The Grizzly, October 30, 1990

Ursinus Honored at Governor\u27s Mansion • Sam Stretton To Speak • Glassmoyer Retires • Heefner New Board President • The Gender of Speech: A Tri-Lambda Lecture • Career Day November 6th • Forbes to Speak to Clergy • Animal Lovers Unite • Mock DWI A Hit • Student Camp Experience • David is Great!! • Presenting Protheatre: The Changeling • Crutcher Leads Team• Muhlenberg Falls • Swimmers Open Season at Relay Meet • Women Running To MAC\u27s • Men Go for MAC Title • Soccer • Letters: Keep Ursinus Clean; Quad Keys Revoked?; Signs Stolen; Security, Please Hold • Environmentally Concerned? Get Active • Bush\u27s Environmental Lip Service • This Time for Real • Nature Versus Nurture: A Step in Solving the Puzzlehttps://digitalcommons.ursinus.edu/grizzlynews/1262/thumbnail.jp

Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees

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 to existing expression data from brains, livers, hearts, testes, and kidneys derived from both species and determined the effects probe numbers have on expression scores of specific transcripts. In all five tissues, probe sets with decreasing numbers of probes showed non-linear trends towards increased variation in expression scores. The relationships between expression variation and probe number in brain data closely matched those observed in simulated expression data sets subjected to random probe masking. However, there is evidence that additional factors affect the observed relationships between gene expression scores and probe number in tissues such as liver and kidney. In parallel, we observed that decreasing the number of probes within probe sets lead to linear increases in both gained and lost inferences of differential cross-species expression in all five tissues, which will affect the interpretation of expression data subject to masking. Conclusion We introduce a readily implemented and updated resource for human and chimpanzee transcriptome analysis through a commonly used microarray platform. Based on empirical observations derived from the analysis of five distinct data sets, we provide novel guidelines for the interpretation of masked data that take the number of probes present in a given probe set into consideration. These guidelines are applicable to other customized applications that involve masking data from specific subsets of probes

mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft

<p>Abstract</p> <p>Background</p> <p>Interactions between the gene products encoded by the mitochondrial and nuclear genomes play critical roles in eukaryotic cellular function. However, the effects mitochondrial DNA (mtDNA) levels have on the nuclear transcriptome have not been defined under physiological conditions. In order to address this issue, we characterized the gene expression profiles of A549 lung cancer cells and their mtDNA-depleted ρ⁰counterparts grown in culture and as tumor xenografts in immune-deficient mice.</p> <p>Results</p> <p>Cultured A549 ρ⁰cells were respiration-deficient and showed enhanced levels of transcripts relevant to metal homeostasis, initiation of the epithelial-mesenchymal transition, and glucuronidation pathways. Several well-established HIF-regulated transcripts showed increased or decreased abundance relative to the parental cell line. Furthermore, growth in culture versus xenograft has a significantly greater influence on expression profiles, including transcripts involved in mitochondrial structure and both aerobic and anaerobic energy metabolism. However, both <it>in vitro </it>and <it>in vivo</it>, mtDNA levels explained the majority of the variance observed in the expression of transcripts in glucuronidation, tRNA synthetase, and immune surveillance related pathways. mtDNA levels in A549 xenografts also affected the expression of genes, such as <it>AMACR </it>and <it>PHYH</it>, involved in peroxisomal lipid metabolic pathways.</p> <p>Conclusion</p> <p>We have identified mtDNA-dependent gene expression profiles that are shared in cultured cells and in xenografts. These profiles indicate that mtDNA-depleted cells could provide informative model systems for the testing the efficacy of select classes of therapeutics, such as anti-angiogenesis agents. Furthermore, mtDNA-depleted cells grown culture and in xenografts provide a powerful means to investigate possible relationships between mitochondrial activity and gene expression profiles in normal and pathological cells.</p

The Grizzly, December 3, 1990

Wismer Hall to be Renovated by Next Fall • Quad Intruder Returns • Politics Honors Projects • Foreign Policy and the Press • Ursinus Offers St. Joseph\u27s Post-MBA Certificates • Dance Marathon Planned • Crazy Toys • Holiday Messages Encouraged • Exam Schedule • Mixed Up • Jane\u27s Addiction Concert Review • European Old Master Prints • At the Playhouse • Attention Skiers • Edie Brickell Reviewed • In the Spotlight • Swimmers Host Double-Header Weekend • Lady Hoopsters Shoot for Title • Are We Going to War? • Why are We Really There? • Hey! Who\u27s the New Guy? • Brain in Brief • Bonnie and SAM (not Clyde)https://digitalcommons.ursinus.edu/grizzlynews/1266/thumbnail.jp

The Grizzly, October 9, 1990

Student Activities Reorganized • Homecoming 1990: Student and Alumnae Festivities • LaRouche Supporter to Speak • Pledging Rules In Effect • EcBa Club Holds First Meeting • The Path to Opportunities • Ursinus Goes South of the Border • Olin Brick Explained • Esther Remembered • Homecoming Festivities • Comedy Brightens Wismer • Pennsylvania Impressionist • Acting Sports • Presenting ProTheatre • Russian Trumpeter • Soccer Team Gets It Together • Grubb\u27s Fearless Predictions • Football Impresses • Field Hockey Rebounds • Harley\u27s Haven • Letters: RAs Question Editorial; Congrats, Now be Quiet! • Classics: Guaranteed to Improve Your Life • Losing Traditions • Grading Our Food Service • Middleton: Man of Many Projectshttps://digitalcommons.ursinus.edu/grizzlynews/1260/thumbnail.jp

The Grizzly, November 13, 1990

Clergy Assembly Meets Ninth Consecutive Year • Career Day: An Information Session for Students • U.S. Energy Policy Anti-American? • The Ursinus Tutoring Program • Being British Without Being English • Election Results • Students React to Reimert Security Doors • Greeks Sponsor Halloween Party • F.W. Olin Foundation • Wilk 3 Protest • The History of Olin Grant • The Changeling • INXS • Television: Whose Reality is it Anyway? • Swimmers Wash Out Washington • Cross-Country Team Pleased with Regionals • Steimy Starts Club • Men\u27s Basketball Looks for Improvement in 1991 Season • Football Finishes Season with a Loss • Letters: No Defense for Personal Abuse; Zeta Chi Missed the Point! • Uncle Sam Wants Everyone • Pre-Med Prognosis Improving • Ursinus Grad in Sticky Situation • Brownback-Anders Meetinghttps://digitalcommons.ursinus.edu/grizzlynews/1264/thumbnail.jp

Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes

<p>Abstract</p> <p>Background</p> <p>A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (<it>Triticum aestivum</it>, genomes AABBDD) and wild tetraploid wheat (<it>Triticum turgidum </it>ssp. <it>dicoccoides</it>, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat.</p> <p>Results</p> <p>Nucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, <it>T. urartu</it>, <it>Aegilops speltoides</it>, and <it>Ae. tauschii</it>, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an <it>Ae. tauschii </it>genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed.</p> <p>Conclusions</p> <p>In a young polyploid, exemplified by <it>T. aestivum</it>, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in <it>T. aestivum </it>is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.</p

Exhaled Aerosol Transmission of Pandemic and Seasonal H1N1 Influenza Viruses in the Ferret

Person-to-person transmission of influenza viruses occurs by contact (direct and fomites) and non-contact (droplet and small particle aerosol) routes, but the quantitative dynamics and relative contributions of these routes are incompletely understood. The transmissibility of influenza strains estimated from secondary attack rates in closed human populations is confounded by large variations in population susceptibilities. An experimental method to phenotype strains for transmissibility in an animal model could provide relative efficiencies of transmission. We developed an experimental method to detect exhaled viral aerosol transmission between unanesthetized infected and susceptible ferrets, measured aerosol particle size and number, and quantified the viral genomic RNA in the exhaled aerosol. During brief 3-hour exposures to exhaled viral aerosols in airflow-controlled chambers, three strains of pandemic 2009 H1N1 strains were frequently transmitted to susceptible ferrets. In contrast one seasonal H1N1 strain was not transmitted in spite of higher levels of viral RNA in the exhaled aerosol. Among three pandemic strains, the two strains causing weight loss and illness in the intranasally infected ‘donor’ ferrets were transmitted less efficiently from the donor than the strain causing no detectable illness, suggesting that the mucosal inflammatory response may attenuate viable exhaled virus. Although exhaled viral RNA remained constant, transmission efficiency diminished from day 1 to day 5 after donor infection. Thus, aerosol transmission between ferrets may be dependent on at least four characteristics of virus-host relationships including the level of exhaled virus, infectious particle size, mucosal inflammation, and viral replication efficiency in susceptible mucosa