Life Sciences Commons^™

Cryptopatches Are Essential For The Development Of Human Galt, Tomonori Nochi, Paul W. Denton, Angela Wahl, J. Victor Garcia

Biology Faculty Publications

Abnormal gut-associated lymphoid tissue (GALT) in humans is associated with infectious and autoimmune diseases, which cause dysfunction of the gastrointestinal (GI) tract immune system. To aid in investigating GALT pathologies in vivo, we bioengineered a human-mouse chimeric model characterized by the development of human GALT structures originating in mouse cryptopatches. This observation expands our mechanistic understanding of the role of cryptopatches in human GALT genesis and emphasizes the evolutionary conservation of this developmental process. Immunoglobulin class switching to IgA occurs in these GALT structures, leading to numerous human IgAproducing plasma cells throughout the intestinal lamina propria. CD4+ T cell depletion …

Evolution Of A Higher Intracellular Oxidizing Environment In Caenorhabditis Elegans Under Relaxed Selection, Joanna Joyner-Matos, Kiley A. Hicks, Dustin Cousins, Michelle Keller, Dee R. Denver, Charles F. Baer, Suzanne Estes

Biology Faculty Publications

We explored the relationship between relaxed selection, oxidative stress, and spontaneous mutation in a set of mutation-accumulation (MA) lines of the nematode Caenorhabditis elegans and in their common ancestor. We measured steady-state levels of free radicals and oxidatively damaged guanosine nucleosides in the somatic tissues of five MA lines for which nuclear genome base substitution and GC-TA transversion frequencies are known. The two markers of oxidative stress are highly correlated and are elevated in the MA lines relative to the ancestor; point estimates of the per-generation rate of mutational decay (DM) of these measures of oxidative stress are similar to …

Germline Transgenic Methods For Tracking Cells And Testing Gene Function During Regeneration In The Axolotl, Shahryar Khattak, Maritta Schuez, Tobias Richter, Dunja Knapp, Saori L. Haigo, Tatiana Sandoval-Guzmán, Kristyna Hradlikova, Annett Duemmler, Ryan R. Kerney, Elly M. Tanaka

Biology Faculty Publications

The salamander is the only tetrapod that regenerates complex body structures throughout life. Deciphering the underlying molecular processes of regeneration is fundamental for regenerative medicine and developmental biology, but the model organism had limited tools for molecular analysis. We describe a comprehensive set of germline transgenic strains in the laboratory-bred salamander Ambystoma mexicanum(axolotl) that open up the cellular and molecular genetic dissection of regeneration. We demonstrate tissue-dependent control of gene expression in nerve, Schwann cells, oligodendrocytes, muscle, epidermis, and cartilage. Furthermore, we demonstrate the use of tamoxifen-induced Cre/loxP-mediated recombination to indelibly mark different cell types. Finally, we inducibly …

Use Of Image Cytometry For Quantification Of Pathogenic Fungi In Association With Host Cells, Charlotte A. Berkes, Leo Li-Ying Chan, Alisha Wilkinson, Benjamin Paradis

Biology Faculty Publications

Studies of the cellular pathogenesis mechanisms of pathogenic yeasts such as Candida albicans, Histoplasma capsulatum, and Cryptococcus neoformans commonly employ infection of mammalian hosts or host cells (i.e. macrophages) followed by yeast quantification using colony forming unit analysis or flow cytometry. While colony forming unit enumeration has been the most commonly used method in the field, this technique has disadvantages and limitations, including slow growth of some fungal species on solid media and low and/or variable plating efficiencies, which is of particular concern when comparing growth of wild-type and mutant strains. Flow cytometry can provide rapid quantitative information regarding yeast …

Stromal Tumor Microenvironment In Chronic Lymphocytic Leukemia: Regulation Of Leukemic Progression, Ashima Shukla, Nagendra K. Chaturvedi, Adam K. Ahrens, Christine E. Cutucache, Amit K. Mittal, Philip Bierman, Dennis D. Weisenburger, Runqing Lu, Shantaram S. Joshi

Biology Faculty Publications

Chronic Lymphocytic Leukemia (CLL), the most prevalent adult leukemia in western countries, which is highly heterogeneous with a very variable clinical outcome. Emerging evidence indicates that the stromal tumor microenvironment (STME) and stromal associated genes (SAG) play important roles in the pathogenesis and progression of CLL. However, the precise mechanisms by which STME and SAG are involved in this process remain unknown. In an attempt to explore the role of STME in this process, we examined the expression levels of stromal associated genes using gene expression profiling (GEP) of CLL cells from lymph nodes (LN) (n=15), bone marrow (BM) (n=18), …

Behavioral And Neurogenomic Transcriptome Changes In Wild-Derived Zebrafish With Fluoxetine Treatment, Ryan Y. Wong, Sarah E. Oxendine, John Godwin

Biology Faculty Publications

Background: Male and female vertebrates typically differ in a range of characteristics, from morphology to physiology to behavior, which are influenced by factors such as the social environment and the internal hormonal and genetic milieu. However, sex differences in gene expression profiles in the brains of vertebrates are only beginning to be understood. Fishes provide a unique complement to studies of sex differences in mammals and birds given that fish show extreme plasticity and lability of sexually dimorphic characters and behaviors during development and even adulthood. Hence, teleost models can give additional insight into sexual differentiation. The goal of …

Species Boundaries And Biogeography Of East African Torrent Frogs Of The Genus Petropedetes (Amphibia: Anura: Petropeditidae), Simon P. Loader, F. Sara Ceccarelli, Mark Wilkinson, Michele Menegon, Jean Mariaux, Rafael O. De Sá, Et Al.

Biology Faculty Publications

Based on morphology there are currently three described East African species of torrent frogs belonging to the tropical African genus Petropedetes (P. dutoiti, P. martiennseni and P. yakusini). Taxonomic uncertainties are evident within this group: a putative new species reported from the Nguru Mountains and the species P. yakusini have a fragmented distribution across the Southern Tanzanian highlands. We conducted a molecular systematic study, sampling populations of East African petropedetids occurring in the mountains of Tanzania (P. martiennseni and P. yakusini), to investigate species boundaries and biogeography. Data provide evidence for the recognition of …

The Identity Of Rana Margaritifera Laurenti, 1768 (Anura, Bufonidae), Esteban O. Lavilla, Ulisses Caramaschi, José A. Langone, José P. Pombal Jr., Rafael O. De Sá

Biology Faculty Publications

Rana margaritifera was described by Laurenti in 1768 and currently is associated to the genus Rhinella, under the combination Rhinella margaritifera. Currently, the R. margaritifera species group consists of 16 recognized species. Further-more, many additional species have been suggested to exist in this group which highlights the ambiguity surrounding the identity of Rhinella margaritifera and impend further description of the species in this group. After an exhaustive bibliographic review, we concluded that the recent designation of a lectotype for R. margaritifera is invalid according with Art. 73, ICZN, 1999. Herein, we designate and provide the description of a …

A Hands-On Activity To Introduce The Effects Of Transmission By An Invasive Species, Barbara May

Biology Faculty Publications

This activity engages students to better understand the impact of transmission by invasive species. Using dice, poker chips, and paper plates, an entire class mimics the spread of an invasive species within a geographic region. The activity can be modified and conducted at the K-16 levels.

Engaging Students In A Bioinformatics Activity To Introduce Gene Structure And Function, Barbara J. May

Biology Faculty Publications

Bioinformatics spans many fields of biological research and plays a vital role in mining and analyzing data. Therefore, there is an ever-increasing need for students to understand not only what can be learned from this data, but also how to use basic bioinformatics tools. This activity is designed to provide secondary and undergraduate biology students to a hands-on activity meant to explore and understand gene structure with the use of basic bioinformatic tools. Students are provided an “unknown” sequence from which they are asked to use a free online gene finder program to identify the gene. Students then predict the …

Unexpected Phylogenetic Positions Of The Genera Rupirana And Crossodactylodes Reveal Insights Into The Biogeography And Reproductive Evolution Of Leptodactylid Frogs, Antoine Foquet, Boris Leonardo Blotto, Maximiliano Manuel Maronna, Vanessa Kruth Verdade, Flora Acuña Juncá, Rafael O. De Sá, Miguel Trefaut Rodrigues

Biology Faculty Publications

Despite major progress in deciphering the amphibian tree of life by molecular phylogenetics, we identified two questions remaining to be answered regarding relationships within Hyloidea, the clade of South American origin that comprises most extant anuran diversity. A few genera like Rupirana and Crossodactylodes have enigmatic phylogenetic positions, and relationships among major lineages within some families like Leptodactylidae remain ambiguous. To resolve these specific questions we used two approaches (1) a complete matrix approach representing >6.6 kb, including most major Hyloidea lineages (61 terminals) combining different methods of phylogenetic reconstruction and measures of node support; and (2) a supermatrix approach …

Using Rnai In C. Elegans To Demonstrate Gene Knockdown Phenotypes In The Undergraduate Biology Lab Setting, Nicole M. Roy

Biology Faculty Publications

RNA interference (RNAi) is a powerful technology used to knock down genes in basic research and medicine. In 2006 RNAi technology using Caenorhabditis elegans (C. elegans) was awarded the Nobel Prize in medicine and thus students graduating in the biological sciences should have experience with this technology. However, students struggle conceptually with the molecular biology behind the RNAi technology and find the technology difficult to grasp. To this end, we have provided a simple, streamlined and inexpensive RNAi procedure using C. elegans that can be adopted in upper level biology classes. By using an unknown RNAi-producing bacteria, students perform novel …

Salamander Hox Clusters Contain Repetitive Dna And Expanded Non-Coding Regions: A Typical Hox Structure For Non-Mammalian Tetrapod Vertebrates?, Stephen Randal Voss, Srikrishna Putta, John A. Walker, Jeramiah J. Smith, Nobuyasu Maki, Panagiotis A. Tsonis

Biology Faculty Publications

Hox genes encode transcription factors that regulate embryonic and post-embryonic developmental processes. The expression of Hox genes is regulated in part by the tight, spatial arrangement of conserved coding and non-coding sequences. The potential for evolutionary changes in Hox cluster structure is thought to be low among vertebrates; however, recent studies of a few non-mammalian taxa suggest greater variation than originally thought. Using next generation sequencing of large genomic fragments (>100 kb) from the red spotted newt (Notophthalamus viridescens), we found that the arrangement of Hox cluster genes was conserved relative to orthologous regions from other vertebrates, but the …

Sprague's Pipit In Clay County, Philip Chu

Biology Faculty Publications

No abstract provided.

The Advertisement Calls And Distribution Of Two Sympatric Species Of Chiasmocleis (Méhely 1904) (Anura, Microhylidae, Gastrophryninae) From The Atlantic Forest, Mauricio C. Florani, Caio Vinicus De Mira Mendes, Iuri Ribeiro Dias, Danilo Silva Ruas, João Fillipe Riva Tonini, Rafael O. De Sá

Biology Faculty Publications

The advertisement calls of Chiasmocleis cordeiroi and C. crucis are described for populations from the municipalities of Igrapiúna and Camacan, respectively, state of Bahia, Brazil. Both calls consist of multipulsed notes produced in series. Differences between the two calls are: dominant frequency, higher in C. cordeiroi (range 4500–4898 Hz; C. crucis range 4069–4435 Hz); note rate, higher in C. cordeiroi (range 6.20–7.46 s/note; C. crucis range 5.17–5.59 s/note); pulse rate, higher in C. cordeiroi (151.82–194.83 s/note; C. crucis range 125.30– 142.12 s/note); and the structure of the modulation patterns of the notes. Moreover, the advertisement calls of C. crucis and …

The Advertisement Calls And Distribution Of Two Sympatric Species Of Chiasmocleis (Méhely 1904) (Anura, Microhylidae, Gastrophryninae) From The Atlantic Forest, Maruicio C. Forlani, Caio Vinicius De Mira Mendes, Iuri Ribeiro Dias, Danilo Silva Ruas, João Filipe Riva Tonini, Rafael O. De Sá

Biology Faculty Publications

The advertisement calls of Chiasmocleis cordeiroi and C. crucis are described for populations from the municipalities of Igrapiúna and Camacan, respectively, state of Bahia, Brazil. Both calls consist of multipulsed notes produced in series. Differences between the two calls are: dominant frequency, higher in C. cordeiroi (range 4500-4898 Hz; C. crucis range 4069-4435 Hz); note rate, higher in C. cordeiroi (range 6.20--7.46 s/note; C. crucis range 5.17-5.59 s/note); pulse rate, higher in C. cordeiroi (151.82-194.83 s/note; C. crucis range 125.30- 142.12 s/note); and the structure of the modulation patterns of the notes. Moreover, the advertisement calls of C. crucis and …

Redbuds And Legumes Subfamilies, W. John Hayden

Biology Faculty Publications

Although legumes constitute one of the largest families of flowering plants in the world, and despite 25 years of celebrating Virginia’s wildflowers, redbud (Cercis canadensis) is the first legume to be recognized as a VNPS Wildflower of the Year. This article addresses the relationships of Cercis with the rest of the legumes (family Fabaceae, or Leguminosae in older literature).

Opposing Mechanisms Drive Richness Patterns Of Core And Transient Bird Species, Jessica R. Coyle, Allen H. Hurlbert, Ethan P. White

Biology Faculty Publications

Studies of biodiversity typically assume that all species are equivalent. However, some species in a community maintain viable populations in the study area, while others occur only occasionally as transient individuals. Here we show that North American bird communities can reliably be divided into core and transient species groups and that the richness of each group is driven by different processes. The richness of core species is influenced primarily by local environmental conditions, while the richness of transient species is influenced primarily by the heterogeneity of the surrounding landscape. This demonstrates that the well-known effects of the local environment and …

The Space Age Sugar Shack, Stephen G. Saupe

Biology Faculty Publications

No abstract provided.

Rectal Transmission Of Transmitted/Founder Hiv-1 Is Efficiently Prevented By Topical 1% Tenofovir In Blt Humanized Mice, Morgan L. Chateau, Paul W. Denton, Michael D. Swanson, Ian Mcgowan, J. Victor Garcia

Biology Faculty Publications

Rectal microbicides are being developed to prevent new HIV infections in both men and women. We focused our in vivo preclinical efficacy study on rectally-applied tenofovir. BLT humanized mice (n = 43) were rectally inoculated with either the primary isolate HIV-1JRCSF or the MSM-derived transmitted/founder (T/F) virus HIV-1THRO within 30 minutes following treatment with topical 1% tenofovir or vehicle. Under our experimental conditions, in the absence of drug treatment we observed 50% and 60% rectal transmission by HIV-1JRCSF and HIV-1THRO, respectively. Topical tenofovir reduced rectal transmission to 8% (1/12; log rank p = 0.03) for HIV-1JRCSF and 0% (0/6; log …

Teaching Physiology Online: Successful Use Of Case Studies In A Graduate Course, Giovanni Casotti, John T. Beneski, Maureen T. Knabb

Biology Faculty Publications

No abstract provided.

Sequencing Of The Sea Lamprey (Petromyzon Marinus) Genome Provides Insights Into Vertebrate Evolution, Jeramiah J. Smith, Shigehiro Kuraku, Carson Holt, Tatjana Sauka-Spengler, Ning Jiang, Michael S. Campbell, Mark D. Yandell, Tereza Manousaki, Axel Meyer, Ona E. Bloom, Jennifer R. Morgan, Joseph D. Buxbaum, Ravi Sachidanandam, Carrie Sims, Alexander S. Garruss, Malcolm Cook, Robb Krumlauf, Leanne M. Wiedemann, Stacia A. Sower, Wayne A. Decatur, Jeffrey A. Hall, Chris T. Amemiya, Nil R. Saha, Katherine M. Buckley, Jonathan P. Rast, Sabyasachi Das, Masayuki Hirano, Nathanael Mccurley, Peng Guo, Nicolas Rohner, Clifford J. Tabin, Paul Piccinelli, Greg Elgar, Magali Ruffier, Bronwen L. Aken, Stephen M.J. Searle, Matthieu Muffato, Miguel Pignatelli, Javier Herrero, Matthew Jones, C. Titus Brown, Yu-Wen Chung-Davidson, Kaben G. Nanlohy, Scot V. Libants, Chu-Yin Yeh, David W. Mccauley, James A. Langeland, Zeev Pancer, Bernd Fritzsch, Pieter J. De Jong, Baoli Zhu, Lucinda L Fulton, Brenda Theising, Paul Flicek, Marianne E. Bronner, Wesley C. Warren, Sandra W. Clifton, Richard K. Wilson, Weiming Li

Biology Faculty Publications

Lampreys are representatives of an ancient vertebrate lineage that diverged from our own ∼500 million years ago. By virtue of this deeply shared ancestry, the sea lamprey (P. marinus) genome is uniquely poised to provide insight into the ancestry of vertebrate genomes and the underlying principles of vertebrate biology. Here, we present the first lamprey whole-genome sequence and assembly. We note challenges faced owing to its high content of repetitive elements and GC bases, as well as the absence of broad-scale sequence information from closely related species. Analyses of the assembly indicate that two whole-genome duplications likely occurred …

The Advertisement Call Of The Poorly Known Leptodactylus Tapiti (Anura, Leptodactylidae), Reuber Albuquerque Brandão, Guilherme Fajardo Roldão Álvares, Rafael O. De Sá

Biology Faculty Publications

The genus Leptodactylus consists of approximately 80 species distributed in four nominal groups (Frost 2011). The fuscus group harbors approximately 30 small species with terrestrial nests, deposited in male built burrows on soft soils. Leptodactylus tapiti Sazima & Bokermann 1978 was described from Veadeiros, currently Alto Paraíso municipality, Goiás State, Brazil. The species is restricted to the region of Chapada dos Veadeiros (Frost 2011), where it occurs in areas of water-saturated soils associated with open fields (Sazima & Bokermann 1978). Since its original description, nothing was published about the species, and its advertisement call remains unknown. Herein, we describe its …

S-Adenosyl-L-Methionine Protects The Probiotic Yest, Saccharomyces Boulardii, From Acid-Induced Cell Death, Nicanor Austriaco, Vincent Cascio, Daniel Gittings, Kristen Merloni, David Laprade

Biology Faculty Publications

Background

Saccharomyces boulardii is a probiotic yeast routinely used to prevent and to treat gastrointestinal disorders, including the antibiotic-associated diarrhea caused by Clostridium difficile infections. However, only 1-3% of the yeast administered orally is recovered alive in the feces suggesting that this yeast is unable to survive the acidic environment of the gastrointestinal tract.

Results

We provide evidence that suggests that S. boulardii undergoes programmed cell death (PCD) in acidic environments, which is accompanied by the generation of reactive oxygen species and the appearance of caspase-like activity. To better understand the mechanism of cell death at the molecular level, we …

Sensory Exploitation And Indicator Models May Explain Red Pelvic Spines In The Brook Stickleback, Culaea Inconstans, Andrew Hodgson, A. Ross Black, Ryan Hull

Biology Faculty Publications

Background: Sensory bias models explaining the evolution of sexually selected traits predict that trait preferences evolve as an artifact of a pre-existing preference for certain components of the environment such as specifically coloured prey. Indicator models, in contrast, predict that sexually selected traits indicate mate condition. We investigate the potential for sensory exploitation and condition indication models to explain the evolution of what appears to be a recently evolved sexually selected trait. Question: Did red pelvic spine coloration in male Turnbull National Wildlife Refuge (TNWR) brook stickleback (Culaea inconstans) evolve to exploit a pre-existing sensory bias for red prey, thus …

A Microarray Analysis Of Gene Expression Patterns During Early Phases Of Newt Lens Regeneration, Konstantinos Sousounis, Christian S. Michel, Marc Bruckskotten, Nobuyasu Maki, Thilo Borchardt, Thomas Braun, Mario Looso, Panagiotis A. Tsonis

Biology Faculty Publications

Purpose: Notophthalmus viridescens, the red-spotted newt, possesses tremendous regenerative capabilities. Among the tissues and organs newts can regenerate, the lens is regenerated via transdifferentiation of the pigment epithelial cells of the dorsal iris, following complete removal (lentectomy). Under normal conditions, the same cells from the ventral iris are not capable of regenerating. This study aims to further understand the initial signals of lens regeneration.

Differential Responses Of Ammonia-Oxidizing Archaea And Bacteria To Long-Term Fertilization In A New England Salt Marsh., Xuefeng Peng, Erik Yando, Erica Hiildebrand, Courtney Dwyer, Anne Kearney, Alex Waciega, Ivan Valiela, Anne E. Bernhard

Biology Faculty Publications

Since the discovery of ammonia-oxidizing archaea (AOA), new questions have arisen about population and community dynamics and potential interactions between AOA and ammonia-oxidizing bacteria (AOB). We investigated the effects of long-term fertilization on AOA and AOB in the Great Sippewissett Marsh, Falmouth, MA, USA to address some of these questions. Sediment samples were collected from low and high marsh habitats in July 2009 from replicate plots that received low (LF), high (HF), and extra high (XF) levels of a mixed NPK fertilizer biweekly during the growing season since 1974. Additional untreated plots were included as controls (C). Terminal restriction fragment …

Revisiting The Relationship Between Regenerative Ability And Aging, Ashley W. Seifert, S. Randal Voss

Biology Faculty Publications

Contrary to the longstanding view that newts (Notophthalamus viridescens), but not axolotls (Ambystoma mexicanum), can regenerate a lens, a recent report in BMC Biology by Panagiotis Tsonis and colleagues shows axolotls indeed possess this ability during early larval stages. In contrast, they show that zebrafish never posses this ability, even as embryos. This underscores the importance of comparing regenerative ability across species and reinforces the need to consider organ regeneration in the context of evolution, development, and aging.

Long-Term Data For Endemic Frog Genera Reveal Potential Conservation Crisis In The Bale Mountains, Ethiopia, David J. Gower, Roman K. Aberra, Silvia Schwaller, Malcolm J. Largen, Ben Collen, Stephen Spawls, Michele Menegon, Breda M. Zimkus, Rafael O. De Sá, Et Al.

Biology Faculty Publications

Populations of many frogs have declined alarmingly in recent years, placing nearly one third of the > 6,000 species under threat of extinction. Declines have been attributed largely to habitat loss, environmental degradation and/or infectious diseases such as chytridiomycosis. Many frogs undergo dramatic natural population fluctuations such that long-term data are required to determine population trends without undue influence of stochastic factors. We present long-term quantitative data (individuals encountered per person hour of searching) for four monotypic frog genera endemic to an Afromontane region of exceptional importance but growing conservation concern: one endemic to the Ethiopian highlands (Spinophrynoides osgoodi) and three …

Ovarian Cycle Activity Varies With Respect To Age And Social Status In Free-Ranging Elephants In Addo Elephant National Park, South Africa, Elizabeth Freeman, Jordana Meyer, Sarah Putman, Bruce A. Schulte, Janine Brown

Biology Faculty Publications

Free-ranging African elephants live in a fission–fusion society, at the centre of which is the matriarch. Matriarchs are generally older females that guide their families to resources and co-ordinate group defense. While much is known about elephant society, knowledge is generally lacking about how age affects the physiology of wild elephants. Investigation of the ovarian activity of free-ranging elephants could provide insight into the reproductive ageing process, with implications for population management. Faecal samples were collected from 46 individuals ranging in age from 14 to 60 years for a 2-year period, and progestagen metabolite analyses were used to examine relationships …