Genetics and Genomics Commons^™

The Drosophila Homolog Of The Mammalian Imprint Regulator, Ctcf, Maintains The Maternal Genomic Imprint In Drosophila Melanogaster, William A. Macdonald, Debashish Menon, Nicholas J. Bartlett, G Elizabeth Sperry, Vanya Rasheva, Victoria Meller, Vett K. Lloyd

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

CTCF is a versatile zinc finger DNA-binding protein that functions as a highly conserved epigenetic transcriptional regulator. CTCF is known to act as a chromosomal insulator, bind promoter regions, and facilitate long-range chromatin interactions. In mammals, CTCF is active in the regulatory regions of some genes that exhibit genomic imprinting, acting as insulator on only one parental allele to facilitate parent-specific expression. In Drosophila, CTCF acts as a chromatin insulator and is thought to be actively involved in the global organization of the genome.

Results

To determine whether CTCF regulates imprinting in Drosophila, we generated CTCF mutant alleles …

Functional Analysis Of B And C Class Floral Organ Genes In Spinach Demonstrates Their Role In Sexual Dimorphism, D Noah Sather, Maja Jovanovic, Edward M. Golenberg

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Evolution of unisexual flowers entails one of the most extreme changes in plant development. Cultivated spinach, Spinacia oleracea L., is uniquely suited for the study of unisexual flower development as it is dioecious and it achieves unisexually by the absence of organ development, rather than by organ abortion or suppression. Male staminate flowers lack fourth whorl primordia and female pistillate flowers lack third whorl primordia. Based on theoretical considerations, early inflorescence or floral organ identity genes would likely be directly involved in sex-determination in those species in which organ initiation rather than organ maturation is regulated. In this …

Primate Phylogenomics: Developing Numerous Nuclear Non-Coding, Non-Repetitive Markers For Ecological And Phylogenetic Applications And Analysis Of Evolutionary Rate Variation, Zuogang Peng, Navin Elango, Derek E. Wildman, Soojin V. Yi

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Genetic analyses are often limited by the availability of appropriate molecular markers. Markers from neutrally evolving genomic regions may be particularly useful for inferring evolutionary histories because they escape the constraints of natural selection. For the majority of taxa however, obtaining such markers is challenging. Advances in genomics have the potential to alleviate the shortage of neutral markers. Here we present a method to develop numerous markers from putatively neutral regions of primate genomes.

Results

We began with the available whole genome sequences of human, chimpanzee and macaque. Using computational methods, we identified a total of 280 potential …

Development Of A Gene Silencing Dna Vector Derived From A Broad Host Range Geminivirus, Edward M. Golenberg, D Noah Sather, Leandria C. Hancock, Kenneth J. Buckley, Natalie M. Villafranco, David M. Bisaro

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Gene silencing is proving to be a powerful tool for genetic, developmental, and physiological analyses. The use of viral induced gene silencing (VIGS) offers advantages to transgenic approaches as it can be potentially applied to non-model systems for which transgenic techniques are not readily available. However, many VIGS vectors are derived from Gemini viruses that have limited host ranges. We present a new, unipartite vector that is derived from a curtovirus that has a broad host range and will be amenable to use in many non-model systems.

Results

The construction of a gene silencing vector derived from the …

Sexual Differentiation Of The Zebra Finch Song System: Potential Roles For Sex Chromosome Genes, Michelle L. Tomaszycki, Camilla Peabody, Kirstin Replogle, David F. Clayton, Robert J. Tempelman, Juli Wade

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Recent evidence suggests that some sex differences in brain and behavior might result from direct genetic effects, and not solely the result of the organizational effects of steroid hormones. The present study examined the potential role for sex-biased gene expression during development of sexually dimorphic singing behavior and associated song nuclei in juvenile zebra finches.

Results

A microarray screen revealed more than 2400 putative genes (with a false discovery rate less than 0.05) exhibiting sex differences in the telencephalon of developing zebra finches. Increased expression in males was confirmed in 12 of 20 by qPCR using cDNA from …

Development And Evaluation Of New Mask Protocols For Gene Expression Profiling In Humans And Chimpanzees, Donna M. Toleno, Gabriel Renaud, Tyra G. Wolfsberg, Munirul Islam, Derek E. Wildman, Kimberly D. Siegmund, Joseph G. Hacia

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Cross-species gene expression analyses using oligonucleotide microarrays designed to evaluate a single species can provide spurious results due to mismatches between the interrogated transcriptome and arrayed probes. Based on the most recent human and chimpanzee genome assemblies, we developed updated and accessible probe masking methods that allow human Affymetrix oligonucleotide microarrays to be used for robust genome-wide expression analyses in both species. In this process, only data from oligonucleotide probes predicted to have robust hybridization sensitivity and specificity for both transcriptomes are retained for analysis.

Results

To characterize the utility of this resource, we applied our mask protocols …

The Caenorhabditis Globin Gene Family Reveals Extensive Nematode-Specific Radiation And Diversification, David Hoogewijs, Sasha De Henau, Sylvia Dewilde, Luc Moens, Marjolein Couvreur, Gaetan Borgonie, Serge N. Vinogradov, Scott W. Roy, Jacques R. Vanfleteren

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Globin isoforms with variant properties and functions have been found in the pseudocoel, body wall and cuticle of various nematode species and even in the eyespots of the insect-parasite Mermis nigrescens. In fact, much higher levels of complexity exist, as shown by recent whole genome analysis studies. In silico analysis of the genome of Caenorhabditis elegans revealed an unexpectedly high number of globin genes featuring a remarkable diversity in gene structure, amino acid sequence and expression profiles.

Results

In the present study we have analyzed whole genomic data from C. briggsae, C. remanei, Pristionchus pacificus and Brugia malayi …

Droid: The Drosophila Interactions Database, A Comprehensive Resource For Annotated Gene And Protein Interactions, Jingkai Yu, Svetlana Pacifico, Guozhen Liu, Russell L. Finley Jr

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Charting the interactions among genes and among their protein products is essential for understanding biological systems. A flood of interaction data is emerging from high throughput technologies, computational approaches, and literature mining methods. Quick and efficient access to this data has become a critical issue for biologists. Several excellent multi-organism databases for gene and protein interactions are available, yet most of these have understandable difficulty maintaining comprehensive information for any one organism. No single database, for example, includes all available interactions, integrated gene expression data, and comprehensive and searchable gene information for the important model organism, Drosophila melanogaster. …

Mcm-Test: A Fuzzy-Set-Theory-Based Approach To Differential Analysis Of Gene Pathways, Lily R. Liang, Vinay Mandal, Yi Lu, Deepak Kumar

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Gene pathway can be defined as a group of genes that interact with each other to perform some biological processes. Along with the efforts to identify the individual genes that play vital roles in a particular disease, there is a growing interest in identifying the roles of gene pathways in such diseases.

Results

This paper proposes an innovative fuzzy-set-theory-based approach, Multi-dimensional Cluster Misclassification test (MCM-test), to measure the significance of gene pathways in a particular disease. Experiments have been conducted on both synthetic data and real world data. Results on published diabetes gene expression dataset and a list …

Molecular Evolution Of The Cytochrome C Oxidase Subunit 5a Gene In Primates, Monica Uddin, Juan C. Opazo, Derek E. Wildman, Chet C. Sherwood, Patrick R. Hof, Morris Goodman, Lawrence I. Grossman

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Many electron transport chain (ETC) genes show accelerated rates of nonsynonymous nucleotide substitutions in anthropoid primate lineages, yet in non-anthropoid lineages the ETC proteins are typically highly conserved. Here, we test the hypothesis that COX5A, the ETC gene that encodes cytochrome c oxidase subunit 5A, shows a pattern of anthropoid-specific adaptive evolution, and investigate the distribution of this protein in catarrhine brains.

Results

In a dataset comprising 29 vertebrate taxa, including representatives from all major groups of primates, there is nearly 100% conservation of the COX5A amino acid sequence among extant, non-anthropoid placental mammals. The most recent common …

Genomic And Gene Regulatory Signatures Of Cryptozoic Adaptation: Loss Of Blue Sensitive Photoreceptors Through Expansion Of Long Wavelength-Opsin Expression In The Red Flour Beetle Tribolium Castaneum, Magdalena Jackowska, Riyue Bao, Zhenyi Liu, Elizabeth C. Mcdonald, Tiffany A. Cook, Markus Friedrich

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Recent genome sequence analysis in the red flour beetle Tribolium castaneum indicated that this highly crepuscular animal encodes only two single opsin paralogs: a UV-opsin and a long wavelength (LW)-opsin; however, these animals do not encode a blue (B)-opsin as most other insects. Here, we studied the spatial regulation of the Tribolium single LW- and UV-opsin gene paralogs in comparison to that of the five opsin paralogs in the retina of Drosophila melanogaster.

Results

In situ hybridization analysis reveals that the Tribolium retina, in contrast with other insect retinas, constitutes a homogenous field of ommatidia that have seven …

Ocpat: An Online Codon-Preserved Alignment Tool For Evolutionary Genomic Analysis Of Protein Coding Sequences, Guozhen Liu, Monica Uddin, Munirul Islam, Morris Goodman, Lawrence I. Grossman, Roberto Romero, Derek E. Wildman

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Rapidly accumulating genome sequence data from multiple species offer powerful opportunities for the detection of DNA sequence evolution. Phylogenetic tree construction and codon-based tests for natural selection are the prevailing tools used to detect functionally important evolutionary change in protein coding sequences. These analyses often require multiple DNA sequence alignments that maintain the correct reading frame for each collection of putative orthologous sequences. Since this feature is not available in most alignment tools, codon reading frames often must be checked manually before evolutionary analyses can commence.

Results

Here we report an online codon-preserved alignment tool (OCPAT) that generates …

Whole Genome Expression Profiling Reveals A Significant Role For Immune Function In Human Abdominal Aortic Aneurysms, Guy M. Lenk, Gerard Tromp, Shantel Weinsheimer, Zoran Gatalica, Ramon Berguer, Helena Kuivaniemi

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Abdominal aortic aneurysms are a common disorder with an incompletely understood etiology. We used Illumina and Affymetrix microarray platforms to generate global gene expression profiles for both aneurysmal (AAA) and non-aneurysmal abdominal aorta, and identified genes that were significantly differentially expressed between cases and controls.

Results

Affymetrix and Illumina arrays included 18,057 genes in common; 11,542 (64%) of these genes were considered to be expressed in either aneurysmal or normal abdominal aorta. There were 3,274 differentially expressed genes with a false discovery rate (FDR) ≤ 0.05. Many of these genes were not previously known to be involved in …

Fm-Test: A Fuzzy-Set-Theory-Based Approach To Differential Gene Expression Data Analysis, Lily R. Liang, Shiyong Lu, Xuena Wang, Yi Lu, Vinay Mandal, Dorrelyn Patacsil, Deepak Kumar

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Microarray techniques have revolutionized genomic research by making it possible to monitor the expression of thousands of genes in parallel. As the amount of microarray data being produced is increasing at an exponential rate, there is a great demand for efficient and effective expression data analysis tools. Comparison of gene expression profiles of patients against those of normal counterpart people will enhance our understanding of a disease and identify leads for therapeutic intervention.

Results

In this paper, we propose an innovative approach, fuzzy membership test (FM-test), based on fuzzy set theory to identify disease associated genes from microarray …

Nymphal Rnai: Systemic Rnai Mediated Gene Knockdown In Juvenile Grasshopper, Ying Dong, Markus Friedrich

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Grasshopper serves as important model system in neuroscience, development and evolution. Representatives of this primitive insect group are also highly relevant targets of pest control efforts. Unfortunately, the lack of genetics or gene specific molecular manipulation imposes major limitations to the study of grasshopper biology.

Results

We investigated whether juvenile instars of the grasshopper species Schistocerca americana are conducive to gene silencing via the systemic RNAi pathway. Injection of dsRNA corresponding to the eye colour gene vermilion into first instar nymphs triggered suppression of ommochrome formation in the eye lasting through two instars equivalent to 10–14 days in …

Phylogenomic Identification Of Five New Human Homologs Of The Dna Repair Enzyme Alkb, Michal A. Kurowski, Ashok S. Bhagwat, Grzegorz Papaj, Janusz M. Bujnicki

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Combination of biochemical and bioinformatic analyses led to the discovery of oxidative demethylation – a novel DNA repair mechanism catalyzed by the Escherichia coli AlkB protein and its two human homologs, hABH2 and hABH3. This discovery was based on the prediction made by Aravind and Koonin that AlkB is a member of the 2OG-Fe²⁺ oxygenase superfamily.

Results

In this article, we report identification and sequence analysis of five human members of the (2OG-Fe²⁺) oxygenase superfamily designated here as hABH4 through hABH8. These experimentally uncharacterized and poorly annotated genes were not associated with the AlkB family …

Mouse Ribonuclease Iii. Cdna Structure, Expression Analysis, And Chromosomal Location, Kristine R. Fortin, Rhonda H. Nicholson, Allen W. Nicholson

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Members of the ribonuclease III superfamily of double-stranded(ds)-RNA-specific endoribonucleases participate in diverse RNA maturation and decay pathways in eukaryotic and prokaryotic cells. A human RNase III orthologue has been implicated in ribosomal RNA maturation. To better understand the structure and mechanism of mammalian RNase III and its involvement in RNA metabolism we determined the cDNA structure, chromosomal location, and expression patterns of mouse RNase III.

Results

The predicted mouse RNase III polypeptide contains 1373 amino acids (~160 kDa). The polypeptide exhibits a single C-terminal dsRNA-binding motif (dsRBM), tandem catalytic domains, a proline-rich region (PRR) and an RS domain. …

A Simple Method For Generating Full Length Cdna From Low Abundance Partial Genomic Clones, Yongxin Wang, Joseph M. Fugaro, Fauzia Siddiq, Chandra Mouli V. Goparaju, Fulvio Lonardo, Anil Wali, John F. Lechner, Harvey I. Pass

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

PCR amplification of target molecules involves sequence specific primers that flank the region to be amplified. While this technique is generally routine, its applicability may not be sufficient to generate a desired target molecule from two separate regions involving intron /exon boundaries. For these situations, the generation of full-length complementary DNAs from two partial genomic clones becomes necessary for the family of low abundance genes.

Results

The first approach we used for the isolation of full-length cDNA from two known genomic clones of Hox genes was based on fusion PCR. Here we describe a simple and efficient method …