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Articles 1 - 20 of 20
Full-Text Articles in Biotechnology
Enabling Precision Medicine Via Standard Communication Of Hts Provenance, Analysis, And Results, Gil Alterovitz, Dennis Dean, Carole Globe, Michael R. Crusoe, Stiam Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkkayastha, Charles H. King, Dan Taylor, Elaine Johanson, Elaine E. Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K. Vora, Jeremy Goecks, Jianchao Yao, Jonas S. Almeida, Jonathon Keeney, Kanakadurga Addepalli, Konstantinos Krampis, Krista M. Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C. Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder
Enabling Precision Medicine Via Standard Communication Of Hts Provenance, Analysis, And Results, Gil Alterovitz, Dennis Dean, Carole Globe, Michael R. Crusoe, Stiam Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkkayastha, Charles H. King, Dan Taylor, Elaine Johanson, Elaine E. Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K. Vora, Jeremy Goecks, Jianchao Yao, Jonas S. Almeida, Jonathon Keeney, Kanakadurga Addepalli, Konstantinos Krampis, Krista M. Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C. Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder
Publications and Research
A personalized approach based on a patient's or pathogen’s unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to findable, accessible, interoperable, and reusable (FAIR) guiding principles. Moreover, effective precision medicine requires standardized reporting that extends beyond wet-lab procedures to computational methods. The BioCompute framework (https://w3id.org/biocompute/1.3.0) enables standardized reporting of genomic sequence data provenance, including provenance domain, usability domain, execution domain, verification kit, and error domain. This framework facilitates communication and promotes interoperability. Bioinformatics computation instances that employ the BioCompute framework are easily relayed, repeated …
Transcriptional Profiling Identifies Potential Genes Associated With Multiple Biotic Stresses In Arabidopsis, Hibatullah Mustafa Al Ashram
Transcriptional Profiling Identifies Potential Genes Associated With Multiple Biotic Stresses In Arabidopsis, Hibatullah Mustafa Al Ashram
Biology Theses
Plants are exposed to many environmental stresses that affect their growth and development. These stresses include biotic stresses (organisms) and abiotic stresses (drought and salinity). Plants respond to these stresses by transcriptional reprogramming and different signaling pathways. Arabidopsis thaliana had shown great sensitivity to the biotic stress: Botrytis cinerea, Alternaria brassicicola, Pseudomonas syringae and the herbivore insect Pieris rapae. The overall goal is to identify common regulated genes that respond to all these biotic stresses to ultimately improve plant stress tolerance in Arabidopsis. The specific aims are to: (1) determine the regulated genes in response to an …
In Vivo Assessment Of Safranal’S Novel Therapeutic Effects On Chemically Induced Hepatic Neoplasia, Ameera Ali M. Almansoori
In Vivo Assessment Of Safranal’S Novel Therapeutic Effects On Chemically Induced Hepatic Neoplasia, Ameera Ali M. Almansoori
Biology Theses
Chronic liver insult leads to fibrosis, which often ends up causing cirrhosis and most of the time that progresses into hepatic neoplasms (early Hepatocellular carcinoma; HCC). HCC is the fifth most common cancer, and the third cause of cancerrelated deaths. Chemotherapy is the most common treatment of cancer patients. HCC is however, chemo-resistant, and the side-effects of chemotherapy are typically exhausting to the patient. Sorafenib is the only anti-HCC drug approved by the U.S Food and Drug Administration. It is a multikinase inhibitor that blocks tumor cells proliferation and angiogenesis. Although sorafenib is successful treating early and mid HCC lesions, …
Theobromine And Related Methylxanthines As Inhibitors Of Primary Amine Oxidase, Padraig Shanahan, Jeffrey O’Sullivan, Keith Tipton, Gemma Kinsella, Barry Ryan, Gary Henehan
Theobromine And Related Methylxanthines As Inhibitors Of Primary Amine Oxidase, Padraig Shanahan, Jeffrey O’Sullivan, Keith Tipton, Gemma Kinsella, Barry Ryan, Gary Henehan
Articles
Methylxanthines are the most widely consumed drugs in the world and evidence of their health benefits has been growing in recent years. Primary Amine Oxidase (PrAO) has been recognised as a therapeutic target for amelioration of inflammatory, vascular and neurodegenerative diseases. Previous work in our laboratories showed that caffeine inhibited Bovine PrAO with a Ki of 1.0mM using benzylamine as substrate.
This study aimed to extend our previous work and explore the possibility that related methylxanthines might influence PrAO activity. While paraxanthine, theophylline and 7-methylxanthine had little effect on PrAO, theobromine was a noncompetitive inhibitor with a Ki of 276±44µM. …
Rnai Targeting Of Manduca Sexta Using Chloroplast-Encoded Long Dsrna, William Burke
Rnai Targeting Of Manduca Sexta Using Chloroplast-Encoded Long Dsrna, William Burke
Electronic Thesis and Dissertation Repository
Pest management strategies are crucial for reducing insect crop damage, and methods with species-specific effect are particularly desirable. Expressing dsRNA with sequence complementarity to a vital gene of feeding pests is a strategy that has shown potential. I modified the chloroplast genome of cultivated tobacco, Nicotiana tabacum, by adding a sequence encoding a 2222 base pair dsRNA complementary to the vacuolar-type H+-ATPase subunit A mRNA of Manduca sexta and demonstrated expression of the product in leaves of the plants. Although feeding this same dsRNA that was synthesized in vitro to larvae knocked down expression of the target …
Directly Light-Regulated Binding Of Rgs-Lov Photoreceptors To Anionic Membrane Phospholipids, Spencer T. Glantz, Erin E. Berlew, Zaynab Jaber, Benjamin S. Schuster, Kevin H. Gardner, Brian Y. Chow
Directly Light-Regulated Binding Of Rgs-Lov Photoreceptors To Anionic Membrane Phospholipids, Spencer T. Glantz, Erin E. Berlew, Zaynab Jaber, Benjamin S. Schuster, Kevin H. Gardner, Brian Y. Chow
Publications and Research
We report natural light–oxygen–voltage (LOV) photoreceptors with a blue light-switched, high-affinity (KD ∼ 10−7 M), and direct electrostatic interaction with anionic phospholipids. Membrane localization of one such photoreceptor, BcLOV4 from Botrytis cinerea, is directly coupled to its flavin photocycle, and is mediated by a polybasic amphipathic helixinthelinker regionbetween the LOV sensor and its C-terminal domain of unknown function (DUF), as revealed through a combination of bioinformatics, computational protein modeling, structure–function studies, and optogenetic assays in yeast and mammalian cell line expression systems. In model systems, BcLOV4 rapidly translocates from the cytosol to plasma membrane (∼1 second). The reversible electrostatic interaction …
Investigation On The Effect Of Pasteurisation On The Bacteria Contamination Of Eggs, Alya Sufiyah Bte Mohamed Subhan
Investigation On The Effect Of Pasteurisation On The Bacteria Contamination Of Eggs, Alya Sufiyah Bte Mohamed Subhan
The International Student Science Fair 2018
This project is a research on bacteria contamination on pasteurised and non-pasteurised eggs. In Singapore, there has been an increase in salmonella cases since 2016. Recently in the US, more than 206 million eggs in supermarkets and grocery chains had to be recalled. This project will explain about the different in bacterial colonies found on seemingly similar eggs.
Mapping Molecular Datasets Back To The Brain Regions They Are Extracted From: Remembering The Native Countries Of Hypothalamic Expatriates And Refugees, Arshad M. Khan, Alice H. Grant, Anais Martinez, Gully Apc Burns, Brendan S. Thatcher, Vishwanath T. Anekonda, Benjamin W. Thompson, Zachary S. Roberts, Daniel H. Moralejo, James E. Blevins
Mapping Molecular Datasets Back To The Brain Regions They Are Extracted From: Remembering The Native Countries Of Hypothalamic Expatriates And Refugees, Arshad M. Khan, Alice H. Grant, Anais Martinez, Gully Apc Burns, Brendan S. Thatcher, Vishwanath T. Anekonda, Benjamin W. Thompson, Zachary S. Roberts, Daniel H. Moralejo, James E. Blevins
Arshad M. Khan, Ph.D.
Same-Sex Marriage And The Baby Carriage: A Post-Obergefell Analysis Of Art Funding For Same-Sex Couples In The United States, Charmaine Mech
Same-Sex Marriage And The Baby Carriage: A Post-Obergefell Analysis Of Art Funding For Same-Sex Couples In The United States, Charmaine Mech
Georgia Journal of International & Comparative Law
No abstract provided.
Characterization Of A Morphogenetic Furrow Specific Gal4 Driver In The Developing Drosophila Eye, Ankita Sarkar, Neha Gogia, Kevin Farley, Lydia C. Payton, Amit Singh
Characterization Of A Morphogenetic Furrow Specific Gal4 Driver In The Developing Drosophila Eye, Ankita Sarkar, Neha Gogia, Kevin Farley, Lydia C. Payton, Amit Singh
Biology Faculty Publications
The ability to express a gene of interest in a spatio-temporal manner using Gal4-UAS system has allowed the use of Drosophila model to study various biological phenomenon. During Drosophila eye development, a synchronous wave of differentiation called Morphogenetic furrow (MF) initiates at the posterior margin resulting in differentiation of retinal neurons. This synchronous differentiation is also observed in the differentiating retina of vertebrates. Since MF is highly dynamic, it can serve as an excellent model to study patterning and differentiation. However, there are not any Gal4 drivers available to observe the gain- of- function or loss- of- function of a …
The Role Of Vitamin D Receptors In Gastric Epithelial Homeostasis, Ifrah Ismail Ali
The Role Of Vitamin D Receptors In Gastric Epithelial Homeostasis, Ifrah Ismail Ali
Biology Theses
The gastric epithelium consists of different types of cells, which are involved in gastric homeostasis by balancing cell proliferation and differentiation. This process involves several signaling molecules such as growth factors, hormones and vitamins. Vitamin D3 (VD3) is engaged in several biological activities. It plays a role in cell differentiation, cell proliferation, immune response and also regulates calcium homeostasis. The biological activities of VD3 are mediated by vitamin D receptor (VDR). Target tissues of VD3 in the gastrointestinal tract were identified earlier in intestine, colon and gastric cancer tissues; however, the normal expression of VDR in stomach is poorly studied. …
Modelling The Micro Environment Of Liver Cancer Using 3d Culture System, Ala’A Abdel Rahim H Al Hrout
Modelling The Micro Environment Of Liver Cancer Using 3d Culture System, Ala’A Abdel Rahim H Al Hrout
Biology Theses
Tumor micro environment has been the focus of many studies that highlighted its essential contribution to tumorigenesis. A two-way communication between the tumor and the surrounding microenvironment sustains and contributes to the growth and metastasis of the tumor by several means, such as extracellular matrix remodeling, fibroblasts activation, epithelial-mesenchymal transition. Hepatocellular carcinoma progression and metastasis have been reported to be highly influenced by diverse microenvironmental elements. The main objective of this study is to create an in vitro model of liver cancer microenvironment that better recapitulate in vivo settings. The proposed model is based on three-dimensional co-culture system of liver …
Anti-Colon Cancer Effect Of Origanum Majorana Essential Oil, Asma Nasser Rashed Alrashedi
Anti-Colon Cancer Effect Of Origanum Majorana Essential Oil, Asma Nasser Rashed Alrashedi
Biology Theses
Plants have been shown to be an excellent source of new drugs, including anticancer agents. Origanum majorana commonly known as marjoram is a plant that is known to possess different therapeutic values including antioxidant andantimicrobial activities.
Our research team has previously tested the ethanolic extract of O. majorana on triple negative breast cancer and published the findings. The ethanolic extract promoted mitotic arrest at G2/M phase, induced apoptosis as well as inhibition of migration and metastasis. The promising potential of the ethanolic extract encouraged us to test the effects of O. majorana essential oil on human colon cancer cell lines. …
Atypical Pkciota Contributes To Poor Prognosis Through Loss Of Apical-Basal Polarity And Cyclin E Overexpression In Ovarian Cancer, Astrid M. Eder, Xiaomei Sui, Daniel G. Rosen, Laura K. Nolden, Kwai Wa Cheng, John P. Lahad, Madhuri Kango-Singh, Karen H. Lu, Carla L. Warneke, Edward N. Atkinson, Isabelle Bedrosian, Khandan Keyomarsi, Wen-Lin Kuo, Joe W. Gray, Jerry C. P. Yin, Jinsong Liu, Georg Halder, Gordon B. Mills
Atypical Pkciota Contributes To Poor Prognosis Through Loss Of Apical-Basal Polarity And Cyclin E Overexpression In Ovarian Cancer, Astrid M. Eder, Xiaomei Sui, Daniel G. Rosen, Laura K. Nolden, Kwai Wa Cheng, John P. Lahad, Madhuri Kango-Singh, Karen H. Lu, Carla L. Warneke, Edward N. Atkinson, Isabelle Bedrosian, Khandan Keyomarsi, Wen-Lin Kuo, Joe W. Gray, Jerry C. P. Yin, Jinsong Liu, Georg Halder, Gordon B. Mills
Madhuri Kango-Singh
We show that atypical PKCι, which plays a critical role in the establishment and maintenance of epithelial cell polarity, is genomically amplified and overexpressed in serous epithelial ovarian cancers. Furthermore, PKCι protein is markedly increased or mislocalized in all serous ovarian cancers. An increased PKCι DNA copy number is associated with decreased progression-free survival in serous epithelial ovarian cancers. In a Drosophila in vivo epithelial tissue model, overexpression of persistently active atypical PKC results in defects in apical-basal polarity, increased Cyclin E protein expression, and increased proliferation. Similar to the Drosophila model, increased PKCι proteins levels are associated with …
Stabilization Of Hypoxia Inducible Factor By Cobalt Chloride Can Alter Renal Transepithelial, Subhra Sankar Nag
Stabilization Of Hypoxia Inducible Factor By Cobalt Chloride Can Alter Renal Transepithelial, Subhra Sankar Nag
ETD Archive
Kidney cyst expansion, stagnant fluid accumulation, and insufficient vascular supply can result in localized chronic ischemia-hypoxia in kidney cysts, as well as in normal renal epithelia adjacent to a cyst. We hypothesize that in normal epithelia near a cyst, the stabilization of Hypoxia Inducible Factor 1a (HIF1a), a major regulator of cellular response to hypoxia, can cause altered paracellular and transcellular transport, transforming a normal absorptive phenotype to a secretory and paracellularly leaky phenotype, leading to cyst expansion. Using 100 µmol/L cobalt chloride (CoCl2), HIF1a was stabilized in cellular nucleus of a mouse cortical collecting duct cell line (mCCD 1296 …
Prospective Study Of The Feasibility Of Point-Of-Care Testing Strategy For Carbapenem-Resistant Organism Detection, Rahul Pannala, Bruce Baldwin, Vijay Aluru, Thomas E. Grys, Jordan Holmes, Laurence J. Miller, M. Edwyn Harrison, Cuong C. Nguyen, Fred C. Tenover, David Persing, Douglas O. Faigel
Prospective Study Of The Feasibility Of Point-Of-Care Testing Strategy For Carbapenem-Resistant Organism Detection, Rahul Pannala, Bruce Baldwin, Vijay Aluru, Thomas E. Grys, Jordan Holmes, Laurence J. Miller, M. Edwyn Harrison, Cuong C. Nguyen, Fred C. Tenover, David Persing, Douglas O. Faigel
Biology Faculty Publications
Background/aims: In an investigator-initiated, prospective study, we evaluated the feasibility of a five-gene sequence point-of-care (POC) testing strategy (Xpert CARBA-R Assay, Cepheid Inc., Sunnyvale, CA, USA), compared to reference laboratory PCR (48 – 72 hours turnaround time, two gene sequences), in patients undergoing endoscopic retrograde cholangiopancreatography (ERCP) and in a hospital outbreak investigation.
Methods: After informed consent, patients undergoing ERCP (September 2015 – April 2016, n = 191) at Mayo Clinic and potential hospital contacts (n = 9) of an index carbapenem-resistant organism (CRO)-positive inpatient were included. Two rectal swabs, one each for reference and POC assays were obtained. The …
Mrub_1283, Mrub_1284 And Mrub_1285 Encode For A Glycine/Betaine Abc Transporter And Are Orthologs Of E. Coli Prov, Prow And Prox, Lan Dang, Dr. Lori Scott
Mrub_1283, Mrub_1284 And Mrub_1285 Encode For A Glycine/Betaine Abc Transporter And Are Orthologs Of E. Coli Prov, Prow And Prox, Lan Dang, Dr. Lori Scott
Meiothermus ruber Genome Analysis Project
ABC transporters are essential for cellular transport; contribute to maintain the homeostasis of the cells. Generally, ABC transporters are multi-subunit; contain essential cytoplasmic factors which are critical to ATP hydrolysis activity. In this paper, we would like to take a closer look to Mrub_1283, Mrub_1284 and Mrub_1285, three consecutive genes in Meiothermus ruber genome. We hypothesize that these genes are in the same operon and encode for ABC glycine/ betaine transporters. To confirm our hypothesis, we utilizes several bioinformatics tools to predict the potential function of Mrub_1283, Mrub_1284 and Mrub_1285 and to search for their orthologs in Escherichia coli genome. …
Pleiotropic And Epistatic Network-Based Discovery: Integrated Networks For Target Gene Discovery, Deborah Weighill, Piet Jones, Manesh Shah, Priya Ranjan, Wellington Muchero, Jeremy Schmutz, Avinash Sreedasyam, David Macaya-Sanz, Robert Sykes, Nan Zhao, Madhavi Z. Martin, Stephen Difazio, Timothy J. Tschaplinski, Gerald Tuskan, Daniel Jacobson
Pleiotropic And Epistatic Network-Based Discovery: Integrated Networks For Target Gene Discovery, Deborah Weighill, Piet Jones, Manesh Shah, Priya Ranjan, Wellington Muchero, Jeremy Schmutz, Avinash Sreedasyam, David Macaya-Sanz, Robert Sykes, Nan Zhao, Madhavi Z. Martin, Stephen Difazio, Timothy J. Tschaplinski, Gerald Tuskan, Daniel Jacobson
Faculty & Staff Scholarship
Biological organisms are complex systems that are composed of functional networks of interacting molecules and macro-molecules. Complex phenotypes are the result of orchestrated, hierarchical, heterogeneous collections of expressed genomic variants. However, the effects of these variants are the result of historic selective pressure and current environmental and epigenetic signals, and, as such, their co-occurrence can be seen as genome-wide correlations in a number of different manners. Biomass recalcitrance (i.e., the resistance of plants to degradation or deconstruction, which ultimately enables access to a plant’s sugars) is a complex polygenic phenotype of high importance to biofuels initiatives. This study makes use …
Range Expansion And The Origin Of Usa300 North American Epidemic Methicillin-Resistant Staphylococcus Aureus, Lavanya Challagundla, Isabella A. Tickler, Xavier Didelot, David C. Coleman, Anna C. Shore, Geoffrey W. Coombs, Daniel O. Sordelli, Eric L. Brown, Robert Skov, Anders Rhod Larsen, Jinnethe Reyes, Iraida E. Robledo, Guillermo J. Vazquez, Paul Rivera, Paul D. Fey, Kurt Stevenson, Shu-Hua Wang, Barry N. Kreiswirth, Jose R. Mediavilla, Cesar A. Arias, Paul J. Planet, Rathel L. Nolan, Fred C. Tenover, Richard V. Goering, D. Ashley Robinson
Range Expansion And The Origin Of Usa300 North American Epidemic Methicillin-Resistant Staphylococcus Aureus, Lavanya Challagundla, Isabella A. Tickler, Xavier Didelot, David C. Coleman, Anna C. Shore, Geoffrey W. Coombs, Daniel O. Sordelli, Eric L. Brown, Robert Skov, Anders Rhod Larsen, Jinnethe Reyes, Iraida E. Robledo, Guillermo J. Vazquez, Paul Rivera, Paul D. Fey, Kurt Stevenson, Shu-Hua Wang, Barry N. Kreiswirth, Jose R. Mediavilla, Cesar A. Arias, Paul J. Planet, Rathel L. Nolan, Fred C. Tenover, Richard V. Goering, D. Ashley Robinson
Biology Faculty Publications
The USA300 North American epidemic (USA300-NAE) clone of methicillin-resistant Staphylococcus aureus has caused a wave of severe skin and soft tissue infections in the United States since it emerged in the early 2000s, but its geographic origin is obscure. Here we use the population genomic signatures expected from the serial founder effects of a geographic range expansion to infer the origin of USA300-NAE and identify polymorphisms associated with its spread. Genome sequences from 357 isolates from 22 U.S. states and territories and seven other countries are compared. We observe two significant signatures of range expansion, including decreases in genetic diversity …
A Comparison Of Three Diagnostic Platforms For The Detection Of Influenza A And B In Children, Furqan Kabir, Marvi Tariq, Fatima Aziz, Syed Imran Rizvi, Shahida Qureshi, Syed Asad Ali, Najeeha Talat Iqbal
A Comparison Of Three Diagnostic Platforms For The Detection Of Influenza A And B In Children, Furqan Kabir, Marvi Tariq, Fatima Aziz, Syed Imran Rizvi, Shahida Qureshi, Syed Asad Ali, Najeeha Talat Iqbal
Department of Paediatrics and Child Health
Background: Viral flu is the predominant cause of hospitalization in young children, which invariably leads to enhanced morbidity and mortality in children in developing countries. Initial treatment of viral flu is based on presumptive diagnosis. Bedside testing is not common in clinical settings because of variable sensitivity and specificity of rapid tests in different settings.
Methods: To address this issue, we evaluated the performance of Binax influenza A/B rapid testing kit against two robust molecular platforms (quantitative real-time polymerase chain reaction [qRT-PCR] and TaqMan array card [TAC]) in 24 nasopharyngeal (NP) swabs, collected from children under 5 years of age. …