Biology Commons^™

Reconstruction Of Family-Level Phylogenetic Relationships Within Demospongiae (Porifera) Using Nuclear Encoded Housekeeping Genes, Malcolm S. Hill, April Hill, Jose Lopez, Kevin J. Peterson

Dartmouth Scholarship

Background: Demosponges are challenging for phylogenetic systematics because of their plastic and relatively simple morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of cellular functions from a diverse group of sponges.

Methodology/Principal Findings: We generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21 newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically defined taxa: Keratosap, Myxospongiaep, Spongillidap, Haploscleromorphap (the …

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.

Metabolism Of Brain Cortex And Cardiac Muscle Mitochondria In Hibernating 13-Lined Ground Squirrels Ictidomys Tridecemlineatus., Kirsten Gallagher, James F Staples

Biology Publications

During bouts of torpor, mitochondrial metabolism is known to be suppressed in the liver and skeletal muscle of hibernating mammals. This suppression is rapidly reversed during interbout euthermic (IBE) phases, when whole-animal metabolic rate and body temperature (T(b)) return spontaneously to euthermic levels. Such mitochondrial suppression may contribute significantly to energy savings, but the capacity of other tissues to suppress mitochondrial metabolism remains unclear. In this study we compared the metabolism of mitochondria from brain cortex and left ventricular cardiac muscle between animals sampled while torpid (stable T(b) near 5°C) and in IBE (stable T(b) near 37°C). Instead of isolating …

Genomics Of A Metamorphic Timing Qtl: Met1 Maps To A Unique Genomic Position And Regulates Morph And Species-Specific Patterns Of Brain Transcription, Robert B. Page, Meredith A. Boley, David K. Kump, Stephen R. Voss

Biology Faculty Publications

Very little is known about genetic factors that regulate life history transitions during ontogeny. Closely related tiger salamanders (Ambystoma species complex) show extreme variation in metamorphic timing, with some species foregoing metamorphosis altogether, an adaptive trait called paedomorphosis. Previous studies identified a major effect quantitative trait locus (met1) for metamorphic timing and expression of paedomorphosis in hybrid crosses between the biphasic Eastern tiger salamander (Ambystoma tigrinum tigrinum) and the paedomorphic Mexican axolotl (Ambystoma mexicanum). We used existing hybrid mapping panels and a newly created hybrid cross to map the met1 genomic region and …

Vegf And Angiopoietin-1 Exert Opposing Effects On Cell Junctions By Regulating The Rho Gef Syx, Siu P. Ngok, Rory Geyer, Miaoliang Liu, Antonis Kourtidis, Sudesh Agrawal, Chuanshen Wu, Himabindu Reddy Seerapu, Laura J. Lewis-Tuffin, Karen L. Moodie, Deborah Huveldt, Ruth Marx, Jay M. Baraban, Peter Storz, Arie Horowitz, Panos Z. Anastasiadis

Dartmouth Scholarship

Vascular endothelial growth factor (VEGF) and Ang1 (Angiopoietin-1) have opposing effects on vascular permeability, but the molecular basis of these effects is not fully known. We report in this paper that VEGF and Ang1 regulate endothelial cell (EC) junctions by determining the localization of the RhoA-specific guanine nucleotide exchange factor Syx. Syx was recruited to junctions by members of the Crumbs polarity complex and promoted junction integrity by activating Diaphanous. VEGF caused translocation of Syx from cell junctions, promoting junction disassembly, whereas Ang1 maintained Syx at the junctions, inducing junction stabilization. The VEGF-induced translocation of Syx from EC junctions was …

Toward The Beginning Of Time: Circadian Rhythms In Metabolism Precede Rhythms In Clock Gene Expression In Mouse Embryonic Stem Cells, Jiffin K. Paulose, Edmund B. Rucker Iii, Vincent M. Cassone

Biology Faculty Publications

The appearance, progression, and potential role for circadian rhythms during early development have previously focused mainly on the suprachiasmatic nucleus (SCN) and peri- and postnatal expression of canonical clock genes. More recently, gene expression studies in embryonic stem cells have shown that some clock genes are expressed in undifferentiated cells; however rhythmicity was only established when cells are directed toward a neural fate. These studies also concluded that a functional clock is not present in ESCs, based solely on their gene expression. The null hypothesis underlying the present study is that embryonic stem cells become rhythmic in both clock gene …

Roles Of The Drosophila Sk Channel (Dsk) In Courtship Memory, Ahmad N. Abou Tayoun, Claudio Pikielny, Patrick J. Dolph

Dartmouth Scholarship

A role for SK channels in synaptic plasticity has been very well-characterized. However, in the absence of simple genetic animal models, their role in behavioral memory remains elusive. Here, we take advantage of Drosophila melanogaster with its single SK gene (dSK) and well-established courtship memory assay to investigate the contribution of this channel to memory. Using two independent dSK alleles, a null mutation and a dominant negative subunit, we show that while dSK negatively regulates the acquisition of short-term memory 30 min after a short training session, it is required for normal long-term memory 24 h after extended …

Skin Regeneration In Adult Axolotls: A Blueprint For Scar-Free Healing In Vertebrates, Ashley W. Seifert, James R. Monaghan, S. Randal Voss, Malcolm Maden

Biology Faculty Publications

While considerable progress has been made towards understanding the complex processes and pathways that regulate human wound healing, regenerative medicine has been unable to develop therapies that coax the natural wound environment to heal scar-free. The inability to induce perfect skin regeneration stems partly from our limited understanding of how scar-free healing occurs in a natural setting. Here we have investigated the wound repair process in adult axolotls and demonstrate that they are capable of perfectly repairing full thickness excisional wounds made on the flank. In the context of mammalian wound repair, our findings reveal a substantial reduction in hemostasis, …

Environmentally Realistic Exposure To The Herbicide Atrazine Alters Some Sexually Selected Traits In Male Guppies, Kausalya Shenoy

Biology Faculty Publications

Male mating signals, including ornaments and courtship displays, and other sexually selected traits, like male-male aggression, are largely controlled by sex hormones. Environmental pollutants, notably endocrine disrupting compounds, can interfere with the proper functioning of hormones, thereby impacting the expression of hormonally regulated traits. Atrazine, one of the most widely used herbicides, can alter sex hormone levels in exposed animals. I tested the effects of environmentally relevant atrazine exposures on mating signals and behaviors in male guppies, a sexually dimorphic freshwater fish. Prolonged atrazine exposure reduced the expression of two honest signals: the area of orange spots (ornaments) and the …

Creation Of A Natural History Information Database With Mobile Device Access For The Pace Campus In Pleasantville, Joshua J. Schwartz, Martina Blackwood

Cornerstone 3 Reports : Interdisciplinary Informatics

No abstract provided.

Testing Phylogenetic Hypotheses Of The Subgenera Of The Freshwater Crayfish Genus Cambarus (Decapoda: Cambaridae)., Jesse W Breinholt, Megan L Porter, Keith A Crandall

Computational Biology Institute

BACKGROUND: The genus Cambarus is one of three most species rich crayfish genera in the Northern Hemisphere. The genus has its center of diversity in the Southern Appalachians of the United States and has been divided into 12 subgenera. Using Cambarus we test the correspondence of subgeneric designations based on morphology used in traditional crayfish taxonomy to the underlying evolutionary history for these crayfish. We further test for significant correlation and explanatory power of geographic distance, taxonomic model, and a habitat model to estimated phylogenetic distance with multiple variable regression.

METHODOLOGY/PRINCIPAL FINDINGS: We use three mitochondrial and one nuclear gene …

Minimum Cost Of Transport In Asian Elephants: Do We Really Need A Bigger Elephant?, V. A. Langman, M. F. Rowe, T. J. Roberts, N. V. Langman, C. R. Taylor

Dartmouth Scholarship

Body mass is the primary determinant of an animal’s energy requirements. At their optimum walking speed, large animals have lower mass-specific energy requirements for locomotion than small ones. In animals ranging in size from 0.8 g (roach) to 260 kg (zebu steer), the minimum cost of transport (COT_min) decreases with increasing body size roughly as COT_min∝body mass (M_b)^{–0.316±0.023} (95% CI). Typically, the variation of COT_min with body mass is weaker at the intraspecific level as a result of physiological and geometric similarity within closely related species. The interspecific relationship estimates that …

Demasculinization And Feminization Of Male Gonads By Atrazine: Consistent Effects Across Vertebrate Classes, Krista A. Mccoy

Integrative Biology Faculty and Staff Publications

Atrazine is the most commonly detected pesticide contaminant of ground water, surface water, and precipitation. Atrazine is also an endocrine disruptor that, among other effects, alters male reproductive tissues when animals are exposed during development. Here, we apply the nine so-called “Hill criteria” (Strength, Consistency, Specificity, Temporality, Biological Gradient, Plausibility, Coherence, Experiment, and Analogy) for establishing cause–effect relationships to examine the evidence for atrazine as an endocrine disruptor that demasculinizes and feminizes the gonads of male vertebrates. We present experimental evidence that the effects of atrazine on male development are consistent across all vertebrate classes examined and we present a …

Cooperative And Antagonistic Contributions Of Two Heterochromatin Proteins To Transcriptional Regulation Of The Drosophila Sex Determination Decision, Hui Li, Janel Rodriguez, Youngdong Yoo, Momin Mohammed Shareef, Ramakrishna Badugu, Jamila I. Horabin, Rebecca Kellum

Biology Faculty Publications

Eukaryotic nuclei contain regions of differentially staining chromatin (heterochromatin), which remain condensed throughout the cell cycle and are largely transcriptionally silent. RNAi knockdown of the highly conserved heterochromatin protein HP1 in Drosophila was previously shown to preferentially reduce male viability. Here we report a similar phenotype for the telomeric partner of HP1, HOAP, and roles for both proteins in regulating the Drosophila sex determination pathway. Specifically, these proteins regulate the critical decision in this pathway, firing of the establishment promoter of the masterswitch gene, Sex-lethal (Sxl). Female-specific activation of this promoter, Sxl(Pe), is essential to females, as it provides SXL …

Septin Filaments Exhibit A Dynamic, Paired Organization That Is Conserved From Yeast To Mammals, Bradley S. Demay, Xiaobo Bai, Louisa Howard, Patricia Occhipinti, Rebecca A. Meseroll, Elias T. Spiliotis, Rudolf Oldenbourg, Amy S. Gladfelter

Dartmouth Scholarship

The septins are conserved, GTP-binding proteins important for cytokinesis, membrane compartmentalization, and exocytosis. However, it is unknown how septins are arranged within higher-order structures in cells. To determine the organization of septins in live cells, we developed a polarized fluorescence microscopy system to monitor the orientation of GFP dipole moments with high spatial and temporal resolution. When GFP was fused to septins, the arrangement of GFP dipoles reflected the underlying septin organization. We demonstrated in a filamentous fungus, a budding yeast, and a mammalian epithelial cell line that septin proteins were organized in an identical highly ordered fashion. Fluorescence anisotropy …

Episodic Radiations In The Fly Tree Of Life, Brian M. Wiegmann, Michelle D. Trautwein, Isaac S. Winkler, Norman B. Barr, Jung-Wook Kim, Christine Lambkin, Matthew Bertone, Brian Cassel, Keith Bayless, Alysha Heimberg

Dartmouth Scholarship

Flies are one of four superradiations of insects (along with beetles, wasps, and moths) that account for the majority of animal life on Earth. Diptera includes species known for their ubiquity (Musca domestica house fly), their role as pests (Anopheles gambiae malaria mosquito), and their value as model organisms across the biological sciences (Drosophila melanogaster). A resolved phylogeny for flies provides a framework for genomic, developmental, and evolutionary studies by facilitating comparisons across model organisms, yet recent research has suggested that fly relationships have been obscured by multiple episodes of rapid diversification. We provide a phylogenomic …

Structure/Function Assessment Of Synapses At Motor Nerve Terminals, Andrew Fredericks Moser Johnstone, Kert Viele, Robin L. Cooper

Biology Faculty Publications

The release of transmitter at neuromuscular junctions (NMJ) of the opener muscle in crayfish is quantal in nature. This NMJ offers the advantage of being able to record quantal events at specific visually identified release sites, thus allowing measurement of the physiological parameters of vesicle release and its response to be directly correlated with synaptic structure.

These experiments take advantage of areas between the varicosities on the nerve terminal that we define as "stems." Stems were chosen as the region to study because of their low synaptic output due to fewer synaptic sites. Through 3D reconstruction from hundreds of serial …

Micrornas Reveal The Interrelationships Of Hagfish, Lampreys, And Gnathostomes And The Nature Of The Ancestral Vertebrate, Alysha M. Heimberg, Richard Cowper-Sal{Middle Dot}Lari, Marie Semon, Philip C. J. Donoghue, Kevin J. Peterson

Dartmouth Scholarship

Hagfish and lampreys are the only living representatives of the jawless vertebrates (agnathans), and compared with jawed vertebrates (gnathostomes), they provide insight into the embryology, genomics, and body plan of the ancestral vertebrate. However, this insight has been obscured by controversy over their interrelationships. Morphological cladistic analyses have identified lampreys and gnathostomes as closest relatives, whereas molecular phylogenetic studies recover a monophyletic Cyclostomata (hagfish and lampreys as closest relatives). Here, we show through deep sequencing of small RNA libraries, coupled with genomic surveys, that Cyclostomata is monophyletic: hagfish and lampreys share 4 unique microRNA families, 15 unique paralogues of more …

Invasive Predators Deplete Genetic Diversity Of Island Lizards, Amandine Gasc, M. C. Duryea, Robert M. Cox, Andrew Kern, Ryan Calsbeek

Dartmouth Scholarship

Invasive species can dramatically impact natural populations, especially those living on islands. Though numerous examples illustrate the ecological impact of invasive predators, no study has examined the genetic consequences for native populations subject to invasion. Here we capitalize on a natural experiment in which a long-term study of the brown anole lizard (Anolis sagrei) was interrupted by rat invasion. An island population that was devastated by rats recovered numerically following rat extermination. However, population genetic analyses at six microsatellite loci suggested a possible loss of genetic diversity due to invasion when compared to an uninvaded island studied over …

Partitioning Of Minimotifs Based On Function With Improved Prediction Accuracy, Sanguthevar Rajasekaran, Tian Mi, Jerlin Camilus Merlin, Aaron Oommen, Patrick R. Gradie, Martin R. Schiller

Life Sciences Faculty Research

Background

Minimotifs are short contiguous peptide sequences in proteins that are known to have a function in at least one other protein. One of the principal limitations in minimotif prediction is that false positives limit the usefulness of this approach. As a step toward resolving this problem we have built, implemented, and tested a new data-driven algorithm that reduces false-positive predictions.

Methodology/Principal Findings

Certain domains and minimotifs are known to be strongly associated with a known cellular process or molecular function. Therefore, we hypothesized that by restricting minimotif predictions to those where the minimotif containing protein and target protein have …

Temporal Regulation Of The Muscle Gene Cascade By Macho1 And Tbx6 Transcription Factors In Ciona Intestinalis, Jamie E. Kugler, Stefan Gazdoiu, Izumi Oda-Ishii, Yale J. Passamaneck, Albert J. Erives, Anna Di Gregorio

Dartmouth Scholarship

For over a century, muscle formation in the ascidian embryo has been representative of 'mosaic' development. The molecular basis of muscle-fate predetermination has been partly elucidated with the discovery of Macho1, a maternal zinc-finger transcription factor necessary and sufficient for primary muscle development, and of its transcriptional intermediaries Tbx6b and Tbx6c. However, the molecular mechanisms by which the maternal information is decoded by cis-regulatory modules (CRMs) associated with muscle transcription factor and structural genes, and the ways by which a seamless transition from maternal to zygotic transcription is ensured, are still mostly unclear. By combining misexpression assays with CRM analyses, …

Seasonal Hippocampal Plasticity In Food-Storing Birds., David F Sherry, Jennifer S Hoshooley

Psychology Publications

Both food-storing behaviour and the hippocampus change annually in food-storing birds. Food storing increases substantially in autumn and winter in chickadees and tits, jays and nutcrackers and nuthatches. The total size of the chickadee hippocampus increases in autumn and winter as does the rate of hippocampal neurogenesis. The hippocampus is necessary for accurate cache retrieval in food-storing birds and is much larger in food-storing birds than in non-storing passerines. It therefore seems probable that seasonal change in caching and seasonal change in the hippocampus are causally related. The peak in recruitment of new neurons into the hippocampus occurs before birds …

Nip/Duoxa Is Essential For Drosophila Embryonic Development And Regulates Oxidative Stress Response., Xiaojun Xie, Jack Hu, Xiping Liu, Hanjuan Qin, Anthony Percival-Smith, Yong Rao, Shawn S C Li

Biochemistry Publications

NIP/DuoxA, originally cloned as a protein capable of binding to the cell fate determinant Numb in Drosophila, was recently identified as a modulator of reactive oxygen species (ROS) production in mammalian systems. Despite biochemical and cellular studies that link NIP/DuoxA to the generation of ROS through the dual oxidase (Duox) enzyme, the in vivo function of NIP/DuoxA has not been characterized to date. Here we report a genetic and functional characterization of nip in Drosophila melanogaster. We show that nip is essential for Drosophila development as nip null mutants die at the 1(st) larval instar. Expression of UAS-nip, but not …

Proteomic Analysis Of Blastema Formation In Regenerating Axolotl Limbs, Nandini Rao, Deepali Jhamb, Derek J. Milner, Bingbing Li, Fengyu Song, Mu Wang, S. Randal Voss, Mathew Palakal, Michael W. King, Behnaz Saranjami, Holly L.D. Nye, Jo Ann Cameron, David L. Stocum

Biology Faculty Publications

BACKGROUND: Following amputation, urodele salamander limbs reprogram somatic cells to form a blastema that self-organizes into the missing limb parts to restore the structure and function of the limb. To help understand the molecular basis of blastema formation, we used quantitative label-free liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS)-based methods to analyze changes in the proteome that occurred 1, 4 and 7 days post amputation (dpa) through the mid-tibia/fibula of axolotl hind limbs.

RESULTS: We identified 309 unique proteins with significant fold change relative to controls (0 dpa), representing 10 biological process categories: (1) signaling, (2) Ca2+ binding and translocation, (3) transcription, …

Ceramide Kinase Regulates Phospholipase C And Phosphatidylinositol 4, 5, Bisphosphate In Phototransduction, Ujjaini Dasgupta, Takeshi Bamba, Salvatore Chiantia, Pusha Karim, Ahmad N. Abou Tayoun

Dartmouth Scholarship

Phosphoinositide-specific phospholipase C (PLC) is a central effector for many biological responses regulated by G-protein-coupled receptors including Drosophila phototransduction where light sensitive channels are activated downstream of NORPA, a PLCbeta homolog. Here we show that the sphingolipid biosynthetic enzyme, ceramide kinase, is a novel regulator of PLC signaling and photoreceptor homeostasis. A mutation in ceramide kinase specifically leads to proteolysis of NORPA, consequent loss of PLC activity, and failure in light signal transduction. The mutant photoreceptors also undergo activity-dependent degeneration. Furthermore, we show that a significant increase in ceramide, resulting from lack of ceramide kinase, perturbs the membrane microenvironment of …

Time's Arrow Flies Like A Bird: Two Paradoxes For Avian Circadian Biology, Vincent M. Cassone, Jiffin K. Paulose, Melissa G. Whitfield-Rucker, Jennifer L. Peters

Biology Faculty Publications

Biological timekeeping in birds is a fundamental feature of avian physiology, behavior and ecology. The physiological basis for avian circadian rhythmicity has pointed to a multi-oscillator system of mutually coupled pacemakers in the pineal gland, eyes and hypothalamic suprachiasmatic nuclei (SCN). In passerines, the role of the pineal gland and its hormone melatonin is particularly important. More recent molecular biological studies have pointed to a highly conserved mechanism involving rhythmic transcription and translation of "clock genes". However, studies attempting to reconcile the physiological role of pineal melatonin with molecular studies have largely failed. Recent work in our laboratory has suggested …

Manipulating Testosterone To Assess Links Between Behavior, Morphology, And Performance In The Brown Anole Anolis Sagrei, Robert M. Cox, Derek S. Stenquist, Justin P. Henningsen, Ryan Calsbeek

Dartmouth Scholarship

Survival and reproductive success are determined by the complex interplay between behavior, physiology, morphology, and performance. When optimal trait combinations along these various phenotypic axes differ between sexes or across seasons, regulatory mechanisms such as sex steroids can often facilitate sex‐specific and/or seasonal trait expression. In this study, we used surgical castration and replacement of exogenous testosterone in adult male brown anoles (Anolis sagrei) to simultaneously examine the effects of testosterone on a suite of morphological (dewlap area, body size), physiological (immune function), behavioral (dewlap, head bob, and push‐up displays), and performance (stamina, sprint speed, bite force) traits. …

Identifying Sleep Regulatory Genes Using A Drosophila Model Of Insomnia, Laurent Seugnet, Yasuko Suzuki, Matthew S. Thimgan, Jeffrey Donlea, Sarah I. Gimbel, Laura Gottschalk, Stephen P. Duntley, Paul J. Shaw

Biological Sciences Faculty Research & Creative Works

Although it is widely accepted that sleep must serve an essential biological function, little is known about molecules that underlie sleep regulation. Given that insomnia is a common sleep disorder that disrupts the ability to initiate and maintain restorative sleep, a better understanding of its molecular underpinning may provide crucial insights into sleep regulatory processes. Thus, we created a line of flies using laboratory selection that share traits with human insomnia. After 60 generations, insomnia-like (ins-l) flies sleep 60 min a day, exhibit difficulty initiating sleep, difficulty maintaining sleep, and show evidence of daytime cognitive impairment. ins-l flies …

N-Acetylcysteine Amide Decreases Oxidative Stress But Not Cell Death Induced By Doxorubicin In H9c2 Cardiomyocytes, Rong Shi, Chuan-Chin Huang, Robert Aronstam, Nuran Ercal, Adam Martin, Yue-Wern Huang

Biological Sciences Faculty Research & Creative Works

Background: While doxorubicin (DOX) is widely used in cancer chemotherapy, long-term severe cardiotoxicity limits its use. This is the first report of the chemoprotective efficacy of a relatively new thiol antioxidant, N-acetylcysteine amide (NACA), on DOX-induced cell death in cardiomyocytes. We hypothesized that NACA would protect H9c2 cardiomyocytes from DOX-induced toxicity by reducing oxidative stress. Accordingly, we determined the ability of NACA to mitigate the cytotoxicity of DOX in H9c2 cells and correlated these effects with the production of indicators of oxidative stress.

Results: DOX at 5 μM induced cardiotoxicity while 1) increasing the generation of reactive oxygen species (ROS), …

Accumulation Of Rhodopsin In Late Endosomes Triggers Photoreceptor Cell Degeneration, Yashodhan Chinchore, Amitavo Mitra, Patrick J. Dolph, Norbert Perrimon

Dartmouth Scholarship

Progressive retinal degeneration is the underlying feature of many human retinal dystrophies. Previous work using Drosophila as a model system and analysis of specific mutations in human rhodopsin have uncovered a connection between rhodopsin endocytosis and retinal degeneration. In these mutants, rhodopsin and its regulatory protein arrestin form stable complexes, and endocytosis of these complexes causes photoreceptor cell death. In this study we show that the internalized rhodopsin is not degraded in the lysosome but instead accumulates in the late endosomes. Using mutants that are defective in late endosome to lysosome trafficking, we were able to show that rhodopsin accumulates …