Genomics Commons^™

Gene Response Profiles For Daphnia Pulex Exposed To The Environmental Stressor Cadmium Reveals Novel Crustacean Metallothioneins, Joseph R. Shaw, John K. Colbourne, Jennifer C. Davey, Stephen P. Glaholt, Thomas H. Hampton, Celia Y. Chen, Carol L. Folt, Joshua W. Hamilton

Dartmouth Scholarship

Genomic research tools such as microarrays are proving to be important resources to study the complex regulation of genes that respond to environmental perturbations. A first generation cDNA microarray was developed for the environmental indicator species Daphnia pulex, to identify genes whose regulation is modulated following exposure to the metal stressor cadmium. Our experiments revealed interesting changes in gene transcription that suggest their biological roles and their potentially toxicological features in responding to this important environmental contaminant.

A Regulator Of Dscam Mutually Exclusive Splicing Fidelity, Sara Olson, Yiannis Savva, Jung Park, Brenton R. Graveley

UCHC Articles - Research

The Down syndrome cell adhesion molecule (Dscam) gene has essential roles in neural wiring and pathogen recognition in Drosophila melanogaster. Dscam encodes 38,016 distinct isoforms via extensive alternative splicing. The 95 alternative exons in Dscam are organized into clusters that are spliced in a mutually exclusive manner. The exon 6 cluster contains 48 variable exons and uses a complex system of competing RNA structures to ensure that only one variable exon is included. Here we show that the heterogeneous nuclear ribonucleoprotein hrp36 acts specifically within, and throughout, the exon 6 cluster to prevent the inclusion of multiple exons. Moreover, hrp36 …

Sampling Daphnia's Expressed Genes: Preservation, Expansion And Invention Of Crustacean Genes With Reference To Insect Genomes, John K. Colbourne, Brian D. Eads, Joseph Shaw, Elizabeth Bohuski, Darren Bauer, Justen Andrews

Dartmouth Scholarship

Functional and comparative studies of insect genomes have shed light on the complement of genes, which in part, account for shared morphologies, developmental programs and life-histories. Contrasting the gene inventories of insects to those of the nematodes provides insight into the genomic changes responsible for their diversification. However, nematodes have weak relationships to insects, as each belongs to separate animal phyla. A better outgroup to distinguish lineage specific novelties would include other members of Arthropoda. For example, crustaceans are close allies to the insects (together forming Pancrustacea) and their fascinating aquatic lifestyle provides an important comparison for understanding the genetic …

Identification Of Synechococcus Sp. Iu 625 Metallothionein Gene And Its Evolutionary Relationship To The Metallothionein Gene Of Other Cyanobacteria, Tin-Chun Chu, Lee Lee, John Gaynor, Quinn Vega, Bonnie Lustigman, Shankar Srinivasan

Tin-Chun Chu, Ph.D.

No abstract provided.

Genomic And Microarray Analysis Of Aromatics Degradation In Geobacter Metallireducens And Comparison To A Geobacter Isolate From A Contaminated Field Site, Jessica E. Butler, Qiang He, Kelly P. Nevin, Zhili He, Jizhong Zhou, Derek R. Lovley

Faculty Publications and Other Works -- General Biology

Background

Groundwater and subsurface environments contaminated with aromatic compounds can be remediated in situ by Geobacter species that couple oxidation of these compounds to reduction of Fe(III)-oxides. Geobacter metallireducens metabolizes many aromatic compounds, but the enzymes involved are not well known.

Results

The complete G. metallireducens genome contained a 300 kb island predicted to encode enzymes for the degradation of phenol, p-cresol, 4-hydroxybenzaldehyde, 4-hydroxybenzoate, benzyl alcohol, benzaldehyde, and benzoate. Toluene degradation genes were encoded in a separate region. None of these genes was found in closely related species that cannot degrade aromatic compounds. Abundant transposons and phage-like genes in …

Comparative Chloroplast Genomics: Analyses Including New Sequences From The Angiosperms Nuphar Advena And Ranunculus Macranthus, Linda A. Raubeson, Rhiannon Peery, Timothy W. Chumley, Chris Dziubek, H. Matthew Fourcade, Jeffrey L. Boore, Robert K. Jansen

All Faculty Scholarship for the College of the Sciences

Background

The number of completely sequenced plastid genomes available is growing rapidly. This array of sequences presents new opportunities to perform comparative analyses. In comparative studies, it is often useful to compare across wide phylogenetic spans and, within angiosperms, to include representatives from basally diverging lineages such as the genomes reported here: Nuphar advena (from a basal-most lineage) and Ranunculus macranthus (a basal eudicot). We report these two new plastid genome sequences and make comparisons (within angiosperms, seed plants, or all photosynthetic lineages) to evaluate features such as the status of ycf15 and ycf68 as protein coding genes, the distribution …

On The Functions Of The H Subunit Of Eukaryotic Initiation Factor 3 In Late Stages Of Translation Initiation, Byung-Hoon Kim, Xue Cai, Justin N. Vaughn, Albrecht G. Von Arnim

Faculty Publications and Other Works -- General Biology

Background

The eukaryotic translation initiation factor 3 (eIF3) has multiple roles during the initiation of translation of cytoplasmic mRNAs. How individual subunits of eIF3 contribute to the translation of specific mRNAs remains poorly understood, however. This is true in particular for those subunits that are not conserved in budding yeast, such as eIF3h.

Results

Working with stable reporter transgenes in Arabidopsis thaliana mutants, it was demonstrated that the h subunit of eIF3 contributes to the efficient translation initiation of mRNAs harboring upstream open reading frames (uORFs) in their 5' leader sequence. uORFs, which can function as devices for translational regulation, …

Maptogenome: A Comparative Genomic Tool That Aligns Transcript Maps To Sequenced Genomes, Srikrishna Putta, Jeramiah J. Smith, Chuck Staben, S. Randal Voss

Biology Faculty Publications

Efforts to generate whole genome assemblies and dense genetic maps have provided a wealth of gene positional information for several vertebrate species. Comparing the relative location of orthologous genes among these genomes provides perspective on genome evolution and can aid in translating genetic information between distantly related organisms. However, large-scale comparisons between genetic maps and genome assemblies can prove challenging because genetic markers are commonly derived from transcribed sequences that are incompletely and variably annotated. We developed the program MapToGenome as a tool for comparing transcript maps and genome assemblies. MapToGenome processes sequence alignments between mapped transcripts and whole genome …

Genome-Wide Patterns Of Nucleotide Polymorphism In Domesticated Rice, Ana Caicedo, S. Williamson, R, Hernandez, A. Boyko, A. Fleded-Alon, T. York, N. Polato, K. Olsen, R. Nielsen, S. Mccouch, C. Bustamante, M. Purugganan

Biology Department Faculty Publication Series

Domesticated Asian rice (Oryza sativa) is one of the oldest domesticated crop species in the world, having fed more people than any other plant in human history. We report the patterns of DNA sequence variation in rice and its wild ancestor, O. rufipogon, across 111 randomly chosen gene fragments, and use these to infer the evolutionary dynamics that led to the origins of rice. There is a genome-wide excess of high-frequency derived single nucleotide polymorphisms (SNPs) in O. sativa varieties, a pattern that has not been reported for other crop species. We developed several alternative models to explain contemporary patterns …

Genome-Wide Patterns Of Nucleotide Polymorphism In Domesticated Rice, Ana Lucia Caicedo, S. H. Williamson, R, D. Hernandez, A. Boyko, A. Fleded-Alon, T. L. York, N. Polato, K. M. Olsen, R. Nielsen, S. Mccouch, C. D. Bustamante, M. D. Purugganan

Ana Lucia Caicedo

Domesticated Asian rice (Oryza sativa) is one of the oldest domesticated crop species in the world, having fed more people than any other plant in human history. We report the patterns of DNA sequence variation in rice and its wild ancestor, O. rufipogon, across 111 randomly chosen gene fragments, and use these to infer the evolutionary dynamics that led to the origins of rice. There is a genome-wide excess of high-frequency derived single nucleotide polymorphisms (SNPs) in O. sativa varieties, a pattern that has not been reported for other crop species. We developed several alternative models to explain contemporary patterns …

Sensory Genes And Mate Choice: Evidence That Duplications, Mutations, And Adaptive Evolution Alter Variation In Mating Cue Genes And Their Receptors, Lisa Horth

Biological Sciences Faculty Publications

Fascinating new data, revealed through gene sequencing, comparative genomics, and genetic engineering, precisely establish which genes are involved in mate choice and mating activity—behaviors that are surprisingly understudied from a genetic perspective. Discussed here are some of the recently identified visual and chemosensory genes that are involved in mate choice and mating behavior. These genes’ products are involved in the production, transmission, and receipt of crucial sensory mate-choice cues that affect fitness. This review exposes newfound evidence that alternative splicing, gene-expression pattern changes, and molecular genetic variation in sensory genes are crucial for both intra- and interspecific mate choice and …

Chess, Chance And Conspiracy, Mark Segal

Mark R Segal

Chess and chance are seemingly strange bedfellows. Luck and/or randomness have no apparent role in move selection when the game is played at the highest levels. However, when competition is at the ultimate level, that of the World Chess Championship (WCC), chess and conspiracy are not strange bedfellows, there being a long and colorful history of accusations levied between participants. One such accusation, frequently repeated, was that all the games in the 1985 WCC (Karpov vs Kasparov) were fixed and prearranged move by move. That this claim was advanced by a former World Champion, Bobby Fischer, argues that it ought …

Does Direct Optimization Produce More Accurate Alignments And Topologies? Poy Vs. Clustalw+Paup*, T. Heath Ogden

T. Heath Ogden

Direct optimization frameworks for simultaneously estimating alignments and phylogenies have recently been developed. One such method, implemented in the program POY, is becoming more common for analyses of variable length sequences (e.g., analyses using ribosomal genes) and for combined evidence analyses (morphology + multiple genes). Simulation of sequences containing insertion and deletion events was performed in order to directly compare a widely used method of multiple sequence alignment (ClustalW) and subsequent parsimony analysis in PAUP* with direct optimization via POY. Data sets were simulated for pectinate, balanced, and random tree shapes under different conditions (clocklike, non-clocklike, and ultrametric). Alignment accuracy …

How Should Gaps Be Treated In Parsimony? A Comparison Of Approaches Using Simulation, T. Heath Ogden

T. Heath Ogden

Simulation with indels was used to produce alignments where true site homologies in DNA sequences were known; the gaps from these datasets were removed and the sequences were then aligned to produce hypothesized alignments. Both alignments were then analyzed under three widely used methods of treating gaps during tree reconstruction under the maximum parsimony principle. With the true alignments, for many cases (82%), there was no diVerence in topological accuracy for the diVerent methods of gap coding. However, in cases where a diVerence was present, coding gaps as a Wfth state character or as separate presence/absence characters outperformed treating gaps …