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Deepep: A Deep Learning Framework For Identifying Essential Proteins, Min Zeng, Min Li, Fang-Xiang Wu, Yaohang Li, Yi Pan 2019 Old Dominion University

Deepep: A Deep Learning Framework For Identifying Essential Proteins, Min Zeng, Min Li, Fang-Xiang Wu, Yaohang Li, Yi Pan

Computer Science Faculty Publications

Background: Essential proteins are crucial for cellular life and thus, identification of essential proteins is an important topic and a challenging problem for researchers. Recently lots of computational approaches have been proposed to handle this problem. However, traditional centrality methods cannot fully represent the topological features of biological networks. In addition, identifying essential proteins is an imbalanced learning problem; but few current shallow machine learning-based methods are designed to handle the imbalanced characteristics. Results: We develop DeepEP based on a deep learning framework that uses the node2vec technique, multi-scale convolutional neural networks and a sampling technique to identify essential proteins ...


Genome-Wide Scans Identify Known And Novel Regions Associated With Prolificacy And Reproduction Traits In A Sub-Saharan African Indigenous Sheep (Ovis Aries), Asrat Tera Dolebo, Negar Khayatzadeh, Aberra Melesse, David Wragg, Mourad Rekik, Aynalem Haile, Barbara Rischkowsky, Max F. Rothschild, Joram M. Mwacharo 2019 Southern Agricultural Research Institute (SARI)

Genome-Wide Scans Identify Known And Novel Regions Associated With Prolificacy And Reproduction Traits In A Sub-Saharan African Indigenous Sheep (Ovis Aries), Asrat Tera Dolebo, Negar Khayatzadeh, Aberra Melesse, David Wragg, Mourad Rekik, Aynalem Haile, Barbara Rischkowsky, Max F. Rothschild, Joram M. Mwacharo

Animal Science Publications

Maximizing the number of offspring born per female is a key functionality trait in commercial- and/or subsistence-oriented livestock enterprises. Although the number of offspring born is closely associated with female fertility and reproductive success, the genetic control of these traits remains poorly understood in sub-Saharan Africa livestock. Using selection signature analysis performed on Ovine HD BeadChip data from the prolific Bonga sheep in Ethiopia, 41 candidate regions under selection were identified. The analysis revealed one strong selection signature on a candidate region on chromosome X spanning BMP15, suggesting this to be the primary candidate prolificacy gene in the breed ...


Review: Innovation Through Research In The North American Pork Industry, R. D. Boyd, C. E. Zier-Rush, A. J. Moeser, M. Culbertson, K. R. Stewart, D. S. Rosero, John F. Patience 2019 Hanor Company

Review: Innovation Through Research In The North American Pork Industry, R. D. Boyd, C. E. Zier-Rush, A. J. Moeser, M. Culbertson, K. R. Stewart, D. S. Rosero, John F. Patience

Animal Science Publications

This article involved a broad search of applied sciences for milestone technologies we deem to be the most significant innovations applied by the North American pork industry, during the past 10 to 12 years. Several innovations shifted the trajectory of improvement or resolved significant production limitations. Each is being integrated into practice, with the exception being gene editing technology, which is undergoing the federal approval process. Advances in molecular genomics have been applied to gene editing for control of porcine reproductive and respiratory syndrome and to identify piglet genome contributions from each parent. Post-cervical artificial insemination technology is not novel ...


Mapping Of Qtl And Identification Of Candidate Genes Conferring Spontaneous Haploid Genome Doubling In Maize (Zea Mays L.), Jiaojiao Ren, Nicholas Boerman, Ruixiang Liu, Penghao Wu, Benjamin Trampe, Kimberly Vanous, Ursula K. Frei, Shaojiang Chen, Thomas Lubberstedt 2019 Xinjiang Agricultural University

Mapping Of Qtl And Identification Of Candidate Genes Conferring Spontaneous Haploid Genome Doubling In Maize (Zea Mays L.), Jiaojiao Ren, Nicholas Boerman, Ruixiang Liu, Penghao Wu, Benjamin Trampe, Kimberly Vanous, Ursula K. Frei, Shaojiang Chen, Thomas Lubberstedt

Agronomy Publications

In vivo doubled haploid (DH) technology is widely used in commercial maize (Zea mays L.) breeding. Haploid genome doubling is a critical step in DH breeding. In this study, inbred lines GF1 (0.65), GF3(0.29), and GF5 (0) with high, moderate, and poor spontaneous haploid genome doubling (SHGD), respectively, were selected to develop mapping populations for SHGD. Three QTL, qshgd1, qshgd2, and qshgd3, related to SHGD were identified by selective genotyping. With the exception of qshgd3, the source of haploid genome doubling alleles were derived from GF1. Furthermore, RNA-Seq was conducted to identify putative candidate genes between GF1 ...


Biotech: Not Just For Geeks, Fred D. Ledley 2019 Bentley University

Biotech: Not Just For Geeks, Fred D. Ledley

Science and Industry

Business students get high marks for scientific literacy


Cgste11 Mediates Cross Tolerance To Multiple Environmental Stressors In Candida Glabrata, Mian Huang, Jibran Khan, Manpreet Kaur, Julian Daniel Torres Vanega, Orlando Andres Aguilar Patiño, Anand Ramasubramanian, Katy Kao 2019 Texas A&M University

Cgste11 Mediates Cross Tolerance To Multiple Environmental Stressors In Candida Glabrata, Mian Huang, Jibran Khan, Manpreet Kaur, Julian Daniel Torres Vanega, Orlando Andres Aguilar Patiño, Anand Ramasubramanian, Katy Kao

Faculty Publications, Biomedical, Chemical, and Materials Engineering

Candida glabrata is a human commensal and an opportunistic human fungal pathogen. It is more closely related to the model yeast Saccharomyces cerevisiae than other Candida spp. Compared with S. cerevisiae, C. glabrata exhibits higher innate tolerance to various environmental stressors, including hyperthermal stress. Here we investigate the molecular mechanisms of C. glabrata adaptation to heat stress via adaptive laboratory evolution. We show that all parallel evolved populations readily adapt to hyperthermal challenge (from 47 °C to 50 °C) and exhibit convergence in evolved phenotypes with extensive cross-tolerance to various other environmental stressors such as oxidants, acids, and alcohols. Genome ...


Comparison Of Montage With Conventional Stereoscopic Seven‑Field Photographs For Assessment Of Etdrs Diabetic Retinopathy Severity, Nam V. Nguyen, Erin M. Vigil, Muhammad Hassan, Muhammad S. Halim, Sean C. Baluyot, Hugo A. Guzman, Rubbia Afridi, Diana V. Do, Yasir J. Sepah 2019 Stanford University & Ocular Imaging Research and Reading Center & University of Nebraska-Lincoln

Comparison Of Montage With Conventional Stereoscopic Seven‑Field Photographs For Assessment Of Etdrs Diabetic Retinopathy Severity, Nam V. Nguyen, Erin M. Vigil, Muhammad Hassan, Muhammad S. Halim, Sean C. Baluyot, Hugo A. Guzman, Rubbia Afridi, Diana V. Do, Yasir J. Sepah

Biochemistry -- Faculty Publications

Background: The ETDRS stereoscopic seven-field (7F) has been a standard imaging and grading protocol for assessment of diabetic retinopathy (DR) severity score in many clinical trials. To the best of our knowledge, the comparison between montage and stereoscopic 7F has not been reported in the literature. Therefore, the main purpose of this study is to compare agreement between montage and stereoscopic seven-field (7F) photographs in the assessment of DR severity.

Methods: Stereoscopic 7F photographs were captured from subjects with DR. Montages of monoscopic 7F images were created using Adobe Photoshop CS6 Extended©. The best quality image of each stereo pair ...


#17 - Detecting The Presence Of Gmos In Tortilla Chips Served U.S. Major Restaurant Chains, Kristen Donahue, Kenneth Levenson, John Senat, Stephany Sifuentes 2019 Georgia Gwinnett College

#17 - Detecting The Presence Of Gmos In Tortilla Chips Served U.S. Major Restaurant Chains, Kristen Donahue, Kenneth Levenson, John Senat, Stephany Sifuentes

Georgia Undergraduate Research Conference (GURC)

Today, consumers are more aware and demand more information about the foods they consume. Transgenic crops, such as BT-corn, are a popular topic of concern among an ever-growing population of health-conscious consumers. Additionally, many U.S. consumers are regularly going out to eat at restaurants instead of cooking at home, with about half of all U.S. food expenditures accounting for food-away-from home. Specifically, chips are becoming a staple of the current American diet and are popular amongst diverse demographics. This study is an attempt to discover if tortilla chips served in common U.S. restaurant chains are genetically modified ...


#18 - Popular Unlabelled Cornmeal Brands Expected To Be Labeled As ‘Bioengineered’ By 2022 In The U.S.: Due To Detection Of Genetic Material, Elvia Encarnacion-Thomas, Jenai DaCosta, Farinaz Panah, Lilly Dishmey-Garrido, Tsion Adula 2019 Georgia Gwinnett College

#18 - Popular Unlabelled Cornmeal Brands Expected To Be Labeled As ‘Bioengineered’ By 2022 In The U.S.: Due To Detection Of Genetic Material, Elvia Encarnacion-Thomas, Jenai Dacosta, Farinaz Panah, Lilly Dishmey-Garrido, Tsion Adula

Georgia Undergraduate Research Conference (GURC)

There is a growing concern in the U.S. about genetically modified (GM) or GMO foods and consumers are demanding proper disclosure. Public Law 114-216 passed July 29, 2016 also known as the ‘GMO labeling bill’, where the USDA established a National Bioengineered Food Disclosure Standard (NBFDS) stating manufacturers are not required to label products if genetic material is undetected3. Bioengineered food is defined as a food that has been modified through the insertion of in vitro recombinant deoxyribonucleic acid techniques, per NBFDS. Because corn is currently in the bioengineered lists of crops and 93% of corn produced in ...


#19 - Testing Usda Certified Organic Soy Noodles For Genetic Modifications, Dhwani Mistry, Kyra Brewer, Salsabile Ibrahim, Vedanti Patel 2019 Georgia Gwinnett College

#19 - Testing Usda Certified Organic Soy Noodles For Genetic Modifications, Dhwani Mistry, Kyra Brewer, Salsabile Ibrahim, Vedanti Patel

Georgia Undergraduate Research Conference (GURC)

Screening USDA Certified Organic Soy noodles for genetic modifications using various DNA and protein analysis tools like DNA isolation, PCR, Gel Electrophoresis, Nano-drop, and ELISA.


Label-Free Microrna Optical Biosensors, Meimei Lai, Gymama Slaughter 2019 Old Dominion University

Label-Free Microrna Optical Biosensors, Meimei Lai, Gymama Slaughter

Bioelectrics Publications

MicroRNAs (miRNAs) play crucial roles in regulating gene expression. Many studies show that miRNAs have been linked to almost all kinds of disease. In addition, miRNAs are well preserved in a variety of specimens, thereby making them ideal biomarkers for biosensing applications when compared to traditional protein biomarkers. Conventional biosensors for miRNA require fluorescent labeling, which is complicated, time-consuming, laborious, costly, and exhibits low sensitivity. The detection of miRNA remains a big challenge due to their intrinsic properties such as small sizes, low abundance, and high sequence similarity. A label-free biosensor can simplify the assay and enable the direct detection ...


In Vitro Investigation Of The Effect Of Camel Milkproteins And Its Fractions On Insulin Receptor Function, Arshida Ashraf 2019 United Arab Emirates University

In Vitro Investigation Of The Effect Of Camel Milkproteins And Its Fractions On Insulin Receptor Function, Arshida Ashraf

Biology Theses

Camel milk (CM) has been reported to have anti-diabetic properties in many in vitro and in vivo studies but the molecular basis of such beneficial properties are still elusive. Recently, camel milk whey proteins (CWPs) have been shown to positively affect the activity of the human insulin receptor (hIR) in cell lines. In this study, we profiled crude CWPs and their hydrolysates as well as camel milk lactoferrin (CMLF) for their pharmacological and functional effects on hIR activity and its downstream signaling in both human embryonic kidney (HEK293) and hepatocarcinoma (HepG2) cell lines. For this, bioluminescence resonance energy transfer (BRET ...


Forensic Evaluation Of 6-Dye Chemistry Kit Composed Of 23 Loi With Casework Samples, Naeema Saleh Al Janaahi 2019 United Arab Emirates University

Forensic Evaluation Of 6-Dye Chemistry Kit Composed Of 23 Loi With Casework Samples, Naeema Saleh Al Janaahi

Biology Theses

Short Tandem Repeats (STRs) are short nucleotide sequence repeats consisting of 2-8 base pairs (bp), representing approximately 3% of human DNA. Markers of STRs have been widely used as genetic markers in forensic DNA analysis and have proven to be an extremely discriminating method for human identification in forensics. The main objective of this research was to evaluate a six-dye STR multiplex assay (Virifiler™ Plus) composed of 23 autosomal STR loci, one insertion/deletion polymorphic marker on the Y chromosome, Amelogenin and two internal quality control markers (IQCS and IQCL) using biological stains found in different crime scenes. The study ...


Multi-Site Photoplethysmography Technology For Blood Pressure Assessment: Challenges And Recommendations, Gabriel Chan, Rachel Cooper, Manish Hosanee, Kaylie Welykholowa, Panayiotis A. Kyriacou, Dingchang Zheng, John Allen, Derek Abbott, Nigel H. Lovell, Richard Fletcher, Mohamed Elgendi 2019 University of British Columbia

Multi-Site Photoplethysmography Technology For Blood Pressure Assessment: Challenges And Recommendations, Gabriel Chan, Rachel Cooper, Manish Hosanee, Kaylie Welykholowa, Panayiotis A. Kyriacou, Dingchang Zheng, John Allen, Derek Abbott, Nigel H. Lovell, Richard Fletcher, Mohamed Elgendi

Open Access Publications by UMMS Authors

Hypertension is one of the most prevalent diseases and is often called the "silent killer" because there are usually no early symptoms. Hypertension is also associated with multiple morbidities, including chronic kidney disease and cardiovascular disease. Early detection and intervention are therefore important. The current routine method for diagnosing hypertension is done using a sphygmomanometer, which can only provide intermittent blood pressure readings and can be confounded by various factors, such as white coat hypertension, time of day, exercise, or stress. Consequently, there is an increasing need for a non-invasive, cuff-less, and continuous blood pressure monitoring device. Multi-site photoplethysmography (PPG ...


Remodeling Of Chlamydomonas Metabolism Using Synthetic Inducers Results In Lipid Storage During Growth, Nishikant Wase, Boqiang Tu, Girish Kumar Rasineni, Ronald Cerny, Ryan Grove, Jiri Adamec, Paul N. Black, Concetta DiRusso 2019 University of Nebraska-Lincoln

Remodeling Of Chlamydomonas Metabolism Using Synthetic Inducers Results In Lipid Storage During Growth, Nishikant Wase, Boqiang Tu, Girish Kumar Rasineni, Ronald Cerny, Ryan Grove, Jiri Adamec, Paul N. Black, Concetta Dirusso

Biochemistry -- Faculty Publications

Microalgae accumulate lipids during stress such as that of nutrient deprivation, concomitant with cessation of growth and depletion of chloroplasts. By contrast, certain small chemical compounds selected by high-throughput screening in Chlamydomonas reinhardtii can induce lipid accumulation during growth, maintaining biomass. Comprehensive pathway analyses using proteomics, transcriptomics, and metabolomics data were acquired from Chlamydomonas cells grown in the presence of one of two structurally distinct lipid activators. WD10784 stimulates both starch and lipid accumulation, whereas WD30030-treated cells accumulate only lipids. The differences in starch accumulation are largely due to differential effects of the two compounds on substrate levels that feed ...


The Catalytic Urease Subunit Urec Is Critical For Bifidobacterium Longum Urea Utilization, YANG LYU 2019 University of Massachusetts Amherst

The Catalytic Urease Subunit Urec Is Critical For Bifidobacterium Longum Urea Utilization, Yang Lyu

Doctoral Dissertations

In the first study, we investigated the utilization of a human milk nitrogen source, urea, by Bifidobacterium. Urea accounts for ~15% in human milk, which is an abundant non-protein nitrogen (NPN). Some bifidobacteria are found to harbor urease gene clusters that potentially enable their hydrolysis of the human milk urea. However, the underlying mechanisms are still unclear. To incisively link the urease gene cluster with bifidobacterial urea utilization, chemical mutagenesis (i.e. ethyl methanesulfonate) was performed on the urease-positive Bifidobacterium longum subsp. suis UMA399. Mutants were selected on differential media and genetic lesions were identified using whole genome sequencing. A ...


Engineering Of An Antibody-Conjugated Nanogel Platform For Targeted Drug Delivery To T Lymphocytes, Mine Canakci 2019 University of Massachusetts Amherst

Engineering Of An Antibody-Conjugated Nanogel Platform For Targeted Drug Delivery To T Lymphocytes, Mine Canakci

Doctoral Dissertations

In an ideal chemotherapy, cytotoxic drugs travel through the bloodstream, reach cells all over the body and preferentially kill abnormal cells. Yet, the hydrophilic or lipophilic property of the small-molecule drugs affects their ability to reach cells from the bloodstream. So, only a small portion of the drug reaches to the diseased tissue. A selective cell killing approach for cancer therapy gained momentum after the realization that cancer cells carry unique set of molecular markers on their cell surface. The development of antibody drug conjugates (ADC) revolutionized the targeted approach for drug delivery. ADCs are composed of cytotoxic agents covalently ...


Investigating The Role Of Lbh During Early Embryonic Development In Xenopus Laevis, Emma Weir 2019 University of Massachusetts Amherst

Investigating The Role Of Lbh During Early Embryonic Development In Xenopus Laevis, Emma Weir

Masters Theses

LBH is a highly conserved protein whose role during vertebrate development is relatively under-studied. In collaboration with the Albertson lab, our lab has previously shown that it is necessary for cranial neural crest cell migration in the zebrafish and in Xenopus laevis. The molecular mechanisms through which it acts are not well understood.

In Xenopus, LBH is a maternally deposited protein. As such, studying its role in early development has not been feasible through the morpholino-mediated knockdown techniques that prevent translation of target genes. Recently, a technique for degrading endogenous proteins was developed, called Trim-Away. This was developed in mammalian ...


Drought Responsive Gene Expression Regulatory Divergence Between Upland And Lowland Ecotypes Of A Perennial C4 Grass, John T. Lovell, Scott Schwartz, David B. Lowry, Eugene V. Shakirov, Jason E. Bonnette, Xiaoyu Weng, Mei Wang, Jenifer Johnson, Avinash Sreedasyam, Christopher Plott, Jerry Jenkins, Jeremy Schmutz, Thomas E. Juenger 2019 Marshall University

Drought Responsive Gene Expression Regulatory Divergence Between Upland And Lowland Ecotypes Of A Perennial C4 Grass, John T. Lovell, Scott Schwartz, David B. Lowry, Eugene V. Shakirov, Jason E. Bonnette, Xiaoyu Weng, Mei Wang, Jenifer Johnson, Avinash Sreedasyam, Christopher Plott, Jerry Jenkins, Jeremy Schmutz, Thomas E. Juenger

Yevgeniy (Eugene) Shakirov

Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C4 grass, Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit ...


Heterologous Expression Of Secreted Bacterial Bpp And Hap Phytases In Plants Stimulates Arabidopsis Thaliana Growth On Phytate., Lia R. Valeeva, Chuluuntsetseg Nyamsuren, Margarita R. Sharipova, Eugene V. Shakirov 2019 Marshall University

Heterologous Expression Of Secreted Bacterial Bpp And Hap Phytases In Plants Stimulates Arabidopsis Thaliana Growth On Phytate., Lia R. Valeeva, Chuluuntsetseg Nyamsuren, Margarita R. Sharipova, Eugene V. Shakirov

Yevgeniy (Eugene) Shakirov

Phytases are specialized phosphatases capable of releasing inorganic phosphate from myo-inositol hexakisphosphate (phytate), which is highly abundant in many soils. As inorganic phosphorus reserves decrease over time in many agricultural soils, genetic manipulation of plants to enable secretion of potent phytases into the rhizosphere has been proposed as a promising approach to improve plant phosphorus nutrition. Several families of biotechnologically important phytases have been discovered and characterized, but little data are available on which phytase families can offer the most benefits toward improving plant phosphorus intake. We have developed transgenic Arabidopsis thaliana plants expressing bacterial phytases PaPhyC (HAP family ...


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