Rna Sequencing Analysis Of The Developing Chicken Retina, Christophe Langouet-Astrie, Annamarie Meinsen, Emily R. Grunwald, Stephen Turner, Raymond A. Enke
Nov 2016
Rna Sequencing Analysis Of The Developing Chicken Retina, Christophe Langouet-Astrie, Annamarie Meinsen, Emily R. Grunwald, Stephen Turner, Raymond A. Enke
JMU CGEMS
RNA sequencing transcriptome analysis using massively parallel next generation sequencing technology provides the capability to understand global changes in gene expression throughout a range of tissue samples. Development of the vertebrate retina requires complex temporal orchestration of transcriptional activation and repression. The chicken embryo (Gallus gallus) is a classic model system for studying developmental biology and retinogenesis. Existing retinal transcriptome projects have been critical to the vision research community for studying aspects of murine and human retinogenesis, however, there are currently no publicly available data sets describing the developing chicken retinal transcriptome. Here we used Illumina RNA sequencing …
Embryonic Development And A Quantitative Model Of Programmed Dna Elimination In Mesocyclops Edax (S. A. Forbes, 1891) (Copepoda: Cyclopoida), Michelle K. Clower, Ashton S. Holub, Rebecca T. Smith, Grace A. Wyngaard
Oct 2016
Embryonic Development And A Quantitative Model Of Programmed Dna Elimination In Mesocyclops Edax (S. A. Forbes, 1891) (Copepoda: Cyclopoida), Michelle K. Clower, Ashton S. Holub, Rebecca T. Smith, Grace A. Wyngaard
JMU CGEMS
The highly programmed fragmentation of chromosomes and elimination of large amounts of nuclear DNA from the presomatic cell lineages (i.e., chromatin diminution), occurs in the embryos of the freshwater zooplankton Mesocyclops edax (S. A. Forbes, 1891) (Crustacea: Copepoda). The somatic genome is reorganized and reduced to a size five times smaller even though the germline genome remains intact. We present the first comprehensive, quantitative model of DNA content throughout embryogenesis in a copepod that possesses embryonic DNA elimination. We used densitometric image analysis to measure the DNA content of polar bodies, germline and somatic nuclei, and excised DNA “droplets.” We …
Connecting Common Genetic Polymorphisms To Protein Function: A Modular Project Sequence For Lecture Or Lab, Christopher E. Berndsen, Byron H. Young, Quinlin J. Mccormick, Raymond A. Enke
Oct 2016
Connecting Common Genetic Polymorphisms To Protein Function: A Modular Project Sequence For Lecture Or Lab, Christopher E. Berndsen, Byron H. Young, Quinlin J. Mccormick, Raymond A. Enke
JMU CGEMS
Single nucleotide polymorphisms (SNPs) in DNA can
result in phenotypes where the biochemical basis may not
be clear due to the lack of protein structures. With the
growing number of modeling and simulation software
available on the internet, students can now participate in
determining how small changes in genetic information
impact cellular protein structure and function. We have
developed a modular series of activities to engage lab or
lecture students in examining the basis for common phenotypes.
The activities range from basic phenotype testing/
observation to DNA sequencing and simulation of
protein structure and dynamics. We provide as an example …
Genomics-Informed Isolation And Characterization Of A Symbiotic Nanoarchaeota System From A Terrestrial Geothermal Environment, Louie Wurch, Richard J. Giannone, Bernard S. Belisle, Carolyn Swift, Sagar Utturkar, Robert L. Hettich, Anna-Louise Reysenbach, Mircea Podar
Jun 2016
Genomics-Informed Isolation And Characterization Of A Symbiotic Nanoarchaeota System From A Terrestrial Geothermal Environment, Louie Wurch, Richard J. Giannone, Bernard S. Belisle, Carolyn Swift, Sagar Utturkar, Robert L. Hettich, Anna-Louise Reysenbach, Mircea Podar
JMU CGEMS
Biological features can be inferred, based on genomic data, for many microbial lineages that
remain uncultured. However, cultivation is important for characterizing an organism’s
physiology and testing its genome-encoded potential. Here we use single-cell genomics to
infer cultivation conditions for the isolation of an ectosymbiotic Nanoarchaeota (‘Nanopusillus
acidilobi’) and its host (Acidilobus, a crenarchaeote) from a terrestrial geothermal environment.
The cells of ‘Nanopusillus’ are among the smallest known cellular organisms (100–
300 nm). They appear to have a complete genetic information processing machinery, but lack
almost all primary biosynthetic functions as well as respiration and ATP synthesis. Genomic
and proteomic …
Direct And Indirect Horizontal Transmission Of The Antifungal Probiotic Bacterium Janthinobacterium Lividum On Green Frog (Lithobates Clamitans) Tadpoles, Eria Rebollar, Stephen J. Simonetti,, William R. Shoemaker,*, Reid N. Harris
Mar 2016
Direct And Indirect Horizontal Transmission Of The Antifungal Probiotic Bacterium Janthinobacterium Lividum On Green Frog (Lithobates Clamitans) Tadpoles, Eria Rebollar, Stephen J. Simonetti,, William R. Shoemaker,*, Reid N. Harris
JMU CGEMS
Amphibian populations worldwide are being threatened by the disease chytridiomycosis, which is caused by Batrachochytrium dendrobatidis. To mitigate the effects of B. dendrobatidis, bioaugmentation of antifungal bacteria has been shown to be a prom- ising strategy. One way to implement bioaugmentation is through indirect horizontal transmission, defined as the transfer of bacteria from a host to the environment and to another host. In addition, direct horizontal transmission among individuals can facilitate the spread of a probiotic in a population. In this study, we tested whether the antifungal bacterium Janthinobacterium lividum could be horizontally transferred, directly or indirectly, in a laboratory …
Vertebrate Hosts As Islands: Dynamics Of Selection, Immigration, Loss, Persistence, And Potential Function Of Bacteria On Salamander Skin, Andrew H. Louden, Arvind Venkataraman, William Van Treuren, Douglas C. Woodhams, Laura Wagner Parfrey, Valerie J. Mckenzie, Rob Knight, Thomas M. Schmidt, Reid N. Harris
Feb 2016
Vertebrate Hosts As Islands: Dynamics Of Selection, Immigration, Loss, Persistence, And Potential Function Of Bacteria On Salamander Skin, Andrew H. Louden, Arvind Venkataraman, William Van Treuren, Douglas C. Woodhams, Laura Wagner Parfrey, Valerie J. Mckenzie, Rob Knight, Thomas M. Schmidt, Reid N. Harris
JMU CGEMS
Skin bacterial communities can protect amphibians from a fungal pathogen; however,
little is known about how these communities are maintained. We used a neutral model of
community ecology to identify bacteria that are maintained on salamanders by selection
or by dispersal from a bacterial reservoir (soil) and ecological drift. We found that 75%
(9/12) of bacteria that were consistent with positive selection, <1% of bacteria that
were consistent with random dispersal and none of the bacteria that were consistent
under negative selection had a 97% or greater match to antifungal isolates. Additionally
we performed an experiment where salamanders were either …
Using “Omics” And Integrated Multi-Omics Approaches To Guide Probiotic Selection To Mitigate Chytridiomycosis And Other Emerging Infectious Diseases, Eria A. Rebollar, Rachael E. Antwis, Matthew H. Becker, Lisa K. Belden, Molly C. Bletz, Robert M. Brucker, Xavier A. Harrison, Myra C. Hughey, Jordan G. Kueneman, Andrew H. Loudon, Valerie Mckenzie, Daniel Medina, Kevin P. C. Minbiole, Louise A. Rollins-Smith, Jenifer B. Walke, Sophie Weiss, Douglas C. Woodhams, Reid N. Harris
Jan 2016
Using “Omics” And Integrated Multi-Omics Approaches To Guide Probiotic Selection To Mitigate Chytridiomycosis And Other Emerging Infectious Diseases, Eria A. Rebollar, Rachael E. Antwis, Matthew H. Becker, Lisa K. Belden, Molly C. Bletz, Robert M. Brucker, Xavier A. Harrison, Myra C. Hughey, Jordan G. Kueneman, Andrew H. Loudon, Valerie Mckenzie, Daniel Medina, Kevin P. C. Minbiole, Louise A. Rollins-Smith, Jenifer B. Walke, Sophie Weiss, Douglas C. Woodhams, Reid N. Harris
JMU CGEMS
Emerging infectious diseases in wildlife are responsible for massive population declines. In amphibians, chytridiomycosis caused by Batrachochytrium dendrobatidis, Bd, has severely affected many amphibian populations and species around the world. One promising management strategy is probiotic bioaugmentation of antifungal bacteria on amphibian skin. In vivo experimental trials using bioaugmentation strategies have had mixed results, and therefore a more informed strategy is needed to select successful probiotic candidates. Metagenomic, transcriptomic, and metabolomic methods, colloquially called “omics,” are approaches that can better inform probiotic selection and optimize selection protocols. The integration of multiple omic data using bioinformatic and statistical tools …
Genomic Characterizationandcomparisonofseven Myoviridae Bacteriophage Infecting Bacillus Thuringiensis, Amber B. Sauder, Mckenzie R. Quinn, Alexis Brouillette, Steven Caruso, Steven Cresawn, Ivan Erill, Lynn Lewis, Kathryn Loesser-Casey, Morgan Pate, Crystal Scott, Stephanie Stockwell, Louise Temple
Jan 2016
Genomic Characterizationandcomparisonofseven Myoviridae Bacteriophage Infecting Bacillus Thuringiensis, Amber B. Sauder, Mckenzie R. Quinn, Alexis Brouillette, Steven Caruso, Steven Cresawn, Ivan Erill, Lynn Lewis, Kathryn Loesser-Casey, Morgan Pate, Crystal Scott, Stephanie Stockwell, Louise Temple
JMU CGEMS
Bacillus thuringiensis Kurstaki, a bacterium that is a source of biopesticides and a safe simulant for pathogenic Bacillus species, was used to isolate seven unique bacteriophages. The phage genomes were sequenced and ranged in size from 158,100 to 163,019 bp encoding 290–299 genes, and the GC content of ~38% was similar to that of the host bacterium. All phages had terminal repeats 2–3 kb long. Three of the phages encoded tRNAs and three contained a self-splicing intron in the DNA polymerase gene. They were categorized as a single cluster (>60% nucleotide conservation) containing three subclusters (>80% nucleotide conservation), supported by genomic synteny …
