Life Sciences Commons^™

Gut Dna Virome Diversity And Its Association With Host Bacteria Regulate Inflammatory Phenotype And Neuronal Immunotoxicity In Experimental Gulf War Illness, Ratanesh K. Seth, Rabia Maqsood, Ayan Mondal, Dipro Bose, Diana Kimono, Larinda A. Holland, Patricia Janulewicz Lloyd, Nancy Klimas, Ronnie Horner, Kimberly Sullivan, Efrem S. Lim, Saurabh Chatterjee

Faculty Publications

Gulf War illness (GWI) is characterized by the persistence of inflammatory bowel disease, chronic fatigue, neuroinflammation, headache, cognitive impairment, and other medically unexplained conditions. Results using a murine model show that enteric viral populations especially bacteriophages were altered in GWI. The increased viral richness and alpha diversity correlated positively with gut bacterial dysbiosis and proinflammatory cytokines. Altered virome signature in GWI mice also had a concomitant weakening of intestinal epithelial tight junctions with a significant increase in Claudin-2 protein expression and decrease in ZO1 and Occludin mRNA expression. The altered virome signature in GWI, decreased tight junction protein level was …

Experimental Evidence Supportive Of The Quantum Dna Model, F. Matthew Mihelic

Faculty Publications

The DNA molecule can be modeled as a quantum logic processor in which electron spin qubits are held coherently in each nucleotide in a logically and thermodynamically reversible enantiomeric symmetry, and can be coherently conducted along the pi-stacking interactions of aromatic nucleotide bases, while simultaneously being spin-filtered via the helicity of the DNA molecule. Entangled electron pairs can be separated by that spin-filtering, held coherently at biological temperatures in the topologically insulated nucleotide quantum gates, and incorporated into separate DNA strands during DNA replication. Two separate DNA strands that share quantum entangled electrons can be mitotically divided into individual cells, …

High Throughput Genomic Sequencing Of Bioaerosols In Broiler Chicken Production Facilities, Kate M. O’Brien, Michael S. Chimenti, Morgan Farnell, Tom Tabler, Thomas Bair, Joey Lynn Bray, Matthew W. Nonnenmann

Faculty Publications

Chronic inhalation exposure to agricultural dust promotes the development of chronic respiratory diseases among poultry workers. Poultry dust is composed of dander, chicken feed, litter bedding and microbes. However, the microbial composition and abundance has not been fully elucidated. Genomic DNA was extracted from settled dust and personal inhalable dust collected while performing litter sampling or mortality collection tasks. DNA libraries were sequenced using a paired-end sequencing-by-synthesis approach on an Illumina HiSeq 2500. Sequencing data showed that poultry dust is predominantly composed of bacteria (64–67%) with a small quantity of avian, human and feed DNA (< 2% of total reads). Staphylococcus sp. AL1, Salinicoccus carnicancri and Lactobacillus crispatus were the most abundant bacterial species in personal exposure samples of inhalable dust. Settled dust had a moderate relative abundance of these species as well as Staphylococcus lentus and Lactobacillus salivarius. There was a statistical difference between the microbial composition of aerosolized and settled dust. Unlike settled dust composition, aerosolized dust composition had little variance between samples. These data provide an extensive analysis of the microbial composition and relative abundance in personal inhalable poultry dust and settled poultry dust.

Large-Scale Identification Of Chemically Induced Mutations In Drosophila Melanogaster., Nele A Haelterman, Lichun Jiang, Yumei Li, Vafa Bayat, Hector Sandoval, Berrak Ugur, Kai Li Tan, Ke Zhang, Danqing Bei, Bo Xiong, Wu-Lin Charng, Theodore Busby, Adeel Jawaid, Gabriela David, Manish Jaiswal, Koen J T Venken, Shinya Yamamoto, Rui Chen, Hugo J Bellen

Faculty Publications

Forward genetic screens using chemical mutagens have been successful in defining the function of thousands of genes in eukaryotic model organisms. The main drawback of this strategy is the time-consuming identification of the molecular lesions causative of the phenotypes of interest. With whole-genome sequencing (WGS), it is now possible to sequence hundreds of strains, but determining which mutations are causative among thousands of polymorphisms remains challenging. We have sequenced 394 mutant strains, generated in a chemical mutagenesis screen, for essential genes on the Drosophila X chromosome and describe strategies to reduce the number of candidate mutations from an average of …

Implications Of The Landauer Limit For Quantum Logic, F. Matthew Mihelic

Faculty Publications

The design of any system of quantum logic must take into account the implications of the Landauer limit for logical bits. Useful computation implies a deterministic outcome, and so any system of quantum computation must produce a final deterministic outcome, which in a quantum computer requires a quantum decision that produces a deterministic qubit. All information is physical, and any bit of information can be considered to exist in a physicality represented as a decision between the two wells of a double well potential in which the energy barrier between the two wells must be greater than kT·ln2. Any proposed …

Enhancing Pcr Amplification Of Dna From Recalcitrant Plant Specimens Using A Trelahose-Based Additive, Tharangamala Samarakoon, Shiao Y. Wang, Mac H. Alford

Faculty Publications

Premise of the study: PCR amplification of DNA extracted from plants is sometimes difficult due to the presence of inhibitory compounds. An effective method to overcome the inhibitory effect of compounds that contaminate DNA from difficult plant specimens is needed.

Methods and Results: The effectiveness of a PCR additive reagent containing trehalose, bovine serum albumin (BSA), and polysorbate‐20 (Tween‐20) (TBT‐PAR) was tested. PCR of DNA extracted from fresh, silica‐dried, and herbarium leaf material of species of Achariaceae, Asteraceae, Lacistemataceae, and Samydaceae that failed using standard techniques were successful with the addition of TBT‐PAR.

Conclusions: The addition of TBT‐PAR during routine …

Environmental Dna Sequencing Primers For Eutardigrades And Bdelloid Rotifers, Byron J. Adams, Jeremy Whiting, Elizabeth K. Costello, Kristen R. Freeman, Andrew P. Martin, Michael S. Robeson, Steve K. Schmidt

Faculty Publications

Background: The time it takes to isolate individuals from environmental samples and then extract DNA from each individual is one of the problems with generating molecular data from meiofauna such as eutardigrades and bdelloid rotifers. The lack of consistent morphological information and the extreme abundance of these classes makes morphological identification of rare, or even common cryptic taxa a large and unwieldy task. This limits the ability to perform large-scale surveys of the diversity of these organisms. Here we demonstrate a culture-independent molecular survey approach that enables the generation of large amounts of eutardigrade and bdelloid rotifer sequence data directly …

Many Species In One: Dna Barcoding Overestimates The Number Of Species When Nuclear Mitochondrial Pseudogenes Are Coamplified, Michael F. Whiting, Hojun Song, Keith A. Crandall, Jennifer E. Buhay

Faculty Publications

Nuclear mitochondrial pseudogenes (numts) are nonfunctional copies of mtDNA in the nucleus that have been found in major clades of eukaryotic organisms.

2c Dna Content Values In Amaranthus (Amaranthaceae) [Abstract], Donald B. Pratt, Shalini N. Jhangiani, Robert J. Wiggers

Faculty Publications

No abstract provided.

Distinguishing Importation From Diversification Of Quinolone-Resistant Neisseria Gonorrhoeae By Molecular Evolutionary Analysis, Keith A. Crandall, Marcos Perez-Losada, Margaret C. Bash, Michael Dan, Jonathan Zenilman, Raphael P. Viscidi

Faculty Publications

Distinguishing the recent introduction of quinolone resistant gonococci into a population from diversification of resistant strains already in the population is important for planning effective infection control strategies. We applied molecular evolutionary analyses to DNA sequences from 9 housekeeping genes and gyrA, parC and porB of 24 quinolone resistant N. gonorrhoeae (QRNG) and 24 quinolone sensitive isolates collected in Israel during 2000-2001. Results- Phylogenetic and eBURST analyses and estimates of divergence time indicated QRNG were introduced on 3 separate occasions and underwent limited diversification by mutation, deletion and horizontal gene transfer. Reconstruction of N. gonorrhoeae demography showed a slowly declining …