Biology Commons^™

Coordinated Regulation Of Myc Trans-Activation Targets By Polycomb And The Trithorax Group Protein Ash1, Julie M. Goodliffe, Michael D. Cole, Eric Wieschaus

Dartmouth Scholarship

The Myc oncoprotein is a transcriptional regulator whose function is essential for normal development. Myc is capable of binding to 10% of the mammalian genome, and it is unclear how a developing embryo controls the DNA binding of its abundant Myc proteins in order to avoid Myc's potential for inducing tumorigenesis.To identify chromatin binding proteins with a potential role in controlling Myc activity, we established a genetic assay for dMyc activity in Drosophila. We conducted a genome-wide screen using this assay, and identified the Trithorax Group protein Ash1 as a modifier of dMyc activity. Ash1 is a histone methyltransferase known …

Search For A Knox Gene In Kalanchöe Pinnatum, Ryan Michael Gleason

Undergraduate Honors Thesis Collection

Knox genes have been found in nearly all eukaryotic organisms. These genes code for a protein that is able to bind DNA. By binding to DNA, it is capable of controlling the expression of other genes. The coded sequence of these genes has been determined in many different organisms, but has yet to be searched for in the air plant, Kalanchoe pinnatum. I did research over the past year in an attempt to find the coded sequence of Kalanchoe's Knox gene. I grew Kalanchoe in Butler's greenhouse to accumulate enough plant material to begin work. I then extracted the RNA …

Shark Bay Prawn And Scallop Fisheries. Draft Review Report, Department Of Fisheries Western Australia

Fisheries Management Papers

In recent times, the Department of Fisheries has received representations from both sectors about the ongoing interaction of the fisheries and their respective management settings. As a result, a decision was made to comprehensively review the fisheries, taking into account matters of fishery sustainability and gear interactions, together with industry economics and market considerations. The review has also addressed research requirements to ensure an appropriate scientific basis for decision-making into the future.

The Carnegie Protein Trap Library: A Versatile Tool For Drosophila Developmental Studies, Anna Allen

Department of Biology Faculty Publications

Metazoan physiology depends on intricate patterns of gene expression that remain poorly known. Using transposon mutagenesis in Drosophila, we constructed a library of 7404 protein trap and enhancer trap lines, the Carnegie collection, to facilitate gene expression mapping at single-cell resolution. By sequencing the genomic insertion sites, determining splicing patterns downstream of the enhanced green fluorescent protein (EGFP) exon, and analyzing expression patterns in the ovary and salivary gland, we found that 600-900 different genes are trapped in our collection. A core set of 244 lines trapped different identifiable protein isoforms, while insertions likely to act as GFP-enhancer traps were …

Assessment Of Genetic Diversity In The Usda And Cip-Fao International Nursery Collections Of Quinoa (Chenopodium Quinoa Willd.) Using Microsatellite Markers [Abstract], S. A. Christensen, Donald B. Pratt, C. Pratt, P. T. Nelson, M. R. Stevens, Eric N. Jellen, C. E. Coleman, D. J. Fairbanks, A. Bonifacio, Peter J. Maughan

Faculty Publications

No abstract provided.

Microarray Challenges In Ecology, Jan E. Kammenga, Michael A. Herman, N. Joop Ouborg, Loretta Johnson, Rainer Bretling

School of Biological Sciences: Faculty Publications

Microarrays are used to measure simultaneously the amount of mRNAs transcribed from many genes. They were originally designed for gene expression profiling in relatively simple biological systems, such as cell lines and model systems under constant laboratory conditions. This poses a challenge to ecologists who increasingly want to use microarrays to unravel the genetic mechanisms underlying complex interactions among organisms and between organisms and their environment. Here, we discuss typical experimental and statistical problems that arise when analyzing genome-wide expression profiles in an ecological context. We show that experimental design and environmental confounders greatly influence the identification of candidate genes …

The Arabidopsis Homologs Of Trithorax (Atx1) And Enhancer Of Zeste (Clf) Establish ‘Bivalent Chromatin Marks’ At The Silent Agamous Locus, Abdelaty Saleh, Ayed Al-Abdallat, Ivan Ndamukong, Raul Alvarez-Venegas, Zoya Avramova

School of Biological Sciences: Faculty Publications

Tightly balanced antagonism between the Polycomb group (PcG) and the Trithorax group (TrxG) complexes maintain Hox expression patterns in Drosophila and murine model systems. Factors belonging to the PcG/TrxG complexes control various processes in plants as well but whether they participate in mechanisms that antagonize, balance or maintain each other’s effects at a particular gene locus is unknown. CURLY LEAF (CLF), an Arabidopsis homolog of enhancer of zeste (EZ) and the ARABIDOPSIS HOMOLOG OF TRITHORAX (ATX1) control the expression of the flower homeotic gene AGAMOUS (AG). Disrupted ATX1 or CLF function results in misexpression of AG, recognizable …

A Practical Approach To Phylogenomics: The Phylogeny Of Ray-Finned Fish (Actinopterygii) As A Case Study, Chenhong Li, Guillermo Orti, Gong Zhang, Guoqing Lu

Biology Faculty Publications

Background: Molecular systematics occupies one of the central stages in biology in the genomic era, ushered in by unprecedented progress in DNA technology. The inference of organismal phylogeny is now based on many independent genetic loci, a widely accepted approach to assemble the tree of life. Surprisingly, this approach is hindered by lack of appropriate nuclear gene markers for many taxonomic groups especially at high taxonomic level, partially due to the lack of tools for efficiently developing new phylogenetic makers. We report here a genome-comparison strategy to identifying nuclear gene markers for phylogenetic inference and apply it to the …

Tissue And Life Stage Distribution Of A Defensin-Like Gene In The Lone Star Tick Amblyomma Americanum, S. Michelle Todd, Daniel E. Sonenshine, Wayne L. Hynes

Biological Sciences Faculty Publications

The transcript sequence of the Amblyomma americanum Linnaeus (Acari: Ixodidae) defensin, termed amercin (amn), was ascertained and a 219-bp amn coding region identified. The gene encodes a 72-amino acid prepropeptide with a putative 37-amino acid mature peptide. This gene shows little similarity to either of the defensins from Amblyomma hebraeum Koch, the only other Amblyomma species for which a defensin has been described. Sequence comparisons with other tick defensins reveal amn to be shorter (6 bp or 2 amino acids) than the Ixodes scapularis Linnaeus (Acari: Ixodidae) and Dermacentor variabilis (Say) (Acari: Ixodidae) defensin sequences. The amercin prepropeptide …

Evaluation Of Genetic Diversity In Wild Chironomid Populations Using Rapd And Hemoglobin Protein As Molecular Biomarkers, Virendrasinh N. Jadeja

Seton Hall University Dissertations and Theses (ETDs)

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Asymmetric Localizations Of Lin-17/Fz And Mig-5/Dsh Are Involved In The Asymmetric B Cell Division In C. Elegans, Mingfu Wu, Michael A. Herman

School of Biological Sciences: Faculty Publications

LIN-44/Wnt and LIN-17/Frizzled (Fz) function in a planar cell polarity (PCP)-like pathway to regulate the asymmetric B cell division in Caenorhabditis elegans. We observed asymmetric localization of LIN-17/Frizzled (Fz) and MIG-5/Disheveled (Dsh) during the B cell division. LIN-17∷GFP was asymmetrically localized within the B cell prior to and after the B cell division and correlated with B cell polarity. Asymmetric localization of LIN-17∷GFP was dependent upon LIN-44/Wnt and MIG-5/Dsh function. The LIN-17 transmembrane domain and a portion of the cysteine-rich domain (CRD) were required for LIN-17 function and asymmetric distribution to the B cell daughters, while the conserved KTXXXW …

The Plant Structure Ontology, A Unified Vocabulary Of Anatomy And Morphology Of A Flowering Plant, Katica Ilic, Elizabeth Kellogg, Pankaj Jaiswal, Felipe Zapata, Peter Stevens, Leszek Vincent, Shulamit Avraham, Leonore Reiser, Anuradha Pujar, Martin Sachs, Noah Whitman, Susan Mccouch, Mary Schaeffer, Doreen Ware, Lincoln Stein, Seung Rhee

Biology Department Faculty Works

Formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require uniform terminology that accurately describes plant anatomy and morphology. This facilitates cross species comparative studies and quantitative comparison of phenotypes and expression patterns. A major drawback is variable terminology that is used to describe plant anatomy and morphology in publications and genomic databases for different species. The same terms are sometimes applied to different plant structures in different taxonomic groups. Conversely, similar structures are named by their species-specific terms. To address this problem, we created the Plant Structure Ontology (PSO), the first generic ontological …

Caenorhabditis Briggsae Methods, Scott Everet Baird, Helen M. Chamberlin

Biological Sciences Faculty Publications

Caenorhabditis briggsae is being developed in parallel to C. elegans as a model system, primarily for the study of evolution. Like C. elegans, C. briggsae is a protandrous hermaphrodite and like C. elegans, its genome has been sequenced. From this point, these two model systems diverge. The development, behavior, and physiology of C. elegans have been characterized through tens of thousands of genetic and molecular studies. Genetic and molecular characterizations of C. briggsae are relatively few. Experimental resources in C. elegans include a high density recombination map that is well integrated with the genome sequence. The C. briggsae …

Review Of "Plant Exploration For Longwood Gardens" By T. Aniśko, Nicholas J. Kaplinsky

Biology Faculty Works

No abstract provided.

The Fat Cadherin Acts Through The Hippo Tumor-Suppressor Pathway To Regulate Tissue Size, Maria Willecke, Fisun Hamaratoglu, Madhuri Kango-Singh, Ryan Udan, Chiao-Lin Chen, Chunyao Tao, Xinwei Zhang, Georg Halder

Biology Faculty Publications

Background: The Hippo tumor-suppressor pathway has emerged as a key signaling pathway that controls tissue size in Drosophila. Merlin, the Drosophila homolog of the human Neurofibromatosis type-2 (NF2) tumor-suppressor gene, and the related protein Expanded are the most upstream components of the Hippo pathway identified so far. However, components acting upstream of Expanded and Merlin, such as transmembrane receptors, have not yet been identified.

Results: Here, we report that the protocadherin Fat acts as an upstream component in the Hippo pathway. Fat is a known tumor-suppressor gene in Drosophila, and fat mutants have severely overgrown imaginal discs. We …

Lobe And Serrate Are Required For Cell Survival During Early Eye Development In Drosophila, Amit Singh, Xiao Shi, Kwang-Wook Choi

Biology Faculty Publications

Organogenesis involves an initial surge of cell proliferation, leading to differentiation. This is followed by cell death in order to remove extra cells. During early development, there is little or no cell death. However, there is a lack of information concerning the genes required for survival during the early cell-proliferation phase. Here, we show that Lobe (L) and the Notch (N) ligand Serrate (Ser), which are both involved in ventral eye growth, are required for cell survival in the early eye disc. We observed that the loss-of-ventral-eye phenotype in L or Ser mutants is due to …

Distance-Based Genome Rearrangement Phylogeny, Li-San Wang, Tandy Warnow, Bernard M.E. Moret, Robert K. Jansen, Linda A. Raubeson

All Faculty Scholarship for the College of the Sciences

Evolution operates on whole genomes through direct rearrangements of genes, such as inversions, transpositions, and inverted transpositions, as well as through operations, such as duplications, losses, and transfers, that also affect the gene content of the genomes. Because these events are rare relative to nucleotide substitutions, gene order data offer the possibility of resolving ancient branches in the tree of life; the combination of gene order data with sequence data also has the potential to provide more robust phylogenetic reconstructions, since each can elucidate evolution at different time scales. Distance corrections greatly improve the accuracy of phylogeny reconstructions from DNA …

Mig-5/Dsh Controls Cell Fate Determination And Cell Migration In C. Elegans, Timothy Walston, Chaobo Guo, Rui Proenca, Mingfu Wu, Michael Herman, Jeff Hardin, Edward Hedgecock

School of Biological Sciences: Faculty Publications

Cell fate determination and cell migration are two essential events in the development of an organism. We identify mig-5, a Dishevelled family member, as a gene that regulates several cell fate decisions and cell migrations that are important during C. elegans embryonic and larval development. In offspring from mig-5 mutants, cell migrations are defective during hypodermal morphogenesis, QL neuroblast migration, and the gonad arm migration led by the distal tip cells (DTCs). In addition to abnormal migration, DTC fate is affected, resulting in either an absent or an extra DTC. The cell fates of the anchor cell in hermaphrodites …

Expression Of The Primary Carbohydrate Component Of The Bordetella Bronchiseptica Biofilm Matrix Is Dependent On Growth Phase But Independent Of Bvg Regulation, Yasuhiko Irie, Andrew Preston, Ming H. Yuk

Biology Faculty Publications

We previously showed that the Bvg virulence control system regulates biofilm formation in Bordetella bronchiseptica (Y. Irie, S. Mattoo, and M. H. Yuk, J. Bacteriol. 186:5692-5698, 2004). Analyses of the extracellular components of B. bronchiseptica biofilm matrix revealed that the major sugar component in the matrix was xylose, and linkage analysis indicated a majority of it to be in a 4-linked polymeric form. The production of xylose was independent of Bvg regulation but instead was dependent on bacterial growth phase. In addition, N-acetyl-glucosamine in the matrix was found to be important for the initial development of the biofilm. These …

Secondary Metabolic Gene Cluster Silencing In Aspergillus Nidulans, J. W. Bok, D. Noordermeer, Shubha Kale Ireland, N. P. Keller

Faculty and Staff Publications

In contrast to most primary metabolism genes, the genes involved in secondary metabolism and certain nutrient utilization pathways are clustered in fungi. Recently a nuclear protein, LaeA, was found to be required for the transcription of several secondary metabolite gene clusters in Aspergillus nidulans. Here we show that LaeA regulation does not extend to nutrient utilization or the spoC1 sporulation clusters. One of the secondary metabolite clusters regulated by LaeA contains the positive regulatory (i.e. aflR) and biosynthetic genes required for biosynthesis of sterigmatocystin (ST), a carcinogenic toxin. Analysis of ST gene cluster expression indicates LaeA regulation of the cluster …

Chironomid Hemoglobin Genetic Diversity As An Indicator Of The New Jersey Hackensack Meadowlands Wetland Health, Lene Marie De Coursin Jacobs

Seton Hall University Dissertations and Theses (ETDs)

Kearny Marsh located within the Hackensack Meadowlands is a freshwater wetland impacted by multiple environmental stressors from human activity. The marsh is located in the northeastern New Jersey metropolitan area. Chironomid larvae, aquatic larvae of midge fly, were analyzed from two Kearny Marsh sample sites, W9 and W22. A previous sediment analysis and toxicity study characterized heavy metal contaminants the marsh. The data results were applied in this thesis study to determine the correlation between environmental stressors and chironomid genetic diversity. Site W9 sediment was impacted by severe levels of total heavy metal contamination, whereas site W22 had just below …

A Subset Of Arabidopsis Ap2 Transcription Factors Mediates Cytokinin Responses In Concert With A Two-Component Pathway, Aaron M. Rashotte, Michael G. Mason, Claire E. Hutchison, Fernando J. Ferreira, G. Eric Schaller, Joseph J. Kieber

Dartmouth Scholarship

The plant hormone cytokinin regulates numerous growth and developmental processes. A signal transduction pathway for cytokinin has been elucidated that is similar to bacterial two-component phosphorelays. In Arabidopsis, this pathway is comprised of receptors that are similar to sensor histidine kinases, histidine-containing phosphotransfer proteins, and response regulators (ARRs). There are two classes of response regulators, the type-A ARRs, which act as negative regulators of cytokinin responses, and the type-B ARRs, which are transcription factors that play a positive role in mediating cytokinin-regulated gene expression. Here we show that several closely related members of the Arabidopsis AP2 gene family of …

In Vitro Expression And Purification Of Class I Mhc Molecules, Loi Cheng

Honors Scholar Theses

The major histocompatibility complex (MHC) is a gene family responsible for many critical functions of the immune system in most vertebrates. The MHC consists of three classes differentiated by their structure and function, and MHC class I encodes antigen binding proteins as well as chaperone and accessory proteins such as tapasin. The purpose of this project is to reconstitute several human MHC class I molecules in their peptide-filled and peptide-deficient forms, and to purify these proteins for biochemical study. The expressed proteins include wild type and mutant variants of the fusion protein human leukocyte antigen HLA-B*0801-fos, and human beta-2-microglobulin (β2m). …

Analysis Of Distal-Less Gene Expression In Ciona Intestinalis, Michelle Cangiano

Senior Honors Projects

Several homeobox-containing genes related to Distal-less (Dlx/Dll) have been isolated from a wide variety of organisms and have been shown to function as developmental regulators. In Drosophila only one Distal-less gene has been identified so far, and in vertebrates many components of the Distal-less family have been characterized. This suggests that, during the evolution of the Chordate phylum, the Dlx genes arose from an ancestral Distal-less gene via gene duplication. Three Dll homeoboxes have been isolated from the protochordate Ciona intestinalis and their clustered arrangement has been described. Since Ciona is regarded as one of the most primitive extant chordates, …

Plasmid Probes For Screening Specific Genes In Large Fragment Dna Libraries, Leah Ferguson

Senior Honors Projects

Heliothis virescens, a member of the lepidopteran family, is of great importance to many people who rely on agriculture as a source of income because it is a pest of many important crops. Because H. virescens feeds on a broad array of hosts including cotton, tobacco, tomato, and soybean it has earned its place as a major nuisance in the United States. Heliothis subflexa is a close taxonomic relative of H. virescens, but the two species differ in that H. subflexa is a specialized herbivore that only feeds on plants in the genus Physalis. Studies have been performed to determine …

Glucocorticoids Exacerbate Obesity And Insulin Resistance In Neuron-Specific Proopiomelanocortin-Deficient Mice, James L. Smart, Virgine Tolle, Malcolm J. Low

Faculty Publications - Department of Biological & Molecular Science

Null mutations of the proopiomelanocortin gene (Pomc–/–) cause obesity in humans and rodents, but the contributions of central versus pituitary POMC deficiency are not fully established. To elucidate these roles, we introduced a POMC transgene (Tg) that selectively restored peripheral melanocortin and corticosterone secretion in Pomc–/– mice. Rather than improving energy balance, the genetic replacement of pituitary POMC in Pomc–/–Tg+ mice aggravated their metabolic syndrome with increased caloric intake and feed efficiency, reduced oxygen consumption, increased subcutaneous, visceral, and hepatic fat, and severe insulin resistance. Pair-feeding of Pomc–/–Tg+ mice to the daily intake of lean controls normalized their rate of …

Linking Direct And Indirect Data On Dispersal: Isolation By Slope In A Headwater Stream Salamander, Winsor H. Lowe, Gene E. Likens, Mark A. Mcpeek, Don C. Buso

Dartmouth Scholarship

There is growing recognition of the need to incorporate information on movement behavior in landscape-scale studies of dispersal. One way to do this is by using indirect indices of dispersal (e.g., genetic differentiation) to test predictions derived from direct data on movement behavior. Mark–recapture studies documented upstream-biased movement in the salamander Gyrinophilus porphyriticus (Plethodontidae). Based on this information, we hypothesized that gene flow in G. porphyriticus is affected by the slope of the stream. Specifically, because the energy required for upstream dispersal is positively related to slope, we predicted gene flow to be negatively related to change in elevation between …

A Broad-Spectrum Mer Operon In A Multi-Drug Resistant Strain Of The Fish Pathogen, Aeromonas Salmonicida, Erin Parry

Honors Theses

Aeromonas salmonicida AS03, a potential fish pathogen, was isolated from Atlantic salmon, Salmo salar, in 2003. This strain was found to be resistant to ≥1000 mM HgCl2 and ≥32 mM phenylmercuric acetate as well as multiple antimicrobials. Mercury (Hg) and antibiotic resistance genes are often located on the same mobile genetic elements, so the genetic determinants of both resistances and the possibility of horizontal gene transfer were examined. Specific PCR primers were used to amplify and sequence distinctive regions of the mer operon. A. salmonicida AS03 was found to have a pDU1358-like broad-spectrum mer operon, containing merB as well as …

Tick Pheromones And Their Use In Tick Control, Daniel E. Sonenshine

Biological Sciences Faculty Publications

Tick pheromones that regulate assembly, attraction/aggregation/attachment, and mating behavior have been described. Most of the compounds regulating these behaviors are purines, substituted phenols, or cholesteryl esters. Other pheromonal compounds include organic acids, hematin, or ecdysteroids. Novel devices have been developed that combine the specific compounds comprising these pheromones with an acaricide. When applied to tick-infested vegetation or directly to the body surfaces of livestock or companion animals, these devices are effective for tick control. This review summarizes the current state of knowledge of tick pheromones. In addition, this review also presents examples illustrating how devices using tick pheromones can offer …

Eye Development At The Houston "Fly Meeting", Amit Singh

Biology Faculty Publications

Meeting report: The 47th Annual Drosophila Research Conference or "Fly Meeting" took place at Houston, Texas, USA from March 29th- April 2nd, 2006, under the aegis of the Genetics Society of America. The Fly Meeting provides an excellent opportunity for fly researchers to present their work and to get a snapshot of recent developments and upcoming trends in their research field. The fruit fly, Drosophila melanogaster, is a very versatile model to study growth, patterning, neural development, evolution, systemetics and various other facets of biomedical science. The topics presented in the meeting covered a very broad spectrum of fly research. …