Exploring The Effects Of Hypoxia On Sulfate Reducing Anaerobes, 2011 University of Rhode Island
Exploring The Effects Of Hypoxia On Sulfate Reducing Anaerobes, Annaliese K. Jones
Senior Honors Projects
Exploring the Effects of Hypoxia on Sulfate Reducing Anaerobes
Annaliese K. Jones
Sponsor: Bethany Jenkins, Cell and Molecular Biology
As a student about to graduate with a degree in Biological Sciences, I find myself faced with the need to find my own independent research interests and scientific voice. As a result of my interests in the fields of both microbiology and ecology, I am drawn to questions surrounding the role and behavior of microorganisms in the environment. With climate change being an issue capturing the attention of a large portion of the scientific community, I have chosen to focus my …
Quantitative Comparison Of Cis-Regulatory Element (Cre) Activities In Transgenic Drosophila Melanogaster, 2011 University of Dayton
Quantitative Comparison Of Cis-Regulatory Element (Cre) Activities In Transgenic Drosophila Melanogaster, William A. Rogers, Thomas M. Williams
Biology Faculty Publications
Gene expression patterns are specified by cis-regulatory element (CRE) sequences, which are also called enhancers or cis-regulatory modules. A typical CRE possesses an arrangement of binding sites for several transcription factor proteins that confer a regulatory logic specifying when, where, and at what level the regulated gene(s) is expressed. The full set of CREs within an animal genome encodes the organism′s program for development1, and empirical as well as theoretical studies indicate that mutations in CREs played a prominent role in morphological evolution2-4. Moreover, human genome wide association studies indicate that genetic variation in CREs …
Protein Trap Lines Of Drosophila To Demonstrate Spatio-Temporal Localization Of Proteins In An Undergraduate Lab, 2011 University of Dayton
Protein Trap Lines Of Drosophila To Demonstrate Spatio-Temporal Localization Of Proteins In An Undergraduate Lab, Oorvashi Roy Puli, Amit Singh
Biology Faculty Publications
The objective of this teaching note is to generate a laboratory exercise, which allows students to get a hands-on experience of a cell biology technique. The short duration of the laboratory classes is the biggest challenge with the development of a cell biology lab for an undergraduate curriculum. Therefore, it is necessary to design a laboratory exercise that enables the students to carry out cell biological assays in the desired time. This laboratory exercise focuses on tracking protein expression levels along a spatial (space) and temporal (time) axis in developing Drosophila melanogaster organ primordium. Here we use the protein trap …
Contribution Of Ectodomain Mutations In Epidermal Growth Factor Receptor To Signaling In Glioblastoma Multiforme, 2011 The University of Texas Graduate School of Biomedical Sciences at Houston
Contribution Of Ectodomain Mutations In Epidermal Growth Factor Receptor To Signaling In Glioblastoma Multiforme, Marta L. Rojas
Dissertations & Theses (Open Access)
CONTRIBUTION OF ECTODOMAIN MUTATIONS IN EPIDERMAL GROWTH FACTOR RECEPTOR TO SIGNALING IN GLIOBLASTOMA MULTIFORME
Publication No._________
Marta Rojas, M.S.
Supervisory Professor: Oliver Bögler, Ph.D.
The Cancer Genome Atlas (TCGA) has conducted a comprehensive analysis of a large tumor cohort and has cataloged genetic alterations involving primary sequence variations and copy number aberrations of genes involved in key signaling pathways in glioblastoma (GBM). This dataset revealed missense ectodomain point mutations in epidermal growth factor receptor (EGFR), but the biological and clinical significance of these mutations is not well defined in the context of gliomas.
In our study, we focused on understanding …
Capture-Recapture Of White-Tailed Deer Using Dna Sampling From Fecal Pellet-Groups, 2011 University of Tennessee, Knoxville
Capture-Recapture Of White-Tailed Deer Using Dna Sampling From Fecal Pellet-Groups, Matthew James Goode
Masters Theses
Reliable density estimates of game and keystone species such as white-tailed deer (Odocoileus virginianus) are desirable to set proper management strategies and for evaluating those strategies over time. However, traditional methods for estimating white-tailed deer density have been inhibited by behavior, densely forested areas that can hamper observation (detection), and invalid techniques of estimating effective trapping area. We wanted to evaluate a noninvasive method of mark-recapture estimation using DNA extracted from fecal pellets as the individual marker and for gender determination, coupled with a spatial detection function to estimate density (Spatially Explicit Capture-Recapture, SECR). We collected pellet groups …
The Incidence Of Plexiform Lesion Formation In Lines Divergently Selected For Ascites, 2011 University of Arkansas
The Incidence Of Plexiform Lesion Formation In Lines Divergently Selected For Ascites, James Mason
Graduate Theses and Dissertations
Complex Vascular Lesions, (CVL) are a common vascular change associated with idiopathicpulmonary arterial hypertension (IPAH). CVL have been characterized in studies using animal models involving, but not limited to, Sprague-Dawley rats and poultry (Abe et al., 2010; Wideman et al., 2011).IPAH has been documented in poultry although no connection has been made with CVLs. The current study characterizes CVL in the lungs from broilers derived from lines divergently selected for 15 generations for ascites susceptibility under conditions of simulated high altitude. The ascites RES and SUS lines were sampled for CVL incidence over time. Both lines were reared in a …
Identification Of Factors Involved In Dna Methylation Of Cpg-Island-Promoters, 2011 The University of Texas Graduate School of Biomedical Sciences at Houston
Identification Of Factors Involved In Dna Methylation Of Cpg-Island-Promoters, Yan Zhang
Dissertations & Theses (Open Access)
Repression of many tumor suppressor genes (TSGs) in cancer is mediated by aberrantly increased DNA methylation levels at promoter CpG islands (CGI). About one-fourth of empirically defined human promoters are surrounded by or contain clustered repetitive elements. It was previously observed that a sharp transition of methylation occurs between highly methylated repetitive elements (SINE or LINE) and unmethylated CGI-promoters (e.g. P16, VHL, CDH and RIL) in normal tissues. The functions that lead to increased CGI methylation in cancer remain poorly understood. We propose that CGI-promoters contain cis-elements for triggering de novo DNA methylation. In the first part of our project, …
Ethnic Disparity In 21-Hydroxylase Gene Mutations Identified In Pakistani Congenital Adrenal Hyperplasia Patient, 2011 Aga Khan University
Ethnic Disparity In 21-Hydroxylase Gene Mutations Identified In Pakistani Congenital Adrenal Hyperplasia Patient, Aysha Habib Khan, Muniba Aban, Jamal Raza, Naeem Ul Haq, Abdul Jabbar, Tariq Moatter
Department of Pathology and Laboratory Medicine
Background: Congenital adrenal hyperplasia (CAH) is a group of autosomal recessive disorders caused by defects in the steroid 21 hydroxylase gene (CYP21A2). We studied the spectrum of mutations in CYP21A2 gene in a multi-ethnic population in Pakistan to explore the genetics of CAH.
Methods: A cross sectional study was conducted for the identification of mutations CYP21A2 and their phenotypic associations in CAH using ARMS-PCR assay.
Results: Overall, 29 patients were analyzed for nine different mutations. The group consisted of two major forms of CAH including 17 salt wasters and 12 simple virilizers. There were 14 phenotypic males and 15 females …
Consequences Of Gene Flow And Transgene Introgression In Hybrids Between Transgenic Brassica Napus And Its Weedy Wild Relative Brassica Rapa, 2011 University of Tennessee - Knoxville
Consequences Of Gene Flow And Transgene Introgression In Hybrids Between Transgenic Brassica Napus And Its Weedy Wild Relative Brassica Rapa, Reginald Jason Millwood
Masters Theses
The adventitious presence of transgenes and their potential impact on the environment has been a topic of concern for many years. To address these concerns the following chapters discuss past and current research of gene flow and introgression, methods for transgene detection and monitoring, and the results from field-level experiments using artificially introgressed advanced generation hybrids. The field studies were designed to be a worst-case scenario where hybrids were produced by hand-crossing transgenic Brassica napus (AACC, 2n = 38) and its weedy wild relative Brassica rapa (AA, 2n = 20). B. napus was transgenic for the green fluorescent protein [m-GFP-5 …
Global And Specific Controls Of Protein Synthesis In Hibernators, 2011 University of Nevada, Las Vegas
Global And Specific Controls Of Protein Synthesis In Hibernators, Peipei Pan
UNLV Theses, Dissertations, Professional Papers, and Capstones
Mammalian hibernation is a highly dynamic physiological process that is composed of a series of torpor bouts, wherein hibernators oscillate between periods of torpor and interbout arousal. Although normally vital to homeostasis, many energetically consumptive processes such as translation or protein synthesis are virtually ceased during hibernation. Earlier studies indicated that protein synthesis had fallen to almost negligible levels. Cap-dependent initiation of translation is well regulated by eukaryotic translation initiation factor 4E (eIF4E) and its binding partner eIF4E-binding protein 1 (4E-BP1) when hibernators cycle in and out the torpor state. Herein, I investigated well-characterized regulatory mechanisms of global and specific …
Afghan Genetic Mysteries, 2011 National Museum of Natural History, CNRS UMR 7206, Paris, France
Afghan Genetic Mysteries, Bernard Dupaigne
Human Biology Open Access Pre-Prints
Letter To The Editor
The Y-Str Genetic Diversity Of An Idaho Basque Population, With Comparison To European Basques And Us Caucasians, 2011 Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
The Y-Str Genetic Diversity Of An Idaho Basque Population, With Comparison To European Basques And Us Caucasians, Josu Zubizarreta, Michael C. Davis, Greg Hampikian
Human Biology Open Access Pre-Prints
Fifty unrelated Basque males from southwest Idaho were typed for the 17 Y-STR loci in the Yfiler multiplex kit (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, YGATA_H4.1 and DYS385a/b). A total of 42 haplotypes were identified, with no more than two individuals sharing a single haplotype. The haplotype diversity (HD) was 0.9935, and gene diversity (D) over loci was 0.457 ± 0.137. The Idaho Basque population was compared to the source population from the Basque autonomous region of Northern Spain and Southern France, as well as a US Caucasian population. The haplotype diversity …
Role Of The Gcn5 Histone Acetyltransferase In Spinocerebellar Ataxia Type 7 And In Immature Neurons, 2011 The University of Texas Graduate School of Biomedical Sciences at Houston
Role Of The Gcn5 Histone Acetyltransferase In Spinocerebellar Ataxia Type 7 And In Immature Neurons, Yi Chun Chen
Dissertations & Theses (Open Access)
Spinocerebellar Ataxia type 7 (SCA7) is a neurodegenerative disease caused by expansion of a CAG repeat encoding a polyglutamine tract in ATXN7, a component of the SAGA histone acetyltransferase (HAT) complex. Previous studies provided conflicting evidence regarding the effects of polyQ-ATXN7 on the activity of Gcn5, the HAT catalytic subunit of SAGA. Here I showed that reducing Gcn5 expression accelerates both cerebellar and retinal degeneration in a mouse model of SCA7. Deletion of Gcn5 in Purkinje cells in mice expressing wild type Atxn7, however, causes only mild ataxia and does not lead to the early lethality observed in SCA7 mice. …
Msh1 Influence On Plant Mitochondrial Genome Recombination And Phenotype In Tobacco, 2011 University of Nebraska-Lincoln
Msh1 Influence On Plant Mitochondrial Genome Recombination And Phenotype In Tobacco, Peibei Sun
School of Biological Sciences: Dissertations, Theses, and Student Research
Plant mitochondrial genomes are composed of unusually complex structures, due to active recombination at numerous repeated sequences in the genome. The maintenance of mitochondrial genome stability is under the control of identifiable nuclear genes. In plants, three nuclear genes (MSH1, RECA3 and OSB1) have been shown to participate in recombination surveillance and the suppression of illegitimate recombination in mitochondria. Disruption of these loci in Arabidopsis results in reproducible mitochondrial genome rearrangements. We demonstrated that repeat-mediated de novo recombination was also enhanced in both Arabidopsis and tobacco during passage through in vitro culture. Furthermore, in vitro conditions led …
The Intracellular Behaviour Of Burkholderia Cenocepacia In Murine Macrophages, 2011 The University of Western Ontario
The Intracellular Behaviour Of Burkholderia Cenocepacia In Murine Macrophages, Jennifer S. Tolman
Electronic Thesis and Dissertation Repository
Burkholderia cenocepacia is an opportunistic pathogen causing life-threatening infections in cystic fibrosis and other immunocompromised patients. The bacterium survives within macrophages by interfering with typical endocytic trafficking, resulting in delayed maturation of a B. cenocepacia-containing phagosome. We hypothesize that B. cenocepacia alters gene expression after internalization by macrophages, inducing genes involved in intracellular survival and host adaptation. Furthermore, we hypothesize that specialized bacterial secretion systems are involved in the interactions between intracellular bacteria and macrophages. In this work, we characterize later-stage infection of macrophages by B. cenocepacia, showing replication within an acidified endosomal compartment suggestive of a phagolysosome. …
Planning Combinatorial Disulfide Cross-Links For Protein Fold Determination, 2011 Dartmouth College
Planning Combinatorial Disulfide Cross-Links For Protein Fold Determination, Fei Xiong, Alan M Friedman, Chris Bailey-Kellogg
Dartmouth Scholarship
Fold recognition techniques take advantage of the limited number of overall structural organizations, and have become increasingly effective at identifying the fold of a given target sequence. However, in the absence of sufficient sequence identity, it remains difficult for fold recognition methods to always select the correct model. While a native-like model is often among a pool of highly ranked models, it is not necessarily the highest-ranked one, and the model rankings depend sensitively on the scoring function used. Structure elucidation methods can then be employed to decide among the models based on relatively rapid biochemical/biophysical experiments.
Exploring The Role Of The Solvent In The Denaturation Of A Protein: A Molecular Dynamics Study Of The Dna Binding Domain Of The 434 Repressor, 2011 University of Massachusetts Medical School
Exploring The Role Of The Solvent In The Denaturation Of A Protein: A Molecular Dynamics Study Of The Dna Binding Domain Of The 434 Repressor, Celia Schiffer, Volker Dötsch, Kurt Wuthrich, Wilfred Van Gunsteren
Celia A. Schiffer
Molecular dynamics simulations of the DNA binding domain of 434 repressor are presented which aim at unraveling the role of solvent in protein denaturation. Four altered solvent models, each mimicking various possible aspects of the addition of a denaturant to the aqueous solvent, were used in the simulations to analyze their effects on the stability of the protein. The solvent was altered by selectively changing the Coulombic interaction between water and protein atoms and between different water molecules. The use of a modified solvent model has the advantage of mimicking the presence of denaturant without having denaturant molecules present in …
Additive Functions In Boolean Models Of Gene Regulatory Network Modules, 2011 Dartmouth College
Additive Functions In Boolean Models Of Gene Regulatory Network Modules, Christian Darabos, Ferdinando Ferdinando Di Cunto, Marco Tomassini, Jason H. Moore
Dartmouth Scholarship
Gene-on-gene regulations are key components of every living organism. Dynamical abstract models of genetic regulatory networks help explain the genome’s evolvability and robustness. These properties can be attributed to the structural topology of the graph formed by genes, as vertices, and regulatory interactions, as edges. Moreover, the actual gene interaction of each gene is believed to play a key role in the stability of the structure. With advances in biology, some effort was deployed to develop update functions in Boolean models that include recent knowledge. We combine real-life gene interaction networks with novel update functions in a Boolean model. We …
Functional Dissection Of The Glucose Signaling Pathways That Regulate The Yeast Glucose Transporter Gene (Hxt) Repressor Rgt1, 2011 University of Southern Mississippi
Functional Dissection Of The Glucose Signaling Pathways That Regulate The Yeast Glucose Transporter Gene (Hxt) Repressor Rgt1, David J. Jouandot Ii, Adhiraj Roy, Jeong-Ho Kim
Faculty Publications
The yeast Rgt1 repressor is a bifunctional protein that acts as a transcriptional repressor and activator. Under glucose-limited conditions, Rgt1 induces transcriptional repression by forming a repressive complex with its corepressors Mth1 and Std1. Here, we show that Rgt1 is converted from a transcriptional repressor into an activator under high glucose conditions and this occurs through two independent but consecutive events mediated by two glucose signaling pathways: (1) disruption of the repressive complex by the Rgt2/Snf3 pathway; (2) phosphorylation of Rgt1 by the cAMP-dependent protein kinase (cAMP-PKA) pathway. Rgt1 is phosphorylated by PKA at four serine residues within its amino-terminal …
Adaptive Evolution Of The Matrix Extracellular Phosphoglycoprotein In Mammals, 2011 Universidade do Porto - Portugal
Adaptive Evolution Of The Matrix Extracellular Phosphoglycoprotein In Mammals, Joao P. Machado, Warren E. Johnson, Stephen J. O'Brien, Vitor Vasconcelos, Agostinho Antunes
Biology Faculty Articles
Background
Matrix extracellular phosphoglycoprotein (MEPE) belongs to a family of small integrin-binding ligand N-linked glycoproteins (SIBLINGs) that play a key role in skeleton development, particularly in mineralization, phosphate regulation and osteogenesis. MEPE associated disorders cause various physiological effects, such as loss of bone mass, tumors and disruption of renal function (hypophosphatemia). The study of this developmental gene from an evolutionary perspective could provide valuable insights on the adaptive diversification of morphological phenotypes in vertebrates.
Results
Here we studied the adaptive evolution of the MEPE gene in 26 Eutherian mammals and three birds. The comparative genomic analyses revealed a high degree …