We analyzed gene expression during t10c12-CLA-induced body fat reduction in a polygenic obese line of mice. Adult mice (N=185) were allotted to a 2x2 factorial experiment consisting of a non-obese (ICR-control) and an obese (M16-selected) line of mice fed a 7% fat, purified diet containing either 1% linoleic acid (LA) or 1% t10c12-CLA. Body weight (BW) gain by day 14 was 12% lower in CLA compared to LA fed mice (P<0.0001). By day 14, t10c12-CLA reduced weights of epididymal, mesenteric and brown adipose tissues as a percentage of BW in both lines by 30, 27 and 58%, respectively, and increased liver weight/BW by 34% (P<0.0001). Total RNA was isolated and pooled (4-5 mice per composite) from epididymal adipose (day 5 & 14) and liver (day 14) of the obese mice to analyze gene expression profiles using Agilent mouse oligo microarray slides (4 per tissue?day) representing >20,000 genes. Numbers of genes differentially expressed by ≥ two fold in epididymal adipose (day 5 & 14) and liver (day 14) were 29, 125, and 80, respectively. Of particular interest in adipose, CLA putatively increased expression of the uncoupling proteins (1 and 2), carnitine palmitoyltransferase (L and M), and carnitine translocase, but decreased expression of PPAR-gamma, GLUT-4, perilipin, caveolin-1, adiponectin and resistin (P<0.01). In conclusion, this experiment has revealed candidate genes that will be useful in elucidating mechanisms underlying the potent anti-adipogenic effects of t10c12-CLA.

Here I used microarrays to identify genes that are activated or repressed by nicotine and caffeine in Drosophila melanogaster. I compared genotypes with differential resistance to each drug in order to select genes that may be involved in resistance to the drugs. Comparison of the genes differentially expressed by both drugs leads me to propose that there are common mechanisms of metabolic resistance to caffeine and nicotine, in particular cytochrome P-450-mediated mechanisms. Caffeine seems to have a more dramatic influence on gene expression than nicotine, in particular on expression of genes involved in energy metabolism. Next, I extended the studies on nicotine resistance to ask whether there are differences in response between two populations of Drosophila. The gene expression patterns of both populations were evaluated separately and in a combined analysis. Most of the differentially expressed genes were up-regulated by nicotine in both populations and in the combined analysis. The induced transcripts were mainly related to protein, nucleic acid, amino acid and energy metabolism, and response to stimulus and stress. Those findings suggest that amino acid and energy metabolism may be important biological processes affected by nicotine and be interesting targets for further investigation related to the nicotine response in Drosophila. The two populations displayed considerable differences in gene expression profiling that may be the result of the observed phenotypic variation for nicotine response between the two populations. Most of the differential expression induced by nicotine seems to be specific to the more resistant population. Finally, I focused on genes whose expression showed significant correlation with survival time on nicotine food. Using a regression approach, it was possible to map quantitative trait transcripts associated to nicotine response. Control expression of alkaline phosphatase and ornithine aminotransferase displayed significant correlation to survival time in drug food. They seem to be linked to regulation of GABA/glutamate neurotransmission and detoxification mechanisms, which ultimately counteracts the stimulatory effects of nicotine.

The genomes of six Streptococcus thermophilus bacteriophages were compared to identify genes that could be targeted by engineered phage defense systems with potentially widespread efficacy. The genes associated with the S. thermophilus phage Sfi21-prototype genome replication module, including a putative primase and a putative helicase, were found to be among the best candidates due to their frequency of distribution in industrial phage isolates, striking sequence conservation between independent isolates, and intrinsic strategic importance in early phage development. Fourteen antisense RNA cassettes targeting the phage k3-derived helicase (hel3) or primase (pri3) genes were expressed in S. thermophilus NCK1125. These constructs consistently reduced the efficiency of plaquing (EOP) of phage k3 to between 5 x 10-1 and 2.0 x 10-3 depending on the (i) gene targeted and (ii) region of the gene that was targeted. The largest antisense RNAs were generally found to confer the largest reductions in EOP, however shorter antisense RNAs designed to the 5' region of the gene retained much of the inhibitory function, especially if they contained sequences complementary to the ribosome binding site. Expression of antisense RNAs correlated with decreased levels of phage encoded primase transcripts, likely due to increased degradation of the dsRNA complex. This, in turn, correlated with diminished phage genome replication and aborted phage development. In a separate study, invariant and highly conserved amino acids within a primase consensus sequence were targeted by site-specific mutation within the S. thermophilus phage k3-encoded putative primase. PCR products containing the desired mutation(s) were cloned and expressed in S. thermophilus NCK1125. The majority of the examined constructs remained sensitive to phage k3, however four constructs conferred strong phage resistance to the bacterial host. The mutated residues resided within a putative ATPase/helicase domain suspected to be critical for primase function in vivo. The co-expression in trans of the K238(A/T) or RR340-341AA mutant proteins suppressed the function of the native, phage-encoded primase protein in a dominant negative fashion via a proposed subunit poisoning mechanism. According to this model, the plasmid-encoded mutant primase subunits are structurally intact and form stable interactions with the native, phage-encoded primase subunits, thus inhibiting their activity. These constructs completely inhibited phage genome synthesis and reduced the efficiencies of plaquing more that nine log cycles. Given the magnitude of the resistance conferred, it was concluded that the putative primase is essential for genome replication in S. thermophilus Sfi21-type phages. Further, it was also clear that host-encoded factors were unable to complement the resultant deficiency. Amber mutations introduced upstream of the transdominant RR340-341AA and K238(A/T) mutations restored phage genome replication and phage sensitivity of the host, indicating that translation was required to confer phage resistance. Residues within a critical oligomerization domain were also identified through genetic analysis. Introduction of an E437A mutation downstream of the transdominant K238T mutation completely suppressed phage resistance, indicating that the E437A mutation precluded the association of the mutant and native subunits. To our knowledge, this is the first use of subunit poisoning to inhibit phage replication in the lactic acid bacteria.

Listeria monocytogenes was the causative agent of the nationwide 2008 outbreak associated with contaminated ready-to-eat meat products. Within the whole genome DNA sequences of the outbreak isolates we previously identified a novel 50kb genomic island, designated as Listeria Genomic Island 1 (LGI1). LGI1 is predicted to contribute to Listeria pathogenesis and/or environmental persistence because it encodes genes related to known virulence factors and mobilization functions, including a putative type IV secretion system and a putative small multidrug resistance efflux pump. The distribution of LGI1 in Canadian L. monocytogenes isolates was determined by PCR screening for LGI1 within 126 isolates from 1987 to 2010 that represented different serotypes and pulsed-field gel electrophoresis (PFGE) patterns. To assess the evolutionary history and genetic diversity of this island, total LGI1 sequences from 15 whole-genome sequences were compared, and from the full study panel of isolates,PCR screening for the chromosomal insertion site and multiple LGI coding sequences were performed. LGI1 was detected almost exclusively in serotype 1/2a isolates, and within those, the isolates predominantly had the same PFGE patterns. These LGI1-encoding isolates also exclusively belonged to the multi-locus sequence typing (MLST)clonal complex 8. LGI1 was highly genetically conserved and it was inserted at the same location within the genome in 65 of the 67 isolates that harboured the island. To study the function and expression of LGI1, antimicrobial susceptibility assays,bioinformatic analyses and real-time reverse-transcription PCR were used. Isolates encoding LGI1 had an increased tolerance to quaternary ammonium compounds commonly used in sanitizing agents (benzalkonium chloride (BCl) and benzethonium chloride (BeCl)) compared to isolates lacking LGI1 (but still highly related by MLST and PFGE). LGI1 is also tightly regulated, with expression of 13 of 16 tested coding sequences only being induced by the presence of sub-inhibitory concentrations of BCl,and one predicted regulator being expressed under all conditions. This study indicates that the vast majority LGI encoding CC8 isolates share a common progenitor L. monocytogenes ancestor that acquired LGI1 in a single evolutionary event. LGI1 has remained genetically conserved since that time, and the functions contributed by this island minimally include an increased tolerance to sanitizer agents.

Listeria monocytogenes was the causative agent of the nationwide 2008 outbreak associated with contaminated ready-to-eat meat products. Within the whole genome DNA sequences of the outbreak isolates we previously identified a novel 50kb genomic island, designated as Listeria Genomic Island 1 (LGI1). LGI1 is predicted to contribute to Listeria pathogenesis and/or environmental persistence because it encodes genes related to known virulence factors and mobilization functions, including a putative type IV secretion system and a putative small multidrug resistance efflux pump. The distribution of LGI1 in Canadian L. monocytogenes isolates was determined by PCR screening for LGI1 within 126 isolates from 1987 to 2010 that represented different serotypes and pulsed-field gel electrophoresis (PFGE) patterns. To assess the evolutionary history and genetic diversity of this island, total LGI1 sequences from 15 whole-genome sequences were compared, and from the full study panel of isolates,PCR screening for the chromosomal insertion site and multiple LGI coding sequences were performed. LGI1 was detected almost exclusively in serotype 1/2a isolates, and within those, the isolates predominantly had the same PFGE patterns. These LGI1-encoding isolates also exclusively belonged to the multi-locus sequence typing (MLST)clonal complex 8. LGI1 was highly genetically conserved and it was inserted at the same location within the genome in 65 of the 67 isolates that harboured the island. To study the function and expression of LGI1, antimicrobial susceptibility assays,bioinformatic analyses and real-time reverse-transcription PCR were used. Isolates encoding LGI1 had an increased tolerance to quaternary ammonium compounds commonly used in sanitizing agents (benzalkonium chloride (BCl) and benzethonium chloride (BeCl)) compared to isolates lacking LGI1 (but still highly related by MLST and PFGE). LGI1 is also tightly regulated, with expression of 13 of 16 tested coding sequences only being induced by the presence of sub-inhibitory concentrations of BCl,and one predicted regulator being expressed under all conditions. This study indicates that the vast majority LGI encoding CC8 isolates share a common progenitor L. monocytogenes ancestor that acquired LGI1 in a single evolutionary event. LGI1 has remained genetically conserved since that time, and the functions contributed by this island minimally include an increased tolerance to sanitizer agents.

Thesis (M.S.) OGI School of Science & Engineering at OHSU, November 2007. / Includes bibliographical references (leaves 41 - 45).

Thesis (M.S.)--University of Delaware, 2008. / Principal faculty advisors: Li Liao, Dept. of Computer & Information Sciences and E. Fidelma Boyd, Dept. of Biological Sciences. Includes bibliographical references.

Thesis (Ph.D.) in Interdisciplinary--University of Maine, 2009. / Includes vita. Includes bibliographical references (leaves 140-170).

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2007. / Includes bibliographical references.

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