Life Sciences Commons^™

Comparative Genomics And Functional Analysis Of Rhamnose Catabolic Pathways And Regulons In Bacteria, Irina A. Rodionova, Xiaoqing Li, Vera Thiel, Sergey Stolyar, Krista Stanton, James K. Fredrickson, Donald A. Bryant, Andrei L. Osterman, Aaron A. Best, Dmitry A. Rodionov

Faculty Publications

L-rhamnose (Rha) is a deoxy-hexose sugar commonly found in nature. L-Rha catabolic pathways were previously characterized in various bacteria including Escherichia coli. Nevertheless, homology searches failed to recognize all the genes for the complete L Rha utilization pathways in diverse microbial species involved in biomass decomposition. Moreover, the regulatory mechanisms of L-Rha catabolism have remained unclear in most species. A comparative genomics approach was used to reconstruct the L-Rha catabolic pathways and transcriptional regulons in the phyla Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, and Thermotogae. The reconstructed pathways include multiple novel enzymes and transporters involved in the utilization of L-Rha and …

Measuring Changes In Tactile Sensitivity In The Hind Paw Of Mice Using An Electronic Von Frey Apparatus, Tijana Martinov, Madison Mack, Akilah Sykes, Devavani Chatterjea

Faculty Publications

Measuring inflammation-induced changes in thresholds of hind paw withdrawal from mechanical pressure is a useful technique to assess changes in pain perception in rodents. Withdrawal thresholds can be measured first at baseline and then following drug, venom, injury, allergen, or otherwise evoked inflammation by applying an accurate force on very specific areas of the skin. An electronic von Frey apparatus allows precise assessment of mouse hind paw withdrawal thresholds that are not limited by the available filament sizes in contrast to classical von Frey measurements. The ease and rapidity of measurements allow for incorporation of assessment of tactile sensitivity outcomes …

The Status Of Plethodon Ainsworthi Lazell: Extinct, Extant, Or Nonexistent?, John G. Himes, David C. Beckett

Faculty Publications

Plethodon ainsworthi Lazell was described as a new species in the slimy salamander (Plethodon glutinosus [Northern Slimy Salamander]) complex from two specimens collected in Jasper County, MS, in 1964. Prior to their designation as the type and paratype of the newly described species in 1998, both specimens were presumably stored in strong formalin for 26 years and thus were in poor condition. Plethodon ainsworthi is distinguished from the sympatric Plethodon mississippi (Mississippi Slimy Salamander) by a more attenuated body, as evidenced by a higher snout-vent length (SVL)/head width (HW) ratio, and shorter limbs. Despite numerous searches between 1991 and …

Cross Amplification Of Microsatellite Loci Developed For Atractosteus Spatula In Atractosteus Tropicus, Sandra Bohn, Enrique Barraza, Caleb Mcmahan, Brian Kreiser

Faculty Publications

Due to recent population declines in tropical gar (Atractosteus tropicus), a greater understanding of its population structure is needed. A key step in gaining this understanding is the development of microsatellite loci for use in this species. For this purpose, 33 microsatellite loci from alligator gar (A. spatula) were screened in 52 individuals from a population in Zanjón del Chino, El Salvador. Twenty-five of these loci successfully amplified in this species, and 9 of those loci were polymorphic in this population. These loci should provide a useful tool for genotyping A. tropicus, both in studying …

The Eps Matrix As An Adaptive Bastion For Biofilms: Introduction To Special Issue, Alan Decho

Faculty Publications

No abstract provided.

The Eps Matrix As An Adaptive Bastion For Biofilms: Introduction To Special Issue, Alan W. Decho

Faculty Publications

No abstract provided.

Knockdown Of Selenocysteine-Specific Elongation Factor In Amblyomma Maculatum Alters The Pathogen Burden Of Rickettsia Parkeri With Epigenetic Control By The Sin3 Histone Deacetylase Corepressor Complex, Steven W. Adamson, Rebecca E. Browning, Khemraj Budachetri, José M.C. Ribeiro, Shahid Karim

Faculty Publications

Selenocysteine is the 21st naturally-occurring amino acid. Selenoproteins have diverse functions and many remain uncharacterized, but they are typically associated with antioxidant activity. The incorporation of selenocysteine into the nascent polypeptide chain recodes the TGA stop codon and this process depends upon a number of essential factors including the selenocysteine elongation factor (SEF). The transcriptional expression of SEF did not change significantly in tick midguts throughout the blood meal, but decreased in salivary glands to 20% at the end of the fast feeding phase. Since selenoprotein translation requires this specialized elongation factor, we targeted this gene for knockdown by RNAi …

Mutational Analysis Of The Rotavirus Nsp4 Enterotoxic Domain That Binds To Caveolin-1, Judith M. Ball, Megan E. Schroeder, Cecelia V. Williams, Friedhelm Schroeder, Rebecca D. Parr

Faculty Publications

Background: Rotavirus (RV) nonstructural protein 4 (NSP4) is the first described viral enterotoxin, which induces early secretory diarrhea in neonatal rodents. Our previous data show a direct interaction between RV NSP4 and the structural protein of caveolae, caveolin-1 (cav-1), in yeast and mammalian cells. The binding site of cav-1 mapped to the NSP4 amphipathic helix, and led us to examine which helical face was responsible for the interaction.

Methods: A panel of NSP4 mutants were prepared and tested for binding to cav-1 by yeast two hybrid and direct binding assays. The charged residues of the NSP4 amphipathic helix were changed …

Morphological Divergence And Flow-Induced Phenotypic Plasticity In A Native Fish From Anthropogenically Altered Stream Habitats, Nathan R. Franssen, Laura K. Stewart, Jacob F. Schaefer

Faculty Publications

Understanding population-level responses to human-induced changes to habitats can elucidate the evolutionary consequences of rapid habitat alteration. Reservoirs constructed on streams expose stream fishes to novel selective pressures in these habitats. Assessing the drivers of trait divergence facilitated by these habitats will help identify evolutionary and ecological consequences of reservoir habitats. We tested for morphological divergence in a stream fish that occupies both stream and reservoir habitats. To assess contributions of genetic-level differences and phenotypic plasticity induced by flow variation, we spawned and reared individuals from both habitats types in flow and no flow conditions. Body shape significantly and consistently …

The Glucose Signaling Network In Yeast, Jeong-Ho Kim, Adhiraj Roy, David Jouandot Ii, Kyu Hong Cho

Faculty Publications

Background

Most cells possess a sophisticated mechanism for sensing glucose and responding to it appropriately. Glucose sensing and signaling in the budding yeast Saccharomyces cerevisiae represent an important paradigm for understanding how extracellular signals lead to changes in the gene expression program in eukaryotes.

Scope of review

This review focuses on the yeast glucose sensing and signaling pathways that operate in a highly regulated and cooperative manner to bring about glucose-induction of HXT gene expression.

Major conclusions

The yeast cells possess a family of glucose transporters (HXTs), with different kinetic properties. They employ three major glucose signaling pathways—Rgt2/Snf3, …

Spatial Warping By Oriented Line Detectors Can Counteract Neural Delays, Don A. Vaughn, David M. Eagleman

Faculty Publications

The slow speed of neural transmission necessitates that cortical visual information from dynamic scenes will lag reality. The "perceiving the present" (PTP) hypothesis suggests that the visual system can mitigate the effect of such delays by spatially warping scenes to look as they will in ~100 ms from now (Changizi, 2001). We here show that the Hering illusion, in which straight lines appear bowed, can be induced by a background of optic flow, consistent with the PTP hypothesis. However, importantly, the bowing direction is the same whether the flow is inward or outward. This suggests that if the warping is …

Zebrafish Cytosolic Carboxypeptidases 1 And 5 Are Essential For Embryonic Development, Peter J. Lyons, Matthew R. Sapio, Lloyd D. Fricker

Faculty Publications

The cytosolic carboxypeptidases (CCPs) are a subfamily of metalloenzymes within the larger M14 family of carboxypeptidases that have been implicated in the post-translational modification of tubulin. It has been suggested that at least four of the six mammalian CCPs function as tubulin deglutamylases. However, it is not yet clear whether these enzymes play redundant or unique roles within the cell. To address this question, genes encoding CCPs were identified in the zebrafish genome. Analysis by quantitative polymerase chain reaction indicated that CCP1, CCP2, CCP5, and CCP6 mRNAs were detectable between 2 h and 8 days postfertilization with highest levels 5–8 …

Day-Night Differences In Neural Activation In Histaminergic And Serotonergic Areas With Putative Projections To The Cerebrospinal Fluid In A Diurnal Brain, Alexandra Castillo-Ruiz, Andrew J. Gall, Laura Smale, Antonio A. Nunez

Faculty Publications

In nocturnal rodents, brain areas that promote wakefulness have a circadian pattern of neural activation that mirrors the sleep/wake cycle, with more neural activation during the active phase than during the rest phase. To investigate whether differences in temporal patterns of neural activity in wake-promoting regions contribute to differences in daily patterns of wakefulness between nocturnal and diurnal species, we assessed Fos expression patterns in the tuberomammillary (TMM), supramammillary (SUM), and raphe nuclei of male grass rats maintained in a 12:12 h light-dark cycle. Day-night profiles of Fos expression were observed in the ventral and dorsal TMM, in the SUM, …

Differential Reconstructed Gene Interaction Networks For Deriving Toxicity Threshold In Chemical Risk Assessment, Yi Yang, Andrew Maxwell, Xiaowei Zhang, Nan Wang, Edward J. Perkins, Chaoyang Zhang, Ping Gong

Faculty Publications

Background: Pathway alterations reflected as changes in gene expression regulation and gene interaction can result from cellular exposure to toxicants. Such information is often used to elucidate toxicological modes of action. From a risk assessment perspective, alterations in biological pathways are a rich resource for setting toxicant thresholds, which may be more sensitive and mechanism-informed than traditional toxicity endpoints. Here we developed a novel differential networks (DNs) approach to connect pathway perturbation with toxicity threshold setting.

Methods: Our DNs approach consists of 6 steps: time-series gene expression data collection, identification of altered genes, gene interaction network reconstruction, differential …

Tnf-Alpha Neutralizing Antibody Blocks Thermal Sensitivity Induced By Compound 48/80-Provoked Mast Cell Degranulation, Devavani Chatterjea, Luisa Paredes, Tijana Martinov, Evelyn Balsells, Juliann Allen, Akilah Sykes, Alyssa Ashbaugh

Faculty Publications

BACKGROUND:
Neuro-inflammatory circuits in the tissue regulate the complex pathophysiology of pain. Protective nociceptive pain serves as an early warning system against noxious environmental stimuli. Tissue-resident mast cells orchestrate the increased thermal sensitivity following injection of basic secretagogue compound 48/80 in the hind paw tissues of ND4 mice. Here we investigated the effects of pre-treatment with TNF-α neutralizing antibody on compound 48/80-provoked thermal hyperalgesia.

METHODS:
We treated ND4 Swiss male mice with intravenous anti-TNF-α antibody or vehicle 30 minutes prior to bilateral, intra-plantar compound 48/80 administration and measured changes in the timing of hind paw withdrawal observed subsequent to mice …

Multitargeting By Turmeric, The Golden Spice: From Kitchen To Clinic (Abstract), Subash C. Gupta, Bokyung Sung, Ji Hye Kim, Sahdeo Prasad, Shiyou Li, Bharat Aggarwal

Faculty Publications

Abstract attached

Transcriptome Sequences Resolve Deep Relationships Of The Grape Family, Jun Wen, Zhiqiang Xiong, Ze-Long Nie, Likai Mao, Yabing Zhu, Xian-Zhao Kan, Stefanie M. Ickert-Bond, Jean Gerrath, Elizabeth A. Zimmer, Xiao-Dong Fang

Faculty Publications

Previous phylogenetic studies of the grape family (Vitaceae) yielded poorly resolved deep relationships, thus impeding our understanding of the evolution of the family. Next-generation sequencing now offers access to protein coding sequences very easily, quickly and cost-effectively. To improve upon earlier work, we extracted 417 orthologous single-copy nuclear genes from the transcriptomes of 15 species of the Vitaceae, covering its phylogenetic diversity. The resulting transcriptome phylogeny provides robust support for the deep relationships, showing the phylogenetic utility of transcriptome data for plants over a time scale at least since the mid-Cretaceous. The pros and cons of transcriptome data for phylogenetic …

Penetration Of Uv-Visible Solar Radiation In The Global Oceans: Insights From Ocean Color Remote Sensing, Zhongping Lee, Chuanmin Hu, Shaoling Shang, Keping Du, Marlon Lewis, Robert Arnone, Robert Brewin

Faculty Publications

Penetration of solar radiation in the ocean is determined by the attenuation coefficient (K-d()). Following radiative transfer theory, K-d is a function of angular distribution of incident light and water's absorption and backscattering coefficients. Because these optical products are now generated routinely from satellite measurements, it is logical to evolve the empirical K-d to a semianalytical K-d that is not only spectrally flexible, but also the sun-angle effect is accounted for explicitly. Here, the semianalytical model developed in Lee et al. (2005b) is revised to account for the shift of phase function between molecular and particulate scattering from the short …

Molecular Characterization Of Tick Salivary Gland Glutaminyl Cyclase, Steven W. Adamson, Rebecca E. Browning, Chien-Chung Chao, Robert C. Bateman Jr., Wei-Mei Ching, Shahid Karim

Faculty Publications

Glutaminyl cyclase (QC) catalyzes the cyclization of N-terminal glutamine residues into pyroglutamate. This post-translational modification extends the half-life of peptides and, in some cases, is essential in binding to their cognate receptor. Due to its potential role in the post-translational modification of tick neuropeptides, we report the molecular, biochemical and physiological characterization of salivary gland QC during the prolonged blood feeding of the black-legged tick (Ixodes scapularis) and the gulf-coast tick (Amblyomma maculatum). QC sequences from I. scapularis and A. maculatum showed a high degree of amino acid identity to each other and other arthropods and …

Experimental Demonstration Of Accelerated Extinction In Source-Sink Metapopulations, John M. Drake, Blaine D. Griffen

Faculty Publications

Population extinction is a fundamental ecological process which may be aggravated by the exchange of organisms between productive (source) and unproductive (sink) habitat patches. The extent to which such source-sink exchange affects extinction rates is unknown. We conducted an experiment in which metapopulation effects could be distinguished from source-sink effects in laboratory populations of Daphnia magna. Time-to-extinction in this experiment was maximized at intermediate levels of habitat fragmentation, which is consistent with a minority of theoretical models. These results provided a baseline for comparison with experimental treatments designed to detect effects of concentrating resources in source patches. These treatments showed …

A Supramolecular Strategy To Assemble Multifunctional Viral Nanoparticles, Limin Chen, Xia Zhao, Yuan Lin, Yubin Huang, Qian Wang

Faculty Publications

Using a one-pot approach driven by the supramolecular interaction between β-cyclodextrin and adamantyl moieties, multifunctional viral nanoparticles can be facilely formulated for biomedical applications.

Jellyfish Body Plans Provide Allometric Advantages Beyond Low Carbon Content, Kylie A. Pitt, Carlos M. Duarte, Cathy H. Lucas, Kelly R. Sutherland, Robert H. Condon, Hermes Mianzan, Jennifer E. Purcell, Kelly L. Robinson, Shin-Ichi Uye

Faculty Publications

Jellyfish form spectacular blooms throughout the world's oceans. Jellyfish body plans are characterised by high water and low carbon contents which enables them to grow much larger than non-gelatinous animals of equivalent carbon content and to deviate from non-gelatinous pelagic animals when incorporated into allometric relationships. Jellyfish have, however, been argued to conform to allometric relationships when carbon content is used as the metric for comparison. Here we test the hypothesis that differences in allometric relationships for several key functional parameters remain for jellyfish even after their body sizes are scaled to their carbon content. Data on carbon and nitrogen …

Study Of Health And Activity In Preschool Environments (Shapes): Study Protocol For A Randomized Trial Evaluating A Multi-Component Physical Activity Intervention In Preschool Children, Karin A. Pfeiffer, Ruth P. Saunders, William H. Brown, Marsha Dowda, Cheryl L. Addy, Russell R. Pate

Faculty Publications

Background: Physical inactivity is a recognized public health concern. Inadequate proportions of children in the U.S, including those of preschool age, are meeting physical activity recommendations. In response to low numbers of preschool children attaining appropriate physical activity levels, combined with the large number of young children who attend preschool, researchers have identified the need to devise interventions to increase physical activity at preschools. However, few multi-component interventions to increase physical activity in preschool children exist. The aims of this study were to observe the effects of a multi-component intervention on physical activity, sedentary behavior, and physical activity energy expenditure …

Human-Relevant Levels Of Added Sugar Consumption Increase Female Mortality And Lower Male Fitness In Mice, James Ruff, Amanda Suchy, Sara Hugentobler, Mirtha Sosa, Bradley Schwartz, Linda Morrison, Sin Gieng, Mark Shigenaga, Wayne Potts

Faculty Publications

Consumption of added sugar has increased over recent decades and is correlated with numerous diseases. Rodent models have elucidated mechanisms of toxicity, but only at concentrations beyond typical human exposure. Here we show that comparatively low levels of added sugar consumption have substantial negative effects on mouse survival, competitive ability, and reproduction. Using Organismal Performance Assays—in which mice fed human-relevant concentrations of added sugar (25% kcal from a mixture of fructose and glucose, modeling high fructose corn syrup) and control mice compete in seminatural enclosures for territories, resources and mates—we demonstrate that fructose/glucose-fed females experience a twofold increase in mortality …

Decades-Long Social Memory In Bottlenose Dolphins, Jason N. Bruck

Faculty Publications

Long-term social memory is important, because it is an ecologically relevant test of cognitive capacity, it helps us understand which social relationships are remembered and it relates two seemingly disparate disciplines: cognition and sociality. For dolphins, long-term memory for conspecifics could help assess social threats as well as potential social or hunting alliances in a very fluid and complex fission-fusion social system, yet we have no idea how long dolphins can remember each other. Through a playback study conducted within a multi-institution dolphin breeding consortium (where animals are moved between different facilities), recognition of unfamiliar versus familiar signature whistles of …

Foot Bone Marrow Edema After A 10-Wk Transition To Minimalist Running Shoes, Sarah T. Ridge, A. Wayne Johnson, Ulrike H. Mitchell, Iain Hunter, Eric Robinson, Brent S. E. Rich, Stephen Douglas Brown

Faculty Publications

Purpose: Minimalist running shoes are becoming a more popular choice for runners in the past few years. However, there is little conclusive evidence about the advantages or disadvantages of running in these shoes. Although performance benefits may exist, injury may also occur from the added stress of running without the benefit of cushioning under the foot. Bone marrow edema can be a manifestation of added stress on the foot. This study measured bone marrow edema in runners’ feet before and after a 10-wk period of transitioning from traditional to minimalist running shoes.

Methods: Thirty-six experienced recreational runners underwent magnetic resonance …

Lesions Of The Intergeniculate Leaflet Lead To A Reorganization In Circadian Regulation And A Reversal In Masking Responses To Photic Stimuli In The Nile Grass Rat, Andrew J. Gall, Laura Smale, Lily Yan, Antonio A. Nunez

Faculty Publications

Light influences the daily patterning of behavior by entraining circadian rhythms and through its acute effects on activity levels (masking). Mechanisms of entrainment are quite similar across species, but masking can be very different. Specifically, in diurnal species, light generally increases locomotor activity (positive masking), and in nocturnal ones, it generally suppresses it (negative masking). The intergeniculate leaflet (IGL), a subdivision of the lateral geniculate complex, receives direct retinal input and is reciprocally connected with the primary circadian clock, the suprachiasmatic nucleus (SCN). Here, we evaluated the influence of the IGL on masking and the circadian system in a diurnal …

Fitness: Philosophical Problems, Grant Ramsey, Charles H. Pence

Faculty Publications

Fitness plays many roles throughout evolutionary theory, from a measure of populations in the wild to a central element in abstract theoretical presentations of natural selection. It has thus been the subject of an extensive philosophical literature, which has primarily centred on the way to understand the relationship between fitness values and reproductive outcomes. If fitness is a probabilistic or statistical quantity, how is it to be defined in general theoretical contexts? How can it be measured? Can a single conceptual model for fitness be offered that applies to all biological cases, or must fitness measures be case-specific? Philosophers have …

Interventions For Improving Nutrition And Physical Activity Behaviors In Adult African American Populations: A Systematic Review, January 2000 Through December 2011, Jennifer Lemacks, Brittny A. Wells, Jasminka Z. Ilich, Penny A. Ralston

Faculty Publications

Introduction The incidence of preventable chronic diseases is disproportionally high among African Americans and could be reduced through diet and physical activity interventions. Our objective was to systematically review the literature on clinical outcomes of diet and physical activity interventions conducted among adult African American populations in the United States. Methods We used the Preferred Reporting Items for Systematic Review and Meta Analysis construct in our review. We searched Medline (PubMed and Ovid), Cochrane, and DARE databases and restricted our search to articles published in English from January 2000 through December 2011. We included studies of educational interventions with clinically …

Rna Interference-Mediated Depletion Of N-Ethylmaleimide Sensitive Fusion Protein And Synaptosomal Associated Protein Of 25 Kda Results In The Inhibition Of Blood Feeding Of The Gulf Coast Tick, Amblyomma Maculatum, Rebecca Browning, Shahid Karim

Faculty Publications

The signalling pathways in tick salivary glands that control ‘sialo‐secretome’ secretion at the tick−host interface remain elusive; however, this complex process is essential for successful feeding and manipulation of the host haemostatic response. Exocytosis of the sialo‐secretome in the salivary glands requires a core of soluble N‐ethylmaleimide‐sensitive fusion (NSF) attachment proteins (SNAPs) and receptor proteins (SNAREs). SNAREs have been identified as the key components in regulating the sialo‐secretome in the salivary gland cells. In this study, we utilized RNA interference to investigate the functional role of two Amblyomma maculatum SNARE complex proteins, AmNSF and AmSNAP‐25, in the tick salivary glands …