Life Sciences Commons^™

Nullomer Derived Anticancer Peptides (Nullops): Differential Lethal Effects On Normal And Cancer Cells In Vitro, Abdelkrim Alileche, Jayita Goswami, William Bourland, Mike Davis, Greg Hampikian

Biology Faculty Publications and Presentations

We demonstrate the first use of the nullomer (absent sequences) approach to drug discovery and development. Nullomers are the shortest absent sequences determined in a species, or group of species. By identifying the shortest absent peptide sequences from the NCBI databases, we screened several potential anti-cancer peptides. In order to improve cell penetration and solubility we added short poly arginine tails (5Rs), and initially solubilized the peptides in1M trehalose. The results for one of the absent sequences 9R (RRRRRNWMWC), and its scrambled version 9S1R (RRRRRWCMNW) are reported here. We refer to these peptides derived from nullomers as PolyArgNulloPs. A control …

When Dna Won't Work, Rick Visser, Greg Hampikian

Biology Faculty Publications and Presentations

Within the criminal justice system, DNA (deoxyribonucleic acid) evidence has often been heralded as the gold standard of forensic science. In a 2009 U.S. Supreme Court decision, Chief Justice Roberts wrote that "DNA testing has an unparalleled ability both to exonerate the wrongly convicted and to identify the guilty. It has the potential to significantly improve both the criminal justice system and police investigative practices." The phrases “unparalleled ability” and “significantly improve” reflect the high standard that DNA has attained in both forensic science and the entire criminal justice system.

Forensic DNA technology has a major advantage over other forensic …

Cephalopod Genomics: A Plan Of Strategies And Organization, Caroline B. Albertin, Laure Bonnaud, C. Titus Brown, Wendy J. Crookes-Goodson, Rute R. Da Fonseca, Carlo Di Cristo, Brian P. Dilkes, Eric Edsinger-Gonzales, Robert M. Freeman Jr., Roger T. Hanlon, Kristen M. Koenig, Annie R. Lindgren, Mark Q. Martindale, Patrick Minx, Leonid L. Moroz, Marie-Therese Nödl, Spencer V. Nyholm, Atsushi Ogura, Judit R. Pungor, Joshua J. C. Rosenthal, Erich M. Schwarz, Shuichi Shigeno, Jan M. Strugnell, Tim Wollesen, Guojie Zhang, Clifton W. Ragsdale

Biology Faculty Publications and Presentations

The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, “Paths to Cephalopod Genomics- Strategies, Choices, Organization,” held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an …

Phylogeny Of A Neotropical Clade In The Gesneriaceae: More Tales Of Convergent Evolution, John L. Clark, Minde M. Funke, Aaron M. Duffy, James F. Smith

Biology Faculty Publications and Presentations

The Gesneriaceae is a family known for convergent evolution of complex floral forms. As a result, defining genera and resolving evolutionary relationships among such genera using morphological data alone has been challenging and often does not accurately reflect monophyletic lineages. The tribe Episcieae is the most diverse within Neotropical Gesneriaceae in terms of its number of species and morphological diversity. As a result, defining genera using floral characters has been historically troublesome. Here we investigate relationships among genera of the tribe using an array of chloroplast DNA, nuclear ribosomal genes, and low-copy nuclear genes to provide resolution for the monophyly …

Identification Of An Amino-Terminal Fragment Of Apolipoprotein E4 That Localizes To Neurofibrillary Tangles Of The Alzheimer’S Disease Brain, Troy T. Rohn, Lindsey W. Catlin, Kendra G. Coonse, Jeffrey W. Habig

Biology Faculty Publications and Presentations

Although the risk factor for harboring the apolipoprotein E4 (apoE4) allele in late-onset Alzheimer’s disease (AD) is well known, the mechanism by which apoE4 contributes to AD pathogenesis has yet to be clarified. Preferential cleavage of the ApoE4 isoform relative to other polymorphic forms appears to be significant, as the resulting fragments are associated with hallmarks of AD. To examine the possible role of apoE4 proteolysis in AD, we designed a site-directed antibody directed at position D172, which would yield a predicted amino-terminal fragment previously identified in AD brain extracts. Western blot analysis utilizing this novel antibody, termed the amino-terminal …

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 …

Landscape Of Transcription In Human Cells, Jainab Khatun

Biology Faculty Publications and Presentations

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell’s regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, …

Oncostatin M Promotes Mammary Tumor Metastasis To Bone And Osteolytic Bone Degradation, Celeste Bolin, Ken Tawara, Caleb Sutherland, Jeff Redshaw, Patrick S. Aranda, Jim Moselhy, Robin Anderson, Cheryl Jorcyk

Biology Faculty Publications and Presentations

Oncostatin M (OSM) is an interleukin-6 (IL-6) family cytokine that has been implicated in a number of biological processes including inflammation, hematopoiesis, immune responses, development, and bone homeostasis. Recent evidence suggests that OSM may promote breast tumor invasion and metastasis. We investigated the role of OSM in the formation of bone metastases in vivo using the 4T1.2 mouse mammary tumor model in which OSM expression was knocked down using shRNA (4T1.2-OSM). 4T1.2-OSM cells were injected orthotopically into Balb/c mice, resulting in a greater than 97% decrease in spontaneous metastasis to bone compared to control cells. Intratibial injection of these same …

An Integrated Encyclopedia Of Dna Elements In The Human Genome, Jainab Khatun

Biology Faculty Publications and Presentations

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence …

Land Snails In Ephemeral Pools At Ottine Swamp, Gonzales County, Texas, Frank J. Dirrigl, Robert H. Mohlenbrock

Biology Faculty Publications and Presentations

We found five species of terrestrial land snails in dried ephemeral pools at Ottine Swamp, Palmetto State Park, Gonzales County, Texas. We recorded four species previously known (Anguispira stronglyodes, Mesomphix friabilis, Olygyra orbiculata, and Rabdotus dealbatus) and added a new occurrence (Mesodon thyroidus) to the list of species in the park.

Se encontraron cinco especies de caracoles terrestres en los fondos secos de unos charcos efímeros en Ottine Swamp, Palmetto State Park, en el condado de Gonzales, Texas. Registramos cuatro especies conocidas anteriormente (Anguispira stronglyodes, Mesomphix friabilis, Olygyra orbiculata y …

Long Noncoding Rnas Are Rarely Translated In Two Human Cell Lines, Jainab Khatun, Brian Risk, Morgan Giddings

Biology Faculty Publications and Presentations

Data from the Encyclopedia of DNA Elements (ENCODE) project show over 9640 human genome loci classified as long noncoding RNAs (lncRNAs), yet only ~100 have been deeply characterized to determine their role in the cell. To measure the protein-coding output from these RNAs, we jointly analyzed two recent data sets produced in the ENCODE project: tandem mass spectrometry (MS/MS) data mapping expressed peptides to their encoding genomic loci, and RNA-seq data generated by ENCODE in long polyA+ and polyA– fractions in the cell lines K562 and GM12878. We used the machinelearning algorithm RuleFit3 to regress the peptide data against RNA …

Sub-Antarctic And High Antarctic Notothenioid Fishes: Ecology And Adaptational Biology Revealed By The Icefish 2004 Cruise Of Rvib Nathaniel B. Palmer, H. William Detrich Iii, Bradley A. Buckley, Daniel F. Doolittle, Christopher D. Jones, Susanne J. Lockhart

Biology Faculty Publications and Presentations

The goal of the ICEFISH 2004 cruise, which was conducted on board RVIB Nathaniel B. Palmer and traversed the transitional zones linking the South Atlantic to the Southern Ocean, was to compare the evolution, ecology, adaptational biology, community structure, and population dynamics of Antarctic notothenioid fishes relative to the cool/temperate notothenioids of the sub-Antarctic. To place this work in a comprehensive ecological context, cruise participants surveyed the benthos and geology of the biogeographic provinces and island shelves on either side of the Antarctic Polar Front (or Antarctic Convergence). Genome-enabled comparison of the responses of cold-living and temperate notothenioids to heat …

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 …

Predicting Occupancy Of Wintering Migratory Birds: Is Microhabitat Information Necessary?, Christopher J. W. Mcclure, Brian W. Rolek, Geoffrey E. Hill

Biology Faculty Publications and Presentations

Information regarding microhabitat, here defined as small-scale vegetation structure, is often useful in predicting use of habitat by birds. Quantifying microhabitat, however, is expensive and labor intensive compared to assessment of habitat at a larger scale, possibly from remotely sensed imagery. To assess the importance of microhabitat information in constructing predictive models of habitat occupancy, we compared occupancy models built on the basis of macro- and microhabitat together and separately. We based our models on counts of wintering migratory bird species and vegetation surveys within Tuskegee National Forest, Alabama, completed during winter 2009. Models built from macrohabitat data only outperformed …

In Vivo Quantification Reveals Extensive Natural Variation In Mitochondrial Form And Function In Caenorhabditis Briggsae, Kiley Ann Hicks, Dana K. Howe, Aubrey Leung, Dee R. Denver, Suzanne Estes

Biology Faculty Publications and Presentations

We have analyzed natural variation in mitochondrial form and function among a set of Caenorhabditis briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic nad5 gene deletion (nad5Δ) that correlates negatively with organismal fitness. We performed in vivo quantification of 24 mitochondrial phenotypes including reactive oxygen species level, membrane potential, and aspects of organelle morphology, and observed significant among- isolate variation in 18 traits. Although several mitochondrial phenotypes were non-linearly associated with nad5Δ levels, most of the among-isolate phenotypic variation could be accounted for by phylogeographic clade membership. In particular, isolate-specific mitochondrial membrane potential …

The Breeding Biology Of The Northern Pygmy Owl: Do The Smallest Of The Small Have An Advantage?, John F. Deshler, Michael T. Murphy

Biology Faculty Publications and Presentations

We explored the breeding biology of the Northern Pygmy-Owl (Glaucidium gnoma) from 2007 to 2009 in a forested reserve in Portland, Oregon. Large body size is often assumed to give animals reproductive advantages, and we tested whether body size affected timing of breeding and examined variation in diet, breeding date, clutch size, and reproductive success to explore whether the presumed benefits of large body size are evident in this species. The average size of 13 clutches was 5.8, and nest success was high (92%); 22 successful nests fledged an average of 5.2 young. Dates of first laying varied …

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 …

A Multi-Gene Phylogeny Of Cephalopoda Supports Convergent Morphological Evolution In Association With Multiple Habitat Shifts In The Marine Environment, Annie R. Lindgren, Molly S. Pankey, Frederick G. Hochberg, Todd H. Oakley

Biology Faculty Publications and Presentations

The marine environment is comprised of numerous divergent organisms living under similar selective pressures, often resulting in the evolution of convergent structures such as the fusiform body shape of pelagic squids, fishes, and some marine mammals. However, little is known about the frequency of, and circumstances leading to, convergent evolution in the open ocean. Here, we present a comparative study of the molluscan class Cephalopoda, a marine group known to occupy habitats from the intertidal to the deep sea. Several lineages bear features that may coincide with a benthic or pelagic existence, making this a valuable group for testing hypotheses …

The Effect Of Human Activities And Their Associated Noise On Ungulate Behavior, Casey L. Brown, Amanda R. Hardy, Jesse R. Barber, Kurt M. Fristrup, Kevin R. Crooks, Lisa M. Angeloni

Biology Faculty Publications and Presentations

Background: The effect of anthropogenic noise on terrestrial wildlife is a relatively new area of study with broad ranging management implications. Noise has been identified as a disturbance that has the potential to induce behavioral responses in animals similar to those associated with predation risk. This study investigated potential impacts of a variety of human activities and their associated noise on the behavior of elk (Cervus elaphus) and pronghorn (Antilocapra americana) along a transportation corridor in Grand Teton National Park.

Methodology/Principal Findings: We conducted roadside scan surveys and focal observations of ungulate behavior while concurrently recording …

Shorter Migration Distances Associated With Higher Winter Temperatures Suggest A Mechanism For Advancing Nesting Phenology Of American Kestrels Falco Sparverius, Julie A. Heath, Karen Steenhof, Mark A. Foster

Biology Faculty Publications and Presentations

Global climate change has affected avian migration patterns and nesting phenology. Changes in one phase of a bird's cycle will most likely affect other stages, but few studies focus simultaneously on multiple life-history events. We used western North American ringing records and Christmas Bird Counts to examine whether changes in migration patterns were concordant with advancing American kestrel Falco sparverius nesting phenology. Consistent with previous findings, male kestrels migrated shorter distances than female kestrels, and kestrels nesting in southern latitudes migrated shorter distances than kestrels nesting in more northern areas. In addition, kestrel migration distance decreased significantly from 1960 to …

Morphology And Phylogeny Of A New Woodruffiid Ciliate, Etoschophrya Inornata Sp. N. (Ciliophora, Colpodea, Platyophryida), With An Account On Evolution Of Platyophryids, William A. Bourland, Greg Hampikian, Peter Vďačný

Biology Faculty Publications and Presentations

We studied the morphology, morphometry, resting cysts and molecular phylogeny of a new woodruffiid ciliate, Etoschophrya inornata, from ephemeral puddles and two lacustrine habitats in Idaho, North-west USA. Up to now, the genus Etoschophrya has included a single species, Etoschophrya oscillatoriophaga, from which our new form is distinguished by (i) the absence of interkinetal cortical granules and, consequently, the absence of extrusible red material in methyl green-pyronin stains, (ii) usually ≥5 adoral membranelles vs. usually four, (iii) greater length and length/width ratio, (iv) prominent cortical furrows vs. inconspicuous and (v) adaptation to non-saline semi-terrestrial and lacustrine habitats in …

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 …

Short Lesson Plan Associated With Increased Acceptance Of Evolutionary Theory And Potential Change In Three Alternate Conceptions Of Macroevolution In Undergraduate Students, Joel K. Abraham, Kathryn E. Perez, Nicholas Downey, Jon C. Herron, Eli Meir

Biology Faculty Publications and Presentations

Undergraduates commonly harbor alternate conceptions about evolutionary biology; these alternate conceptions often persist, even after intensive instruction, and may influence acceptance of evolution. We interviewed undergraduates to explore their alternate conceptions about macroevolutionary patterns and designed a 2-h lesson plan to present evidence that life has evolved. We identified three alternate conceptions during our interviews: that newly derived traits would be more widespread in extant species than would be ancestral traits, that evolution proceeds solely by anagenesis, and that lineages must become more complex over time. We also attempted to measure changes in the alternate conceptions and levels of acceptance …

Environmental Flows Recommendations Report. Final Submission To The Environmental Flows Advisory Group, Rio Grande, Rio Grande Estuary, And Lower Laguna Madre Basin And Bay Stakeholders Committee, And Texas Commission On Environmental Quality, Hudson R. Deyoe, David Buzan, Jude A. Benavides, Carlos Marin, R. J. Edwards, W. Pulich Jr.

Biology Faculty Publications and Presentations

No abstract provided.

Anti-Invasive And Anti-Adhesive Activities Of A Recombinant Disintegrin, R-Viridistatin 2, Derived From The Prairie Rattlesnake (Crotalus Viridis Viridis), Sara E. Lucena, Ying Jia, Julio G. Soto, Jessica Parral, Esteban Cantu, Jeremy Brannon, Kristina Lardner, Carla J. Ramos, Agustin I. Seoane, Elda. E. Sánchez

Biology Faculty Publications and Presentations

Snake venom disintegrins inhibit platelet aggregation and have anti-cancer activities. In this study, we report the cloning, expression, and functional activities of a recombinant disintegrin, r-viridistatin 2 (GenBank ID: JQ071899), from the Prairie rattlesnake. r-Viridistatin 2 was tested for anti-invasive and anti-adhesive activities against six different cancer cell lines (human urinary bladder carcinoma (T24), human fibrosarcoma (HT-1080), human skin melanoma (SK-Mel-28), human colorectal adenocarcinoma (CaCo-2), human breast adenocarcinoma (MDA-MB-231) and murine skin melanoma (B16F10)). r-Viridistatin 2 shares 96% and 64% amino acid identity with two other Prairie rattlesnake medium-sized disintegrins, viridin and viridistatin, respectively. r-Viridistatin 2 was able to …

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 …

Presentation Tips, Zen Faulkes

Biology Faculty Publications and Presentations

Giving a talk? This short book offers lots of bite-sized tips and tricks to make your next presentation better. The book is divided into three sections: "Planning what to say" on organizing your thoughts and approach; "Planning what to show" on designing slides; and "The talk itself" on the delivery on the day.

Effectiveness Of Pan Trapping As A Rapid Bioinventory Method Of Freshwater Shoreline Insects Of Subtropical Texas, Frank J. Dirrigl Jr.

Biology Faculty Publications and Presentations

Pan trapping proves to be an effective method for field surveying insects, especially Diptera. This manuscript examines the effectiveness of the method for the rapid bioinventory of freshwater shoreline insects. Pan traps at ground level, above ground, and elevated and of different colors were evaluated for their ability to attract and capture insects. Abundance (n), taxonomic richness (T), and hierarchical diversity indices (H′) allowed for the determination of efficacy among methods. Yellow pan (n = 141, T = 10, H′ = 1.15) and elevated yellow pan traps (n = 113, T = 5, H′ = 1.18) were most effective at …

Host Plant Use By Competing Acacia-Ants: Mutualists Monopolize While Parasites Share Hosts, Stefanie Kautz, Daniel J. Ballhorn, Johannes Kroiss, Steffen U. Pauls, Corrie S. Moreau, Sascha Eilmus, Erhard Strohm, Martin Heil

Biology Faculty Publications and Presentations

Protective ant-plant mutualisms that are exploited by non-defending parasitic ants represent prominent model systems for ecology and evolutionary biology. The mutualist Pseudomyrmex ferrugineus is an obligate plant-ant and fully depends on acacias for nesting space and food. The parasite Pseudomyrmex gracilis facultatively nests on acacias and uses host-derived food rewards but also external food sources. Integrative analyses of genetic microsatellite data, cuticular hydrocarbons and behavioral assays showed that an individual acacia might be inhabited by the workers of several P. gracilis queens, whereas one P. ferrugineus colony monopolizes one or more host trees. Despite these differences in social organization, neither …