social and behavioral, and outcomes research in order to reduce colon cancer incidence and mortality among the Egyptian population. For the US, the Transdisciplinary Collaborative Center will advance discovery, implementation, and dissemination in the areas of: 1) identifying high-risk populations based on ethnicity and environmental exposures; 2) developing and implementing culturally appropriate interventions to increase colorectal cancer survivorship; and 3) development and dissemination of culturally appropriate messages to enhance colorectal cancer prevention in multicultural communities.
Year 1 Project Progress Summary (Submitted June 2017)
The objective of this project, led collaboratively by the University of Alabama at Birmingham (UAB) and the University of Alexandria Faculty of Medicine (UAFM), is to establish Transdisciplinary Collaborative Center (TCC) for Colorectal Cancer Research in Egypt. The Center’s long-term goal is to reduce the high rates of illness and death due to colorectal cancer in the Egyptian population.
The first aim of the project is to identify demographic and socio-cultural factors associated with using screening for the prevention and early detection of colon cancer in Egypt. To do this we will conduct focus groups with Egyptians with no history of colorectal cancer as well as interviews with Egyptian primary care physicians and specialists. During this reporting period, procedures and protocols were established. Four UAB investigators visited Alexandria from 3/5/2017 – 3/11/2017 and trained focus group facilitators and interviewers on procedures and protocols for obtaining informed consent and conducting focus group sessions and qualitative interviews. All documents, including the focus group guide, interview guide, consent forms and demographic intake forms have been translated from English to Arabic, with back translation for verification. The focus group and interview guides were pilot tested with staff being trained as facilitators, co-facilitators and interviewers during the March training week. A comprehensive operations manual has been developed to serve as a guide for staff conducting the focus groups and qualitative interviews. The UAB IRB has approved the project and the AUFM has granted provision approval with final approval expected with the month. Recruitment and implementation of focus groups and qualitative interviews is planned for July-August 2017.
Our second aim is to identify sub-populations in Egypt at high-risk for aggressive colorectal cancer. We will do this through identifying and validating the clinical utility of molecular markers identified in US colorectal cancer tissues in tissues collected form Egyptian patents. These will be used to predict response to therapy, disease recurrence, and survival in Egyptian patients. During this reporting period, extensive planning has occurred. The Material Transfer Agreement been submitted to UAB to permit the exchange colorectal cancer tissues and data between UAB and Alexandria.
Our third aim focusses on survivorship by identifying dietary and physical activity patterns among colorectal cancer survivors in Egypt. The March visit of UAB investigators to Alexandria also included training on the collection dietary and physical activity data. Investigators have identified culturally appropriate 24-hour dietary recall measures and physical activity measurement protocols and they are in the process of being translated. The IRB HSP is being finalized pending the translation of all forms. Investigators from Alexandria will travel to UAB in August, 2017 to observe and participate in data collection of dietary and physical activity data. Recruitment of Egyptian participants will begin in September of 2017.
Our final aim it to ensure sustainability through a structured research training program for Egyptian investigators. This will be accomplished through a research training program that includes a face-to-face intensive training, distance-based didactic learning component, mentoring, and research experience through a short-term internship on UAB campus. During this reporting period, two training sessions occurred in Alexandria, Egypt. One was a scientific day in January, 2017 entitled, “Nutrition and Cancer: An Optimistic Look” and included several sessions on colon cancer prevention, screening, treatment, and management led by Egyptian investigators on this project. One UAB investigator also presented several sessions. As mentioned earlier, four UAB investigators led a face-to-face training week in March, 2017 that included the topics of focus group facilitation, qualitative interviewing, and physical activity and dietary data collection. A total of 25 Egyptians were trained in these qualitative and quantitative data collection methods.
The significance of this project is that the TCC will serve as the basis for a fully developed cancer research program in Egypt that will continue to grow after the end of the current funding and implement independent intervention studies in the areas of basic, clinical, social and behavioral, and outcomes research in order to reduce colon cancer incidence and mortality among the Egyptian population. For the US, the TCC will advance discovery, implementation, and dissemination in the areas of: 1) identifying high-risk populations based on ethnicity and environmental exposures; 2) developing and implementing culturally appropriate interventions to increase colorectal cancer survivorship; and 3) development and dissemination of culturally appropriate messages to enhance colorectal cancer prevention in multicultural communities.
Year 2 Project Progress Summary (Submitted July 2018)
The objective of this project, led collaboratively by the University of Alabama at Birmingham (UAB) and the University of Alexandria Faculty of Medicine (UAFM), is to establish a Transdisciplinary Collaborative Center (TCC) for Colorectal Cancer Research in Egypt. The Center’s long-term goal is to reduce the high rates of illness and death due to colorectal cancer in the Egyptian population.
The first aim of the project is to identify demographic and socio-cultural factors associated with using screening for the prevention and early detection of colon cancer in Egypt. To do this, we are conducting focus groups with Egyptians with no history of colorectal cancer as well as interviews with Egyptian primary care physicians and specialists. During this reporting period, we have conducted physician interviews (N=13) and focus groups (N=5). The remainder (3 physician interviews and 3 focus groups) will be completed by July 31, 2018. One UAB team member (Mona Fouad, PI) traveled to Alexandria in October, 2017 to meet with 2 new Egyptian Team members, Dr. Doaa Genena and Dr. Fayek Elwsky, update the AUFM Dean of the School of Medicine and the university President on the project, and observe focus groups in progress and offer advice.
Two Egyptian medical students, who have been conducting the focus group interviews, visited UAB from January 2 through January 18. They were trained in qualitative data collection and analysis, as well as cancer health disparities. From April 21-29, 3 investigators from UAB traveled to Alexandria to work with the medical students mentioned above and 3 others to analyze data collected.
Our second aim is to identify sub-populations in Egypt at high-risk for aggressive colorectal cancer. We will do this through identifying and validating the clinical utility of molecular markers identified in US colorectal cancer tissues in tissues collected form Egyptian patients. These will be used to predict response to therapy, disease recurrence, and survival in Egyptian patients. UAB investigators are planning to host 2 Egyptian pathologists in September, 2018.
Our third aim focusses on survivorship by identifying dietary and physical activity patterns among colorectal cancer survivors in Egypt. We have received IRB approval and are ready to begin collecting data in July 2018 (after the conclusion of Ramadan). A detailed operations manual has been developed for use by data collectors, and the April visit of UAB investigators (mentioned in Aim 1 above) to Alexandria included training new Egyptian team members on procedures for data collection in Aim 3. Training and practice was offered on the collection dietary and physical activity data as well as research methods and research ethics. Four nutrition students and 3 faculty members were trained.
Our final aim is to ensure sustainability through a structured research training program for Egyptian investigators. This is being accomplished through an ongoing research training program that includes a face-to-face intensive training, discussed above. A total of 12 Egyptians, including students, junior faculty and early career physicians, participated in training during this period.
The will serve as the basis for a fully developed cancer research program in Egypt that will continue to grow after the end of the current funding and implement independent intervention studies in the areas of basic, clinical, social and behavioral, and outcomes research in order to reduce colon cancer incidence and mortality among the Egyptian population. For the US, the TCC will advance discovery, implementation, and dissemination in the areas of: 1) identifying high-risk populations based on ethnicity and environmental exposures; 2) developing and implementing culturally appropriate interventions to increase colorectal cancer survivorship; and 3) development and dissemination of culturally appropriate messages to enhance colorectal cancer prevention in multicultural communities.
Year 3 Project Progress Summary (Submitted June 2019)
The objective of this project, led collaboratively by the University of Alabama at Birmingham (UAB) and the University of Alexandria Faculty of Medicine (UAFM), is to establish a Transdisciplinary Collaborative Center for Colorectal Cancer Research in Egypt. The Center’s long-term goal is to reduce the high rates of illness and death due to colorectal cancer in the Egyptian population.
The first aim of the project is to identify demographic and socio-cultural factors associated with using screening for the prevention and early detection of colon cancer in Egypt. To do this, we have conducted focus groups with Egyptians with no history of colorectal cancer as well as interviews with Egyptian primary care physicians and specialists. During this reporting period, we have completed physician interviews (N=17) and focus groups (N=7). In September, an Alexandria University Faculty of Medicine medical student traveled to UAB to complete research training and analyze all physician interview data. Plans for completion of Aim 1 were discussed during a visit to UAB by Dr. Waleed Arafat, PI and Dr. Salah Abdelmoneim, investigator in December of 2018. Another Alexandria University Faculty of Medicine medical student traveled to UAB and was trained worked on the focus group analysis in January of 2019. Preliminary data was used by UAB investigators collaborating with Egyptian partners, to submit a UAB internal pilot grant application, which was awarded in May of 2019.
Our second aim is to identify sub-populations in Egypt at high-risk for aggressive colorectal cancer. During this reporting period, tissue samples were identified and sent to the University of Alabama at Birmingham and analysis is ongoing to identify and validate the clinical utility of molecular markers identified in U.S. colorectal cancer tissues and tissues from Alexandrian patients. Two Egyptian research fellows have visited the University of Alabama at Birmingham have been trained to conduct the analysis. The microbiome profile of Egyptian colorectal patients have been analyzed via 16S rRNA gene sequencing data from paired biopsies from colorectal patients. This analysis has revealed that young colorectal cancer patients have an absence of specific beneficial microbiota.
Our third aim focusses on survivorship by identifying dietary and physical activity patterns among colorectal cancer survivors in Egypt. In November of 2018, three University of Alabama at Birmingham investigators traveled to Alexandria to complete training with nutrition students who would be serving as data collectors. And, in April of 2019, Dr. Doaa Genena, investigator, traveled to the University of Alabama at Birmingham to receive final training on accelerometer utilization and collaborate with investigators on study protocols. Data collection has begun and we have completed data collection on 11 participants. Participant recruitment is ongoing in both public and private clinics as we aim to recruit 120 colorectal cancer survivors into the study.
Our final aim is to ensure sustainability through a structured research training program for Egyptian investigators. This is being accomplished through an ongoing training program that includes a face-to-face intensive training. During this reporting, in November of 2018, three UAB investigators led a face-to-face training that included the topics physical activity and dietary data collection. Five students (3 males, 2 females), 1 junior faculty (female) participated in training. In addition, four Egyptian medical students from the Alexandria University Faculty of Medicine traveled to UAB for training. Two medical students were trained on qualitative methods and worked on analysis of Aim 1 data. Also, two medical technology students from Alexandria University rotated in Dr. Upender Manne’s (co-investigator) laboratory in the Wallace Tumor Institute, UAB Comprehensive Cancer Center, to learn several routine laboratory techniques including, immunohistochemistry, cell culture and western blot techniques in order to complete analysis on tissue samples. Finally, in May, 2019 two workshops were held in Alexandria in conjunction with the Alexandria Society for Cancer Patient’s Care 11th Annual Conference offered jointly by investigators part of the research team. The Cancer Biomarker Development and Validation workshop, led by Dr. Upender Manne and several other UAB researchers, was attended by 55 Egyptian clinicians, scientists and students. The Clinical Investigator Training Program was by invitation. Fifteen Egyptians participated in the training.
The significance of this project is that the TCC will serve as the basis for a fully developed cancer research program in Egypt that will continue to grow after the end of the current funding and implement independent intervention studies in the areas of basic, clinical, social and behavioral, and outcomes research in order to reduce colon cancer incidence and mortality among the Egyptian population. For the US, the TCC will advance discovery, implementation, and dissemination in the areas of: 1) identifying high-risk populations based on ethnicity and environmental exposures; 2) developing and implementing culturally appropriate interventions to increase colorectal cancer survivorship; and 3) development and dissemination of culturally appropriate messages to enhance colorectal cancer prevention in multicultural communities.
Year 4 Project Progress Summary (Submitted May 2020)
The objective of this project, led collaboratively by the University of Alabama at Birmingham (UAB) and the University of Alexandria Faculty of Medicine (UAFM), is to establish a Transdisciplinary Collaborative Center for Colorectal Cancer Research in Egypt. The Center’s long-term goal is to reduce the high rates of illness and death due to colorectal cancer in the Egyptian population.
The first aim of the project is to identify demographic and socio-cultural factors associated with using screening for the prevention and early detection of colon cancer in Egypt. To do this, we have conducted focus groups with Egyptians with no history of colorectal cancer as well as interviews with Egyptian primary care physicians and specialists. During the last reporting period, we completed physician interviews (N=17) and focus groups (N=7). The focus during this reporting period has been completing analysis of the focus group data and writing and submitting papers for publications and abstracts for presentation.
Investigators have published a paper, based on the physician interview data, in The Oncologist, entitled “Designing an Effective Colorectal Cancer Screening Program in Egypt: A Qualitative Study of Perceptions of Egyptian Primary Care Physicians and Specialists.” Additionally, a submission, "Barriers and Facilitators to Colorectal Cancer Screening in Egypt: Examining the Perceptions of Physicians and Residents in Alexandria," has been accepted for a poster presentation at the 8th Annual Symposium on Global Cancer Research, Washington DC, April 17. Although the conference was cancelled due to COVID-19, the abstract was selected for publication in a special issue of ASCO JCO Global Oncology Journal.
Papers under development include one based on focus group findings and one that combines physician interview and focus group findings. A research intern (3rd year medical student) from UAB is assisting with the papers, as are two Egyptian junior scholars.
Our second aim is to identify sub-populations in Egypt at high-risk for aggressive colorectal cancer. During this reporting period, tissue samples were identified and sent to the University of Alabama at Birmingham and analysis is ongoing to identify and validate the clinical utility of molecular markers identified in U.S. colorectal cancer tissues and tissues from Alexandrian patients. Two Egyptian research fellows have visited the University of Alabama at Birmingham have been trained to conduct the analysis. The microbiome profile of Egyptian colorectal patients have been analyzed via 16S rRNA gene sequencing data from paired biopsies from colorectal patients. This analysis has revealed that young colorectal cancer patients have an absence of specific beneficial microbiota. Our third aim focusses on survivorship by identifying dietary and physical activity patterns among colorectal cancer survivors in Egypt. During this reporting period we extended the eligibility criteria to survivors in active treatment. We have also expanded to another oncology clinic and utilized medical students to assist with recruiting. The medical students went through an organized training in which they learned about the ethical conduct of studies, designing research studies, doctor-patient communication and recruitment. These revisions to our protocol greatly increased enrollment. We are currently at 48 participants enrolled. One issue that continues is that participants are refusing to wear the accelerometer (only 18 have chosen to wear it). Further, a major challenge has been the fact that recruitment had to cease in March because of COVID-19 related restrictions.
Because enrollment is currently on hold, we are currently analyzing the data we have collected to this point. The physical activity data is currently being analyzed by project investigators, and the 24 hour diet recall data will be analyzed at the National Nutrition Institute in Cairo when it reopen after the COVID-19 shut down.
Publications are currently under development for this aim.
Our final aim is to ensure sustainability through a structured research training program for Egyptian investigators. This is being accomplished through an ongoing training program that includes a face-to-face intensive training.
UAB investigators communicated with Aim 1 trainees through Whatsapp throughout the reporting period to provide additional capacity building. Two Egyptian scholars have visited UAB during this period. Two additional Egyptian junior scholars, continue to work on analyzing Aim 1 data, as well as with project investigators on a related pilot grant that was funded during the last reporting. Finally, a UAB medical student, began a research experience focusing on Aim 1.
As an outcome of the pilot project that emerged from this grant, 14 medical students at Alexandria University Faculty of Medicine were trained by project investigators in the last reporting period in research methods, doctor-patient communication, and research ethics. The students put his knowledge into practice this reporting period by collecting data in Aim 3 in order to expedite the recruitment process.
The significance of this project is that the TCC will serve as the basis for a fully developed cancer research program in Egypt that will continue to grow after the end of the current funding and implement independent intervention studies in the areas of basic, clinical, social and behavioral, and outcomes research in order to reduce colon cancer incidence and mortality among the Egyptian population. For the US, the TCC will advance discovery, implementation, and dissemination in the areas of: 1) identifying high-risk populations based on ethnicity and environmental exposures; 2) developing and implementing culturally appropriate interventions to increase colorectal cancer survivorship; and 3) development and dissemination of culturally appropriate messages to enhance colorectal cancer prevention in multicultural communities.
Year 5 Project Progress Summary (Submitted June 2021)
The objective of this project, led collaboratively by the University of Alabama at Birmingham (UAB) and the University of Alexandria Faculty of Medicine (UAFM), is to establish a Transdisciplinary Collaborative Center for Colorectal Cancer Research in Egypt. The Center’s long-term goal is to reduce the high rates of illness and death due to colorectal cancer in the Egyptian population. The first aim of the project is to identify demographic and socio-cultural factors associated with using screening for the prevention and early detection of colon cancer in Egypt. To do this, we have conducted focus groups with Egyptians with no history of colorectal cancer as well as interviews with Egyptian primary care physicians and specialists. During the last reporting period, our focus has been writing and submitting papers for publications and abstracts for presentation. Investigators have published an abstract, “Barriers to and Facilitators of Colorectal Cancer Screening in Egypt: Examining the Perceptions of Physicians and Residents in Alexandria” in JCO Global Oncology, and are also currently revising a paper for re-submission, “Development of a theory based, culturally relevant intervention to promote colorectal cancer screening in Egypt.” The paper is based on findings from this aim, both the physician interviews and focus groups, which served as the basis for intervention development. Our team has made several presentations including to the UAB Sparkman Center for Global Health in October of 2020, entitled the “Development of a theory based, culturally relevant intervention to promote colorectal cancer screening in Egypt,” and in April of 2021, we presented “Examining the Results of a Culturally Relevant Intervention to Promote Colorectal Cancer Screening in Egypt: Findings and Next Steps” to the UAB Division of Preventive Medicine Grand Rounds in Birmingham, Alabama. Our team made two presentations to the Third Annual Egyptian Pelvic Pathology Oncology Group Society of Pelvic Surgeons Conference (EPOG 2021), which took place February 11-13, 2021 in Alexandria, Egypt. One was entitled, “Egyptian US Collaborative Project: The Development and Implementation of a Colorectal Cancer Screening Intervention” and the other, “A collaboration between The Alexandria University Faculty of Medicine & The University of Alabama at Birmingham.” We also presented two posters at international conferences. In March, we presented a poster to the Consortium of Universities for Global Health entitled “Engaging Medical Students to Implement a Colorectal Screening Intervention in Egypt” and to the 9th Annual Symposium on Global Cancer Research, in March, 2021, entitled “Examining a Culturally Relevant Intervention to Promote Colorectal Cancer Screening in Egypt,” A research intern (3rd year medical student) from UAB is assisting with the papers, as are two Egyptian junior scholars.
Our second aim is to identify sub-populations in Egypt at high-risk for aggressive colorectal cancer. As recent retrospective study showed that Egyptian CRC patients have unique clinical behavior in terms of epidemiological profile and survival pattern, molecular studies are needed to unleash the molecular behavior of Egyptian CRC patients in terms of gene expression and microbiome profiling. The team has completed the analysis of the microbiome-tumor gene expression and mucosal immunity crosstalk in colorectal cancer to identify specific biomarkers for high-risk populations. We concluded that the altered expression of immune-related genes is linked with microbiome dysbiosis. Moreover, microbiome dysbiosis in CRC tumors was characterized by overabundance of specific microbiota, that can be further investigated as biomarkers. We proposed also that multiple microbiota that influence tumor gene expression, might be candidates as therapeutic targets. We are currently revising a manuscript for publication, entitled, “Investigating the microbiome-tumor gene expression and mucosal immunity crosstalk in Egyptian colorectal cancer”.
Our third aim focusses on survivorship by identifying dietary and physical activity patterns among colorectal cancer survivors in Egypt. We have completed data collected of our quantitative aim. Physical activity data has been analyzed and two presentations have been made during this reporting period. We presented “Physical activity among colorectal cancer survivors” to the the Third Annual Egyptian Pelvic Pathology Oncology Group Society of Pelvic Surgeons Conference (EPOG 2021) in February in Alexandria. And, a poster was presented to the 9th Annual Symposium on Global Cancer Research: “Self-Reported Physical Activity Patterns among Colorectal Cancer Survivors in Egypt.” The abstract will be published in an upcoming issue of AACR’s Cancer Epidemiology, Biomarkers, & Prevention. Our team has just received the dietary intake data that was analyzed by the National Nutrition Institute in Cairo; further analysis in ongoing and manuscripts for publication are under development. Finally, we are conducting one-on-one interviews with colorectal cancer survivors to understand their experience with diet and physical activity as well as how they experience cancer treatment during COVID-19. We plan to complete interviews in June and begin analysis of the data.
Our final aim is to ensure sustainability through a structured research training program for Egyptian investigators. This is being accomplished through an ongoing training program that includes a face-to-face and remote intensive training. UAB investigators communicated with Egyptian trainees through Whatsapp and Zoom meetings throughout this reporting period to provide capacity building and mentoring, even though travel was restricted due to COVID-19.