Life Sciences Commons^™

Identification Of G1-Regulated Genes In Normally Cycling Human Cells, Maroun J. Beyrouthy, Karen E. Alexander, Amy Baldwin, Michael L. Whitfield, Hank W. Bass, Dan Mcgee, Myra M. Hurt

Dartmouth Scholarship

Background: Obtaining synchronous cell populations is essential for cell-cycle studies. Methods such as serum withdrawal or use of drugs which block cells at specific points in the cell cycle alter cellular events upon re-entry into the cell cycle. Regulatory events occurring in early G1 phase of a new cell cycle could have been overlooked. Methodology and Findings: We used a robotic mitotic shake-off apparatus to select cells in late mitosis for genome-wide gene expression studies. Two separate microarray experiments were conducted, one which involved isolation of RNA hourly for several hours from synchronous cell populations, and one experiment which examined …

Meeting Report: Methylmercury In Marine Ecosystems—From Sources To Seafood Consumers, Celia Y. Chen, Nancy Serrell, David C. Evers, Bethany J. Fleishman, Kathleen F. Lambert, Jeri Weiss, Robert P. Mason, Michael S. Bank

Dartmouth Scholarship

Mercury and other contaminants in coastal and open-ocean ecosystems are an issue of great concern globally and in the United States, where consumption of marine fish and shellfish is a major route of human exposure to methylmercury (MeHg). A recent National Institute of Environmental Health Sciences–Superfund Basic Research Program workshop titled “Fate and Bioavailability of Mercury in Aquatic Ecosystems and Effects on Human Exposure,” convened by the Dartmouth Toxic Metals Research Program on 15–16 November 2006 in Durham, New Hampshire, brought together human health experts, marine scientists, and ecotoxicologists to encourage cross-disciplinary discussion between ecosystem and human health scientists and …

The Role Of Causal Processes In The Neutral And Nearly Neutral Theories, Michael R. Dietrich, Roberta L. Millstein

Dartmouth Scholarship

The neutral and nearly neutral theories of molecular evolution are sometimes characterized as theories about drift alone, where drift is described solely as an outcome, rather than a process. We argue, however, that both selection and drift, as causal processes, are integral parts of both theories. However, the nearly neutral theory explicitly recognizes alleles and/or molecular substitutions that, while engaging in weakly selected causal processes, exhibit outcomes thought to be characteristic of random drift. A narrow focus on outcomes obscures the significant role of weakly selected causal processes in the nearly neutral theory.

Medial Temporal Lobe Bold Activity At Rest Predicts Individual Differences In Memory Ability In Hhealthy Young Adults, Gagan S. Wig, Scott T. Grafton, Kathryn E. Demos, George L. Wolford, Steven E. Petersen, William M. Kelley

Dartmouth Scholarship

Human beings differ in their ability to form and retrieve lasting long-term memories. To explore the source of these individual differences, we used functional magnetic resonance imaging to measure blood-oxygen-level-dependent (BOLD) activity in healthy young adults (n = 50) during periods of resting fixation that were interleaved with periods of simple cognitive tasks. We report that medial temporal lobe BOLD activity during periods of rest predicts individual differences in memory ability. Specifically, individuals who exhibited greater magnitudes of task-induced deactivations in medial temporal lobe BOLD signal (as compared to periods of rest) demonstrated superior memory during offline testing. This relationship …

Pseudomonas Aeruginosa-Candida Albicans Interactions: Localization And Fungal Toxicity Of A Phenazine Derivative, Jane Gibson, Arpanah Sood, Deborah A. Hogan

Dartmouth Scholarship

Phenazines are redox-active small molecules that play significant roles in the interactions between pseudomonads and diverse eukaryotes, including fungi. When Pseudomonas aeruginosa and Candida albicans were cocultured on solid medium, a red pigmentation developed that was dependent on P. aeruginosa phenazine biosynthetic genes. Through a genetic screen in combination with biochemical experiments, it was found that a P. aeruginosa-produced precursor to pyocyanin, proposed to be 5-methyl-phenazinium-1-carboxylate (5MPCA), was necessary for the formation of the red pigmentation. The 5MPCA-derived pigment was found to accumulate exclusively within fungal cells, where it retained the ability to be reversibly oxidized and reduced, and its …

Evolution Acts On Enhancer Organization To Fine-Tune Gradient Threshold Readouts, Justin Crocker, Yoichiro Tamori, Albert Erives

Dartmouth Scholarship

The elucidation of principles governing evolution of gene regulatory sequence is critical to the study of metazoan diversification. We are therefore exploring the structure and organizational constraints of regulatory sequences by studying functionally equivalent cis-regulatory modules (CRMs) that have been evolving in parallel across several loci. Such an independent dataset allows a multi-locus study that is not hampered by nonfunctional or constrained homology. The neurogenic ectoderm enhancers (NEEs) of Drosophila melanogaster are one such class of coordinately regulated CRMs. The NEEs share a common organization of binding sites and as a set would be useful to study the relationship …

Identification Of Two Gene Clusters And A Transcriptional Regulator Required For Pseudomonas Aeruginosa Glycine Betaine Catabolism, Matthew J. Wargo, Benjamin S. Szwergold, Deborah A. Hogan

Dartmouth Scholarship

Glycine betaine (GB), which occurs freely in the environment and is an intermediate in the catabolism of choline and carnitine, can serve as a sole source of carbon or nitrogen in Pseudomonas aeruginosa. Twelve mutants defective in growth on GB as the sole carbon source were identified through a genetic screen of a nonredundant PA14 transposon mutant library. Further growth experiments showed that strains with mutations in two genes, gbcA (PA5410) and gbcB (PA5411), were capable of growth on dimethylglycine (DMG), a catabolic product of GB, but not on GB itself. Subsequent nuclear magnetic resonance (NMR) experiments with 1,2-(13)C-labeled choline …

Ovarian Development In Mice Requires The Gata4-Fog2 Transcription Complex, Nikolay L. Manuylov, Fatima O. Smagulova, Lyndsay Leach, Sergei G. Tevosian

Dartmouth Scholarship

We have demonstrated previously that mammalian sexual differentiation requires both the GATA4 and FOG2 transcriptional regulators to assemble the functioning testis. Here we have determined that the sexual development of female mice is profoundly affected by the loss of GATA4-FOG2 interaction. We have also identified the Dkk1 gene, which encodes a secreted inhibitor of canonical beta-catenin signaling, as a target of GATA4-FOG2 repression in the developing ovary. The tissue-specific ablation of the beta-catenin gene in the gonads disrupts female development. In Gata4(ki/ki); Dkk1(-/-) or Fog2(-/-); Dkk1(-/-) embryos, the normal ovarian gene expression pattern is partially restored. Control of ovarian development …

Evolution Of The Holozoan Ribosome Biogenesis Regulon, Seth J. Brown, Michael D. Cole, Albert J. Erives

Dartmouth Scholarship

The ribosome biogenesis (RiBi) genes encode a highly-conserved eukaryotic set of nucleolar proteins involved in rRNA transcription, assembly, processing, and export from the nucleus. While the mode of regulation of this suite of genes has been studied in the yeast, Saccharomyces cerevisiae, how this gene set is coordinately regulated in the larger and more complex metazoan genomes is not understood. Here we present genome-wide analyses indicating that a distinct mode of RiBi regulation co-evolved with the E(CG)-binding, Myc:Max bHLH heterodimer complex in a stem-holozoan, the ancestor of both Metazoa and Choanoflagellata, the protozoan group most closely related to animals. These …

Metabolic Engineering Of A Thermophilic Bacterium To Produce Ethanol At High Yield, A. Joe Shaw, Kara K. Podkaminer, Sunil G. Desai, John S. Bardsley, Stephen R. Rogers, Philip G. Thorne, David A. Hogsett, Lee R. Lynd

Dartmouth Scholarship

We report engineering Thermoanaerobacterium saccharolyticum, a thermophilic anaerobic bacterium that ferments xylan and biomass-derived sugars, to produce ethanol at high yield. Knockout of genes involved in organic acid formation (acetate kinase, phosphate acetyltransferase, and L-lactate dehydrogenase) resulted in a strain able to produce ethanol as the only detectable organic product and substantial changes in electron flow relative to the wild type. Ethanol formation in the engineered strain (ALK2) utilizes pyruvate:ferredoxin oxidoreductase with electrons transferred from ferredoxin to NAD(P), a pathway different from that in previously described microbes with a homoethanol fermentation. The homoethanologenic phenotype was stable for >150 generations …

The Bile Response Repressor Brer Regulates Expression Of The Vibrio Cholerae Breab Efflux System Operon, Francisca A. Cerda-Maira, Carol S. Ringelberg, Ronald K. Taylor

Dartmouth Scholarship

Enteric pathogens have developed several resistance mechanisms to survive the antimicrobial action of bile. We investigated the transcriptional profile of Vibrio cholerae O1 El Tor strain C6706 under virulence gene-inducing conditions in the presence and absence of bile. Microarray analysis revealed that the expression of 119 genes was affected by bile. The mRNA levels of genes encoding proteins involved in transport were increased in the presence of bile, whereas the mRNA levels of genes encoding proteins involved in pathogenesis and chemotaxis were decreased. This study identified genes encoding transcriptional regulators from the TetR family (vexR and breR) and …

Habitat-Mediated Foraging Limitations Drive Survival Bottlenecks For Juvenile Salmon, Brian P. Kennedy, Keith H. Nislow, Carol L. Folt

Dartmouth Scholarship

Realistic population models and effective conservation strategies require a thorough understanding of mechanisms driving stage-specific mortality. Mortality bottlenecks for many species occur in the juvenile stage and are thought to result from limitation on food or foraging habitat during a "critical period" for growth and survival. Without a way to account for maternal effects or to measure integrated consumption rates in the field, it has been virtually impossible to test these relationships directly. Hence uncertainties about mechanisms underlying such bottlenecks remain. In this study we randomize maternal effects across sites and apply a new method for measuring consumption integrated over …

The Leaf Ionome As A Multivariable System To Detect A Plant's Physiological Status, Ivan R. Baxter, Olga Vitek, Brett Lahner, Balasubramaniam Muthukumar, Monica Borghi, Joe Morrissey, Mary Lou Guerinot, David E. Salt

Dartmouth Scholarship

The contention that quantitative profiles of biomolecules contain information about the physiological state of the organism has motivated a variety of high-throughput molecular profiling experiments. However, unbiased discovery and validation of biomolecular signatures from these experiments remains a challenge. Here we show that the Arabidopsis thaliana (Arabidopsis) leaf ionome, or elemental composition, contains such signatures, and we establish statistical models that connect these multivariable signatures to defined physiological responses, such as iron (Fe) and phosphorus (P) homeostasis. Iron is essential for plant growth and development, but potentially toxic at elevated levels. Because of this, shoot Fe concentrations are …

A Protein Methylation Pathway In Chlamydomonas Flagella Is Active During Flagellar Resorption, Mark J. Schneider, Megan Ulland, Roger D. Sloboda

Dartmouth Scholarship

During intraflagellar transport (IFT), the regulation of motor proteins, the loading and unloading of cargo and the turnover of flagellar proteins all occur at the flagellar tip. To begin an analysis of the protein composition of the flagellar tip, we used difference gel electrophoresis to compare long versus short (i.e., regenerating) flagella. The concentration of tip proteins should be higher relative to that of tubulin (which is constant per unit length of the flagellum) in short compared with long flagella. One protein we have identified is the cobalamin-independent form of methionine synthase (MetE). Antibodies to MetE label flagella in a …

Fish Distributions And Nutrient Cycling In Streams: Can Fish Create Biogeochemical Hotspots, Peter B. Mcintyre, Alexander S. Flecker, Michael J. Vanni, James M. Hood, Brad W. Taylor, Steven A. Thomas

Dartmouth Scholarship

Rates of biogeochemical processes often vary widely in space and time, and characterizing this variation is critical for understanding ecosystem functioning. In streams, spatial hotspots of nutrient transformations are generally attributed to physical and microbial processes. Here we examine the potential for heterogeneous distributions of fish to generate hotspots of nutrient recycling. We measured nitrogen (N) and phosphorus (P) excretion rates of 47 species of fish in an N-limited Neotropical stream, and we combined these data with population densities in each of 49 stream channel units to estimate unit- and reach-scale nutrient recycling. Species varied widely in rates of N …

Nectar Secondary Compounds Affect Self-Pollen Transfer: Implications For Female And Male Reproduction, Rebecca E. Irwin, Lynn S. Adler

Dartmouth Scholarship

Pollen movement within and among plants affects inbreeding, plant fitness, and the spatial scale of genetic differentiation. Although a number of studies have assessed how plant and floral traits influence pollen movement via changes in pollinator behavior, few have explored how nectar chemical composition affects pollen transfer. As many as 55% of plants produce secondary compounds in their nectar, which is surprising given that nectar is typically thought to attract pollinators. We tested the hypothesis that nectar with secondary compounds may benefit plants by encouraging pollinators to leave plants after visiting only a few flowers, thus reducing self-pollen transfer. We …

Mucosal Immunity In Toxoplasma Gondii Infection, J. Schulthess, D. Fourreau, S. Darche, B. Meresse, L. Kasper, N. Cerf-Bensussan, D. Buzoni-Gatel

Dartmouth Scholarship

Toxoplasma gondii is an intracellular parasite that frequently infects a large spectrum of warm-blooded animals. This parasite induces abortion and establishes both chronic and silent infections, particularly in the brain. Parasite penetration into the host activates a strong anti-parasite immune response. In the present paper, we will discuss the interplay between innate and adaptive immunity that occurs within the infected intestine to clear the parasite and to maintain intestinal homeostasis despite the exacerbation of an inflammatory immune response.

Chloroplast Fe(Iii) Chelate Reductase Activity Is Essential For Seedling Viability Under Iron Limiting Conditions, Jeeyon Jeong, Christopher Cohu, Loubna Kerkeb, Marinus Pilon, Erin L. Connolly, Mary Lou Guerinot

Dartmouth Scholarship

Photosynthesis, heme biosynthesis, and Fe-S cluster assembly all take place in the chloroplast, and all require iron. Reduction of iron via a membrane-bound Fe(III) chelate reductase is required before iron transport across membranes in a variety of systems, but to date there has been no definitive genetic proof that chloroplasts have such a reduction system. Here we report that one of the eight members of the Arabidopsis ferric reductase oxidase (FRO) family, FRO7, localizes to the chloroplast. Chloroplasts prepared from fro7 loss-of-function mutants have 75% less Fe(III) chelate reductase activity and contain 33% less iron per microgram of chlorophyll than …

Integration Host Factor Positively Regulates Virulence Gene Expression In Vibrio Cholerae, Emily Stonehouse, Gabriela Kovacikova, Ronald K. Taylor, Karen Skorupski

Dartmouth Scholarship

Virulence gene expression in Vibrio cholerae is dependent upon a complex transcriptional cascade that is influenced by both specific and global regulators in response to environmental stimuli. Here, we report that the global regulator integration host factor (IHF) positively affects virulence gene expression in V. cholerae. Inactivation of ihfA and ihfB, the genes encoding the IHF subunits, decreased the expression levels of the two main virulence factors tcpA and ctx and prevented toxin-coregulated pilus and cholera toxin production. IHF was found to directly bind to and bend the tcpA promoter region at an IHF consensus site centered at position 162 …

Hops Proofreads The Trans-Snare Complex For Yeast Vacuole Fusion, Vincent J. Starai, Christopher M. Hickey, William Wickner

Dartmouth Scholarship

No abstract provided.

Molecular Evolution, Michael Dietrich

Dartmouth Scholarship

Comprised of essays by top scholars in the field, this volume offers detailed overviews of philosophical issues raised by biology.

Mechanistic Home Range Models And Resource Selection Analysis: A Reconciliation And Unification, Paul R. Moorcroft, Alex Barnett

Dartmouth Scholarship

In the three decades since its introduction, resource selection analysis (RSA) has become a widespread method for analyzing spatial patterns of animal relocations obtained from telemetry studies. Recently, mechanistic home range models have been proposed as an alternative framework for studying patterns of animal space-use. In contrast to RSA models, mechanistic home range models are derived from underlying mechanistic descriptions of individual movement behavior and yield spatially explicit predictions for patterns of animal space-use. In addition, their mechanistic underpinning means that, unlike RSA, mechanistic home range models can also be used to predict changes in space-use following perturbation. In this …

The Mads-Domain Transcriptional Regulator Agamous-Like15 Promotes Somatic Embryo Development In Arabidopsis And Soybean, Dhiraj Thakare, Weining Tang, Kristine Hill, Sharyn E. Perry

Dartmouth Scholarship

The MADS-domain transcriptional regulator AGAMOUS-LIKE15 (AGL15) has been reported to enhance somatic embryo development when constitutively expressed. Here we report that loss-of-function mutants of AGL15, alone or when combined with a loss-of-function mutant of a closely related family member, AGL18, show decreased ability to produce somatic embryos. If constitutive expression of orthologs of AGL15 is able to enhance somatic embryo development in other species, thereby facilitating recovery of transgenic plants, then AGL15 may provide a valuable tool for crop improvement. To test this idea in soybean (Glycine max), a full-length cDNA encoding a putative ortholog of AGL15 was isolated from …

Drinking-Water Arsenic Exposure Modulates Gene Expression In Human Lymphocytes From A U.S. Population, Angeline S. Andrew, David A. Jewell, Rebecca A. Mason, Michael L. Whitfield, Jason H. Moore, Margaret R. Karagas

Dartmouth Scholarship

Background:

Arsenic exposure impairs development and can lead to cancer, cardiovascular disease, and diabetes. The mechanism underlying these effects remains unknown. Primarily because of geologic sources of contamination, drinking-water arsenic levels are above the current recommended maximum contaminant level of 10 μg/L in the northeastern, western, and north central regions of the United States.

Objectives:

We investigated the effects of arsenic exposure, defined by internal biomarkers at levels relevant to the United States and similarly exposed populations, on gene expression.

Methods:

We conducted separate Affymetrix microarray-based genomewide analyses of expression patterns. Peripheral blood lymphocyte samples from 21 controls interviewed (1999–2002) …

Minimal Components Of The Rna Polymerase Ii Transcription Apparatus Determine The Consensus Tata Box, Gudrun Bjornsdottir, Lawrence C. Myers

Dartmouth Scholarship

In Saccharomyces cerevisiae, multiple approaches have arrived at a consensus TATA box sequence of TATA(T/A)A(A/T)(A/G). TATA-binding protein (TBP) affinity alone does not determine TATA box function. To discover how a minimal set of factors required for basal and activated transcription contributed to the sequence requirements for a functional TATA box, we performed transcription reactions using highly purified proteins and CYC1 promoter TATA box mutants. The TATA box consensus sequence is a good predictor of promoter activity. However, several nonconsensus sequences are almost fully functional, indicating that mechanistic requirements are not the only selective pressure on the TATA box. We …

Systems Approach Identifies An Organic Nitrogen-Responsive Gene Network That Is Regulated By The Master Clock Control Gene Cca1, Rodrigo A. Gutierrez, Trevor L. Stokes, Karen Thum, Xiaodong Xu, Mariana Obertello, Manpreet S. Katari, Milos Tanurdzic, Alexis Dean, Damion C. Nero, C Robertson Mcclung, Gloria M. Coruzzi

Dartmouth Scholarship

Understanding how nutrients affect gene expression will help us to understand the mechanisms controlling plant growth and development as a function of nutrient availability. Nitrate has been shown to serve as a signal for the control of gene expression in Arabidopsis. There is also evidence, on a gene-by-gene basis, that downstream products of nitrogen (N) assimilation such as glutamate (Glu) or glutamine (Gln) might serve as signals of organic N status that in turn regulate gene expression. To identify genome-wide responses to such organic N signals, Arabidopsis seedlings were transiently treated with ammonium nitrate in the presence or absence of …

The Tempo And Mode Of Three‐Dimensional Morphological Evolution In Male Reproductive Structures, Mark A. Mcpeek, Li Shen, John Z. Torrey, Hany Farid

Dartmouth Scholarship

Various evolutionary forces may shape the evolution of traits that influence the mating decisions of males and females. Phe- notypic traits that males and females use to judge the species identify of potential mates should evolve in a punctuated fashion, changing significantly at the time of speciation but changing little between speciation events. In contrast, traits experiencing sexual selection or sexually antagonistic interactions are generally expected to change continuously over time because of the directional selection pressures imposed on one sex by the actions of the other. To test these hy- potheses, we used spherical harmonic representations of the shapes …

Orchestration Of The S-Phase And Dna Damage Checkpoint Pathways By Replication Forks From Early Origins, Julie M. Caldwell, Yinhuai Chen, Kaila L. Schollaert, James F. Theis, George F. Babcock, Carol S. Newlon, Yolanda Sanchez

Dartmouth Scholarship

The S-phase checkpoint activated at replication forks coordinates DNA replication when forks stall because of DNA damage or low deoxyribonucleotide triphosphate pools. We explore the involvement of replication forks in coordinating the S-phase checkpoint using dun1Δ cells that have a defect in the number of stalled forks formed from early origins and are dependent on the DNA damage Chk1p pathway for survival when replication is stalled. We show that providing additional origins activated in early S phase and establishing a paused fork at a replication fork pause site restores S-phase checkpoint signaling to chk1Δ dun1Δ cells and relieves the reliance …

Darwin's Gift To Science And Religion, Michael Dietrich

Dartmouth Scholarship

Review of Darwin's Gift to Science and Religion by Francisco Ayala, 2007.

Variation In Molybdenum Content Across Broadly Distributed Populations Of Arabidopsis Thaliana Is Controlled By A Mitochondrial Molybdenum Transporter (Mot1), Ivan Baxter, Balasubramaniam Muthukumar, Hyeong Cheol Park, Peter Buchner, Brett Lahner, John Danku, Keyan Zhao, Joohyun Lee, Malcolm J. Hawkesford, Mary Lou Guerinot, David E. Salt

Dartmouth Scholarship

Molybdenum (Mo) is an essential micronutrient for plants, serving as a cofactor for enzymes involved in nitrate assimilation, sulfite detoxification, abscisic acid biosynthesis, and purine degradation. Here we show that natural variation in shoot Mo content across 92 Arabidopsis thaliana accessions is controlled by variation in a mitochondrially localized transporter (Molybdenum Transporter 1 - MOT1) that belongs to the sulfate transporter superfamily. A deletion in the MOT1 promoter is strongly associated with low shoot Mo, occurring in seven of the accessions with the lowest shoot content of Mo. Consistent with the low Mo phenotype, MOT1 expression in low Mo accessions …