Search

We report here the complete genome sequences of 44 phages infecting Arthrobacter sp. strain ATCC 21022. These phages have double-stranded DNA genomes with sizes ranging from 15,680 to 70,707 bp and G+C contents from 45.1% to 68.5%. All three tail types (belonging to the families Siphoviridae , Myoviridae , and Podoviridae ) are represented.

Bacteriophages AlleyCat, Edugator, and Guillsminger were isolated on Mycobacterium smegmatis mc 2 155 from enriched soil samples. All are members of mycobacteriophage subcluster K5, with genomes of 62,112 to 63,344 bp. Each genome contains 92 to 99 predicted protein-coding genes and one tRNA. Guillsminger is the first mycobacteriophage to carry an IS 1380 family transposon.

The KDM4/JMJD2 family of histone demethylases is amplified in human cancers. However, little is known about their physiologic or tumorigenic roles. We have identified a conserved and unappreciated role for the JMJD2A/KDM4A H3K9/36 tridemethylase in cell cycle progression. We demonstrate that JMJD2A protein levels are regulated in a cell cycle-dependent manner and that JMJD2A overexpression increased chromatin accessibility, S phase progression, and altered replication timing of specific genomic loci. These phenotypes depended on JMJD2A enzymatic activity. Strikingly, depletion of the only C. elegans homolog, JMJD-2, slowed DNA replication and increased ATR/p53-dependent apoptosis. Importantly, overexpression of HP1γ antagonized JMJD2A-dependent progression through S phase, and depletion of HPL-2 rescued the DNA replication-related phenotypes in jmjd-2(-/-) animals. Our findings describe a highly conserved model whereby JMJD2A regulates DNA replication by antagonizing HP1γ and controlling chromatin accessibility.

Chromatin-modifying enzymes play a fundamental role in regulating chromatin structure so that DNA replication is spatially and temporally coordinated. For example, the lysine demethylase 4A/Jumonji domain-containing 2A (KDM4A/JMJD2A) is tightly regulated during the cell cycle. Overexpression of JMJD2A leads to altered replication timing and faster S phase progression. In this study, we demonstrate that degradation of JMJD2A is regulated by the proteasome. JMJD2A turnover is coordinated through the SKP1-Cul1-F-box ubiquitin ligase complex that contains cullin 1 and the F-box and leucine-rich repeat protein 4 (FbxL4). This complex interacted with JMJD2A. Ubiquitin overexpression restored turnover and blocked the JMJD2A-dependent faster S phase progression in a cullin 1-dependent manner. Furthermore, increased ubiquitin levels decreased JMJD2A occupancy and BrdU incorporation at target sites. This study highlights a finely tuned mechanism for regulating histone demethylase levels and emphasizes the need to tightly regulate chromatin modifiers so that the cell cycle occurs properly.

Background Western Kentucky University is a member of a select group of colleges and universities chosen to participate in a national science experiment designed to improve undergraduate science education. To introduce freshman students to authentic research, the Howard Hughes Medical Institute’s Science Education Alliance (HHMI SEA) has implemented an innovative program to introduce genomics into the classroom. The program draws on themes and techniques from biology, microbiology, molecular biology, genomics and bioinformatics. The WKU course is called “Genome Discovery and Exploration” (GDE); WKU Genome Discovery and Exploration Program [http://bioweb.wku.edu/asp/wkungri/]. During the fall semester, students isolate bacterial viruses from the environment and characterize them using a variety of techniques including DNA analysis and electron microscopy. Over the winter break, the complete DNA sequence of one of the viruses isolated by the GDE students is determined. During the spring semester, GDE students learn how use computer programs (e.g. Consed, Glimmer, Genemark, BLAST and Phamerator) to identify all the viral genes and to make genome wide comparisons to identify evolutionary relationships. All course participants and the SEA staff are connected via the internet to share and analyze data, troubleshoot, and discuss results. Near the end of the spring semester, HHMI hosts a research symposium for course faculty and one student from each institution to report on their discoveries and experiences. As unique phages are characterized on campuses nationwide, students will have the opportunity to publish their research for the broader scientific community. This hands-on experience with the tools of Bioinformatics is an outstanding training opportunity and this unique program has helped the WKU Biology Department create an introductory pipeline to research experiences that complements our existing and planned instructional programs and allows freshman to engage in the thrill of discovery.

Background In order to develop treatments or preventive measures for auditory hair cell loss, an understanding of both the process of auditory hair cell regeneration and factors that influence this process, is needed. Our previous microarray analysis showed that growth hormone (GH) was significantly upregulated during zebrafish auditory hair cell regeneration, coupled with cell proliferation [1,2]. We further tested the effects of GH on zebrafish auditory hair cell regeneration by injecting GH after sound exposure and found that GH can efficiently promote post-trauma auditory hair cell regeneration, which may be achieved through stimulating proliferation and suppressing apoptosis [3]. In the current study, we used Next Generation Sequencing (NGS) to examine the possible GH pathways involved in zebrafish auditory hair cell regeneration.

Background Toxoplasmosis, caused by the protozoan parasite Toxoplasma gondii is a major cause of morbidity and mortality in patients with AIDS and an important cause of miscarriage, stillbirth and congenital disease in newborns. Previous studies have provided evidence that dietary supplementation with vitamin E and selenium is harmful during experimental toxoplasmosis in mice, whereas a diet deficient in vitamin E and selenium results in decreased numbers of tissue cysts in the brain and dramatically reduced brain pathology. The overall goal of the present study was to determine the impact of dietary supplementation with antioxidants on gene expression in the brains of non-infected mice and in mice infected with T. gondii using microarray analysis. RNA was isolated from the brains of C57BL/6 mice, and an Agilent Oligo Whole Mouse Genome Microarray (Agilent Technologies, Inc.) was performed. A total of 48 chips were normalized by Z ratios and the Data Driven Harr Fisch Normalization methods. Differentially expressed genes were identified by applying thresholds to identify significant values and the results were compared between the normalization methods. These differentially expressed genes and their respective fold change ratios were used in Ingenuity Pathway Analysis (IPA) software to analyze the pathways involved with these genes.

Material and methods The Wizard007 bacteriophage was isolated from a soil sample taken at N36° 49’36.8” W87° 29’42.5” in Hopkinsville, KY. It was plaque purified on Mycobacterium smegmatis and DNA was isolated using the Promega Wizard DNA purification kit. The DNA was sequenced at the Virginia Commonwealth University by Roche 454 DNA sequencing. The genome quality was confirmed in Consed [1] and found to be 51,034 bp in length. Genes were called from the assembled sequence with a workflow consisting of Glimmer [2], GeneMark [3], tRNAscan [4], and SDFinder to identify potential gene features. Gbrowse [5], Apollo [6], and BLAST [7] were used to call and annotate genes. A 10 base 3’ overhang was found at the ends by ligating the genomic DNA and sequencing a PCR product produced across the ligated ends.

A method is described for the analysis of the isotope distribution in malate(C-2,3). In a single test-tube reaction, the inner carbon atoms of malate are enzymically converted to acetate and are stereospecifically incorporated into citrate as acetyl-CoA. A rapid method for obtaining the intramolecular isotope distribution in citrate(C-1,2) permits calculation of the isotope distribution and specific activity of the original malate carbon atoms. The error is less than 3%. This method is relevant to the recently reported problem of anomalous isotope distributions in the organic acids of C3 plants following short-term photosynthesis in 14CO2.

Materials and methods In this study we compared the codon frequencies between the phages that carry tRNA in their genome (Clusters A2, A3, A5, A6, A9, C1, C2, E, J, K1, L1, L2, M) to those phages without tRNA in their genome (Clusters A1, A4, B1, B2, D, F1, G) in order to determine whether the tRNAs being carried by the mycobacteriophages were needed to survive in M. smegmatis. The phages with embedded tRNAs were drawn from http:// phagesdb.org/data/. The coding sequences for the mycobacteriophages were obtained from NCBI GenBank [2]. Codon frequencies were derived for each mycobacteriophage and a BoxWhiskerChart (Figure 1) was made using a program written in Mathematica. To determine which codons may require expression of phage tRNAs, Figure 1 plot regions for phages containing tRNA (red) that show frequencies in excess of those not containing tRNA (blue) have been circled in magenta. Only a few codons meet this criteria: ACT, ATG, CAG***, CGT, GAC**, GAG*, TAC, TAT, TGG. A significant number of mycobacteriophages lay outside the non-tRNA phage boundaries for codons CAG, GAC

The University of Tennessee (UT), the Oak Ridge National Laboratory (ORNL), and the Kentucky Biomedical Research Infrastructure Network (KBRIN), have collaborated over the past eleven years to share research and educational expertise in bioinformatics. One result of this collaboration is the joint sponsorship of an annual regional summit to bring together researchers, educators and students who are interested in bioinformatics from a variety of research and educational institutions. This summit provides unique opportunities for collaboration and forging links between members of the various institutions. This year, the Eleventh Annual UT-ORNL-KBRIN Bioinformatics Summit was held at the Seelbach Hilton Hotel in Louisville, Kentucky from March 30-April 1, 2012. A total of 232 participants pre-registered for the summit, with 126 from various Kentucky institutions and 80 from various Tennessee institutions. A number of additional participants came from universities and research institutions from other states and countries, e.g. University of Arkansas Medical Sciences, Michigan State University, University of Cincinnati, Iowa State University, etc. Eighty-four registrants were faculty, with an additional 68 students, 37 staff, and 32 postdoctoral participants (with 12 undeclared). The conference program consisted of three days of presentations. The first day included a pre-summit of talks by Kentucky researchers and a workshop on Next-Generation Sequencing technologies. The next two days were dedicated to scientific presentations divided into four plenary sessions on Next-Generation Sequencing, Medical Informatics, Metagenomics, and Behavioral and Comparative Genomics. The Medical Informatics session was followed by four short talks, selected from 47 submitted poster abstracts.

* Correspondence: claire.rinehart@wku.edu Department of Biology, Western Kentucky University, Bowling Green, KY, 42101, USA Figure 1 Seven predicted pham 6714 structures superimposed into a single model matching methyltransferase structures. PDB files were rendered using UCSF Chimera (http://www.cgl.ucsf.edu/chimera/). Proteins include MeeZee gp 78, JN243856.1; Backyardigan gp 74, JF704093.1; and ShiLan gp 70, JN020143.1 Kapadia and Rinehart BMC Bioinformatics 2013, 14(Suppl 17):A10 http://www.biomedcentral.com/1471-2105/14/S17/A10