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Articles 7861 - 7890 of 9784

Full-Text Articles in Genetics and Genomics

Kdr-Lacz-Expressing Cells Are Involved In Ovarian And Testis-Specific Vascular Development, Suggesting A Role For Vegfa In The Regulation Of This Vasculature, Rebecca C. Bott, Debra T. Summers, Anna M. Fuller, Ryann M. Mcfee, Ningxia Lu, Renee M. Mcfee, Andrea S. Cupp Oct 2010

Kdr-Lacz-Expressing Cells Are Involved In Ovarian And Testis-Specific Vascular Development, Suggesting A Role For Vegfa In The Regulation Of This Vasculature, Rebecca C. Bott, Debra T. Summers, Anna M. Fuller, Ryann M. Mcfee, Ningxia Lu, Renee M. Mcfee, Andrea S. Cupp

Department of Animal Science: Faculty Publications

Our objectives were to evaluate kinase insert domain protein receptor (KDR)-β-galactosidase (LacZ) expression as a marker for vascular development during gonadal morphogenesis and to determine whether any novel non-angiogenic KDR-LacZ expression was present in mouse testes or ovaries. Gonads were collected from mice expressing LacZ driven by the Kdr promoter (KDRLacZ) from embryonic day 11 (E11) through postnatal day 60 (P60). At E11.5, mesonephric cells expressing KDR-LacZ seemed to migrate into the developing testis and surrounded developing seminiferous cords. Cells expressing KDR-LacZ appeared in the ovary with no apparent migration from the adjacent mesonephros, suggesting a different origin of endothelial …


Complete Plastid Genome Sequences Of Three Rosids (Castanea, Prunus, Theobroma): Evidence For At Least Two Independent Transfers Of Rpl22 To The Nucleus, Robert K. Jansen, Christopher Saski, Seung-Bum Lee, Anne K. Hansen, Henry Daniell Oct 2010

Complete Plastid Genome Sequences Of Three Rosids (Castanea, Prunus, Theobroma): Evidence For At Least Two Independent Transfers Of Rpl22 To The Nucleus, Robert K. Jansen, Christopher Saski, Seung-Bum Lee, Anne K. Hansen, Henry Daniell

Publications

Functional gene transfer from the plastid to the nucleus is rare among land plants despite evidence that DNA transfer to the nucleus is relatively frequent. During the course of sequencing plastid genomes from representative species from three rosid genera (Castanea, Prunus, Theobroma) and ongoing projects focusing on the Fagaceae and Passifloraceae, we identified putative losses of rpl22 in these two angiosperm families. We further characterized rpl22 from three species of Passiflora and one species of Quercus and identified sequences that likely represent pseudogenes. In Castanea and Quercus, both members of the Fagaceae, we identified a …


Dorsal Eye Selector Pannier (Pnr) Suppresses The Eye Fate To Define Dorsal Margin Of The Drosophila Eye, Sarah M. Oros, Meghana Tare, Madhuri Kango-Singh, Amit Singh Oct 2010

Dorsal Eye Selector Pannier (Pnr) Suppresses The Eye Fate To Define Dorsal Margin Of The Drosophila Eye, Sarah M. Oros, Meghana Tare, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

Axial patterning is crucial for organogenesis. During Drosophila eye development, dorso-ventral (DV) axis determination is the first lineage restriction event. The eye primordium begins with a default ventral fate, on which the dorsal eye fate is established by expression of the GATA-1 transcription factor pannier (pnr). Earlier, it was suggested that loss of pnr function induces enlargement in the dorsal eye due to ectopic equator formation. Interestingly, we found that in addition to regulating DV patterning, pnr suppresses the eye fate by downregulating the core retinal determination genes eyes absent (eya), sine oculis (so) and dacshund (dac) to define the …


Using The R Package Crlmm For Genotyping And Copy Number Estimation, Robert B. Scharpf, Rafael Irizarry, Walter Ritchie, Benilton Carvalho, Ingo Ruczinski Sep 2010

Using The R Package Crlmm For Genotyping And Copy Number Estimation, Robert B. Scharpf, Rafael Irizarry, Walter Ritchie, Benilton Carvalho, Ingo Ruczinski

Johns Hopkins University, Dept. of Biostatistics Working Papers

Genotyping platforms such as Affymetrix can be used to assess genotype-phenotype as well as copy number-phenotype associations at millions of markers. While genotyping algorithms are largely concordant when assessed on HapMap samples, tools to assess copy number changes are more variable and often discordant. One explanation for the discordance is that copy number estimates are susceptible to systematic differences between groups of samples that were processed at different times or by different labs. Analysis algorithms that do not adjust for batch effects are prone to spurious measures of association. The R package crlmm implements a multilevel model that adjusts for …


The Armadillo Repeat Protein Pf16 Is Essential For Flagellar Structure And Function In Plasmodium Male Gametes, Ursula Straschil, Arthur M. Talman, David J. P. Ferguson, Karen A. Bunting, Zhengyao Xu, Elizabeth Bailes, Robert E. Sinden, Anthony A. Holder, Elizabeth F. Smith Sep 2010

The Armadillo Repeat Protein Pf16 Is Essential For Flagellar Structure And Function In Plasmodium Male Gametes, Ursula Straschil, Arthur M. Talman, David J. P. Ferguson, Karen A. Bunting, Zhengyao Xu, Elizabeth Bailes, Robert E. Sinden, Anthony A. Holder, Elizabeth F. Smith

Dartmouth Scholarship

Malaria, caused by the apicomplexan parasite Plasmodium, threatens 40% of the world's population. Transmission between vertebrate and insect hosts depends on the sexual stages of the life-cycle. The male gamete of Plasmodium parasite is the only developmental stage that possesses a flagellum. Very little is known about the identity or function of proteins in the parasite's flagellar biology. Here, we characterise a Plasmodium PF16 homologue using reverse genetics in the mouse malaria parasite Plasmodium berghei. PF16 is a conserved Armadillo-repeat protein that regulates flagellar structure and motility in organisms as diverse as green algae and mice. We show that …


Physical Interaction Between Vivid And White Collar Complex Regulates Photoadaptation In Neurospora, Chen-Hui H. Chen, Bradley S. Demay, Amy S. Gladfelter, Jay Dunlap, Jennifer J. Loros Sep 2010

Physical Interaction Between Vivid And White Collar Complex Regulates Photoadaptation In Neurospora, Chen-Hui H. Chen, Bradley S. Demay, Amy S. Gladfelter, Jay Dunlap, Jennifer J. Loros

Dartmouth Scholarship

Photoadaptation, the ability to attenuate a light response on prolonged light exposure while remaining sensitive to escalating changes in light intensity, is essential for organisms to decipher time information appropriately, yet the underlying molecular mechanisms are poorly understood. In Neurospora crassa, VIVID (VVD), a small LOV domain containing blue-light photoreceptor protein, affects photoadaptation for most if not all light-responsive genes. We report that there is a physical interaction between VVD and the white collar complex (WCC), the primary blue-light photoreceptor and the transcription factor complex that initiates light-regulated transcriptional responses in Neurospora. Using two previously characterized VVD mutants, we show …


Hepatitis C Virus Core-Derived Peptides Inhibit Genotype 1b Viral Genome Replication Via Interaction With Ddx3x, Chaomin Sun, Cara T. Pager, Guangxiang Luo, Peter Sarnow, Jamie H. D. Cate Sep 2010

Hepatitis C Virus Core-Derived Peptides Inhibit Genotype 1b Viral Genome Replication Via Interaction With Ddx3x, Chaomin Sun, Cara T. Pager, Guangxiang Luo, Peter Sarnow, Jamie H. D. Cate

Microbiology, Immunology, and Molecular Genetics Faculty Publications

The protein DDX3X is a DEAD-box RNA helicase that is essential for the hepatitis C virus (HCV) life cycle. The HCV core protein has been shown to bind to DDX3X both in vitro and in vivo. However, the specific interactions between these two proteins and the functional importance of these interactions for the HCV viral life cycle remain unclear. We show that amino acids 16-36 near the N-terminus of the HCV core protein interact specifically with DDX3X both in vitro and in vivo. Replication of HCV replicon NNeo/C-5B RNA (genotype 1b) is significantly suppressed in HuH-7-derived cells expressing green fluorescent …


Sialic Acid Transport And Catabolism Are Cooperatively Regulated By Siar And Crp In Nontypeable Haemophilus Influenzae, Jason W. Johnston, Haider Shamsulddin, Anne-Frances Miller, Michael A. Apicella Sep 2010

Sialic Acid Transport And Catabolism Are Cooperatively Regulated By Siar And Crp In Nontypeable Haemophilus Influenzae, Jason W. Johnston, Haider Shamsulddin, Anne-Frances Miller, Michael A. Apicella

Microbiology, Immunology, and Molecular Genetics Faculty Publications

BACKGROUND: The transport and catabolism of sialic acid, a critical virulence factor for nontypeable Haemophilus influenzae, is regulated by two transcription factors, SiaR and CRP.

RESULTS: Using a mutagenesis approach, glucosamine-6-phosphate (GlcN-6P) was identified as a co-activator for SiaR. Evidence for the cooperative regulation of both the sialic acid catabolic and transport operons suggested that cooperativity between SiaR and CRP is required for regulation. cAMP was unable to influence the expression of the catabolic operon in the absence of SiaR but was able to induce catabolic operon expression when both SiaR and GlcN-6P were present. Alteration of helical phasing supported …


Integrating Evolutionary And Functional Approaches To Infer Adaptation At Specific Loci, Jay F. Storz, Christopher W. Wheat Sep 2010

Integrating Evolutionary And Functional Approaches To Infer Adaptation At Specific Loci, Jay F. Storz, Christopher W. Wheat

Jay F. Storz Publications

Inferences about adaptation at specific loci are often exclusively based on the static analysis of DNA sequence variation. Ideally, population-genetic evidence for positive selection serves as a stepping-off point for experimental studies to elucidate the functional significance of the putatively adaptive variation. We argue that inferences about adaptation at specific loci are best achieved by integrating the indirect, retrospective insights provided by population-genetic analyses with the more direct, mechanistic insights provided by functional experiments. Integrative studies of adaptive genetic variation may sometimes be motivated by experimental insights into molecular function, which then provide the impetus to perform population genetic tests …


Association Between Chronic Liver And Colon Inflammation During The Development Of Murine Syngeneic Graft-Versus-Host Disease, Jason Anthony Brandon, Jacqueline Perez-Rodriguez, C. Darrell Jennings, Donald A. Cohen, Vishal J. Sindhava, Subbarao Bondada, Alan M. Kaplan, J. Scott Bryson Sep 2010

Association Between Chronic Liver And Colon Inflammation During The Development Of Murine Syngeneic Graft-Versus-Host Disease, Jason Anthony Brandon, Jacqueline Perez-Rodriguez, C. Darrell Jennings, Donald A. Cohen, Vishal J. Sindhava, Subbarao Bondada, Alan M. Kaplan, J. Scott Bryson

Microbiology, Immunology, and Molecular Genetics Faculty Publications

The murine model of cyclosporine A (CsA)-induced syngeneic graft-versus-host disease (SGVHD) is a bone marrow (BM) transplantation model that develops chronic colon inflammation identical to other murine models of CD4+ T cell-mediated colitis. Interestingly, SGVHD animals develop chronic liver lesions that are similar to the early peribiliary inflammatory stages of clinical chronic liver disease, which is frequently associated with inflammatory bowel disease (IBD). Therefore, studies were initiated to investigate the chronic liver inflammation that develops in the SGVHD model. To induce SGVHD, mice were lethally irradiated, reconstituted with syngeneic BM, and treated with CsA. All of the SGVHD animals …


Bpab, A Novel Protein Encoded By The Lyme Disease Spirochete's Cp32 Prophages, Binds To Erp Operator 2 Dna, Logan H. Burns, Claire A. Adams, Sean P. Riley, Brandon L. Jutras, Amy Bowman, Alicia M. Chenail, Anne E. Cooley, Laura A. Haselhorst, Alisha M. Moore, Kelly Babb, Michael G. Fried, Brian Stevenson Sep 2010

Bpab, A Novel Protein Encoded By The Lyme Disease Spirochete's Cp32 Prophages, Binds To Erp Operator 2 Dna, Logan H. Burns, Claire A. Adams, Sean P. Riley, Brandon L. Jutras, Amy Bowman, Alicia M. Chenail, Anne E. Cooley, Laura A. Haselhorst, Alisha M. Moore, Kelly Babb, Michael G. Fried, Brian Stevenson

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Borrelia burgdorferi produces Erp outer surface proteins throughout mammalian infection, but represses their synthesis during colonization of vector ticks. A DNA region 5′ of the start of erp transcription, Operator 2, was previously shown to be essential for regulation of expression. We now report identification and characterization of a novel erp Operator 2-binding protein, which we named BpaB. erp operons are located on episomal cp32 prophages, and a single bacterium may contain as many as 10 different cp32s. Each cp32 family member encodes a unique BpaB protein, yet the three tested cp32-encoded BpaB alleles all bound to the same DNA …


Conidia But Not Yeast Cells Of The Fungal Pathogen Histoplasma Capsulatum Trigger A Type I Interferon Innate Immune Response In Murine Macrophages, Diane O. Inglis, Charlotte A. Berkes, Davina R. Hocking Murray, Anita Sil Sep 2010

Conidia But Not Yeast Cells Of The Fungal Pathogen Histoplasma Capsulatum Trigger A Type I Interferon Innate Immune Response In Murine Macrophages, Diane O. Inglis, Charlotte A. Berkes, Davina R. Hocking Murray, Anita Sil

Biology Faculty Publications

Histoplasma capsulatum is the most common cause of fungal respiratory infections and can lead to progressive disseminated infections, particularly in immunocompromised patients. Infection occurs upon inhalation of the aerosolized spores, known as conidia. Once inside the host, conidia are phagocytosed by alveolar macrophages. The conidia subsequently germinate and produce a budding yeast-like form that colonizes host macrophages and can disseminate throughout host organs and tissues. Even though conidia are the predominant infectious particle for H. capsulatum and are the first cell type encountered by the host during infection, very little is known at a molecular level about conidia or about …


Genetic Variants In Nuclear-Encoded Mitochondrial Genes Influence Aids Progression, Sher L. Hendrickson, J. A. Lautenberger, Leslie Wei Chinn, Michael Malasky, Lawrence Kingsley, James J. Goedert, Gregory D. Kirk, Edward Gomperts, Susan Buchbinder, Jennifer L. Troyer, Stephen J. O'Brien Sep 2010

Genetic Variants In Nuclear-Encoded Mitochondrial Genes Influence Aids Progression, Sher L. Hendrickson, J. A. Lautenberger, Leslie Wei Chinn, Michael Malasky, Lawrence Kingsley, James J. Goedert, Gregory D. Kirk, Edward Gomperts, Susan Buchbinder, Jennifer L. Troyer, Stephen J. O'Brien

Biology Faculty Articles

Background: The human mitochondrial genome includes only 13 coding genes while nuclear-encoded genes account for 99% of proteins responsible for mitochondrial morphology, redox regulation, and energetics. Mitochondrial pathogenesis occurs in HIV patients and genetically, mitochondrial DNA haplogroups with presumed functional differences have been associated with differential AIDS progression.

Methodology/Principal Findings: Here we explore whether single nucleotide polymorphisms (SNPs) within 904 of the estimated 1,500 genes that specify nuclear-encoded mitochondrial proteins (NEMPs) influence AIDS progression among HIV-1 infected patients. We examined NEMPs for association with the rate of AIDS progression using genotypes generated by an Affymetrix 6.0 genotyping array of 1,455 …


Splice Factor Sfrs6: Regulation By P53 And Effect On Il-24 Splicing, Erin L. Schmidt Sep 2010

Splice Factor Sfrs6: Regulation By P53 And Effect On Il-24 Splicing, Erin L. Schmidt

Loma Linda University Electronic Theses, Dissertations & Projects

Alternative splicing of RNA transcripts is emerging as a major mechanism for expanding the proteome. Splice pattern changes are found in numerous diseases and cancers, indicating the importance of tight control over this process. While the mechanism of splicing has been described in detail, it is less clear how a cell is able to modify its splicing patterns in response to different conditions. Our lab previously demonstrated that DNA damage can induce SFRS6, the gene coding for splicing factor SRp55, thereby leading to changes in the splicing patterns of several target genes related to survival and apoptosis. We also …


Genome Sequence Of The Model Mushroom Schizophyllum Commune, Robin A. Ohm, Jan F. De Jong, Luis G. Lugones, Andrea Aerts, Erika Kothe, Jason E. Stajich, Ronald P. De Vries, Eric Record, Anthony Levasseur, Scott E. Baker, Kirk A. Bartholomew, Pedro M. Coutinho, Susann Erdmann, Thomas J. Fowler, Allen C. Gathmen, Vincent Lombard, Bernard Henrissat, Nicole Knabe, Ursula Kues, Walt W. Lily Sep 2010

Genome Sequence Of The Model Mushroom Schizophyllum Commune, Robin A. Ohm, Jan F. De Jong, Luis G. Lugones, Andrea Aerts, Erika Kothe, Jason E. Stajich, Ronald P. De Vries, Eric Record, Anthony Levasseur, Scott E. Baker, Kirk A. Bartholomew, Pedro M. Coutinho, Susann Erdmann, Thomas J. Fowler, Allen C. Gathmen, Vincent Lombard, Bernard Henrissat, Nicole Knabe, Ursula Kues, Walt W. Lily

Biology Faculty Publications

Much remains to be learned about the biology of mushroom-forming fungi, which are an important source of food, secondary metabolites and industrial enzymes. The wood-degrading fungus Schizophyllum commune is both a genetically tractable model for studying mushroom development and a likely source of enzymes capable of efficient degradation of lignocellulosic biomass. Comparative analyses of its 38.5-megabase genome, which encodes 13,210 predicted genes, reveal the species's unique wood-degrading machinery. One-third of the 471 genes predicted to encode transcription factors are differentially expressed during sexual development of S. commune. Whereas inactivation of one of these, fst4, prevented mushroom formation, inactivation of another, …


Ovaries And Germline Cysts And Their Evolution In Dermaptera (Insecta), Wacław Tworzydło, Szczepan M. Biliński, Petr Kočárek, Fabian Haas Sep 2010

Ovaries And Germline Cysts And Their Evolution In Dermaptera (Insecta), Wacław Tworzydło, Szczepan M. Biliński, Petr Kočárek, Fabian Haas

All Peer-Reviewed Publications

We studied the ovary structure and initial stages of oogenesis in 15 representatives of several dermapteran taxa, including the epizoic Arixeniina. In all examined species, the ovaries are meroistic-polytrophic. The ovaries of the basal taxa ('Pygidicranidae', 'Diplatyidae', and Labiduridae) are composed of elongated ovarioles, attached to short lateral oviducts. In these groups, ovarioles contain several (more than 30) ovarian follicles in a linear arrangement. In the Eudermaptera, the ovaries are composed of 1-6 (Spongiphoridae) or 20-40 (Forficulidae, Chelisochidae) short ovarioles (containing 2 ovarian follicles only) that open to strongly elongated lateral oviducts. In all investigated dermapterans, the ovarian follicles are …


G-Lattices For An Unrooted Perfect Phylogeny, Monica Grigg Aug 2010

G-Lattices For An Unrooted Perfect Phylogeny, Monica Grigg

Mathematical Sciences Technical Reports (MSTR)

We look at the Pure Parsimony problem and the Perfect Phylogeny Haplotyping problem. From the Pure Parsimony problem we consider structures of genotypes called g-lattices. These structures either provide solutions or give bounds to the pure parsimony problem. In particular, we investigate which of these structures supports an unrooted perfect phylogeny, a condition that adds biological interpretation. By understanding which g-lattices support an unrooted perfect phylogeny, we connect two of the standard biological inference rules used to recreate how genetic diversity propagates across generations.


A Perturbation Method For Inference On Regularized Regression Estimates, Jessica Minnier, Lu Tian, Tianxi Cai Aug 2010

A Perturbation Method For Inference On Regularized Regression Estimates, Jessica Minnier, Lu Tian, Tianxi Cai

Harvard University Biostatistics Working Paper Series

No abstract provided.


Gene Cooption And Convergent Evolution Of Oxygen Transport Hemoglobins In Jawed And Jawless Vertebrates, Federico G. Hoffmann, Juan C. Opazo, Jay F. Storz Aug 2010

Gene Cooption And Convergent Evolution Of Oxygen Transport Hemoglobins In Jawed And Jawless Vertebrates, Federico G. Hoffmann, Juan C. Opazo, Jay F. Storz

Jay F. Storz Publications

Natural selection often promotes evolutionary innovation by coopting preexisting genes for new functions, and this process may be greatly facilitated by gene duplication. Here we report an example of cooptive convergence where paralogous members of the globin gene superfamily independently evolved a specialized O2 transport function in the two deepest branches of the vertebrate family tree. Specifically, phylogenetic evidence demonstrates that erythroidspecific O2 transport hemoglobins evolved independently from different ancestral precursor proteins in jawed vertebrates (gnathostomes) and jawless fish (cyclostomes, represented by lamprey and hagfish). A comprehensive phylogenetic analysis of the vertebrate globin gene superfamily revealed that the …


Development Of Pyrf-Based Genetic System For Targeted Gene Deletion In Clostridium Thermocellum And Creation Of A Pta Mutant, Shital A. Tripathi, Daniel G. Olson, D. Aaron Argyros, Bethany B. Miller, Trisha F. Barrett, Daniel M. Murphy, Jesse D. Mccool, Anne K. Warner, Vineet B. Rajgarhia, Lee R. Lynd, David A. Hogsett, Nicky C. Caiazza Aug 2010

Development Of Pyrf-Based Genetic System For Targeted Gene Deletion In Clostridium Thermocellum And Creation Of A Pta Mutant, Shital A. Tripathi, Daniel G. Olson, D. Aaron Argyros, Bethany B. Miller, Trisha F. Barrett, Daniel M. Murphy, Jesse D. Mccool, Anne K. Warner, Vineet B. Rajgarhia, Lee R. Lynd, David A. Hogsett, Nicky C. Caiazza

Dartmouth Scholarship

We report development of a genetic system for making targeted gene knockouts in Clostridium thermocellum, a thermophilic anaerobic bacterium that rapidly solubilizes cellulose. A toxic uracil analog, 5-fluoroorotic acid (5-FOA), was used to select for deletion of the pyrF gene. The ΔpyrF strain is a uracil auxotroph that could be restored to a prototroph via ectopic expression of pyrF from a plasmid, providing a positive genetic selection. Furthermore, 5-FOA was used to select against plasmid-expressed pyrF, creating a negative selection for plasmid loss. This technology was used to delete a gene involved in organic acid production, namely pta, which encodes …


The Small Regulatory Rna Ryhb Regulates Icsa Expression In Shigella Flexneri, Nick Egan, Helen J. Wing Aug 2010

The Small Regulatory Rna Ryhb Regulates Icsa Expression In Shigella Flexneri, Nick Egan, Helen J. Wing

Undergraduate Research Opportunities Program (UROP)

Shigella flexneri is a gram negative non-motile, non-spore forming, rod-shaped bacterium responsible for bacillary dysentery in humans. The master regulator, VirF, initiates a cascade of virulence gene activation by acting as a transcription factor for the gene encoding the global regulator, VirB (1). Production of VirB is also negatively regulated by the regulatory small RNA (sRNA), RyhB 2). Regulatory sRNAs are untranslated RNA molecules involved in the regulation of both transcription and translation. RyhB, a 90 nt sRNA, was first identified in E. coli and subsequently found in all Shigella species. In Shigella this sRNA is maximally expressed in response …


Phylogenetic Studies Of Newly Isolated Freshwater Magnetospirilla Using Cbb And Mam Genes, Nathan Viloria, Christopher T. Lefevre, Dennis A. Bazylinski Aug 2010

Phylogenetic Studies Of Newly Isolated Freshwater Magnetospirilla Using Cbb And Mam Genes, Nathan Viloria, Christopher T. Lefevre, Dennis A. Bazylinski

Undergraduate Research Opportunities Program (UROP)

The phylogeny and general relatedness of prokaryotes is determined by comparisons of the sequences of rRNA genes, most commonly the 16S rRNA gene. Comparisons between other gene sequences have been used for this purpose and some have supported conclusions from 16S rRNA genes while others have not. In this study, 13 new magnetospirilla were phylogenetically characterized using the sequences of the 16S rRNA gene as well as the genes for forms I and II ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) (cbbL and cbbM, respectively) and for two magnetosome membrane proteins unique to magnetotactic bacteria, mamJ and mamK. Polymerase chain reaction (PCR) with degenerate …


Genetically Modifying Arabidopsis Thaliana With A Gene From Drought-Tolerant Xerophyte Larrea Tridentata (Creosote Bush), Norris Lam, Liyuan A. Zhang, Lingkun Gu, Qingxi J. Shen Aug 2010

Genetically Modifying Arabidopsis Thaliana With A Gene From Drought-Tolerant Xerophyte Larrea Tridentata (Creosote Bush), Norris Lam, Liyuan A. Zhang, Lingkun Gu, Qingxi J. Shen

Undergraduate Research Opportunities Program (UROP)

L. tridentata, or desert creosote bush, is a xerophytic C3 plant native to the American Southwest, and is known to have evolutionarily developed sophisticated cellular mechanisms to deal with periods of intense abiotic stress. Particularly, complex signaling pathways in L. tridentata allow it to survive in periods of severe water deficiency. Through the findings of Zou et al. [5,6], LtWRKY21 synergistically works with abscisic acid (ABA) to transactivate both ABA-inducible HVA1 and HVA22 promoters. In addition, as ABA and gibberellic acid (GA) pathways are known to act antagonistically. Expectantly, the findings of Zou et al. suggest that LtWRKY21 activates ABA …


Antibiotic Resistance In Bacillus Subtilis As Affected By Transcriptional Derepression And The Stringent Response, Brandon Eisinger, Ronald E. Yasbin, Eduardo A. Robleto Aug 2010

Antibiotic Resistance In Bacillus Subtilis As Affected By Transcriptional Derepression And The Stringent Response, Brandon Eisinger, Ronald E. Yasbin, Eduardo A. Robleto

Undergraduate Research Opportunities Program (UROP)

Bacterial cells under conditions of starvation or prolonged non-lethal selective pressures accumulate mutations in highly transcribed genes. This process is part of cellular programs to increase genetic diversity in conditions of stress, also known as stationary phase or stress-induced mutagenesis. This experiment investigated mutation frequencies for antibiotic resistance as affected by the stringent response. The stringent response is a global cellular process that initiates at the cessation of growth and mediates changes in gene expression that repress synthesis of ribosome components. We used Bacillus subtilis strains that differ in RelA proficiency. The relA gene controls the synthesis of (p)ppGpp, the …


Examination Of Germination Receptors Of B. Subtilis And B. Megaterium, Shruti Patel, Alessio Luinetti, Ernesto Abel-Santos, Eduardo Robleto Aug 2010

Examination Of Germination Receptors Of B. Subtilis And B. Megaterium, Shruti Patel, Alessio Luinetti, Ernesto Abel-Santos, Eduardo Robleto

Undergraduate Research Opportunities Program (UROP)

Many bacterial species including those in the Bacilli group form spores as a mechanism to survive harsh conditions such as extreme temperature, radiation, chemicals, and nutrient starvation. By forming spores, they can remain metabolically dormant for an extended period and revert to their vegetative form when environment becomes favorable. This resumption of metabolism and growth is marked by a process called germination that is triggered by exogenous nutrients such as amino acids, sugars, and nucleotides. The (Ger) germination receptors that are postulated to respond to these germinants, in the case of B. subtilis and B. megaterium, are a complex of …


Impact Of Historical Climate Change On The Genetic Structure Of The Great Basin Pocket Mouse, Perognathus Parvus, Ashwitha Francis, Mallory E. Eckstut, Brett R. Riddle Aug 2010

Impact Of Historical Climate Change On The Genetic Structure Of The Great Basin Pocket Mouse, Perognathus Parvus, Ashwitha Francis, Mallory E. Eckstut, Brett R. Riddle

Undergraduate Research Opportunities Program (UROP)

The dynamics of genetic patterns, such as genetic differentiation within and between populations and the geographic distribution of genetic lineages, are often influenced by historical events (such as climatic changes) that have substantially impacted regional biodiversity (the study of phylogeography; Avise, 20001). The magnitude of genetic differentiation among populations is often increased if suitable habitat is reduced, because there is restricted migration among populations. When migration is restricted, the populations may become genetically differentiated from conspecific populations and, over time, may become independent lineages that follow distinctive evolutionary trajectories (Stebbins, 19523; Nevo & Beiles, 19892; Thomas et al., 19984). In …


Evaluating Snow Microbial Assemblages, Jenny Lam, Jessica K. Guy, Ryan Brock, Matt Oates, Alison E. Murray Aug 2010

Evaluating Snow Microbial Assemblages, Jenny Lam, Jessica K. Guy, Ryan Brock, Matt Oates, Alison E. Murray

Undergraduate Research Opportunities Program (UROP)

Psychrophiles are organisms that grow optimally below 20C (1). The US Great Basin is home to many mountain peaks with an abundance of alpine snow environments perfect for psychrophilic habitation. We analyzed samples from three different locations, Wheeler Peak, Pacific Crest Trail, and Mount Conness, characterizing and comparing the psychrophilic communities at varying depth intervals in the snow. Polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) showed no notable difference in community structure with depth, but there was a distinct difference when comparing different snow environments (i.e. shaded vs. full sun exposure). The chlorophyll concentration decreased as the …


Evaluation Of Virb Binding Site Contribution To The Regulation Of The Icsp Promoter In Shigella Flexneri, Juan C. Duhart, Maria I. Castellanos, Helen J. Wing Aug 2010

Evaluation Of Virb Binding Site Contribution To The Regulation Of The Icsp Promoter In Shigella Flexneri, Juan C. Duhart, Maria I. Castellanos, Helen J. Wing

Undergraduate Research Opportunities Program (UROP)

Shigella species are gram-negative, rod-shaped bacteria that are closely related to Escherichia coli. Virulent Shigella spp. are intracellular pathogens that invade, replicate and spread through epithelial cells of the lower intestine and cause bacillary dysentery in humans. This disease is characterized by a robust inflammatory response that results in fever, abdominal pain, and bloody diarrhea (3). According to the CDC, approximately 14,000 cases are reported each year in the United States alone. This number however, does not reflect the actual incidence of this disease as many cases go unreported. The molecular pathogenesis of these bacteria lies in the large virulence …


Modifying The Amino Acid Sequence In The Surface-Exposed Loops Of The Omptin Family Of Proteins To Determine Their Effect On Function, Natiera Magnuson, Eun-Hae Kim, Christian Ross, Helen J. Wing Aug 2010

Modifying The Amino Acid Sequence In The Surface-Exposed Loops Of The Omptin Family Of Proteins To Determine Their Effect On Function, Natiera Magnuson, Eun-Hae Kim, Christian Ross, Helen J. Wing

Undergraduate Research Opportunities Program (UROP)

The omptin family of proteins consists of proteases which lie in the outer membrane of some gram-negative, pathogenic bacteria such as Escherichia coli (OmpT), Shigella flexneri (IcsP), Salmonella typhimurium (PgtE), and Yersinia pestis (Pla). These proteases are highly conserved, sharing approximately 50% sequence identity and a β-barrel shape (fig. 1D). The differences in the structure of these four proteins are in the surface-exposed loop region surrounding the active site, but not in the active site itself [4]. These proteases are important for the virulence of many bacteria. For example, OmpT of E. coli cleaves an antimicrobial peptide secreted by epithelial …


Cross-Reactivity Of Antibodies Against Leptospiral Recurrent Uveitis-Associated Proteins A And B (Lrua And Lrub) With Eye Proteins, Ashutosh Verma, Pawan Kumar, Kelly Babb, John F. Timoney, Brian Stevenson Aug 2010

Cross-Reactivity Of Antibodies Against Leptospiral Recurrent Uveitis-Associated Proteins A And B (Lrua And Lrub) With Eye Proteins, Ashutosh Verma, Pawan Kumar, Kelly Babb, John F. Timoney, Brian Stevenson

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Infection by Leptospira interrogans has been causally associated with human and equine uveitis. Studies in our laboratories have demonstrated that leptospiral lipoprotein LruA and LruB are expressed in the eyes of uveitic horses, and that antibodies directed against LruA and LruB react with equine lenticular and retinal extracts, respectively. These reactivities were investigated further by performing immunofluorescent assays on lenticular and retinal tissue sections. Incubation of lens tissue sections with LruA-antiserum and retinal sections with LruB-antiserum resulted in positive fluorescence. By employing two-dimensional gel analyses followed by immunoblotting and mass spectrometry, lens proteins cross-reacting with LruA antiserum were identified to …