Genetics and Genomics Commons^™

Reducing False-Positive Prediction Of Minimotifs With A Genetic Interaction Filter, Jerlin Camilus Merlin, Sanguthevar Rajasekaran, Tian Mi, Martin Schiller

Life Sciences Faculty Research

Background

Minimotifs are short contiguous peptide sequences in proteins that have known functions. At its simplest level, the minimotif sequence is present in a source protein and has an activity relationship with a target, most of which are proteins. While many scientists routinely investigate new minimotif functions in proteins, the major web-based discovery tools have a high rate of false-positive prediction. Any new approach that reduces false-positives will be of great help to biologists.

Methods and Findings

We have built three filters that use genetic interactions to reduce false-positive minimotif predictions. The basic filter identifies those minimotifs where the source/target …

Dna Secondary Structures And Their Contribution To Mutagenesis In B. Subtilis Stationary Phase Cells, Carmen Vallin, Holly Anne Martin, Christian Ross, Ronald Yasbin, Eduardo Robleto

McNair Poster Presentations

It is widely known and accepted that the cause of many mutations in cells are generated during the replication process of actively dividing cells, however more recent research has shown that mutations also arise in non growing conditions, a phenomenon known as stationary phase mutagenesis. Much of what is known come from studies in eukaryotic and bacterial models. It has been proposed that in non-growing cells, the process of transcription plays an important role in mutagenesis. We test the hypothesis that DNA secondary structures, formed during transcription, promote mutagenesis. The transcription-generated structures are speculated to be prone to by blocking …

Transcriptome Analysis Of Glue Secretion In Drosophila, William Mccurdy, Pawel Parafianowicz, Andrew Andres

McNair Poster Presentations

Steroid hormones control important developmental and physiological responses in animals, including humans. It is known that when a cell is exposed to a steroid hormone, there is an immediate change in the genes that are expressed into proteins. Of notable importance is steroid regulation in the salivary glands of larval Drosophila melanogaster and the corresponding physiological responses that are governed by treatment with the conserved insect steroid, 20-hydroxyecdysone (20E). Exposure to the steroid hormone 20E causes a change in gene expression that facilitates the secretion of glue glycoproteins from inside the cells into the lumen of the tissue. Altered gene …

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 …

The Role Of A Transcription Factor In Regulating Rice Response To Drought Stress, Diana Ha, Liyuan A. Zhang, Jeffery Shen

Undergraduate Research Opportunities Program (UROP)

The current water shortage is a major concern in regard to our global climate change crisis. A decrease in the availability of water will have direct effects on the development of plants. Some crops, such as Oryza sativa, or commonly known as rice, requires an abundant amount of water for adequate growth. With the water shortage crisis, it will become extremely difficult to harvest such crops to meet the world’s food demand. However, many plants have evolved mechanisms for overcoming and tolerating stresses such as drought. My research focuses on studying the proteins involved with these mechanisms. The WRKY superfamily …

Combination Of Virb Binding Site Mutations To Evaluate Collective Impact On Icsp Promoter Activity In Shigella Flexneri, Pashtana Usufuzy, Juan C. Duhart, Maria I. Castellanos, Helen Wing

Undergraduate Research Opportunities Program (UROP)

Shigella flexneri is a gram-negative, invasive bacterial pathogen that afflicts the human colonic epithelium, causing shigellosis, an illness triggering severe dysentery. The World Health Organization cites the disease burden of shigellosis near 90 million episodes and 108,000 deaths per year.

The motility and spread of Shigella is modulated by icsP, a virulence gene. The transcription factor VirB positively regulates many virulence genes encoded by the Shigella virulence plasmid. Two distal binding sites of VirB have been shown to regulate the promoter activity of icsP, despite their location of more than 1 kb upstream of the transcription start site. Five VirB …

Magnetosome Genes In The Gammaproteobacterium Strain Bw-2, Lucero Rivera, Denis Trubitsyn, Dennis A. Bazylinski

Undergraduate Research Opportunities Program (UROP)

Magnetotactic bacteria (MTB) biomineralize intracellular nanometer-sized, magnetic crystals surrounded by a lipid bilayer membrane known as magnetosomes. These crystals, which consist of magnetite (Fe3O4) or greigite (Fe3S4), causes the cell to align along the geomagnetic field lines as they swim, a phenomenon known as magnetotaxis. Strain BW-2 is a magnetite-producing magnetotactic bacterium isolated from Badwater Basin, Death Valley National Park (California) and is one of only two species of MTB that are known to phylogenetically belong to the Gammaproteobacteria class of the Proteobacteria phylum. The biomineralization of magnetite in magnetotactic bacteria is mediated by a series of genes that include …

Inactivation Of Spo0a Gene Increases Stationary Phase Mutagenesis In Bacillus Subtilis, Denisse Reyes, Amanda Prisbrey, Holly Martin, Eduardo Robleto

Undergraduate Research Opportunities Program (UROP)

Stationary phase mutagenesis occurs when a population of cells acquires mutations conferring escape from nongrowing or stress conditions. This type of mutations is observed in nutritionally starved cells. Because the mutations occur after the onset of stress and in cells that are in non-replicative conditions, elucidating the underlying mechanisms contributes novel views to the process of evolution and apply to the formation of cancer in human cells and antibiotic resistance in microbial pathogens. Studies have shown that in Bacillus subtilis, the Mfd protein which is a transcription repair coupling factor is necessary for this phenomenon to occur. Here, we investigate …

Investigating The Origin Of Coprolites From Three Great Basin Caves, Chelsey Vandrisse, Duane P. Moser, David Rhode

Undergraduate Research Opportunities Program (UROP)

The study of coprolites (mummified feces) is a relatively new endeavor, which enables investigations of the health and diet of ancient people and provides some of the oldest evidence to date for the human habitation in North America (2). In this project, 18 coprolites were examined from archeological digs at three Great Basin caves: the Bonneville Estates Rockshelter (UT), Hidden Cave (NV), and Top of the Terrace Rockshelter (UT). The main objectives were: 1) to verify human origin through the presence of mitochondrial DNA (mtDNA) and 2) assuming human origin, characterize intestinal microflora of Native Americans prior to European contact. …

Isolation, Characterization, And Genome Sequence Of The First Representative Of A Novel Class Within The Chloroflexi That Is Abundant In Some U.S. Great Basin Hot Springs And May Play Important Roles In N And C Cycling, Jeremy A. Dodsworth, Senthil K. Murugapiran, Jonathan Gevorkian, James Han, Tanja Woyke, Susan M. Lucas, Sam Pitluck, Len Pennacchio, Lynne Goodwin, Brian P. Hedlund

Undergraduate Research Opportunities Program (UROP)

A thermophilic, facultatively microaerophilic, heterotrophic bacterium, designated strain JAD2, was isolated from sediments of Great Boiling Spring (GBS), an ~80oC, circumneutral hot spring in the Great Basin GB). The strain grew anaerobically on yeast extract or peptone with an optimal growth temperature of 70-75oC. Growth was stimulated by addition of 0.01 atm O2 to the culture vessel headspace, but was inhibited by higher concentrations (0.2 atm). Cells of JAD2 formed non-motile filaments ranging from 10 to >300 μm in length, which typically decreased in length during stationary phase. 16S rRNA gene-targeted pyrotag sequencing and clone library data suggest that close …

Dna Secondary Structures And Their Contribution To Mutagenesis In B. Subtilis Stationary Phase Cells, Carmen Vallin, Holly Martin, Christian Ross, Ronald Yasbin, Eduardo Robleto

Undergraduate Research Opportunities Program (UROP)

It is widely known and accepted that the cause of many mutations in cells are generated during the replication process of actively dividing cells, however more recent research has shown that mutations also arise in non growing conditions, a phenomenon known as stationary phase mutagenesis. Much of what is known come from studies in eukaryotic and bacterial models. It has been proposed that in non~growing cells, the process of transcription plays an important role in mutagenesis. We test the hypothesis that DNA secondary structures, formed during transcription, promote mutagenesis. The transcription-generated structures are speculated to be prone to mutations by …

Evaluating Species Responses To Climate Change Using Ecological Niche Modeling And Genetic Data, Jeanette Perry

Undergraduate Research Opportunities Program (UROP)

The current and projected future warming trends together with degradation of habitats throughout much of the Great Basin and Columbian Plateau represent real threats to many species occupying these regions. If we can determine the impacts of past climatic changes on the distribution of species, we can obtain a better understanding of the future impacts of projected climatic trends on many species in these regions. My results with the Great Basin Pocket Mouse (Perognathus parvus) may be relevant to conservation ecologists and resource managers attempting to protect several Endangered Species Act candidates, such as the pygmy cottontail (Brachylagus idahoensis). I …

The Role Of Historical And Contemporary Processes On Phylogeographic Structure And Genetic Diversity In The Northern Cardinal, Cardinalis Cardinalis, Brian T. Smith, Patricia Escalante, Blanca E. Hernandez-Banos, Adolfo G. Navarro-Siguenza, Sievert Rohwer, John Klicka

Ornithology Program (HRC)

Background

Earth history events such as climate change are believed to have played a major role in shaping patterns of genetic structure and diversity in species. However, there is a lag between the time of historical events and the collection of present-day samples that are used to infer contemporary population structure. During this lag phase contemporary processes such as dispersal or non-random mating can erase or reinforce population differences generated by historical events. In this study we evaluate the role of both historical and contemporary processes on the phylogeography of a widespread North American songbird, the Northern Cardinal, Cardinalis cardinalis …

Molecular Evolution And Historical Biogeography Of New World Birds, Brian T. Smith

UNLV Theses, Dissertations, Professional Papers, and Capstones

Deciphering the patterns of how biodiversity has evolved across time and space has remained a fundamental objective for biologists for the last 200 years. Researchers are faced with the challenge of interpreting the complexity of evolutionary patterns that have been generated over the deep history of the Earth. The advancement of DNA sequencing technology has yielded a new and powerful genetic toolkit that has allowed biologists to address novel evolutionary questions. For my dissertation research, I used molecular genetics and a statistical framework to study the evolution and historical biogeography of birds distributed in North and South America. My dissertation …

Oral Presentation: Plant Genes And Drought Tolerance, Norris Lam

Festival of Communities: UG Symposium (Posters)

Research has shown that a gene from C3 xerophyte Larrea tridentata (creosote bush), LtWRKY21, is involved in pathways governing creosote bush’s high tolerance to environmental stress. By understanding the way in which creosote bush adapts to drought, crop plants can be engineered to be more drought tolerant during times of imminent global climate change. To study the underlying mechanisms of creosote bush drought response, the LtWRKY21 gene was mobilized into the model organism Arabidopsis thaliana. Chlorophyll degradation, cellular electrolyte leakage, and water content in leaves will serve as indicators of drought tolerance in LtWRKY21-transgenic A. thaliana after treatment in chemically …

Stationary Phase Mutagenesis In Bacillus Subtilisis Independent Of Genome Replication, Mark Upchurch, Holly Martin, Eduardo Robleto

Festival of Communities: UG Symposium (Posters)

Stationary phase mutagenesis is defined as cellular mechanisms that produce genetic diversity in cells experiencing conditions of stress. These processes are associated with many biological phenomena, including those that produce the formation of cancers in animal cells and other degenerative diseases. Also, these mechanisms are associated with the accumulation of beneficial mutations in bacteria, but follow stochastic processes and are controlled by genetic factors. The current models explaining the generation of stress-induced mutations are predicated on the formation of DNA replication intermediates that are formed during the repair of damaged DNA or during DNA replication and transcription encounters. Here we …

Role Of Hydrodynamic Behavior Of Dna Molecules In Dielectrophoretic Polarization Under The Action Of An Electric Field, Hui Zhao

Mechanical Engineering Faculty Research

A continuum model is developed to predict the dielectrophoretic polarizability of coiled DNA molecules under the action of an alternating current electric field. The model approximates the coiled DNA molecule as a charged porous spherical particle. The model explains the discrepancies among scaling laws of polarizability of different-sized DNA molecules with contour length and such discrepancies are attributed to different hydrodynamic behavior. With zero or one fitting parameter, theoretical predictions are in good agreement with various experimental data, even though in experiments there are some uncertainties in regard to certain parameters.

Environmental Influence On Brain, Behavior, And Gene Expression In Drosophila, Xia Wang

UNLV Theses, Dissertations, Professional Papers, and Capstones

Brain development and behavior are sensitive to environmental stimuli. To gain an understanding of how and to what extent environmental variations, particularly with regard to thermal stress and sensory input, affect brain development, function, and genomic activity, in this dissertation, three interrelated studies were conducted in Drosophila melanogaster.

The first study examined the effects of ecologically-relevant hyperthermia stress on development of the Drosophila mushroom body (MB), a conserved sensory integration and associative center in the insect brain. A daily hyperthermic episode throughout larval and pupal development was shown to severely disrupt MB anatomy by reducing intrinsic Kenyon cell neuron …

Transcriptional Regulation Of Shigella Virulence Plasmid-Encoded Genes By Virb And Crp, Christopher Thomas Hensley

UNLV Theses, Dissertations, Professional Papers, and Capstones

Shigella flexneri is a species of Gram-negative intracellular pathogens that causes bacillary dysentery in humans. Shigella relies on the precise transcriptional regulation of virulence genes, encoded by a large virulence plasmid, for invasion and infection of human colonic epithelial cells. The transcription of most identified virulence genes are regulated through a cascade controlled by the primary regulator of virulence genes, VirF, and the global transcriptional regulator, VirB. Currently, few studies have addressed how individual Shigella virulence genes are precisely regulated for optimal expression during specific stages of pathogenesis and within the constraints of the regulatory cascade. This work addresses how …

Reconstructing Species Responses To Past Climatic Changes Using Niche Modeling And Genetic Data, Tereza Jezkova

UNLV Theses, Dissertations, Professional Papers, and Capstones

Glacial – interglacial cycles have a pronounced impact on species distributions and genetic structure. Many species shift their distributions to lower latitudes and altitudes during the colder glacial periods and expand northwards and up the elevation during warmer interglacial periods. Some species however are capable of adapting to changing environment which allows them to persist in place despite climatic changes. I explored how climatic changes after the last glacial maximum (LGM) effected two species inhabiting the deserts of western North America: one mammal (Chisel-toothed Kangaroo Rat, Dipodomys microps) and one reptile (Desert Horned Lizard, Phrynosoma platyrhinos). I used …

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

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

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

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

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

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

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

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

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 …

The Larval Salivary Gland Of Drosophila Melangogaster: A Model System For Temporal And Spatial Steroid Hormone Regulation, Benjamin Constantino

UNLV Theses, Dissertations, Professional Papers, and Capstones

Drosophila melanogaster provides an ideal model organism to test genetic and molecular biological mechanisms within the context of a living animal. For over one hundred years Drosophila continues to produce a boundless extent of informative and important scientific data providing crucial insight into development, disease progression and genetic interactions. A century as a model organism allowed for the development of an abundance of unique genetic and molecular tools allowing researchers to tease apart cellular mechanisms with very little limitation. From the whole adult body to tissue function to molecular networks, if a biological question arises it most likely can be …