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Truncation Of Type Iv Pilin Induces Mucoidy In Pseudomonas Aeruginosa Strain Pao579, T. Ryan Withers, F. Heath Damron, Yeshi Yin, Hongwei D. Yu 2013 Marshall University

Truncation Of Type Iv Pilin Induces Mucoidy In Pseudomonas Aeruginosa Strain Pao579, T. Ryan Withers, F. Heath Damron, Yeshi Yin, Hongwei D. Yu

Biochemistry and Microbiology

Pseudomonas aeruginosa is a Gram negative, opportunistic pathogen that uses the overproduction of alginate, a surface polysaccharide, to form biofilms in vivo. Overproduction of alginate, also known as mucoidy, affords the bacterium protection from the host's defenses and facilitates the establishment of chronic lung infections in individuals with cystic fibrosis. Expression of the alginate biosynthetic operon is primarily controlled by the alternative sigma factor AlgU (AlgT/σ22). In a nonmucoid strain, AlgU is sequestered by the transmembrane antisigma factor MucA to the cytoplasmic membrane. AlgU can be released from MucA via regulated intramembrane proteolysis by proteases AlgW and ...


Assessing Methods For Assigning Snps To Genes In Gene-Based Tests Of Association Using Common Variants, Ashley Petersen, Carolina Alvarez, Scott DeClaire, Nathan L. Tintle 2013 University of Washington

Assessing Methods For Assigning Snps To Genes In Gene-Based Tests Of Association Using Common Variants, Ashley Petersen, Carolina Alvarez, Scott Declaire, Nathan L. Tintle

Department of Biostatistics Faculty Publications

Gene-based tests of association are frequently applied to common SNPs (MAF>5%) as an alternative to single-marker tests. In this analysis we conduct a variety of simulation studies applied to five popular gene-based tests investigating general trends related to their performance in realistic situations. In particular, we focus on the impact of non-causal SNPs and a variety of LD structures on the behavior of these tests. Ultimately, we find that non-causal SNPs can significantly impact the power of all gene-based tests. On average, we find that the “noise” from 6–12 non-causal SNPs will cancel out the “signal” of one ...


Intratracheal Instillation Of Cerium Oxide Nanoparticles Induces Hepatic Toxicity In Male Sprague-Dawley Rats, Siva Krishna Nalabotu, Madhukar Babu Kolli, William E. Triest, Jane Y. Ma, Nandini DPK Manne, Anjaiah Katta, Hari S. Addagarla, Kevin M. Rice, Eric R. Blough 2013 Marshall University

Intratracheal Instillation Of Cerium Oxide Nanoparticles Induces Hepatic Toxicity In Male Sprague-Dawley Rats, Siva Krishna Nalabotu, Madhukar Babu Kolli, William E. Triest, Jane Y. Ma, Nandini Dpk Manne, Anjaiah Katta, Hari S. Addagarla, Kevin M. Rice, Eric R. Blough

Kevin M Rice

Background: Cerium oxide (CeO2) nanoparticles have been posited to have both beneficial and toxic effects on biological systems. Herein, we examine if a single intratracheal instillation of CeO2 nanoparticles is associated with systemic toxicity in male Sprague-Dawley rats. Methods and results: Compared with control animals, CeO2 nanoparticle exposure was associated with increased liver ceria levels, elevations in serum alanine transaminase levels, reduced albumin levels, a diminished sodium-potassium ratio, and decreased serum triglyceride levels (P < 0.05). Consistent with these data, rats exposed to CeO2nanoparticles also exhibited reductions in liver weight (P < 0.05) and dose-dependent hydropic degeneration, hepatocyte enlargement, sinusoidal ...


The Genochip: A New Tool For Genetic Anthropology, Eran Elhaik, Elliott Greenspan, Sean Staats, Thomas Krahn, Chris Tyler-Smith, Yali Xue, Sergio Tofanelli, Francesco Cucca, Luca Pagani, Li Jin, Hui Li, Theodore G. Schurr, Bennett Greenspan, R. Spencer Wells, Genographic Consortium 2013 University of Pennsylvania

The Genochip: A New Tool For Genetic Anthropology, Eran Elhaik, Elliott Greenspan, Sean Staats, Thomas Krahn, Chris Tyler-Smith, Yali Xue, Sergio Tofanelli, Francesco Cucca, Luca Pagani, Li Jin, Hui Li, Theodore G. Schurr, Bennett Greenspan, R. Spencer Wells, Genographic Consortium

Department of Anthropology Papers

The Genographic Project is an international effort aimed at charting human migratory history. The project is nonprofit and non-medical, and, through its Legacy Fund, supports locally led efforts to preserve indigenous and traditional cultures. Although the first phase of the project was focused on uniparentally inherited markers on the Y-chromosome and mitochondrial DNA (mtDNA), the current phase focuses on markers from across the entire genome to obtain a more complete understanding of human genetic variation. Although many commercial arrays exist for genome-wide single-nucleotide polymorphism (SNP) genotyping, they were designed for medical genetic studies and contain medically related markers that are ...


Genomics Unbound: The Scientific And Legal Case Against Patents Based On Naturally Occurring Dna Sequences, Fazal Khan 2013 University of Georgia School of Law

Genomics Unbound: The Scientific And Legal Case Against Patents Based On Naturally Occurring Dna Sequences, Fazal Khan

Scholarly Works

While there have been mixed opinions as to whether gene patents were dead in light of Prometheus,this Article argues that a proper understanding of patent law, genomics, and public policy concerns should lead to no other result. The primary focus of this piece is to rebut certain vested interests in the biotechnology industry and affirm the normative claim that gene patents improperly fetter genomics research and development. First, through the lens of the Myriad case, we will recount why there was such a strong public interest movement against recognizing such patents. Specifically, we will show how patents on naturally ...


Intratracheal Instillation Of Cerium Oxide Nanoparticles Induces Hepatic Toxicity In Male Sprague-Dawley Rats, Siva Krishna Nalabotu, Madhukar Babu Kolli, William E. Triest, Jane Y. Ma, Nandini DPK Manne, Anjaiah Katta, Hari S. Addagarla, Kevin M. Rice, Eric R. Blough 2013 Marshall University

Intratracheal Instillation Of Cerium Oxide Nanoparticles Induces Hepatic Toxicity In Male Sprague-Dawley Rats, Siva Krishna Nalabotu, Madhukar Babu Kolli, William E. Triest, Jane Y. Ma, Nandini Dpk Manne, Anjaiah Katta, Hari S. Addagarla, Kevin M. Rice, Eric R. Blough

Eric Blough

Background: Cerium oxide (CeO2) nanoparticles have been posited to have both beneficial and toxic effects on biological systems. Herein, we examine if a single intratracheal instillation of CeO2 nanoparticles is associated with systemic toxicity in male Sprague-Dawley rats. Methods and results: Compared with control animals, CeO2 nanoparticle exposure was associated with increased liver ceria levels, elevations in serum alanine transaminase levels, reduced albumin levels, a diminished sodium-potassium ratio, and decreased serum triglyceride levels (P < 0.05). Consistent with these data, rats exposed to CeO2nanoparticles also exhibited reductions in liver weight (P < 0.05) and dose-dependent hydropic degeneration, hepatocyte enlargement, sinusoidal ...


Role Of Iron In Ethanol Derived Hepatic Stress, Jesse A. Thornton 2013 Marshall University

Role Of Iron In Ethanol Derived Hepatic Stress, Jesse A. Thornton

Theses, Dissertations and Capstones

Chronic alcohol abuse is the third leading cause of preventable death in the United States. Ethanol metabolism causes liver injury through alterations in hepatic metabolic state, redox status, and acetaldehyde adduct formations. Increased iron absorption is associated with chronic ethanol consumption and may play a role in ethanol induced oxidative stress. We tested the hypothesis that normal labile iron in the liver plays a role in ethanol related pathological stress, using C57/Bl6 mice pair-fed Lieber-DeCarli liquid ethanol diets for 11 and 22 weeks. Normal iron group mice received 55mg/kg iron as ferric citrate, whereas the low iron groups ...


Meckel Gruber Syndrome: Second Trimester Diagnosis Of A Case In A Non-Consanguineous Marriage, Areej Alam, Mehreen Adhi, Raffat Bano, Aisha Zubair, Ammara Mushtaq 2013 Dow University of Health Sciences

Meckel Gruber Syndrome: Second Trimester Diagnosis Of A Case In A Non-Consanguineous Marriage, Areej Alam, Mehreen Adhi, Raffat Bano, Aisha Zubair, Ammara Mushtaq

Department of Obstetrics & Gynaecology

Meckel-Gruber Syndrome (MKS) is a rare, autosomal recessive genetic disorder, incompatible with life. It is characterized by enlarged polycystic kidneys and post axial polydactyly. Foetal or neonatal death is caused by pulmonary hypoplasia. We report a case of a 35 year old woman who presented at 7 weeks of gestation of her sixth pregnancy. A transabdominal anomaly ultrasound performed for her current pregnancy at 18 weeks of gestation showed features consistent with MKS. The termination of pregnancy was declined and a live newborn female was delivered via an emergency caeserean section at 34 weeks of gestation due to previous history ...


The Krüppel-Like Factor 2 And Krüppel-Like Factor 4 Genes Interact To Maintain Endothelial Integrity In Mouse Embryonic Vasculogenesis, Aditi R. Chiplunkar, Benjamin C. Curtis, Gabriel L. Eades, Megan S. Kane, Sean J. Fox, Jack L. Haar, Joyce A. Lloyd 2013 Virginia Commonwealth University

The Krüppel-Like Factor 2 And Krüppel-Like Factor 4 Genes Interact To Maintain Endothelial Integrity In Mouse Embryonic Vasculogenesis, Aditi R. Chiplunkar, Benjamin C. Curtis, Gabriel L. Eades, Megan S. Kane, Sean J. Fox, Jack L. Haar, Joyce A. Lloyd

Human and Molecular Genetics Publications

Background Krüppel-like Factor 2 (KLF2) plays an important role in vessel maturation during embryonic development. In adult mice, KLF2 regulates expression of the tight junction protein occludin, which may allow KLF2 to maintain vascular integrity. Adult tamoxifen-inducible Krüppel-like Factor 4 (KLF4) knockout mice have thickened arterial intima following vascular injury. The role of KLF4, and the possible overlapping functions of KLF2 and KLF4, in the developing vasculature are not well-studied.

Results Endothelial breaks are observed in a major vessel, the primary head vein (PHV), in KLF2-/-KLF4-/- embryos at E9.5. KLF2-/-KLF4-/- embryos die by E10.5, which is ...


Nucleoside Reverse Transcriptase Inhibitors And Ototoxicity: A Review Of The Literature, Erinn Reinbolt 2013 University of Redlands

Nucleoside Reverse Transcriptase Inhibitors And Ototoxicity: A Review Of The Literature, Erinn Reinbolt

Undergraduate Honors Theses

In December 2011, the World Health Organization released a report estimating the number of worldwide HIV/AIDS cases at 30 million. HIV/AIDS is an antiretroviral disease that affects the immune system by destroying cells vital to the body's immune response. This is accomplished by two general mechanisms: killing host cells, and killing uninfected neighboring cells. Both mechanisms are based on manipulation of the genetic information contained within ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) of a type of immune cell called the CD4 cell.


The Expanding Genomic Landscape Of Autism: Discovering The 'Forest' Beyond The 'Trees', Valerie Wailin Hu 2013 George Washington University

The Expanding Genomic Landscape Of Autism: Discovering The 'Forest' Beyond The 'Trees', Valerie Wailin Hu

Biochemistry and Molecular Medicine Faculty Publications

Autism spectrum disorders (ASDs) are neurodevelopmental disorders characterized by significant deficits in reciprocal social interactions, impaired communication, and restricted, repetitive behaviors. Because ASDs are among the most heritable of neuropsychiatric disorders, much of autism research has focused on the search for genetic variants in protein-coding genes (i.e., the "trees"). However, no single gene can account for more than 1% of the cases of ASD. Yet, genome-wide association studies have often identified statistically significant associations of genetic variations in regions of DNA that do not code for proteins (i.e., intergenic regions). There is increasing evidence that such noncoding regions ...


Pax3 Expression, Protein Modifications And Downstream Target Gene Profiling In Melanocytes And Melanoma Cells, Danielle Bartlett 2013 Edith Cowan University

Pax3 Expression, Protein Modifications And Downstream Target Gene Profiling In Melanocytes And Melanoma Cells, Danielle Bartlett

Theses: Doctorates and Masters

PAX3 is a transcription factor. It plays a major role in the development of melanocytes in the embryo. As a result of alternative splicing, the gene gives rise to eight different transcripts which encode proteins that have differing structures and are therefore likely to activate different downstream target genes. The presence of post-translational modifications has also been shown to alter the functions of the proteins.

PAX3 regulates the maintenance of undifferentiated melanoblasts and mediates pathways involved in proliferation, migration and survival. It has been shown to be expressed in melanoblasts, adult melanocytes, naevi and in most melanoma cells. This implies ...


Expression And Function Of Cd9 In Melanoma Cells, Jun Fan, Guo-Zhang Zhu, Richard Niles 2012 Marshall University

Expression And Function Of Cd9 In Melanoma Cells, Jun Fan, Guo-Zhang Zhu, Richard Niles

Jun Fan

CD9, a member of the tetraspanin family, functions as an organizer in “tetraspanin webs,” through interacting with other cell adhesion molecules. It plays a role in differentiation, fertilization, and cell migration. We investigated the expression and function of CD9 in melanoma. CD9 protein expression in B16 mouse melanoma and six human melanoma cell lines was decreased compared to normal melanocytes. B16F1 clones stably overexpressing CD9 had reduced ability to form colonies in soft agar; however, paradoxically these overexpressing clones had increased ability to invade Matrigel. Similarly, transient overexpression of CD9 in the human metastatic melanoma cell line WM9 dramatically decreased ...


The Mycoplasma Genitalium Mg_454 Gene Product Resists Killing By Organic Hydroperoxides, Sankaralingam Saikolappan, Smitha Sasindran, Hongwei Yu, Joel Basema, Subramanian Dhandayuthapani 2012 Marshall University

The Mycoplasma Genitalium Mg_454 Gene Product Resists Killing By Organic Hydroperoxides, Sankaralingam Saikolappan, Smitha Sasindran, Hongwei Yu, Joel Basema, Subramanian Dhandayuthapani

Hongwei Yu

Mycoplasma genitalium is the smallest self-replicating organism and a successful human pathogen associated with a range of genitourinary maladies. As a consequence of its restricted genome size, genes that are highly conserved in other bacteria are absent in M. genitalium. Significantly, genes that encode antioxidants like superoxide dismutase and catalase-peroxidase are lacking. Nevertheless, comparative genomics has revealed that MG_454 of M. genitalium encodes a protein with putative function as an organic hydroperoxide reductase (Ohr). In this study, we found that an M. genitalium transposon mutant that lacks expression of MG_454 was sensitive to killing by t-butyl hydroperoxide and cumene hydroperoxide ...


Persistent Infections And Immunity In Cystic Fibrosis, Hongwei Yu, Nathan Head 2012 Marshall University

Persistent Infections And Immunity In Cystic Fibrosis, Hongwei Yu, Nathan Head

Hongwei Yu

Cystic fibrosis (CF) is the most common autosomal recessive lethal disease in the Caucasian population. Chronic respiratory infections with Pseudomonas aeruginosa, neutrophil-dominated airway inflammation and progressive lung damage are the major causes of morbidity and mortality in CF. Two persistent infection phenotypes expressed by this bacterium are biofilm and mucoidy. Biofilm, also called the microcolony mode of growth is the surface-associated adherent bacterial community, while mucoidy refers to a phenotype conducive to copious amounts of mucoid exopolysaccharide (MEP)/alginate that provides a matrix for mature biofilms conferring resistance to host defenses and antibiotics. Recent completion of the whole genomic sequence ...


Expression And Function Of Cd9 In Melanoma Cells, Jun Fan, Guo-Zhang Zhu, Richard Niles 2012 Marshall University

Expression And Function Of Cd9 In Melanoma Cells, Jun Fan, Guo-Zhang Zhu, Richard Niles

Richard M Niles

CD9, a member of the tetraspanin family, functions as an organizer in “tetraspanin webs,” through interacting with other cell adhesion molecules. It plays a role in differentiation, fertilization, and cell migration. We investigated the expression and function of CD9 in melanoma. CD9 protein expression in B16 mouse melanoma and six human melanoma cell lines was decreased compared to normal melanocytes. B16F1 clones stably overexpressing CD9 had reduced ability to form colonies in soft agar; however, paradoxically these overexpressing clones had increased ability to invade Matrigel. Similarly, transient overexpression of CD9 in the human metastatic melanoma cell line WM9 dramatically decreased ...


Identification Of Conserved Splicing Motifs In Mutually Exclusive Exons Of 15 Insect Species, Patricia Buendia, John Tyree, Robert Laredo, Shu-Ning Hsu 2012 INFOTECH Soft, Inc., Miami, Florida

Identification Of Conserved Splicing Motifs In Mutually Exclusive Exons Of 15 Insect Species, Patricia Buendia, John Tyree, Robert Laredo, Shu-Ning Hsu

School of Computing and Information Sciences

Background: During alternative splicing, the inclusion of an exon in the final mRNA molecule is determined by nuclear proteins that bind cis-regulatory sequences in a target pre-mRNA molecule. A recent study suggested that the regulatory codes of individual RNA-binding proteins may be nearly immutable between very diverse species such as mammals and insects. The model system Drosophila melanogaster therefore presents an excellent opportunity for the study of alternative splicing due to the availability of quality EST annotations in FlyBase.

Methods: In this paper, we describe an in silico analysis pipeline to extract putative exonic splicing regulatory sequences from a multiple ...


Gene Patents No More? Deciphering The Meaning Of Prometheus, Fazal Khan, Lindsay Kessler 2012 University of Georgia School of Law

Gene Patents No More? Deciphering The Meaning Of Prometheus, Fazal Khan, Lindsay Kessler

Scholarly Works

When Congress enacted the United States Patent Act in 1952, it specified that patentable subject matter included anything “under the sun that is made by man.” Three decades ago the United States Patent and Trademark Office (USPTO) issued the first gene patent and ushered in a brave new gold rush. Some genes are associated with specific diseases, so being able to identify these sequences is an essential first step for developing genomic diagnostic tests and therapies. The problem with gene patents is that they allow modern-day prospectors to cordon off access to naturally occurring DNA sequences and exclude others from ...


A Proposal To Test The Effects Of Factor Ecat1 On Pluripotency, From Reprogramming To Differentiation Of Human Somatic Cells, Vritti R. Goel 2012 Scripps College

A Proposal To Test The Effects Of Factor Ecat1 On Pluripotency, From Reprogramming To Differentiation Of Human Somatic Cells, Vritti R. Goel

CMC Senior Theses

The field of stem cell research has been growing more because of the interest in using stem cells to cure diseases and heal injuries. Human embryonic stem cells, because of the controversy surrounding them—and subsequently the difficulties in acquiring samples of the existing aging cell lines—can only be used in limited capacities. While the development of induced pluripotent stem cells in the last decade has allowed the field to progress closer to medical treatments, the low efficiency of reprogramming a somatic cell to a pluripotent state, and the vast molecular and genomic differences between human embryonic stem cells ...


Mitochondrial Genome Sequence Analysis: A Custom Bioinformatics Pipeline Substantially Improves Affymetrix Mitochip V2.0 Call Rate And Accuracy, Hongbo M. Xie, Juan C. Perin, Theodore G. Schurr, Matthew C. Dulik, Sergey I. Zhadanov, Joseph A. Baur, Michael P. King, Emily Place, Colleen Clarke, Michael Grauer, Jonathan Schug, Avni Santani, Anthony Albano, Cecilia Kim, Vincent Procaccio, Hakon Hakonarson, Xiaowu Gai, Marni J. Falk 2011 University of Pennsylvania

Mitochondrial Genome Sequence Analysis: A Custom Bioinformatics Pipeline Substantially Improves Affymetrix Mitochip V2.0 Call Rate And Accuracy, Hongbo M. Xie, Juan C. Perin, Theodore G. Schurr, Matthew C. Dulik, Sergey I. Zhadanov, Joseph A. Baur, Michael P. King, Emily Place, Colleen Clarke, Michael Grauer, Jonathan Schug, Avni Santani, Anthony Albano, Cecilia Kim, Vincent Procaccio, Hakon Hakonarson, Xiaowu Gai, Marni J. Falk

Department of Anthropology Papers

Background

Mitochondrial genome sequence analysis is critical to the diagnostic evaluation of mitochondrial disease. Existing methodologies differ widely in throughput, complexity, cost efficiency, and sensitivity of heteroplasmy detection. Affymetrix MitoChip v2.0, which uses a sequencing-by-genotyping technology, allows potentially accurate and high-throughput sequencing of the entire human mitochondrial genome to be completed in a cost-effective fashion. However, the relatively low call rate achieved using existing software tools has limited the wide adoption of this platform for either clinical or research applications. Here, we report the design and development of a custom bioinformatics software pipeline that achieves a much improved call ...


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