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Molecular Genetics

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Articles 331 - 360 of 523

Full-Text Articles in Genetics

Spontaneous Dna Damage To The Nuclear Genome Promotes Senescence, T Redox Imbalance And Aging, Andria R. Robinson, Matthew J. Yousefzadeh, Tania A. Rozgaja, Jin Wang, Xuesen Li, Jeremy S. Tilstra, Chelsea H. Feldman, Siobhan Q. Gregg, Caroline H. Johnson, Erin M. Skoda, Marie-Celine Frantz, Harris Bell-Temin, Hannah Pope-Varsalona, Aditi U. Gurkar, Luigi A. Nasto, Rena A.S. Robinson, Heike Fuhrmann-Stroissnigg, Jolanta Czerwinska, Sara J. Mcgowan, Nadiezhda Cantu-Madellin, Jamie B. Harris, Salony Maniar, Mark A. Ross, Christy E. Trussoni, Nicholas F. Larusso, Eugenia Cifuentes-Pagano, Patrick J. Pagano, Barbara Tudek, Nam V. Vo, Lora H. Rigatti, Patricia L. Opresko, Donna B. Stolz, Simon C. Watkins, Christin E. Burd, Claudette M. St, Croix, Gary Siuzdak, Nathan A. Yates, Paul D. Robbins, Yinsheng Wang, Peter Wipf, Eric E. Kelley, Laura J. Neidernhofer Jan 2018

Spontaneous Dna Damage To The Nuclear Genome Promotes Senescence, T Redox Imbalance And Aging, Andria R. Robinson, Matthew J. Yousefzadeh, Tania A. Rozgaja, Jin Wang, Xuesen Li, Jeremy S. Tilstra, Chelsea H. Feldman, Siobhan Q. Gregg, Caroline H. Johnson, Erin M. Skoda, Marie-Celine Frantz, Harris Bell-Temin, Hannah Pope-Varsalona, Aditi U. Gurkar, Luigi A. Nasto, Rena A.S. Robinson, Heike Fuhrmann-Stroissnigg, Jolanta Czerwinska, Sara J. Mcgowan, Nadiezhda Cantu-Madellin, Jamie B. Harris, Salony Maniar, Mark A. Ross, Christy E. Trussoni, Nicholas F. Larusso, Eugenia Cifuentes-Pagano, Patrick J. Pagano, Barbara Tudek, Nam V. Vo, Lora H. Rigatti, Patricia L. Opresko, Donna B. Stolz, Simon C. Watkins, Christin E. Burd, Claudette M. St, Croix, Gary Siuzdak, Nathan A. Yates, Paul D. Robbins, Yinsheng Wang, Peter Wipf, Eric E. Kelley, Laura J. Neidernhofer

Faculty & Staff Scholarship

Accumulation of senescent cells over time contributes to aging and age-related diseases. However, what drives senescence in vivo is not clear. Here we used a genetic approach to determine if spontaneous nuclear DNA damage is sufficient to initiate senescence in mammals. Ercc1-/Δ mice with reduced expression of ERCC1-XPF endonuclease have impaired capacity to repair the nuclear genome. Ercc1-/Δ mice accumulated spontaneous, oxidative DNA damage more rapidly than wild-type (WT) mice. As a consequence, senescent cells accumulated more rapidly in Ercc1-/Δ mice compared to repair-competent animals. However, the levels of DNA damage and senescent cells in Ercc1-/Δ mice never exceeded that …

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Effects Of Gli-Similar 3 Knockout Mutations On The Expression Of Insulin Transcription And Pancreatic Islet Development In Zebrafish, Dylan James Hammrich Jan 2018

Effects Of Gli-Similar 3 Knockout Mutations On The Expression Of Insulin Transcription And Pancreatic Islet Development In Zebrafish, Dylan James Hammrich

Murray State Theses and Dissertations

Blood glucose homeostasis is a critical component in the physiological health of vertebrates. Regulation of blood glucose levels is the responsibility of the endocrine pancreas, which excretes hormones to the bloodstream in response to changes in glucose concentrations. The hormones excreted from the pancreas include insulin, which is secreted form the β cells of the pancreas and signals uptake of excess glucose by the peripheral tissues, and glucagon, which is secreted from the α cells and signals release of glucose to the bloodstream through gluconeogenesis in the liver. The Krüppel-like zinc finger protein Gli-Similar 3 (Glis3) is a transcription factor …

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Increased Fxyd1 And Pgc-1Α Mrna After Blood Flow-Restricted Running Is Related To Fibre Type-Specific Ampk Signalling And Oxidative Stress In Human Muscle, Danny Christiansen, Robyn M. Murphy, Christos G. Stathis, David Bishop Jan 2018

Increased Fxyd1 And Pgc-1Α Mrna After Blood Flow-Restricted Running Is Related To Fibre Type-Specific Ampk Signalling And Oxidative Stress In Human Muscle, Danny Christiansen, Robyn M. Murphy, Christos G. Stathis, David Bishop

Research outputs 2014 to 2021

Aim: This study explored the effects of blood flow restriction (BFR) on mRNA responses of PGC-1α (total, 1α1, and 1α4) and Na+,K+-ATPase isoforms (NKA; α1-3, β1-3, and FXYD1) to an interval running session and determined whether these effects were related to increased oxidative stress, hypoxia, and fibre type-specific AMPK and CaMKII signalling, in human skeletal muscle. Methods: In a randomized, crossover fashion, 8 healthy men (26 ± 5 year and 57.4 ± 6.3 mL kg−1 min−1) completed 3 exercise sessions: without (CON) or with blood flow restriction (BFR), or in systemic hypoxia (HYP, ~3250 m). A muscle sample was collected …

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Adverse Pregnancy Outcomes And Imbalance In Angiogenic Growth Mediators And Oxidative Stress Biomarkers Is Associated With Advanced Maternal Age Births: A Prospective Cohort Study In Ghana, Enoch Odame Anto, William K. Owiredu, Samuel A. Sakyi, Cornelius A. Turpin, Richard K. Ephraim, Linda A. Fondjo, Christian Obirikorang, Eric Adua, Emmanuel Acheampong Jan 2018

Adverse Pregnancy Outcomes And Imbalance In Angiogenic Growth Mediators And Oxidative Stress Biomarkers Is Associated With Advanced Maternal Age Births: A Prospective Cohort Study In Ghana, Enoch Odame Anto, William K. Owiredu, Samuel A. Sakyi, Cornelius A. Turpin, Richard K. Ephraim, Linda A. Fondjo, Christian Obirikorang, Eric Adua, Emmanuel Acheampong

Research outputs 2014 to 2021

Background Advanced maternal age (AMA) has been associated with negative pregnancy outcomes. Oxidative stress (OS) and defective placental dysfunction are contributing factors. This study determined the association between AMA and adverse pregnancy outcomes, OS biomarkers and angiogenic growth mediators (AGMs) in normal pregnancies. Methods This prospective cohort study conducted at the Obstetrics and Gynaecology (O&G) Department of the Komfo Anokye Teaching Hospital (KATH) finally included 175 normal pregnant women comprising, 58 AMA (35–45 years), 55 (30–34 years) and 62 optimal childbearing age (20–29 years). Venous blood samples were collected at 28–32 weeks for soluble fms-like tyrosine kinase-1 (sFlt-1), placental growth …

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Snd1-Targeted Gene Therapy For Hepatocellular Carcinoma, Bryan D. Mckiver Jan 2018

Snd1-Targeted Gene Therapy For Hepatocellular Carcinoma, Bryan D. Mckiver

Theses and Dissertations

Staphylococcal nuclease and tudor-domain containing 1 (SND1) is an oncogene for a wide variety of cancers, including hepatocellular carcinoma (HCC). SND1 is a multifunctional protein regulating gene expression of proto-oncogenes and tumor suppressor genes, making SND1 a prime target for developing cancer therapeutics. This notion is especially attributed to HCC as most patients are diagnosed in advanced stages and the therapeutic options available for these patients are severely limited. In this study, we evaluated the therapeutic potential of a replication-defective adenovirus vector delivering SND1 shRNA (Ad.SND1sh) to human HCC cell lines, HepG3, HuH-7, and Hep3B. Adenovirus infection in HCC cells …

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การจำแนกลักษณะทางโมเลกุลของเชื้อ Escherichia Coli ที่สร้างเอนไซม์ Extended-Spectrum Beta-Lactamases ที่แยกได้จากสุกรและประชากรในอำเภอเมือง จังหวัดลำพูน, จักรพงษ์ สีนามะ Jan 2018

การจำแนกลักษณะทางโมเลกุลของเชื้อ Escherichia Coli ที่สร้างเอนไซม์ Extended-Spectrum Beta-Lactamases ที่แยกได้จากสุกรและประชากรในอำเภอเมือง จังหวัดลำพูน, จักรพงษ์ สีนามะ

Chulalongkorn University Theses and Dissertations (Chula ETD)

ปัจจุบันพบเชื้อ Escherichia coli ที่สร้างเอนไซม์ extended-spectrum beta-lactamase (ESBL) แพร่กระจายในชุมชนอย่างกว้างขวาง เชื้อแบคทีเรียดังกล่าวสามารถพบได้ว่าเป็นเชื้อประจำถิ่นในลำไส้ของคน และสัตว์ รวมไปถึงสามารถพบได้ในสิ่งแวดล้อมทั่วไป ซึ่งอาจกลายเป็นแหล่งเก็บกักเชื้อแบคทีเรียดื้อสารต้านจุลชีพ ที่สามารถแพร่กระจายในชุมชนต่างๆ ทั่วโลก การศึกษาครั้งนี้ทำการจำแนกลักษณะทางโมเลกุลของเชื้อ E. coli ที่สร้างเอนไซม์ ESBL ซึ่งแยกได้จากสุกรในฟาร์มปศุสัตว์และประชากรในชุมชน ในพื้นที่อำเภอเมือง จังหวัดลำพูน เพื่อศึกษารูปแบบของยีนที่ควบคุมการสร้างเอนไซม์ ESBL และศึกษาหาความสัมพันธ์ของเชื้อในกลุ่มตัวอย่างทั้งสอง เชื้อ E. coli ที่สร้างเอนไซม์ ESBL จำนวนทั้งสิ้น 212 สายพันธุ์ แยกได้จากอุจจาระของสุกรและประชากรที่มีสุขภาพดี และทำการจำแนกยีนที่ควบคุมการสร้างเอนไซม์ ESBL ได้แก่ ยีน blaCTX-M ยีน blaTEM และยีน blaSHV ด้วยเทคนิค multiplex-PCR และเทคนิค whole genome sequencing และศึกษาความสัมพันธ์ของเชื้อ E. coli ที่สร้างเอนไซม์ ESBL ที่แยกได้จากทั้งสองกลุ่มตัวอย่างด้วยเทคนิค multilocus sequence typing ผลการศึกษาพบว่าเชื้อ E. coli ที่สร้างเอนไซม์ ESBL ส่วนใหญ่เป็นเชื้อดื้อยาหลายขนาน และมักดื้อยากลุ่ม fluoroquinolones ยากลุ่ม aminoglycosides และยา trimethoprim/sulfamethoxazole ในขณะที่เชื้อทุกสายพันธุ์ดื้อต่อยา ampicillin ยา ceftriaxone และยา cefotaxime ยีนที่ควบคุมการสร้างเอนไซม์ ESBL ที่พบมากที่สุดได้แก่ ยีน blaCTX-M ซึ่งพบได้ 95.75% รองลงมาคือยีน blaTEM และยีน blaSHV พบได้ 62.73% และ 2.40% ตามลำดับ โดย subgroup ของยีนที่ควบคุมการสร้างเอนไซม์ ESBL ที่พบมากที่สุด ได้แก่ ยีน blaCTX-M-55 …

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An Undergraduate Laboratory Manual For Analyzing A Crispr Mutant With A Predicted Role In Regeneration, Susan Walsh, Ashley Becker, Paxton S. Sickler, Damian G. Clarke, Erin Jimenez Nov 2017

An Undergraduate Laboratory Manual For Analyzing A Crispr Mutant With A Predicted Role In Regeneration, Susan Walsh, Ashley Becker, Paxton S. Sickler, Damian G. Clarke, Erin Jimenez

Faculty Publications

Exposing students to undergraduate research has reportedly improved students’ development of knowledge and skills in the laboratory, self-efficacy, satisfaction with their research, retention, and perseverance when faced with obstacles. Furthermore, utilizing authentic course-based undergraduate research experiences (CUREs) includes all students enrolled in the class, giving those who may not otherwise have access to an independent undergraduate research project an opportunity to engage in the scientific process in context of an original, unanswered question. In the fall of 2016, second semester introductory biology students conducted a semester-long research project on the transcription factor Lin28a to determine the effect of Lin28a on …

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Characterization Of A Novel Mitochondrial Plasmid In Brassica, Mackenzie Strehle Oct 2017

Characterization Of A Novel Mitochondrial Plasmid In Brassica, Mackenzie Strehle

UCARE: Research Products

Possessing some of the largest and most complex genomes of any eukaryotic organelles, plant mitochondria are notorious for their rapidly rearranging genetic framework. In addition to containing a large and complex mitochondrial genome, the mitochondria of several plants in the genus Brassica have also been shown to contain an independent, self-replicating linear plasmid. Interestingly, the plasmid appears to be able to move independently between the cytoplasm and the mitochondria, and it can be paternally inherited, unlike the rest of the mitochondrial genome. The plasmid also has features similar to those of adenoviruses, including terminal inverted repeats and covalently bound proteins …

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Itraq-Based Proteomics Analysis And Network Integration For Kernel Tissue Development In Maize, Long Zhang, Yongbin Dong, Qilei Wang, Chunguang Du, Wenwei Xiong, Xinyu Li, Sailan Zhu, Yuling Li Aug 2017

Itraq-Based Proteomics Analysis And Network Integration For Kernel Tissue Development In Maize, Long Zhang, Yongbin Dong, Qilei Wang, Chunguang Du, Wenwei Xiong, Xinyu Li, Sailan Zhu, Yuling Li

Department of Biology Faculty Scholarship and Creative Works

Grain weight is one of the most important yield components and a developmentally complex structure comprised of two major compartments (endosperm and pericarp) in maize (Zea mays L.), however, very little is known concerning the coordinated accumulation of the numerous proteins involved. Herein, we used isobaric tags for relative and absolute quantitation (iTRAQ)-based comparative proteomic method to analyze the characteristics of dynamic proteomics for endosperm and pericarp during grain development. Totally, 9539 proteins were identified for both components at four development stages, among which 1401 proteins were non-redundant, 232 proteins were specific in pericarp and 153 proteins were specific in …

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Performing A Genetic Screen To Identify Factors That Promote Lncrna-Dependent Gene Repression, Chrishan Fernando, Cecilia Yiu, Sara Cloutier, Siwen Wang, Elizabeth Tran Aug 2017

Performing A Genetic Screen To Identify Factors That Promote Lncrna-Dependent Gene Repression, Chrishan Fernando, Cecilia Yiu, Sara Cloutier, Siwen Wang, Elizabeth Tran

The Summer Undergraduate Research Fellowship (SURF) Symposium

Long non-coding RNAs (lncRNAs) were once thought not to have useful functions in organisms but rather to be products of aberrant transcription. However, roles are being found for lncRNAs in beneficial processes such as controlling gene expression. In some of these cases, lncRNAs form R-loops in vivo. R-loops are nucleic acid structures consisting of hybridized strands of single-stranded DNA (ssDNA) and single-stranded RNA (ssRNA) as well as the displaced strand of ssDNA. Formation of these R-loops is important for gene regulation by the lncRNAs. However, factors that promote formation of lncRNA R-loops are not known. The gene PHO84 is being …

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Optimizing A Method For Simultaneous Recovery Of Proteins And Dna From Fingerprints, Steven Kranes Aug 2017

Optimizing A Method For Simultaneous Recovery Of Proteins And Dna From Fingerprints, Steven Kranes

Student Theses

DNA testing on touched objects is a valuable tool in forensic investigations, but DNA is usually present in low amounts, causing poor STR typing results. For touch DNA evidence, there is a clear need for additional individualization, especially for highly probative samples. This could be achieved by testing genetically variable proteins. The goal of this project was to develop a DNA/protein co-extraction method to facilitate DNA and protein testing on the same evidence item. Existing DNA extraction methods were carefully adjusted to allow for downstream mass spectrometry analysis. Initial experiments on saliva and fingerprints placed on glass suggested that trypsin …

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Functional Consequences Of Rna Exosome Complex Alteration By Conformational Changes And Cofactor Binding, Jaeil Han Aug 2017

Functional Consequences Of Rna Exosome Complex Alteration By Conformational Changes And Cofactor Binding, Jaeil Han

Dissertations and Theses (Open Access)

The RNA exosome is an essential 3’-5 ribonuclease that processes or degrades a variety of RNA species in eukaryotes. It is composed of nine structural cores and one catalytic subunit, Rrp44. Structural studies captured two different conformations of Rrp44, Rrp44ch (channel) and Rrp44da (direct-access). The Rrp44ch appears to recruit RNA substrates from the central channel formed by the core subunits, while the substrate is directly recruited to Rrp44da bypassing the central channel. Although in vivo function of the Rrp44ch-exosome is extensively studied, the function or even the presence of the Rrp44da-exosome in …

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A Rapid Colorimetric Peptide Nucleic Acid Loop-Mediated Isothermal Amplification Assay For The Detection Of The Idh1 Mutation In Glioblastoma, Edward J. Raack Jul 2017

A Rapid Colorimetric Peptide Nucleic Acid Loop-Mediated Isothermal Amplification Assay For The Detection Of The Idh1 Mutation In Glioblastoma, Edward J. Raack

All NMU Master's Theses

The IDH1 mutation is an important diagnostic and prognostic biomarker used to characterize glioblastoma (GBM). Patients harboring the IDH1 mutation have improved overall survival following maximal resection. Knowledge of the IDH1 mutation status allows the surgeon to modify the surgical plan; however, no existing molecular test can provide this information intraoperatively. We designed a novel colorimetric peptide nucleic acid loop-mediated isothermal amplification (PNA-LAMP) method that rapidly detects the IDH1 R132H mutation in GBM. PNA-LAMP amplifies target DNA under isothermal conditions with high specificity and speed. The PNA prevents amplification of wild-type IDH1 DNA, while allowing amplification of the R132H variant …

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Body Size Regulation Via Bmp Signaling In Caenorhabditis Elegans, Uday Madaan Jun 2017

Body Size Regulation Via Bmp Signaling In Caenorhabditis Elegans, Uday Madaan

Dissertations, Theses, and Capstone Projects

The body size of an organism can be a crucial determinant of access to nutrition, reproductive success and overall survival in the wild. However, how body size of an individual is determined is incompletely understood. Body size is a complex trait determined by multiple pathways and genes, making it difficult to understand the role of individual genes and pathways in determining overall size. In Caenorhabditis elegans, a homolog of Bone Morphogenetic Proteins (BMP) is a major regulator of body size; functional loss of DBL-1 leads to a small body size. Due to a drastic change in body size in dbl-1 …

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The Population Genetics Of Morro Bay Eelgrass (Zostera Marina), Julia Gardner Harencar Jun 2017

The Population Genetics Of Morro Bay Eelgrass (Zostera Marina), Julia Gardner Harencar

Master's Theses

Seagrass populations are in decline worldwide. Zostera marina (eelgrass), one of California’s native seagrasses, is no exception to this trend. In the last 8 years, Morro Bay, California has lost 95% of its eelgrass. Eelgrass is an ecosystem engineer, providing important ecosystem services such as sediment stabilization, nutrient cycling, and nursery habitats for fish. The failure of recent restoration efforts necessitates a better understanding of the causes of eelgrass decline in this estuary. Previous research on eelgrass in California has demonstrated a link between population genetic diversity and eelgrass bed health, ecosystem functioning, and resilience to disturbance and extreme climatic …

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The 'Pseudomonas Aeruginosa' Psl Polysaccharide Is A Social But Noncheatable Trait In Biofilms, Yasuhiko Irie, Aled E. Roberts, Kasper N. Kragh, Vernita D. Gordon, Jaime B. Hutchison, Rosalind J. Allen, Gavin Melaugh, Thomas Bjarnsholt, Stuart A. West, Stephen P. Diggle Jun 2017

The 'Pseudomonas Aeruginosa' Psl Polysaccharide Is A Social But Noncheatable Trait In Biofilms, Yasuhiko Irie, Aled E. Roberts, Kasper N. Kragh, Vernita D. Gordon, Jaime B. Hutchison, Rosalind J. Allen, Gavin Melaugh, Thomas Bjarnsholt, Stuart A. West, Stephen P. Diggle

Biology Faculty Publications

Extracellular polysaccharides are compounds secreted by microorganisms into the surrounding environment, and they are important for surface attachment and maintaining structural integrity within biofilms. The social nature of many extracellular polysaccharides remains unclear, and it has been suggested that they could function as either cooperative public goods or as traits that provide a competitive advantage. Here, we empirically tested the cooperative nature of the PSL polysaccharide, which is crucial for the formation of biofilms in Pseudomonas aeruginosa. We show that (i) PSL is not metabolically costly to produce; (ii) PSL provides populationlevel benefits in biofilms, for both growth and antibiotic …

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The Santa Ana Speckled Dace (Rhinichthys Osculus): Phylogeography And Molecular Evolution Of The Mitochondrial Dna Control Region, James Jay Vanmeter Jun 2017

The Santa Ana Speckled Dace (Rhinichthys Osculus): Phylogeography And Molecular Evolution Of The Mitochondrial Dna Control Region, James Jay Vanmeter

Electronic Theses, Projects, and Dissertations

The purpose of this genetic study of the Santa Ana Speckled Dace Rhinichthys osculus was three-fold. The first goal was to characterize the molecular structure of the mtDNA control region of R. osculus. An 1143 base-pair region of the mitochondrial DNA genome, which included the complete control region was sequenced for all individuals. Analysis of the sequence data revealed that the molecular structure of the speckled dace control region was similar to the molecular structure described for other vertebrate taxa. The speckled dace control region contains three major domains, which vary in base frequency as well as in the frequency …

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Dna Sequences Of The Mitochondrial Cytochrome C Oxidase I (Coi) Genes From Deep Sea Fishes. Cruises Dp01 And Dp02 From May 2015 - August 2015, Andrea Bernard, Max Weber, Kimberly A. Finnegan, Mahmood S. Shivji, Ron Eytan May 2017

Dna Sequences Of The Mitochondrial Cytochrome C Oxidase I (Coi) Genes From Deep Sea Fishes. Cruises Dp01 And Dp02 From May 2015 - August 2015, Andrea Bernard, Max Weber, Kimberly A. Finnegan, Mahmood S. Shivji, Ron Eytan

DEEPEND Datasets

The deep sea ecosystem is believed to contain the highest biomass of fish in the oceans. However, the taxonomic diversity in this ecosystem is incompletely described and likely to be vastly underestimated. DNA sequence data (barcodes) have become a key tool to discover hidden biodiversity. We generated mitochondrial DNA barcode datasets based on the Cytochrome c oxidase I (COI) gene from deep sea fishes. These data were analyzed using phylogenetic and statistical methods to reveal cryptic species and make taxonomic linkages between adult fishes and their early life stages. These datasets were generated from fishes collected in the Northern Gulf …

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Does Genotype Correlate With Phenotype? Evaluating Ruffed Lemur (Varecia Spp.) Color Vision Using Subject Mediated Automatic Remote Testing Apparatus (Smarta), Raymond Vagell May 2017

Does Genotype Correlate With Phenotype? Evaluating Ruffed Lemur (Varecia Spp.) Color Vision Using Subject Mediated Automatic Remote Testing Apparatus (Smarta), Raymond Vagell

Theses and Dissertations

Ruffed lemur (Varecia spp.) color vision research was conducted using a multidisciplinary approach: psychophysics, genetic analysis, technology, and animal training. The behavioral manifestation of Varecia spp. trichromacy was shown using a touchscreen apparatus (SMARTA). Trichromats performed better than dichromats when discriminating red from green (G2 = 78.10, p < 0.001).

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Phenotypic Variation And Genetic Purity Of The Original 'Prime-Jim®' X 'Arapaho' Population, Loren M. Luther May 2017

Phenotypic Variation And Genetic Purity Of The Original 'Prime-Jim®' X 'Arapaho' Population, Loren M. Luther

Horticulture Undergraduate Honors Theses

In 2013, Castro et al., produced the first linkage map for primocane-fruiting blackberries using the cross ‘Prime-Jim®’ x ‘Arapaho.’ This mapping population has been maintained since the original experiment with the hopes of conducting future studies. Further research was determined to be needed on the population to better characterize additional phenotypic traits, and since nine years had passed since the seedlings were established, there was a need to assess the continued genetic purity of the population using molecular methods. Phenotypic data was collected to analyze the variation of the population including soluble solids content, titratable acidity, average weight, shape, and …

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Mrub_2294, Mrub_2293, And Mrub_1942 Genes Are Orthologs Of E. Coli B2476, B1131, And B4006 Genes, Respectively, Lindsay Popp, Dr. Lori Scott Jan 2017

Mrub_2294, Mrub_2293, And Mrub_1942 Genes Are Orthologs Of E. Coli B2476, B1131, And B4006 Genes, Respectively, Lindsay Popp, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

No abstract provided.

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Mrub_1304, Mrub_2007 And Mrub_2006 Are Orthologs Of E. Coli B_3189, B_3972, And B_0091, Respectively Within The Peptidoglycan Biosynthesis Pathway, Mylaun E. Griffith, Dr. Lori Scott Jan 2017

Mrub_1304, Mrub_2007 And Mrub_2006 Are Orthologs Of E. Coli B_3189, B_3972, And B_0091, Respectively Within The Peptidoglycan Biosynthesis Pathway, Mylaun E. Griffith, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

No abstract provided.

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Mrub_0860, Mrub_0701 And Mrub_2285 Are Orthologous To E. Coli B2892, B2562 And B3863 Within The Recfor Pathway For Homologous Recombination, Bailey Englund, Dr. Lori Scott Jan 2017

Mrub_0860, Mrub_0701 And Mrub_2285 Are Orthologous To E. Coli B2892, B2562 And B3863 Within The Recfor Pathway For Homologous Recombination, Bailey Englund, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tool associated with the Guiding Education through Novel Investigation – Annotation Collaboration Toolkit (GENI-ACT) to predict the gene function. We investigated the biological function of the genes Mrub_0860, Mrub_0701,and Mrub_2285. We predicted that Mrub_0860 (DNA coordinates 842934..844868 on the forward strand) encodes for the enzyme single-stranded DNA-specific exonuclease, which is in the first step of homologous recombination via the RecFOR pathway (KEGG map number 03440). The E. coli K12 MG1655 ortholog is predicted to be b2892, which has the gene identifier …

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Iron Metabolism Genes In Browsing And Grazing Rhinoceroses: Implications For Iron Overload Disorder, Lorien Salyer Jan 2017

Iron Metabolism Genes In Browsing And Grazing Rhinoceroses: Implications For Iron Overload Disorder, Lorien Salyer

Undergraduate Honors Thesis Projects

Iron overload disorder is a serious condition that affects many animals of conservation interest, including rhinoceroses. Iron overload disorder is only found in browsing rhinos (African black, Diceros bicornis, and Sumatran, Dicerorhinus sumatrensis) but not in grazing species (African white, Ceratotherium simum, and greater one-horned, Rhinoceros unicornis). Iron overload is connected with many of the other health issues seen in captive browsing rhinoceroses, so it is vitally important that the iron metabolism process is studied to improve the existing husbandry procedures of these critically endangered animals. The objective of this study was to characterize genes related to …

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An Undergraduate Cell Biology Lab: Western Blotting To Detect Proteins From Drosophila Eye, Neha Gogia, Ankita Sarkar, Amit Singh Jan 2017

An Undergraduate Cell Biology Lab: Western Blotting To Detect Proteins From Drosophila Eye, Neha Gogia, Ankita Sarkar, Amit Singh

Biology Faculty Publications

We have developed an undergraduate laboratory to allow detection and localization of proteins in the compound eye of Drosophila melanogaster, a.k.a fruit fly. This lab was a part of the undergraduate curriculum of the cell biology laboratory course aimed to demonstrate the use of Western Blotting technique to study protein localization in the adult eye of Drosophila. Western blotting, a two-day laboratory exercise, can be used to detect the presence of proteins of interests from total protein isolated from a tissue. The first day involves isolation of proteins from the tissue and SDS-PAGE (sodium dodecyl sulfate-polyacrylamide) gel …

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Real-Time Quantitative Pcr To Demonstrate Gene Expression In An Undergraduate Lab, Abijeet Singh Mehta, Amit Singh Jan 2017

Real-Time Quantitative Pcr To Demonstrate Gene Expression In An Undergraduate Lab, Abijeet Singh Mehta, Amit Singh

Biology Faculty Publications

The objective of this teaching note is to develop a laboratory exercise, which allows students to get a hands-on experience of a molecular biology technique to analyze gene expression. The short duration of the biology laboratory for an undergraduate curriculum is the biggest challenge with the development of new labs. An important part of cell biology or molecular biology undergraduate curriculum is to study gene expression. There are many labs to study gene expression in qualitative manner. The commonly used reporter gene expression studies are primarily qualitative. However, there is no hands-on experience exercise to quantitatively determine gene expression. Therefore, …

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Epigenetic Editing To Validate Findings From Methylome-Wide Association Studies Of Neuropsychiatric Disorders, Robin F. Chan Jan 2017

Epigenetic Editing To Validate Findings From Methylome-Wide Association Studies Of Neuropsychiatric Disorders, Robin F. Chan

Theses and Dissertations

DNA methylation is necessary for learning, memory consolidation and has been implicated in a number of neuropsychiatric disorders. Obtaining high quality and comprehensive data for the three common forms of methylation in brain is challenging for methylome-wide association studies (MWAS). To address this we optimized a panel of enrichment methods for screening the brain methylome. Results show that these enrichment techniques approach the coverage and fidelity of the current gold standard bisulfite based techniques. Our MBD-based method can also be used with low amounts of genomic material from limited human biomaterials. Psychiatric disorders have high prevalence and are often chronic …

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Pnpase In C. Elegans: Mutagenic Analysis To Complement Knockdown Studies, Danielle K. Seibert Jan 2017

Pnpase In C. Elegans: Mutagenic Analysis To Complement Knockdown Studies, Danielle K. Seibert

Theses and Dissertations

PNPase is a gene implicated as a potential target for cancer therapy; human mutations also present with deafness, myopathies, and neuropathies. In this study, C. elegans was used to investigate the effect of knocking out PNPase in a whole animal. C. elegans knockdown studies have reported an extended lifespan via an increase in ROS production. Further noted are larger mitochondria and an increase in fzo-1 expression. Knockout animals previously constructed using CRISPR/Cas9 were used for this study. We aimed to confirm these findings validating previous studies. It was discovered that PNPase knockout animals demonstrated a similar lifespan extension that was …

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Cullin-4 Regulates Wingless And Jnk Signaling-Mediated Cell Death In The Drosophila Eye., Meghana Tare, Ankita Sarkar, Shimpi Bedi, Madhuri Kango-Singh, Amit Singh Dec 2016

Cullin-4 Regulates Wingless And Jnk Signaling-Mediated Cell Death In The Drosophila Eye., Meghana Tare, Ankita Sarkar, Shimpi Bedi, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

In all multicellular organisms, the fundamental processes of cell proliferation and cell death are crucial for growth regulation during organogenesis. Strict regulation of cell death is important to maintain tissue homeostasis by affecting processes like regulation of cell number, and elimination of unwanted/unfit cells. The developing Drosophila eye is a versatile model to study patterning and growth, where complex signaling pathways regulate growth and cell survival. However, the molecular mechanisms underlying regulation of these processes is not fully understood. In a gain-of-function screen, we found that misexpression of cullin-4 (cul-4), an ubiquitin ligase, can rescue reduced eye mutant phenotypes. Previously, …

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A Bioinformatics Methodology For The Annotation And Analysis Of Sperm Chromatin Remodeling Proteins In Sequenced Drosophila Species, Zain A. Alvi Dec 2016

A Bioinformatics Methodology For The Annotation And Analysis Of Sperm Chromatin Remodeling Proteins In Sequenced Drosophila Species, Zain A. Alvi

Seton Hall University Dissertations and Theses (ETDs)

Spermatogenesis is the process by which mature functional spermatozoa are formed, and is initiated in the stem cell niche of the testes. During the post-meiotic stage of spermatogenesis, spermiogenesis, transition proteins facilitate the transformation of chromatin from a histone-based nucleosome structure to a protamine-based nucleosome structure. This study is aimed at analyzing genomic, transcript, and protein sequences of transition proteins in 13 sequenced Drosophila species. The Drosophila melanogaster spermatid specific transition protein-like protein (Tpl94D) was used as the reference sequence in this study. An extensive bioinformatics approach was employed in establishing the Tpl94D orthologs. We identified …

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