Biology Commons^™

An Insight Into The Sialome Of The Lone Star Tick, Ambylomma Americanum, With A Glimpse On Its Time Dependent Gene Expression, Shahid Karim, José M.C. Ribeiro

Faculty Publications

Hard ticks feed for several days or weeks on their hosts. Blood feeding is assisted by tick saliva, which is injected in the host skin regularly, alternating with blood ingestion. Tick saliva contains hundreds or thousands of different peptides and other bioactive compounds that assist feeding by inhibiting their hosts’ blood clotting, platelet aggregation, vasoconstriction, as well as pain and itching. Immunomodulatory and antimicrobial peptides are also found in tick saliva. Molecular characterization of tick salivary compounds, or its sialome (from the Greek sialos = saliva), helps identification of possible antigens that might confer anti-tick immunity, as well as identifying …

Inferring Pathway Dysregulation In Cancers From Multiple Types Of Omic Data, Shelley M. Macneil, William E. Johnson, Dean Y. Li, Stephen R. Piccolo, Andrea H. Bild

Faculty Publications

Although in some cases individual genomic aberrations may drive disease development in isolation, a complex interplay among multiple aberrations is common. Accordingly, we developed Gene Set Omic Analysis (GSOA), a bioinformatics tool that can evaluate multiple types and combinations of omic data at the pathway level. GSOA uses machine learning to identify dysregulated pathways and improves upon other methods because of its ability to decipher complex, multigene patterns. We compare GSOA to alternative methods and demonstrate its ability to identify pathways known to play a role in various cancer phenotypes. Software implementing the GSOA method is freely available from https://bitbucket.org/srp33/gsoa …

Histone Deacetylase 6 (Hdac6) Promotes The Pro-Survival Activity Of 14-3-3Ζ Via Deacetylation Of Lysines Within The 14-3-3Ζ Binding Pocket, Jeffrey B. Mortenson, Lisa N. Heppler, Courtney J. Banks, Vajira K. Weerasekara, Matthew D. Whited, Stephen R. Piccolo, William E. Johnson, J. Will Thompson, Joshua L. Andersen

Faculty Publications

The phospho-binding protein 14-3-3ζ acts as a signaling hub controlling a network of interacting partners and oncogenic pathways. We show here that lysines within the 14-3-3ζ binding pocket and protein-protein interface can be modified by acetylation. The positive charge on two of these lysines, Lys49 and Lys120, is critical for coordinating 14-3-3ζ-phosphoprotein interactions. Through screening, we identified HDAC6 as the Lys49/Lys120 deacetylase. Inhibition of HDAC6 blocks 14-3-3ζ interactions with two well described interacting partners, Bad and AS160, which triggers their dephosphorylation at Ser112 and Thr642, respectively. Expression of an acetylation-refractory K49R/K120R mutant of 14-3-3ζ rescues both the HDAC6 inhibitor-induced loss …

Molecular And Phenotypic Characterization Of Methicillin-Resistant Staphylococcus Aureus Isolates Causing Bacteremia At A Major Hospital In Southern Mississippi, Dhritiman Samanta, Justin Batte, Stephanie N. Brown, Angela G. Crosby, Luis A. Marcos, Mohamed O. Elasri

Faculty Publications

Staphylococcus aureus is the predominant cause of bacteremia worldwide. We assessed the molecular epidemiology and antibiotic resistance of methicillin-resistant S aureus isolates causing bacteremia in southern Mississippi. Diverse genetic backgrounds in terms of staphylococcal cassette chromosome mec, pulsed-field gel electrophoresis, and multilocus sequence typing types of methicillin-resistant S aureus were identified as causing bacteremia in Mississippi. A strong association of Panton-Valentine leukocidin genes with elevated vancomycin minimum inhibitory concentration is one of the important findings of our study.

Biocontrol And Plant Growth-Promoting Activity Of Rhizobacteria From Chinese Fields With Contaminatd Soils, Xuefie Wang, Dmitri V. Mavrodi, Linfeng Ke, Olga V. Mavrodi, Mingming Yang, Linda S. Thomashow, Na Zheng, David M. Weller, Jibin Zhang

Faculty Publications

The aim of this study was to inventory the types of plant growth‐promoting rhizobacteria (PGPR) present in the rhizosphere of plants grown in soils contaminated with heavy metals, recalcitrant organics, petroleum sewage or salinity in China. We screened 1223 isolates for antifungal activity and about 24% inhibited Rhizoctonia solani or Sclerotinia sclerotiorum. Twenty‐four strains inhibitory to R. solani, Gaeumannomyces graminis var. tritici and/or S. sclerotiorum and representing the dominant morphotypes were assayed for PGPR activity. Seven strains contained phlD, prnD, pltC or phzF genes and produced the antibiotics 2,4‐diacetylphloroglucinol, pyrrolnitrin, pyoluteorin and phenazines respectively. Six strains contained acdS, which encodes …

Draft Genome Sequence Of The Phenazine-Producing Pseudomonas Fluorescens Strain 2-79, Kai Nesemann, Susanna A. Braus-Stromeyer, Andrea Thuermer, Rolf Daniel, Dmitri V. Mavrodi, Linda S. Thomashow, David M. Weller, Gerard H. Braus

Faculty Publications

Pseudomonas fluorescens strain 2-79, a natural isolate of the rhizosphere of wheat (Triticum aestivum L.), possesses antagonistic potential toward several fungal pathogens. We report the draft genome sequnce of strain 2-79, which comprises 5,674 protein-coding sequences.

The Candidate Cancer Gene Database: A Database Of Cancer Driver Genes From Forward Genetic Screens In Mice, Kenneth L. Abbott, Erik T. Nyre, Juan Abrahante, Yen Yi Ho, Rachel Isaksson Vogel, Timothy K. Starr

Faculty Publications

Identification of cancer driver gene mutations is crucial for advancing cancer therapeutics. Due to the overwhelming number of passenger mutations in the human tumor genome, it is difficult to pinpoint causative driver genes. Using transposon mutagenesis in mice many laboratories have conducted forward genetic screens and identified thousands of candidate driver genes that are highly relevant to human cancer. Unfortunately, this information is difficult to access and utilize because it is scattered across multiple publications using different mouse genome builds and strength metrics. To improve access to these findings and facilitate metaanalyses, we developed the Candidate Cancer Gene Database (CCGD, …

Satrat: Staphylococcus Aureus Transcript Regulatory Network Analysis Tool, Tamilselvi Gopal, Vijayaraj Nagarajan, Mohamed O. Elasri

Faculty Publications

Staphylococcus aureus is a commensal organism that primarily colonizes the nose of healthy individuals. S. aureus causes a spectrum of infections that range from skin and soft-tissue infections to fatal invasive diseases. S. aureus uses a large number of virulence factors that are regulated in a coordinated fashion. The complex regulatory mechanisms have been investigated in numerous high-throughput experiments. Access to this data is critical to studying this pathogen. Previously, we developed a compilation of microarray experimental data to enable researchers to search, browse, compare, and contrast transcript profiles. We have substantially updated this database and have built a novel …

Effects Of Urbanization On The Occurrence Of Batrachochytrium Dendrobatidis: Do Urban Environments Provide Refuge From The Amphibian Chytrid Fungus?, Daniel Saenz, Taylor L. Hall, Matthew Kwiatkowski

Faculty Publications

Batrachochytrium dendrobatidis (Bd) is a widespread pathogenic fungus that is known to cause the disease, chytridiomycosis, which can be lethal to many amphibians. We compared occurrence rates on spring peepers (Pseudacris crucifer) in urban and forested breeding sites in eastern Texas, USA. All study sites were at approximately the same latitude and altitude, and samples were collected at the same time of year to isolate differences in Bd infection rates between habitat types. We found significant differences (p<0.001) in the occurrence of Bd between habitats; with dramatically lower rates of occurrence at urban sites (19.5 %), compared to forested sites (62.9 …

Morphologic And Taxonomic Analysis Of The Weedy And Cultivated Amaranthus Hybridus Species Complex, Dinesh Adhikary, Donald B. Pratt

Faculty Publications

The hybridus species complex of the genus Amaranthus is a group of weedy and cultivated plants from the New World that are considered difficult to identify. Classification schemes have varied between a single species approach, Amaranthus hybridus s.l., and a five species approach that recognizes the widespread weedy A. hybridus s.s., the South American endemic A. quitensis, and the three cultivated taxa (A. hypochondriacus, A. cruentus, and A. caudatus) as distinct species. The goals of this study were to analyze patterns of floral variation within the species complex and to determine distinguishing morphological features of …

Special Speciation, Lyn L. Countryman, Jill D. Maroo

Faculty Publications

Considerable anecdotal evidence indicates that some of the most difficult concepts that both high school and undergraduate elementary-education students struggle with are those surrounding evolutionary principles, especially speciation. It’s no wonder that entry-level biology students are confused, when biologists have multiple definitions of “species.” We developed this speciation activity to provide clarity and allow students a hands-on experience with a speciation model.

Diet Of Larval Ambystoma Altamiranoi From Llano De Los Axolotes, Mexico, J. A. Lemos-Espinal, Geoffrey R. Smith, G. A. Woolrich-Pina

Faculty Publications

No abstract provided.

Amphibians And Reptiles Of The State Of Hidalgo, Mexico, J. A. Lemos-Espinal, Geoffrey R. Smith

Faculty Publications

No abstract provided.

Thermal Ecology, Sexual Dimorphism, And Diet Of Xenosaurus Tzacualtipantecus From Hidalgo, Mexico, J. Garcia-Rico, A. Diaz De La Vega-Pere, Geoffrey R. Smith, J. A. Lemos-Espinal, G. A. Woolrich-Pina

Faculty Publications

No abstract provided.

Metazoan Parasites Of Antarctic Fishes, Mehmet Cemal Oğuz, Yahya Tepe, Mark C. Belk, Richard A. Heckmann, Burçak Aslan, Meryem Gürgen, Rodney A. Bray, Ülker Akgül

Faculty Publications

To date, there have been nearly 100 papers published on metazoan parasites of Antarctic fishes, but there has not yet been any compilation of a species list of fish parasites for this large geographic area. Herein, we provide a list of all documented occurrences of monogenean, cestode, digenean, acanthocephalan, nematode, and hirudinean parasites of Antarctic fishes. The list includes nearly 250 parasite species found in 142 species of host fishes. It is likely that there are more species of fish parasites, which are yet to be documented from Antarctic waters.

An Efficient Algorithm To Explore Liquid Association On A Genome-Wide Scale, Tina Gunderson, Yen Yi Ho

Faculty Publications

Background: The growing wealth of public available gene expression data has made the systemic studies of how genes interact in a cell become more feasible. Liquid association (LA) describes the extent to which coexpression of two genes may vary based on the expression level of a third gene (the controller gene). However, genome-wide application has been difficult and resource-intensive. We propose a new screening algorithm for more efficient processing of LA estimation on a genome-wide scale and apply its use to a data set. Results: On a test subset of the data, the fast screening algorithm achieved >99.8 agreement with …

Using Phylogenetically-Informed Annotation (Pia) To Search For Light-Interacting Genes In Transcriptomes From Non-Model Organisms, Daniel Isaac Speiser, M Sabrina Pankey, Alexandera K. Zaharoff, Barbara A. Battelle, Heather D. Bracken-Grissom, Jesse W. Breinholt, Seth M. Bybee, Thomas W. Cronin, Anders Garm, Annie R. Lindgren, Nipam H. Patel, Megan L. Porter, Meredith E. Protas, Ajna S. Rivera, Jeanne M. Serb, Kirk S. Zigler, Keith A. Crandall, Todd H. Oakley

Faculty Publications

Background

Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees for every gene of interest and each time a new data set is analyzed. In response, we employed existing tools for phylogenetic analysis …

Viability Costs Of Reproduction And Behavioral Compensation In Western Mosquitofish (Gambusia Affinis), Clinton T. Laidlaw, Jacob M. Condon, Mark C. Belk

Faculty Publications

The cost of reproduction hypothesis suggests that current reproduction has inherent tradeoffs with future reproduction. These tradeoffs can be both in the form of energy allocated to current offspring as opposed to somatic maintenance and future reproduction (allocation costs), or as an increase in mortality as a result of morphological or physiological changes related to reproduction (viability costs). Individuals may be able to decrease viability costs by altering behavior. Female western mosquitofish, Gambusia affinis experience a reduction in swimming ability as a consequence of pregnancy. We test for a viability cost of reproduction, and for behavioral compensation in pregnant female …

Residency Time As An Indicator Of Reproductive Restraint In Male Burying Beetles, Ashlee N. Smith, Mark C. Belk, J. Curtis Creighton

Faculty Publications

The cost of reproduction theory posits that there are trade-offs between current and future reproduction because resources that are allocated to current offspring cannot be used for future reproductive opportunities. Two adaptive reproductive strategies have been hypothesized to offset the costs of reproduction and maximize lifetime fitness. The terminal investment hypothesis predicts that as individuals age they will allocate more resources to current reproduction as a response to decreasing residual reproductive value. The reproductive restraint hypotheses predicts that as individuals age they will allocate fewer resources to current reproduction to increase the chance of surviving for an additional reproductive opportunity. …

A Comparison Of The Caulobacter Na1000 And K31 Genomes Reveals Extensive Genome Rearrangements And Differences In Metabolic Potential, Kurt Ash, Theta Brown, Tynetta Watford, Latia E. Scott, Craig Stephens, Bert Ely

Faculty Publications

The genus Caulobacter is found in a variety of habitats and is known for its ability to thrive in low-nutrient conditions. K31 is a novel Caulobacter isolate that has the ability to tolerate copper and chlorophenols, and can grow at 4°C with a doubling time of 40 h. K31 contains a 5.5 Mb chromosome that codes for more than 5500 proteins and two large plasmids (234 and 178 kb) that code for 438 additional proteins. A comparison of the K31 and the Caulobacter crescentus NA1000 genomes revealed extensive rearrangements of gene order, suggesting that the genomes had been randomly scrambled. …

Antiviral Responses In Mouse Embryonic Stem Cells: Differential Development Of Cellular Mechanisms In Type I Interferon Production And Response, Ruoxing Wang, Jundi Wang, Dhiraj Acharya, Amber M. Paul, Fengwei Bai, Faqing Huang, Yan-Lin Guo

Faculty Publications

We have recently reported that mouse embryonic stem cells (mESCs) are deficient in expressing type I interferons (IFNs) in response to viral infection and synthetic viral RNA analogs (Wang, R., Wang, J., Paul, A. M., Acharya, D., Bai, F., Huang, F., and Guo, Y. L. (2013) J. Biol. Chem. 288, 15926–15936). Here, we report that mESCs are able to respond to type I IFNs, express IFN-stimulated genes, and mediate the antiviral effect of type I IFNs against La Crosse virus and chikungunya virus. The major signaling components in the IFN pathway are expressed in mESCs. Therefore, the basic molecular mechanisms …

Robust Meta-Analysis Shows That Glioma Transcriptional Subtyping Complements Traditional Approaches, Sanghoon Lee, Stephen Piccolo, Kristina Allen-Brady

Faculty Publications

Background Gliomas traditionally have been sub-classified
based on histopathological observations. However, this ap-
proach is subject to inter-observer variability, and histopatho-
logical features may not reflect the biological mechanisms that
drive tumor growth. High-throughput transcriptional profiling
has shown promise in objectively and reproducibly identify-
ing glioma subtypes. Most prior studies have typically used
only modest sample sizes and have sometimes overlooked
important data-processing steps to ensure sample quality and
to evaluate the robustness of quantitative findings. The pur-
pose of our study was to define robust glioma subtypes by
applying rigorous preprocessing and validation steps to 1,952
microarray samples aggregated …

Identification And Characterization Of An Operon, Msaabcr, That Controls Virulence And Biofilm Development In Staphlococcus Aureus, Gyan S. Sahukhal, Mohamed O. Elasri

Faculty Publications

Background

Community-acquired, methicillin-resistant Staphylococcus aureus strains often cause localized infections in immunocompromised hosts, but some strains show enhanced virulence leading to severe infections even among healthy individuals with no predisposing risk factors. The genetic basis for this enhanced virulence has yet to be determined. S. aureus possesses a wide variety of virulence factors, the expression of which is carefully coordinated by a variety of regulators. Several virulence regulators have been well characterized, but others have yet to be thoroughly investigated. Previously, we identified the msa gene as a regulator of several virulence genes, biofilm development, and antibiotic resistance. We also …

Male-Male Clasping May Be Part Of An Alternative Reproductive Tactic In Xenopus Laevis, Heather J. Rhodes, Rachel J. Stevenson, Courtney L. Ego

Faculty Publications

No abstract provided.

Genomic Classification Of The Ras Network Identifies A Personalized Treatment Strategy For Lung Cancer, Nader N. El-Chaar, Stephen R. Piccolo, Kenneth M. Boucher, Adam L. Cohen, Jeffrey T. Chang, Philip J. Moos, Andrea H. Bild

Faculty Publications

Better approaches are needed to evaluate a single patient's drug response at the genomic level. Targeted therapy for signaling pathways in cancer has met limited success in part due to the exceedingly interwoven nature of the pathways. In particular, the highly complex RAS network has been challenging to target. Effectively targeting the pathway requires development of techniques that measure global network activity to account for pathway complexity. For this purpose, we used a gene-expression-based biomarker for RAS network activity in non-small cell lung cancer (NSCLC) cells, and screened for drugs whose efficacy was significantly highly correlated to RAS network activity. …

Prior Experience Affects Allocation To Current Reproduction In A Burying Beetle, Eric J. Billman, J. Curtis Creighton, Mark C. Belk

Faculty Publications

The cost of reproduction hypothesis predicts that the level of reproductive investment to current reproduction is constrained by an individual’s future reproductive potential or residual reproductive value. Therefore, age, or differences between young and old individuals in residual reproductive value, is expected to influence reproductive investment. However, recent theoretical work suggests that residual reproductive value is also influenced by an individual’s state or condition which may in part be determined by prior reproductive experience. We evaluated the reproductive investment of same-aged female burying beetles (Nicrophorus orbicollis) to determine how prior reproductive experience affects current reproduction. Consistent with previous …

Correction Of The Caulobacter Crescentus Na1000 Genome Annotation, Bert Ely, Latia Etheredge Scott

Faculty Publications

Bacterial genome annotations are accumulating rapidly in the GenBank database and the use of automated annotation technologies to create these annotations has become the norm. However, these automated methods commonly result in a small, but significant percentage of genome annotation errors. To improve accuracy and reliability, we analyzed the Caulobacter crescentus NA1000 genome utilizing computer programs Artemis and MICheck to manually examine the third codon position GC content, alignment to a third codon position GC frame plot peak, and matches in the GenBank database. We identified 11 new genes, modified the start site of 113 genes, and changed the reading …

Structural And Functional Analyses Of A Glutaminyl Cyclase From Ixodes Scapularis Reveal Metal-Independent Catalysis And Inhibitor Binding, Kai-Fa Huang, Hui-Ling Hsu, Shahid Karim, Andrew H.-J. Wang

Faculty Publications

Glutaminyl cyclases (QCs) from mammals and Drosophila are zinc-dependent enzymes that catalyze N-terminal pyroglutamate formation of numerous proteins and peptides. These enzymes have been found to be critical for the oviposition and embryogenesis of ticks, implying that they are possible physiological targets for tick control. Here, 1.10–1.15 Å resolution structures of a metal-independent QC from the black-legged tick Ixodes scapularis (Is-QC) are reported. The structures exhibit the typical scaffold of mammalian QCs but have two extra disulfide bridges that stabilize the central β-­sheet, resulting in an increased thermal stability. Is-QC contains ∼0.5 stoichiometric zinc ions, which could …

Morphological Divergence Driven By Predation Environment Within And Between Species Of Brachyrhaphis Fishes, Spencer J. Ingley, Eric J. Billman, Mark C. Belk, Jerald B. Johnson

Faculty Publications

Natural selection often results in profound differences in body shape among populations from divergent selective environments. Predation is a well-studied driver of divergence, with predators having a strong effect on the evolution of prey body shape, especially for traits related to escape behavior. Comparative studies, both at the population level and between species, show that the presence or absence of predators can alter prey morphology. Although this pattern is well documented in various species or population pairs, few studies have tested for similar patterns of body shape evolution at multiple stages of divergence within a taxonomic group. Here, we examine …

A Field Guide To Genomics Research, Andrea H. Bild, Jeffrey T. Chang, W. Evan Johnson, Stephen R. Piccolo

Faculty Publications

High-throughput technologies are enabling scientists to profile genomes, transcriptomes, proteomes, and metabolomes at an unprecedented scale [1]. All this “-omics” research (let's call it genomics for simplicity) is exciting—and game changing—but it's also fraught with dangers for the tenderfoot. Here, we've put together a brief “field guide” for those wishing to visit the genomics frontier, in which we use caricatures to illustrate various pitfalls that can beset those who inhabit this new territory. By documenting the behaviors of these common types, we hope to guide researchers in their quest to apply sound practices when designing genomics experiments and analyzing …