Utilization of Probabilistic Models in Short Read Assembly from Second-Generation Sequencing

With the advent of cheaper and faster DNA sequencing technologies, assembly methods have greatly changed. Instead of outputting reads that are thousands of base pairs long, new sequencers parallelize the task by producing read lengths between 35 and 400 base pairs. Reconstructing an organism’s genome from these millions of reads is a computationally expensive task. Our algorithm solves this problem by organizing and indexing the reads using n-grams, which are short, fixed-length DNA sequences of length n. These n-grams are used to efficiently locate putative read joins, thereby eliminating the need to perform an exhaustive search over all possible read pairs. Our goal was develop a novel n-gram method for the assembly of genomes from next-generation sequencers. Specifically, a probabilistic, iterative approach was utilized to determine the most likely reads to join through development of a new metric that models the probability of any two arbitrary reads being joined together. Tests were run using simulated short read data based on randomly created genomes ranging in lengths from 10,000 to 100,000 nucleotides with 16 to 20x coverage. We were able to successfully re-assemble entire genomes up to 100,000 nucleotides in length.

Mate Expulsions in Females Across the Menstrual Cycle

Female mate preferences are complex due to their greater selectivity in mates according to the good genes sexual selection theory. Additionally, research shows that female’s behaviors and mate preferences change cyclically due to the importance of attracting amate when conception risk is highest. However, research has not examined whether there is a relationship between menstrual cycle changes and mate expulsion (the casting off of a mate or ending a relationship). The present research examined whether fertility riskaffects mate expulsion decisions. Female participants completed a questionnaire which included demographic questions, such as information about the length and date of their menstrual cycle, mate expulsion scenarios, and a social desirability scale. Effects ofcurrent relationship status (a demographic measure) were also examined. If fertility risk does have an influence, the following patterns were hypothesized. High fertility women will be less likely to expel their mate due to an increased chance of conception and a need for access to parental investment resources from their mate. The results obtained indicate that fertility risks do not influence female’s decisions to expel their mates. Current relationship status in conjunction with fertility risk does affect mate expulsion. Thesefindings are discussed in terms of prior research and evolutionary theory.

Friendship As A Relationship Infiltration Tactic During Human Mate Poaching: An Experimental Investigation

Previous research has characterized human mate poaching as a prevalent alternative mating strategy that entails risks and costs typically not present during general romantic courtship and attraction. This study is the first to experimentally investigate friendship between a poacher and poachee as a risk mitigation tactic. Participants (N = 382) read a vignette that differed by whether the poacher was male/female and whether the poacher and poachee were friends/acquaintances. Participants assessed the likelihood of the poacher being successful and incurring costs. They also rated the poacher and poachee on several personality and mate characteristics. Results revealed that friendship increased the perceived likelihood of success of a mate poaching attempt and decreased the perceived likelihood of several risks typically associated with mate poaching. However, friend-poachers were rated less favorably than acquaintance-poachers across measures of warmth, nurturance, and friendliness. These findings are interpreted using an evolutionary perspective. This study complements and builds upon previous findings and is the first experimental investigation of tactics mate poachers may use to mitigate risks inherent in mate poaching.

Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing

With the advent of high through-put sequencing (HTS), the emerging science of metagenomics is transforming our understanding of the relationships of microbial communities with their environments. While metagenomics aims to catalogue the genes present in a sample through assessing which genes are actively expressed, metatranscriptomics can provide a mechanistic understanding of community inter-relationships. To achieve these goals, several challenges need to be addressed from sample preparation to sequence processing, statistical analysis and functional annotation. Here we use an inbred non-obese diabetic (NOD) mouse model in which germ-free animals were colonized with a defined mixture of eight commensal bacteria, to explore methods of RNA extraction and to develop a pipeline for the generation and analysis of metatranscriptomic data. Applying the Illumina HTS platform, we sequenced 12 NOD cecal samples prepared using multiple RNA-extraction protocols. The absence of a complete set of reference genomes necessitated a peptide-based search strategy. Up to 16% of sequence reads could be matched to a known bacterial gene. Phylogenetic analysis of the mapped ORFs revealed a distribution consistent with ribosomal RNA, the majority from Bacteroides or Clostridium species. To place these HTS data within a systems context, we mapped the relative abundance of corresponding Escherichia coli homologs onto metabolic and protein-protein interaction networks. These maps identified bacterial processes with components that were well-represented in the datasets. In summary this study highlights the potential of exploiting the economy of HTS platforms for metatranscriptomics.

Angiogenic factors and acute-phase proteins in serum samples of preeclampsia and HELLP patients: a matched-pair analysis

To investigate the serum level distribution of angiogenic markers (PlGF, endoglin, sFlt-1) and acute-phase proteins (SAA, CRP) in patients with HELLP syndrome or preeclampsia (PE) including matched controls.