Biology Commons^™

Reducing The Impact Of Pcr-Mediated Recombination In Molecular Evolution And Environmental Studies Using A New-Generation High-Fidelity Dna Polymerase, Daniel J.G. Lahr, Laura A. Katz

Biological Sciences: Faculty Publications

PCR-mediated recombination can greatly impact estimates of diversity, both in environmental studies and in analyses of gene family evolution. Here we measure chimera (PCR-mediated recombinant) formation by analyzing a mixture of eight partial actin sequences isolated from the amoeba Arcella hemisphaerica amplified under a variety of conditions that mimic standard laboratory situations. We further compare a new-generation proofreading processivity-enhanced polymerase to both a standard proofreading enzyme and previously published results. Proofreading polymerases are preferred over other polymerases in instances where evolutionary inferences must be made. Our analyses reveal that reducing the initial template concentration is as critical as reducing the …

Molecular Data Are Transforming Hypotheses On The Origin And Diversification Of Eukaryotes, Yonas I. Tekle, Laura Wegener Parfrey, Laura A. Katz

Biological Sciences: Faculty Publications

The explosion of molecular data has transformed hypotheses on both the origin of eukaryotes and the structure of the eukaryotic tree of life. Early ideas about the evolution of eukaryotes arose through analyses of morphology by light microscopy and, later, electron microscopy. Though such studies have proven powerful at resolving more recent events, theories on origins and diversification of eukaryotic life have been substantially revised in light of analyses of molecular data including gene and, increasingly, whole-genome sequences. By combining these approaches, progress has been made in elucidating the origin and diversification of eukaryotes. Yet many aspects of the evolution …

Genome-Wide Identification Of H-Ns-Controlled, Temperature-Regulated Genes In Escherichiacoli K-12, Christine A. White-Ziegler, Talya R. Davis

Biological Sciences: Faculty Publications

DNA microarrays demonstrate that H-NS controls 69% of the temperature regulated genes in Escherichia coli K-12. H-NS is shown to be a common regulator of multiple iron and other nutrient acquisition systems preferentially expressed at 37°C and of general stress response, biofilm formation, and cold shock genes highly expressed at 23°C.

Tissue Targeted Embryonic Chimeras: Zebrafish Gastrula Cell Transplantation, Elizabeth R. Deschene, Michael J. Barresi

Biological Sciences: Faculty Publications

Certain fundamental questions in the field of developmental biology can only be answered when cells are placed in novel environments or when small groups of cells in a larger context are altered. Watching how one cell interacts with and behaves in a unique environment is essential to characterizing cell functions. Determining how the localized misexpression of a specific protein influences surrounding cells provides insightful information on the roles that protein plays in a variety of developmental processes. Our lab uses the zebrafish model system to uniquely combine genetic approaches with classical transplantation techniques to generate genotypic or phenotypic chimeras. We …

The Impact Of Repeated Rounds Of Mass Drug Administration With Diethylcarbamazine Plus Albendazole On Bancroftian Filariasis In Papua New Guinea, Gary J. Weil, Will Kastens, Melinda Susapu, Sandra J. Laney, Steven A. Williams, Christopher L. King, James W. Kazura, Moses J. Bockarie

Biological Sciences: Faculty Publications

Background: This study employed various monitoring methods to assess the impact of repeated rounds of mass drug administration (MDA) on bancroftian filariasis in Papua New Guinea, which has the largest filariasis problem in the Pacific region.

Methodology/Principal Findings: Residents of rural villages near Madang were studied prior to and one year after each of three rounds of MDA with diethylcarbamazine plus albendazole administered per World Health Organization (WHO) guidelines. The mean MDA compliance rate was 72.9%. Three rounds of MDA decreased microfilaremia rates (Mf, 1 ml night blood by filter) from 18.6% pre-MDA to 1.3% after the third MDA (a …

Living Where The Flow Is Right: How Flow Affects Feeding In Bryozoans, Marney C. Pratt

Biological Sciences: Faculty Publications

Bryozoans are suspension feeding colonial animals that remain attached to the substratum or other surfaces. How well a bryozoan can feed in a particular flow regime could help determine the distribution and abundance of that bryozoan. I tested how velocity of flow affects feeding rate in four species of bryozoans in the laboratory and how these species perform in different flow regimes in the field. I found that one species, Membranipora membranacea, had a higher ingestion rate than did the other three species at all velocities of flow tested. Membranipora also had a higher rate of ingestion at intermediate velocities, …

Determinants Of Success In National Programs To Eliminate Lymphatic Filariasis: A Perspective Identifying Essential Elements And Research Needs, Dominique Kyelem, Gautam Biswas, Moses J. Bockarie, Mark Bradley, Maged El-Setouhy, Peter U. Fischer, Ralph H. Henderson, James W. Kazura, Patrick J. Lammie, Sammy M. Njenga, Eric A. Ottesen, Kapa Ramaiah, Frank O. Richardson, Gary J. Weil, Steven A. Williams

Biological Sciences: Faculty Publications

The Global Programme to Eliminate Lymphatic Filariasis (GPELF) was launched in 2000. To understand why some national programs have been more successful than others, a panel of individuals with expertise in LF elimination efforts met to assess available data from programs in 8 countries. The goal was to identify: 1) the factors determining success for national LF elimination programs (defined as the rapid, sustained reduction in microfilaremia/ antigenemia after repeated mass drug administration [MDA]); 2) the priorities for operational research to enhance LF elimination efforts.

Of more than 40 factors identified, the most prominent were 1) initial level of LF …

Patterns Of Body And Tail Length And Body Mass In Sciuridae, Virginia Hayssen

Biological Sciences: Faculty Publications

For squirrels, physical size varies with ancestry, locomotion, and sex. Body length has little variation associated with subfamilies or tribes but varies significantly among genera within tribes. Thus, patterns in body size among genera represent more recent evolutionary pressures. Flying squirrels weigh less than similarly sized tree or ground squirrels but ecological profile and ancestry are confounded for flying squirrels. Tail length has clear relationships with ecological profile in squirrels. Tail length is shorter in ground squirrels, longer in tree squirrels, and longest in flying squirrels. In addition, in arboreal squirrels, females have longer tails, relative to body length, than …

A Reverse Transcriptase-Pcr Assay For Detecting Filarial Infective Larvae In Mosquitoes, Sandra J. Laney, Caitlin J. Buttaro, Sabato Visconti, Nils Pilotte, Reda M.R. Ramzy, Gary J. Weil, Steven A. Williams

Biological Sciences: Faculty Publications

Background: Existing molecular assays for filarial parasite DNA in mosquitoes cannot distinguish between infected mosquitoes that contain any stage of the parasite and infective mosquitoes that harbor third stage larvae (L3) capable of establishing new infections in humans. We now report development of a molecular L3-detection assay for Brugia malayi in vectors based on RT-PCR detection of an L3-activated gene transcript.

Methodology/Principal Findings: Candidate genes identified by bioinformatics analysis of EST datasets across the B. malayilife cycle were initially screened by PCR using cDNA libraries as templates. Stage-specificity was confirmed using RNA isolated from infected mosquitoes. Mosquitoes were collected daily …

Reproduction Within Marmotine Ground Squirrels (Sciuridae, Xerinae, Marmotini): Patterns Among Genera, Virginia Hayssen

Biological Sciences: Faculty Publications

The sciurid tribe Marmotini has a distinctive, highly specialized reproductive profile characterized by annually produced litters of many offspring, each of small mass and fast growth rate. However, not all genera of marmotines follow the reproductive profile of the tribe. In fact, included in the tribe are squirrels with the highest and lowest energetic investment into reproduction of the entire family. Because of its large litter size, Ammospermophilus has the largest energetic investment into reproduction of nearly all squirrels. Also, Ammospermophilus is not limited to 1 litter per year. At the opposite extreme, Marmota has the smallest energetic investment into …

Reproductive Effort In Squirrels: Ecological, Phylogenetic, Allometric, And Latitudinal Patterns, Virginia Hayssen

Biological Sciences: Faculty Publications

The distinctive features of reproduction in squirrels are the lack of allometric influences on the duration of reproductive investment; the strong allometric influences on offspring mass; and a trade-off between number and size of young, suggesting an important developmental component to reproduction. Lengths of gestation and lactation do not vary with body size but neonatal and weaning mass do. Apparently, the major constraint on reproduction in squirrels is not resources per se (food, calories, minerals, or water) but rather the length of time such resources are available. Squirrels adjust growth rate to fit the timing of resource abundance. Within the …

Tasting Phenylthiocarbamide (Ptc): A New Integrative Genetics Lab With An Old Flavor, Robert B. Merritt, Lou Ann Bierwert, Barton Slatko, Michael P. Weiner, Jessica Ingram, Kristianna Sciarra, Evan Weiner

Biological Sciences: Faculty Publications

First reported in the early 1930s, variation in the ability to taste phenylthiocarbamide (PTC) has since become one of the most widely studied of all human genetic traits. Guo and Reed (2001) provide an excellent review of work on this polymorphism prior to the identification and sequencing of the PTC gene by Kim et al. (2003), and Wooding (2006) provides a stimulating historical review of the role various scientists have played in the study of PTC taste sensitivity and the importance of these studies in relation to natural selection. Identification of the PTC gene and a number of subsequent …

Human Cardiac-Specific Cdna Array For Idiopathic Dilated Cardiomyopathy: Sex-Related Differences, Georges E. Haddad, Lori J. Saunders, Seth D. Crosby, Maria Carles, Federica Del Monte, Kindra King, Michael R. Bristow, Francis G. Spinale, Thomas E. Macgillivray, Marc J. Semigran, G. William Dec, Steven A. Williams, Roger J. Hajjar, Judith K. Gwathmey

Biological Sciences: Faculty Publications

Idiopathic dilated cardiomyopathy (IDCM) constitutes a large portion of patients with heart failure of unknown etiology. Up to 50% of all transplant recipients carry this clinical diagnosis. Female-specific gene expression in IDCM has not been explored. We report sex-related differences in the gene expression profile of ventricular myocardium from patients undergoing cardiac transplantation. We produced and sequenced subtractive cDNA libraries, using human left ventricular myocardium obtained from male transplant recipients with IDCM and nonfailing human heart donors. With the resulting sequence data, we generated a custom human heart failure microarray for IDCM containing 1,145 cardiac-specific oligonucleotide probes. This array was …

The Dynamic Nature Of Eukaryotic Genomes, Laura Wegener Parfrey, Daniel J.G. Lahr, Laura A. Katz

Biological Sciences: Faculty Publications

Analyses of diverse eukaryotes reveal that genomes are dynamic, sometimes dramatically so. In numerous lineages across the eukaryotic tree of life, DNA content varies within individuals throughout life cycles and among individuals within species. Discovery of examples of genome dynamism is accelerating as genome sequences are completed from diverse eukaryotes. Though much is known about genomes in animals, fungi, and plants, these lineages represent only 3 of the 60-200 lineages of eukaryotes. Here, we discuss diverse genomic strategies in exemplar eukaryotic lineages, including numerous microbial eukaryotes, to reveal dramatic variation that challenges established views of genome evolution. For example, in …

Broadly Sampled Multigene Trees Of Eukaryotes, Hwan Su Yoon, Jessica Grant, Yonas I. Tekle, Min Wu, Benjamin C. Chaon, Jeffrey C. Cole, John M. Logsdon, David J. Patterson, Debashish Bhattacharya, Laura A. Katz

Biological Sciences: Faculty Publications

Background. Our understanding of the eukaryotic tree of life and the tremendous diversity of microbial eukaryotes is in flux as additional genes and diverse taxa are sampled for molecular analyses. Despite instability in many analyses, there is an increasing trend to classify eukaryotic diversity into six major supergroups: the 'Amoebozoa', 'Chromalveolata', 'Excavata', 'Opisthokonta', 'Plantae', and 'Rhizaria'. Previous molecular analyses have often suffered from either a broad taxon sampling using only single-gene data or have used multigene data with a limited sample of taxa. This study has two major aims: (1) to place taxa represented by 72 sequences, 61 of which …

An Unidentified Filarial Species And Its Impact On Fitness In Wild Populations Of The Black-Footed Ferret (Mustela Nigripes), Samantha M. Wisely, Jo Gayle Howard, Steven A. Williams, Odile Bain, Rachel M. Santymire, Katherine D. Bardsley, Elizabeth S. Williams

Biological Sciences: Faculty Publications

Disease can threaten the restoration of endangered species directly by substantially decreasing host survival or indirectly via incremental decreases in survival and reproduction. During a biomedical survey of reintroduced populations of the highly endangered black-footed ferret from 2002 to 2005, microfilariae discovered in the blood were putatively identified as Dirofilaria immitis, and widespread screening was initiated using a commercially available antigen-based ELISA test. A subset of animals (n = 16) was screened for D. immitis using a highly sensitive PCR-based assay. Microfilariae were also molecularly and morphologically characterized. Of 198 animals at six reintroduction sites, 12% had positive results using …

Low Temperature (23 °C) Increases Expression Of Biofilm-, Cold-Shock- And Rpos-Dependent Genes In Escherichia Coli K-12, Christine A. White-Ziegler, Suzin Um, Natalie M. Pérez, Abby L. Berns, Amy J. Malhowski, Sarah Young

Biological Sciences: Faculty Publications

Temperature serves as a cue to regulate gene expression in Escherichia coli and other bacteria. Using DNA microarrays, we identified 297 genes whose expression is increased at 23 6C compared to 37 6C in E. coli K-12. Of these genes, 122 are RpoS-controlled, confirming genome-wide the model that low temperature serves as a primary cue to trigger the general stress response. Several genes expressed at 23 6C overlap with the cold-shock response, suggesting that strategies used to adapt to sudden shifts in temperature also mediate long-term growth at 23 6C. Another category of genes more highly expressed at 23 6C …

Draft Genome Of The Filarial Nematode Parasite Brugia Malayi, Elodie Ghedin, Shiliang Wang, David Spiro, Elisabet Caler, Qi Zhao, Jonathan Crabtree, Jonathan E. Allen, Arthur L. Delcher, David B. Guiliano, Diego Miranda-Saavedra, Samuel V. Angiuoli, Todd Creasy, Paolo Amedeo, Brian Haas, Najib M. El-Sayed, Jennifer R. Wortman, Tamara Feldblyum, Luke Tallon, Michael Schatz, Martin Shumway, Hean Koo, Steven L. Salzberg, Seth Schobel, Mihaela Pertea, Mihai Pop, Owen White, Geoffrey J. Barton, Clotilde K.S. Carlow, Michael J. Crawford, Jennifer Daub, Et Al, Steven A. Williams

Biological Sciences: Faculty Publications

Parasitic nematodes that cause elephantiasis and river blindness threaten hundreds of millions of people in the developing world. We have sequenced the ∼90 megabase (Mb) genome of the human filarial parasite Brugia malayi and predict ∼11,500 protein coding genes in 71 Mb of robustly assembled sequence. Comparative analysis with the free-living, model nematode Caenorhabditis elegans revealed that, despite these genes having maintained little conservation of local synteny during ∼350 million years of evolution, they largely remain in linkage on chromosomal units. More than 100 conserved operons were identified. Analysis of the predicted proteome provides evidence for adaptations of B. malayi …

Human Body Temperature (37°C) Increases The Expression Of Iron, Carbohydrate, And Amino Acid Utilization Genes In Escherichia Coli K-12, Christine A. White-Ziegler, Amy J. Malhowski, Sarah Young

Biological Sciences: Faculty Publications

Using DNA microarrays, we identified 126 genes in Escherichia coli K-12 whose expression is increased at human body temperature (37°C) compared to growth at 23°C. Genes involved in the uptake and utilization of amino acids, carbohydrates, and iron dominated the list, supporting a model in which temperature serves as a host cue to increase expression of bacterial genes needed for growth. Using quantitative real-time PCR, we investigated the thermoregulatory response for representative genes in each of these three categories (hisJ, cysP, srlE, garP, fes, and cirA), along with the fimbrial gene papB. Increased expression at 37°C compared to 23°C was …

Spatial Variation In Sea Urchins, Fish Predators, And Bioerosion Rates On Coral Reefs Of Belize, Jocelyn Brown-Saracino, Paulette Peckol, H. Allen Curran, Martha L. Robbart

Biological Sciences: Faculty Publications

Although sea urchins are critical for controlling macroalgae on heavily fished coral reefs, high densities threaten reefs, as urchins are also prodigous bioeroders. This study examined urchin population characteristics, bioerosion rates, their fish predators (Labridae), and potential competitors (Scaridae) on unprotected reefs and a reef within a marine protected area (MPA) in the lagoonal regions off Belize. Urchin density (<1 >m-2) and bioerosion rates (∼0.2 kg CaCO3m-2year-1) were lowest and members of the Labridae were the highest (∼20 fish 200 m-3) within the MPA, while several unprotected reefs had higher (∼18-40 m-2) urchin densities, lower Labridae abundances (1-3 fish 200 …

Hiring Criteria In Biology Departments Of Academic Institutions, Christine M. Fleet, Meredith F.N. Rosser, Rebecca A. Zufall, Marney C. Pratt, Tracy S. Feldman, Paula P. Lemons

Biological Sciences: Faculty Publications

We surveyed faculty in the biology departments of US institutions of higher education to compare the experience and training valued by faculty at hiring institutions with the experience and training most graduate students receive. Our data show that associate, baccalaureate, and master's institutions value teaching experience and skills more highly than research skills. In contrast, doctoral institutions place a higher value on the ability to publish research and obtain outside funding. These findings provide quantitative and qualitative insight into discrepancies between the values of those who train graduate students in biology and the expectations of the institutions likely to hire …

A Real-Time Pcr-Based Assay For Detection Of Wuchereria Bancrofti Dna In Blood And Mosquitoes, Ramakrishna U. Rao, Laura J. Atkinson, Reda M.R. Ramzy, Hanan H. Helmy, Hoda A. Farid, Moses J. Bockarie, Melinda Susapu, Sandra J. Laney, Steven A. Williams, Gary J. Weil

Biological Sciences: Faculty Publications

We developed and evaluated real-time polymerase chain reaction (PCR) assays for detecting Wuchereria bancrofti DNA in human blood and in mosquitoes. An assay based on detection of the W. bancrofti “LDR” repeat DNA sequence was more sensitive than an assay for Wolbachia 16S rDNA. The LDR-based assay was sensitive for detecting microfilarial DNA on dried membrane filters or on filter paper. We also compared real-time PCR with conventional PCR (C-PCR) for detecting W. bancrofti DNA in mosquito samples collected in endemic areas in Egypt and Papua New Guinea. Although the two methods had comparable sensitivity for detecting filarial DNA in …

Generality Of Vertebrate Developmental Patterns: Evidence For A Dermomyotome In Fish, S. H. Devoto, W. Stoiber, C. L. Hammond, P. Steinbacher, J. R. Haslett, M. J.F. Barresi, S. E. Patterson, E. G. Adiarte, S. M. Hughes

Biological Sciences: Faculty Publications

The somitic compartment that gives rise to trunk muscle and dermis in amniotes is an epithelial sheet on the external surface of the somite, and is known as the dermomyotome. However, despite its central role in the development of the trunk and limbs, the evolutionary history of the dermomyotome and its role in nonamniotes is poorly understood. We have tested whether a tissue with the morphological and molecular characteristics of a dermomyotome exists in nonamniotes. We show that representatives of the agnathans and of all major clades of gnathostomes each have a layer of cells on the surface of the …

Characterization Of A Novel Filarial Serine Protease Inhibitor, Ov-Spi-1, From Onchocerca Volvulus, With Potential Multifunctional Roles During Development Of The Parasite, Louise Ford, David B. Guiliano, Yelena Oksov, Asim K. Debnath, Jing Liu, Steven A. Williams, Mark L. Blaxter, Sara Lustigman

Biological Sciences: Faculty Publications

A novel filarial serine protease inhibitor (SPI) from the human parasitic nematode Onchocerca volvulus, Ov-SPI-1, was identified through the analysis of a molting third-stage larvae expressed sequence tag dataset. Subsequent analysis of the expressed sequence tag datasets of O. volvulus and other filariae identified four other members of this family. These proteins are related to the low molecular weight SPIs originally isolated from Ascaris suumwhere they are believed to protect the parasite from host intestinal proteases. The two Ov-spi transcripts are up-regulated in the molt- ing larvae and adult stages of the development of the parasite. Recombinant Ov-SPI-1 is an …

Hedgehog Regulated Slit Expression Determines Commissure And Glial Cell Position In The Zebrafish Forebrain, Michael J.F. Barresi, Lara D. Hutson, Chi Bin Chien, Rolf O. Karlstrom

Biological Sciences: Faculty Publications

Three major axon pathways cross the midline of the vertebrate forebrain early in embryonic development: the postoptic commissure (POC), the anterior commissure (AC) and the optic nerve. We show that a small population of Gfap+ astroglia spans the midline of the zebrafish forebrain in the position of, and prior to, commissural and retinal axon crossing. These glial 'bridges' form in regions devoid of the guidance molecules slit2 and slit3, although a subset of these glial cells express slit1a. We show that Hh signaling is required for commissure formation, glial bridge formation, and the restricted expression of the guidance molecules slit1a, …

Increased Action Potential Firing Rates Of Layer 2/3 Pyramidal Cells In The Prefrontal Cortex Are Significantly Related To Cognitive Performance In Aged Monkeys, Yu Ming Chang, Douglas L. Rosene, Ronald J. Killiany, Lisa A. Mangiamele, Jennifer I. Luebke

Biological Sciences: Faculty Publications

The neurobiological substrates of significant age-related deficits in higher cognitive abilities mediated by the prefrontal cortex (PFC) are unknown. To address this issue, whole-cell current-clamp recordings were used to compare the intrinsic membrane and action potential (AP) firing properties of layer 2/3 pyramidal cells in PFC slices from young and aged behaviorally characterized rhesus monkeys. Most aged subjects demonstrated impaired performance in Delayed Non-Match to Sample (DNMS) task acquisition, DNMS 2 min delay and the Delayed Recognition Span task. Resting membrane potential and membrane time constant did not differ in aged relative to young cells, but input resistance was significantly …

Rich Mesic Forests: Edaphic And Physiographic Drivers Of Community Variation In Western Massachusetts, J. Bellemare, G. Motzkin, D. R. Foster

Biological Sciences: Faculty Publications

Rich Mesic Forest, a Northeastern variant of the species-rich Mixed Mesophytic Forest association of eastern North America, is an Acer saccharum-dominated forest type typically associated with calcareous bedrock and nutrient-rich, mull soils. Rich Mesic Forest (RMF) is a priority for conservation in the Northeast due to its limited areal extent, high plant species richness, and numerous rare taxa, yet the community characteristics and environmental correlates of this forest type are incompletely understood. This study undertook a quantitative classification of RMF of the northeastern edge of the Berkshire Plateau in western Massachusetts. Cluster analysis of data from ten sites identified two …

Filarial Genomics, Steven A. Williams

Biological Sciences: Faculty Publications

No abstract provided.

Effect Of Zooid Spacing On Bryozoan Feeding Success: Is Competition Or Facilitation More Important?, Marney C. Pratt

Biological Sciences: Faculty Publications

Most Recent bryozoan species are encrusting sheets, and many of these colonies have densely packed feeding zooids. In this study, I tested whether tight packing of feeding zooids affects food capture. Colonies of a bryozoan with an encrusting sheet form (Membranipora membranacea) were dissected to produce individuals whose feeding zooids were (1) closely packed, (2) more widely spaced, or (3) isolated. For each type, rates of particle ingestion were measured in still water and in a freestream velocity of 2.7 cm s-1. Ingestion rate increased when zooids were closest together, probably because of reduced refiltration and increased feeding current strength …

Multiple Roles For Hedgehog Signaling In Zebrafish Pituitary Development, Jennifer L. Sbrogna, Michael J.F. Barresi, Rolf O. Karlstrom

Biological Sciences: Faculty Publications

The endocrine-secreting lobe of the pituitary gland, or adenohypophysis, forms from cells at the anterior margin of the neural plate through inductive interactions involving secreted morphogens of the Hedgehog (Hh), fibroblast growth factor (FGF), and bone morphogenetic protein (BMP) families. To better understand when and where Hh signaling influences pituitary development, we have analyzed the effects of blocking Hh signaling both pharmacologically (cyclopamine treatments) and genetically (zebrafish Hh pathway mutants). While current models state that Shh signaling from the oral ectoderm patterns the pituitary after placode induction, our data suggest that Shh plays a direct early role in both pituitary …