Climate Change and Student Behavior: Recommendations for the University of Richmond

We, the Environmental Studies Senior Seminar Class of 2008, choose to recognize climate change as an imminent threat. After rigorous examination of the scientific, social, and political aspects of climate change, we initially wanted to help construct the carbon emissions inventory required in the PCC. However, citing their ability to build the inventory through existing University institutions, our administration steered us towards the Scope 3 emissions inventory, a component which focuses on student behavior. While we found Scope 3 too limiting, we decided our goal as a class was to impact student climate change awareness on campus. Therefore, we separated into three “working groups” and developed three distinct projects to meet our goal: 1) develop a database of projects and initiatives other universities have implemented to address climate change; 2) execute a comprehensive survey of the student body’s understanding of global climate change and energy consumption patterns and; 3) present the University of Richmond with options and recommendations for addressing climate change on campus. Our goal is to inspire individual responses to climate change. Raising awareness does not indicate everyone will or should agree with our beliefs and convictions, but it will enable individuals to come to their own conclusions. We wholeheartedly believe climate change is an issue we cannot disregard and we stand by the belief that the risk of doing nothing is the biggest danger of them all. Paper prepared for the Environmental Studies Senior Seminar Faculty Advisor: Dr. David Salisbur

Loss of Y Chromosome in the Malignant Peripheral Nerve Sheet Tumor of a Patient with Neurofibromatosis Type 1

Neurofibromatosis type 1 (NF1) is one of the most commonly inherited autosomal dominant disorders. In order to determine whether genomic alterations and/or chromosomal aberrations involved in the malignant progression of NF1 were present in a Korean patient with NF1, molecular and cytogenetic analyses were performed on the pathologically normal, benign, and malignant tissues and primary cells cultured from those tissues of the patient. The comparative genomic hybridization (CGH) array revealed a Y chromosome loss in the malignant peripheral nerve sheet tumor (MPNST) tissue. G-banding analysis of 50 metaphase cells showed normal chromosomal patterns in the histopathologically normal and benign cultured cells, but a mosaic Y chromosome loss in the malignant cells. The final karyotype for the malignant cells from MPNST tissue was 45,X,-Y[28]/46,XY[22]. The data suggest that the somatic Y chromosome loss may be involved in the transformation of benign tumors to MPNSTs

Species-level functional profiling of metagenomes and metatranscriptomes.

Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community's known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways. Relative to pure translated search, HUMAnN2 is faster and produces more accurate gene family profiles. We applied HUMAnN2 to study clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species' genomic versus transcriptional contributions, and strain profiling. Further, we introduce 'contributional diversity' to explain patterns of ecological assembly across different microbial community types

Genome-wide SNPs analysis of indigenous Zebu breeds in Pakistan

Prospects of high throughput technology in animal genetics makes easy to investigate hidden genetic variation in farm animal's genetic resources. However, many SNPs technologies are currently practicing in animal genetics. In this study, we investigated genome wide SNPs variations and its distribution across the indigenous cattle population in Pakistan using Illumina Bovine HD (777K) SNPs bead chip. A total of 136 individuals from ten different breeds were genotyped and after filtration 500, 939 SNPs markers were used for further analysis. The mean minor allele frequency (MAF) was 0.23, 0.20, 0.22, 0.22, 0.20, 0.18, 0.20, 0.22, 0.21 and 0.18 observed for Achi, Bhagnari, Cholistani, Dhanni, Dajal, Kankraj, Lohani, Red sindi, Sahiwal and Tharparkar cattle, respectively. Significant difference (P0.05) within breeds and remaining 36% were considered as monomorphic markers. Average observed (Ho) and expected (HE) heterozygosity values 0.662 and 0.640 were estimated among these breeds. In conclusion, this preliminary study results revealed that these SNPs variation level could potentially be used for genetic characterization of zebu cattle breeds and could also be used to estimate genetic potential of these cattle breeds for livestock improvement in country

Phylogenomics of non-model ciliates based on transcriptomic analyses

© The Author(s) 2015. This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited. The attached file is the published version of the article

The interplay of descriptor-based computational analysis with pharmacophore modeling builds the basis for a novel classification scheme for feruloyl esterases

One of the most intriguing groups of enzymes, the feruloyl esterases (FAEs), is ubiquitous in both simple and complex organisms. FAEs have gained importance in biofuel, medicine and food industries due to their capability of acting on a large range of substrates for cleaving ester bonds and synthesizing high-added value molecules through esterification and transesterification reactions. During the past two decades extensive studies have been carried out on the production and partial characterization of FAEs from fungi, while much less is known about FAEs of bacterial or plant origin. Initial classification studies on FAEs were restricted on sequence similarity and substrate specificity on just four model substrates and considered only a handful of FAEs belonging to the fungal kingdom. This study centers on the descriptor-based classification and structural analysis of experimentally verified and putative FAEs; nevertheless, the framework presented here is applicable to every poorly characterized enzyme family. 365 FAE-related sequences of fungal, bacterial and plantae origin were collected and they were clustered using Self Organizing Maps followed by k-means clustering into distinct groups based on amino acid composition and physico-chemical composition descriptors derived from the respective amino acid sequence. A Support Vector Machine model was subsequently constructed for the classification of new FAEs into the pre-assigned clusters. The model successfully recognized 98.2% of the training sequences and all the sequences of the blind test. The underlying functionality of the 12 proposed FAE families was validated against a combination of prediction tools and published experimental data. Another important aspect of the present work involves the development of pharmacophore models for the new FAE families, for which sufficient information on known substrates existed. Knowing the pharmacophoric features of a small molecule that are essential for binding to the members of a certain family opens a window of opportunities for tailored applications of FAEs

The extraordinary evolutionary history of the reticuloendotheliosis viruses

The reticuloendotheliosis viruses (REVs) comprise several closely related amphotropic retroviruses isolated from birds. These viruses exhibit several highly unusual characteristics that have not so far been adequately explained, including their extremely close relationship to mammalian retroviruses, and their presence as endogenous sequences within the genomes of certain large DNA viruses. We present evidence for an iatrogenic origin of REVs that accounts for these phenomena. Firstly, we identify endogenous retroviral fossils in mammalian genomes that share a unique recombinant structure with REVs—unequivocally demonstrating that REVs derive directly from mammalian retroviruses. Secondly, through sequencing of archived REV isolates, we confirm that contaminated Plasmodium lophurae stocks have been the source of multiple REV outbreaks in experimentally infected birds. Finally, we show that both phylogenetic and historical evidence support a scenario wherein REVs originated as mammalian retroviruses that were accidentally introduced into avian hosts in the late 1930s, during experimental studies of P. lophurae, and subsequently integrated into the fowlpox virus (FWPV) and gallid herpesvirus type 2 (GHV-2) genomes, generating recombinant DNA viruses that now circulate in wild birds and poultry. Our findings provide a novel perspective on the origin and evolution of REV, and indicate that horizontal gene transfer between virus families can expand the impact of iatrogenic transmission events

Extensive Copy-Number Variation of Young Genes across Stickleback Populations

MM received funding from the Max Planck innovation funds for this project. PGDF was supported by a Marie Curie European Reintegration Grant (proposal nr 270891). CE was supported by German Science Foundation grants (DFG, EI 841/4-1 and EI 841/6-1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript