Genetics and Genomics Commons^™

Phylotranscriptomics To Bring The Understudied Into The Fold: Monophyletic Ostracoda, Fossil Placement, And Pancrustacean Phylogeny, Todd H. Oakley, Joanna M. Wolfe, Annie R. Lindgren, Alexander K. Zaharoff

Biology Faculty Publications and Presentations

An ambitious, yet fundamental goal for comparative biology is to understand the evolutionary relationships for all of life. However, many important taxonomic groups have remained recalcitrant to inclusion into broader scale studies. Here, we focus on collection of 9 new 454 transcriptome data sets from Ostracoda, an ancient and diverse group with a dense fossil record, which is often undersampled in broader studies. We combine the new transcriptomes with a new morphological matrix (including fossils) and existing expressed sequence tag, mitochondrial genome, nuclear genome, and ribosomal DNA data. Our analyses lead to new insights into ostracod and pancrustacean phylogeny. We …

Differential Virus Host-Ranges Of The Fuselloviridae Of Hyperthermophilic Archaea: Implications For Evolution In Extreme Environments, Ruben M. Ceballos, Caleb D. Marceau, Joshua O. Marceau, Steven Morris, Adam J. Clore, Kenneth M. Stedman

Biology Faculty Publications and Presentations

An emerging model for investigating virus-host interactions in hyperthermophilic Archaea is the Fusellovirus-Sulfolobus system. The host, Sulfolobus, is a hyperthermophilic acidophile endemic to sulfuric hot springs worldwide. The Fuselloviruses, also known as Sulfolobus Spindle-shaped Viruses (SSVs), are "lemon" or "spindle"-shaped double-stranded DNA viruses, which are also found worldwide. Although a few studies have addressed the host-range for the type virus, Sulfolobus Spindle-shaped Virus 1 (SSV1), using common Sulfolobus strains, a comprehensive host-range study for SSV-Sulfolobus systems has not been performed. Herein, we examine six bona fide SSV strains (SSV1, SSV2, SSV3, SSVL1, SSVK1, SSVRH) and their respective infection characteristics on …

Antisense Transcription Is Pervasive But Rarely Conserved In Enteric Bacteria, Rahul Raghavan, D. B. Sloan, H. Ochman

Biology Faculty Publications and Presentations

Noncoding RNAs, including antisense RNAs (asRNAs) that originate from the complementary strand of protein-coding genes, are involved in the regulation of gene expression in all domains of life. Recent application of deep-sequencing technologies has revealed that the transcription of asRNAs occurs genome-wide in bacteria. Although the role of the vast majority of asRNAs remains unknown, it is often assumed that their presence implies important regulatory functions, similar to those of other noncoding RNAs. Alternatively, many antisense transcripts may be produced by chance transcription events from promoter-like sequences that result from the degenerate nature of bacterial transcription factor binding sites. To …

Selfish Little Circles: Transmission Bias And Evolution Of Large Deletion-Bearing Mitochondrial Dna In Caenorhabditis Briggsae Nematodes, Katie A. Clark, Dana K. Howe, Kristin Gafner, Danika Kusuma, Sita Ping, Suzanne Estes

Biology Faculty Publications and Presentations

Selfish DNA poses a significant challenge to genome stability and organismal fitness in diverse eukaryotic lineages. Although selfish mitochondrial DNA (mtDNA) has known associations with cytoplasmic male sterility in numerous gynodioecious plant species and is manifested as petite mutants in experimental yeast lab populations, examples of selfish mtDNA in animals are less common. We analyzed the inheritance and evolution of mitochondrial DNA bearing large heteroplasmic deletions including nad5 gene sequences (nad5Δ mtDNA), in the nematode Caenorhabditis briggsae. The deletion is widespread in C. briggsae natural populations and is associated with deleterious organismal effects. We studied the inheritance patterns of nad5Δ …

A Novel Virus Genome Discovered In An Extreme Environment Suggests Recombination Between Unrelated Groups Of Rna And Dna Viruses, Geoffrey S. Diemer, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Background: Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to resolve deep evolutionary histories of the known major virus groups. Metagenomics offers a potential means of establishing a more comprehensive view of viral evolution as vast amounts of new sequence data becomes available for comparative analysis.

Results: Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar …

A Genetic Study Of Ssv1, The Prototypical Fusellovirus, Eric Iverson, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Viruses of thermophilic Archaea are unique in both their structures and genomic sequences. The most widespread and arguably best studied are the lemon-shaped fuselloviruses. The spindle-shaped virus morphology is unique to Archaea but widespread therein. The best studied fusellovirus is SSV1 from Beppu, Japan, which infects Sulfolobus solfataricus. Very little is known about the function of the genes in the SSV1 genome. Recently we have developed genetic tools to analyze these genes. In this study, we have deleted three SSV1 open reading frames (ORFs) ranging from completely conserved to poorly conserved: VP2, d244, and b129. Deletion of the universally conserved …

Pseudoscorpion Mitochondria Show Rearranged Genes And Genome-Wide Reductions Of Rna Gene Sizes And Inferred Structures, Yet Typical Nucleotide Composition Bias, Sergey Ovchinnikov, Susan E. Masta

Biology Faculty Publications and Presentations

Pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. No mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of Chelicerata possess unusual features, including short rRNA genes and tRNA genes that lack sequence to encode arms of the canonical cloverleaf-shaped tRNA. Additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes.

We sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order Pseudoscorpiones. We find that these genomes possess unusually short tRNA genes that do …

A Selective Force Favoring Increased G+C Content In Bacterial Genes, Rahul Raghavan, Yogeshwar D. Kelkar, Howard Ochman

Biology Faculty Publications and Presentations

Bacteria display considerable variation in their overall base compositions, which range from 13% to over 75% G+C. This variation in genomic base compositions has long been considered to be a strictly neutral character, due solely to differences in the mutational process; however, recent sequence comparisons indicate that mutational input alone cannot produce the observed base compositions, implying a role for natural selection. Because bacterial genomes have high gene content, forces that operate on the base composition of individual genes could help shape the overall genomic base composition. To explore this possibility, we tested whether genes that encode the same protein …

Causes And Consequences Of Mitochondrial Variation In Caenorhabditid Nematodes, Kiley Ann Hicks

Dissertations and Theses

Mitochondria are dynamic organelles that harbor their own stream-lined genome and generate much of the ATP necessary to sustain eukaryotic life via an electron transport chain (ETC). Because of the central role for mitochondria in organismal physiology, mitochondrial genetic and phenotypic variation can alter organismal fitness and affect population genetic and evolutionary outcomes. Despite the far-reaching relevance of mitochondria to evolutionary processes and human health, we lack a basic understanding of the causes and consequences of mitochondrial genetic and phenotypic variation. In this thesis, I quantified mitochondrial reactive oxygen species (ROS), membrane potential (δΨM), and mitochondrial morphological traits within Caenorhabditis …

Effects Of Reactive Oxygen Species On Life History Traits Of Caenorhabditis Elegans, Samson William Smith

Dissertations and Theses

Evolutionary life history theory predicts that tradeoffs among fitness-related phenotypes will occur as a result of resource limitations and/or physiological constraints. Such tradeoffs are defined as the cost(s) incurred on one component of fitness (e.g., reproduction) by the increased expression of another fitness-related trait (e.g., longevity). Only recently have researchers begun to investigate the mechanistic bases of life history tradeoffs. A recent proposal is that reactive oxygen species (ROS) have a central role in shaping life history traits and tradeoffs. Research on disparate animal taxa has highlighted strong correlations between oxidative stress resistance and fitness-related life history traits, for example. …

Functional Promiscuity Of The Cog0720 Family, Gabriela Phillips, Laura L. Grochowski, Shilah Bonnett, Huimin Xu, Marc Bailly, Crysten Haas-Blaby, Basma El Yacoubi, Dirk Iwata-Reuyl, Robert H. White, Valérie De Crécy-Lagard

Chemistry Faculty Publications and Presentations

The biosynthesis of GTP derived metabolites such as tetrahydrofolate (THF), biopterin (BH4), and the modified tRNA nucleosides queuosine (Q) and archaeosine (G⁺) relies on several enzymes of the Tunnel-fold superfamily. A subset of these proteins include the 6-pyruvoyl-tetrahydropterin (PTPS-II), PTPS-III, and PTPS-I homologs, all members of the COG0720 family, that have been previously shown to transform 7,8-dihydroneopterin triphosphate (H₂NTP) into different products. PTPS-II catalyzes the formation of 6-pyruvoyltetrahydropterin in the BH₄ pathway. PTPS-III catalyzes the formation of 6-hydroxylmethyl-7,8-dihydropterin in the THF pathway. PTPS-I catalyzes the formation of 6-carboxy-5,6,7,8-tetrahydropterin in the Q pathway. Genes of these …

Genome-Wide Detection Of Novel Regulatory Rnas In E. Coli, Rahul Raghavan, Eduardo Groisman, Howard Ochman

Biology Faculty Publications and Presentations

The intergenic regions in bacterial genomes can contain regulatory leader sequences and small RNAs (sRNAs), which both serve to modulate gene expression. Computational analyses have predicted the presence of hundreds of these noncoding regulatory RNAs in Escherichia coli; however, only about 80 have been experimentally validated. By applying a deep-sequencing approach, we detected and quantified the vast majority of the previously validated regulatory elements and identified 10 new sRNAs and nine new regulatory leader sequences in the intergenic regions of E. coli. Half of the newly discovered sRNAs displayed enhanced stability in the presence of the RNA-binding protein …

Complexity Through Recombination: From Chemistry To Biology, Niles Lehman, Carolina Diaz Arenas, Wesley A. White, Francis J. Schmidt

Chemistry Faculty Publications and Presentations

Recombination is a common event in nature, with examples in physics, chemistry, and biology. This process is characterized by the spontaneous reorganization of structural units to form new entities. Upon reorganization, the complexity of the overall system can change. In particular the components of the system can now experience a new response to externally applied selection criteria, such that the evolutionary trajectory of the system is altered. In this work we explore the link between chemical and biological forms of recombination. We estimate how the net system complexity changes, through analysis of RNA-RNA recombination and by mathematical modeling. Our results …

Metagenomes From High-Temperature Chemotrophic Systems Reveal Geochemical Controls On Microbial Community Structure And Function, William P. Inskeep, Douglas B. Rusch, Zackary J. Jay, Markus J. Herrgard, Mark A. Kozubal, Toby H. Richardson, Richard E. Macur, Natsuko Hamamura, Ryan Dem. Jennings, Bruce W. Fouke, Anna-Louise Reysenbach, Frank Roberto, Mark Young, Ariel Schwartz, Eric S. Boyd, Jonathan H. Badger, Eric J. Mathur, Alice C. Ortmann, Mary Bateson, Gill Geesey

Biology Faculty Publications and Presentations

The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14-15,000 Sanger reads per site) was obtained for five hightemperature (>65°C) chemotrophic microbial communities sampled from …

Reconstructability Analysis As A Tool For Identifying Gene-Gene Interactions In Studies Of Human Diseases, Stephen Shervais, Patricia L. Kramer, Shawn K. Westaway, Nancy J. Cox, Martin Zwick

Complex Systems Faculty Publications and Presentations

There are a number of common human diseases for which the genetic component may include an epistatic interaction of multiple genes. Detecting these interactions with standard statistical tools is difficult because there may be an interaction effect, but minimal or no main effect. Reconstructability analysis (RA) uses Shannon’s information theory to detect relationships between variables in categorical datasets. We applied RA to simulated data for five different models of gene-gene interaction, and find that even with heritability levels as low as 0.008, and with the inclusion of 50 non-associated genes in the dataset, we can identify the interacting gene pairs …

Quasispecies-Like Behavior Observed In Catalytic Rna Populations Evolving In A Test Tube, Carolina Diaz Arenas, Niles Lehman

Chemistry Faculty Publications and Presentations

Background: During the RNA World, molecular populations were probably very small and highly susceptible to the force of strong random drift. In conjunction with Muller's Ratchet, this would have imposed difficulties for the preservation of the genetic information and the survival of the populations. Mechanisms that allowed these nascent populations to overcome this problem must have been advantageous.

Results: Using continuous in vitro evolution experimentation with an increased mutation rate imposed by MnCl2, it was found that clonal 100-molecule populations of ribozymes clearly exhibit certain characteristics of a quasispecies. This is the first time this has been seen …

Rearrangement Of The Rna Polymerase Subunit H And The Lower Jaw In Archaeal Elongation Complexes, Sebastian Grünberg, Christoph Reich, Mirijam E. Zeller, Michael S. Bartlett, Michael Thomm

Biology Faculty Publications and Presentations

The lower jaws of archaeal RNA polymerase and eukaryotic RNA polymerase II include orthologous subunits H and Rpb5, respectively. The tertiary structure of H is very similar to the structure of the C-terminal domain of Rpb5, and both subunits are proximal to downstream DNA in pre-initiation complexes. Analyses of reconstituted euryarchaeal polymerase lacking subunit H revealed that H is important for open complex formation and initial transcription. Eukaryotic Rpb5 rescues activity of the ΔH enzyme indicating a strong conservation of function for this subunit from archaea to eukaryotes. Photochemical cross-linking in elongation complexes revealed a striking structural rearrangement of RNA …

One Rna Plays Three Roles To Provide Catalytic Activity To A Group I Intron Lacking An Endogenous Internal Guide Sequence, Nilesh Vaidya, Niles Lehman

Chemistry Faculty Publications and Presentations

Catalytic RNA molecules possess simultaneously a genotype and a phenotype. However, a single RNA genotype has the potential to adopt two or perhaps more distinct phenotypes as a result of differential folding and/or catalytic activity. Such multifunctionality would be particularly significant if the phenotypes were functionally inter-related in a common biochemical pathway. Here, this phenomenon is demonstrated by the ability of the Azoarcus group I ribozyme to function when its canonical internal guide sequence (GUG) has been removed from the 5? end of the molecule, and added back exogenously in trans. The presence of GUG triplets in noncovalent fragments of …

Dna Before Proteins? Recent Discoveries In Nucleic Acid Catalysis Strengthen The Case, Aaron Steven Burton, Niles Lehman

Chemistry Faculty Publications and Presentations

An RNA-DNA World could arise from an all-RNA system with the development of as few as three ribozymes— a DNA-dependent RNA polymerase, an RNA-dependent DNA polymerase, and a catalyst for the production of DNA nucleotides. A significant objection to DNA preceding proteins is that RNA has not been shown to catalyze the production of DNA. However, RNA- and DNAzymes have been recently discovered that catalyze chemical reactions capable of forming deoxyribose, such as mixed aldol condensation of 5’-glyceryl- and 3’- glycoaldehyde-terminated DNA strands. Thus, the only remaining obstacles to RNA-catalyzed in vitro DNA synthesis are alterations of substrate and template …

Mechanisms Of Covalent Self-Assembly Of The Azoarcus Ribozyme From Four Fragment Oligonucleotides, Will E. Draper, Eric John Hayden, Niles Lehman

Chemistry Faculty Publications and Presentations

RNA oligomers of length 40–60 nt can self-assemble into covalent versions of the Azoarcus group I intron ribozyme. This process requires a series of recombination reactions in which the internal guide sequence of a nascent catalytic complex makes specific interactions with a complement triplet, CAU, in the oligomers. However, if the CAU were mutated, promiscuous self-assembly may be possible, lessening the dependence on a particular set of oligomer sequences. Here, we assayed whether oligomers containing mutations in the CAU triplet could still self-construct Azoarcus ribozymes. The mutations CAC, CAG, CUU and GAU all inhibited self-assembly to some degree, but did …

Ordering Genetic Algorithm Genomes With Reconstructability Analysis: Discrete Models, Stephen Shervais, Martin Zwick

Complex Systems Faculty Publications and Presentations

The building block hypothesis implies that genetic algorithm effectiveness is influenced by the relative location of epistatic genes on the chromosome. We demonstrate this with a discrete-valued problem, based on Kauffman’s NK model, and show that information-theoretic reconstructability analysis can be used to decide on optimal gene ordering.

The Hyperthermophilic Archaeon Sulfolobus: From Exploration To Exploitation, Stan J.J. Brouns, Thijs J.G. Ettema, Kenneth M. Stedman, Jasper Walther, Hauke Smith, Ambrosius P.L. Snijders, Mark Young, Rolf Bernander, Phillip C. Wright, Betina Siebers, John Van Der Oost

Biology Faculty Publications and Presentations

In the early 1970s, Sulfolobus was first isolated by Thomas Brock and co-workers from sulfur-rich acidic hot springs in Yellowstone National Park. Sulfolobus became one of the model organisms of Archaea in general, and of Crenarchaea in particular. Many of its unusual physiological characteristics have been investigated, and several of its thermostable enzymes have been studied in considerable detail. For fundamental reasons, and because of its potential for industrial applications, Sulfolobus has been selected for a genome sequence project. The recent completion of the Sulfolobus solfataricus genome has set the stage for a series of postgenome research lines that will …

Ordering Genetic Algorithm Genomes With Reconstructability Analysis, Stephen Shervais, Martin Zwick

Complex Systems Faculty Publications and Presentations

The building block hypothesis implies that genetic algorithm effectiveness is influenced by the relative location of epistatic genes on the chromosome. We find that this influence exists, but depends on the generation in which it is measured. Early in the search process it may be more effective to have epistatic genes widely separated. Late in the search process, effectiveness is improved when they are close together. The early search effect is weak but still statistically significant; the late search effect is much stronger and plainly visible. We demonstrate both effects with a set of simple problems, and show that infonnation-theoretic …

Human Genomics Of Biotechnology, Brian Bluelake, Bob Wang, Serin Hudson, Fatih Ersan, Aaron Freier

Engineering and Technology Management Student Projects

Biotechnology is the term for the techniques of managing biological systems for human benefit. A biological system can range from a single cell organism to different types of plants, animals, and to the very complicated human being. Biotechnology includes a great range of scientific and technological disciplines and has a great variety of important applications in biology, medicine, agriculture, and various industries. In our report, we shall only focus on one of the most active frontiers of today's biotechnology-human genomics.

Analysis Of Mitochondrial Dna Restriction Fragment Patterns In Killer Whales, Orcinus Orca, Tracy Alison Stevens

Dissertations and Theses

The mitochondrial DNA restriction fragment patterns of killer whales (Orcinus orca) were investigated in order to determine the level of genetic differentiation that exists between killer whales from various geographic locations. Twenty one killer whales were examined, seventeen of which were captive killer whales that originated from the North Atlantic and Northeast Pacific Oceans. Two were captive-born animals and two were killer whales that stranded along the Northeast Pacific coast.

DNA was extracted from blood and/or tissue samples, cleaved with a variety of restriction endonucleases and the DNA fragments were separated by horizontal agarose gel electrophoresis. The DNA …

Gibbon Classification: The Issue Of Species And Subspecies, Erin Lee Osterud

Dissertations and Theses

Gibbon classification at the species and subspecies levels has been hotly debated for the last 200 years. This thesis explores the reasons for this debate. Authorities agree that siamang, concolor, kloss and hoolock are species, while there is complete lack of agreement on lar, agile, moloch, Mueller's and pileated. The disagreement results from the use and emphasis of different character traits, and from debate on the occurrence and importance of gene flow.

Double Cross: Agriculture And Genetics, 1930 To 1960, Tracy Scott Lebenzon

Dissertations and Theses

This paper discusses the role of genetic technology and application in agriculture between 1930 and 1960. Topics covered include the role of genetics and the relationship that theory, education, administration, professionalism, economic and social considerations bore to genetics.

Molecular Cloning Of Spinach Chloroplast Dna Isolated By Alkaline Lysis, Robert Gray Drager

Dissertations and Theses

Chloroplast genomes of land plants show conservation of structure and gene arrangement. The spinach chloroplast genome is comprised of a covalently closed. circular DNA molecule of 150 kilobases and is typical of these plants. Approximately 20% of the proteins found in the spinach chloroplast are encoded by the chloroplast genome and translated on chloroplast ribosomes. The remainder are encoded on chromosomes in the nucleus, translated on cytoplasmic ribosomes and transported into the chloroplast.

Spinach chloroplast DNA was isolated from crude 2 chloroplast preparations by a new method. Chloroplasts were lysed with alkaline sodium dodecyl sulfate, contaminating macromolecules precipitated with acidified …

Restriction Mapping And Expression Of Recombinant Plasmids Containing The Arsenic Resistance Genes Of The Plasmid R45, Terry M. Coons

Dissertations and Theses

The trivalent (arsenite) and pentavalent (arsenate) forms of arsenic are introduced into the environment through the use of arsenic in herbicides, pesticides, fertilizers, and the smelting of arsenic-bearing ores. Bacteria resistant to arsenic are readily isolated from surface waters, sewage, and clinical infections. Although some bacterial resistance is provided by inducible phosphate transport systems that discriminate against arsenate, marked resistance is carried on bacterial plasmids.

A 6.9 kilobase fragment previously derived from one such plasmid, R45, and containing the genes for inducible resistance to arsenite and arsenate was ligated into the cloning vectors puce and pUC9 in opposite orientations and …

Audiological Characteristics Of The Monge Family Of Costa Rica, Christine Moulton

Dissertations and Theses

The audiological characteristics of the Monge family of Costa Rica were investigated in a sample of fifty-two affected members and twelve unaffected members. Through laboratory analysis by staff personnel from the University of Costa Rica and audiological test results obtained in the present investigation, it was concluded that affected Monge members demonstrate a slowly progressive low frequency sensorineural hearing loss of autosomal dominant transmission. The initial site of lesion appears to be the apical portion of the cochlea, with significant onset occurring during early childhood following normal speech and language acquisition. The rate at which the hearing loss progresses and …