Eating Is a Bitch

Produced by the Center on Disability Studies, University of Hawai'i at Manoa, Honolulu, Hawai'i and The School of Social Sciences, The University of Texas at Dallas, Richardson, Texas for The Society for Disability Studies

Liger, Tigons and Bears (Oh My!): The Genomic Consequences of Inter-species Hybridization

What makes a species? Driven largely by our natural inclination to categorize, we tend to think of all living things in discrete units – species – related to each other in a clearly defined taxonomic hierarchy into which every one fits neatly. New species emerge as evolutionary changes accumulate within one, leading to reproductive barriers that eventually split that one species into two. Hybrids, however, challenge this notion. As more and more genomes are sequenced, scientists are beginning to discover how common hybridization is in the wild, and that speciation may not be the directional – and irreversible – process we thought we understood. Through the remarkable and complex story of the evolution of the polar bear, I will discuss how hybridization may help to shape genomic diversity in wild populations, including aiding the survival of species during periods of dramatic environmental change. I will ask the question: is there really such a thing as a brown bear

Conformational energy calculations of tyrocidine

The minimum energy conformation of the cyclic decapeptide tyrocidine was calculated using the Empirical Conformational Energy Program for Peptides (ECEPP). Half of the amino acid sequence of tyrocidine is identical to the amino acid sequence found in the cyclic decapeptide gramicidin-S. Hence this study focuses on the conformation of the decapeptide that is not contained in gramicidin-S. This study calculates the conformation of a tripeptide ASN-GLN-TYR without the consideration of the presence of a beta bend formation because there is a low probability that a beta bend exists in this location. Two of the lowest energy conformations found in this study have an 82 % probability of occurrence. Computer graphics representations of these conformations show the presence of hydrogen bonding and compact appearance

Assets, Race, and Educational Choices

Assets, Race, and Educational Choice

Management of E-Resources Cataloging Workflows at the University of Maryland, College Park

In 2011, one of the authors, a staff member of the Metadata Services Department at the University of Maryland, College Park, created an electronic resources cataloging management database (ERCM) to manage the details of MARC record set loads to the online catalog. After attending the NISO Standards update session entitled “The NISO ERM Data Standards and Best Practices Review” presentation at the 2012 Annual Conference of the American Library Association, at which cataloging workflow support was referred to as a problem area in electronic resources management, she decided to follow up with an investigation of the nature of the problem and to explore its relevancy to the ERCM. This article will inform metadata services departments about the management of constantly changing electronic resources cataloging workflows and also discuss cataloging workflow as it pertains to Electronic Resources Management System (ERMS) development

A novel NGS library preparation method to characterize native termini of fragmented DNA.

Biological and chemical DNA fragmentation generates DNA molecules with a variety of termini, including blunt ends and single-stranded overhangs. We have developed a Next Generation Sequencing (NGS) assay, XACTLY, to interrogate the termini of fragmented DNA, information traditionally lost in standard NGS library preparation methods. Here we describe the XACTLY method, showcase its sensitivity and specificity, and demonstrate its utility in in vitro experiments. The XACTLY assay is able to report relative abundances of all lengths and types (5' and 3') of single-stranded overhangs, if present, on each DNA fragment with an overall accuracy between 80-90%. In addition, XACTLY retains the sequence of each native DNA molecule after fragmentation and can capture the genomic landscape of cleavage events at single nucleotide resolution. The XACTLY assay can be applied as a novel research and discovery tool for fragmentation analyses and in cell-free DNA

Recovery of DNA from Footprints in the Snow

The recovery of trace amounts of DNA has been demonstrated to be a reliable tool in conservation genetics and has become a key component of modern forensic casework. To date, genetic data have been successfully recovered from a variety of sources, including biological fluids, faeces, clothing, and even directly from fingerprints. However, to our knowledge and despite their widespread occurrence and clear potential as a source of DNA, genetic information has not previously been recovered directly from footprints. Here, we extract and amplify mitochondrial DNA from a snow footprint, <48-hours old, made by a Swedish Arctic Fox (Alopex lagopus). Our results demonstrate that it is possible to recover sufficient DNA from recent footprints to accurately type the source of the print, with implications for conservation biology and forensic science

Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: Subtype G is a circulating recombinant form

Human immunodeficiency virus type I (HIV-1) is classified in nine subtypes (A to D, F, G, H, J, and K), a number of subsubtypes, and several circulating recombinant forms (CRFs). Due to the high level of genetic diversity within HIV-1 and to its worldwide distribution, this classification system is widely used in fields as diverse as vaccine development, evolution, epidemiology, viral fitness, and drug resistance. Here, we demonstrate how the high recombination rates of HIV-1 may confound the study of its evolutionary history and classification. Our data show that subtype G, currently classified as a pure subtype, has in fact a recombinant history, having evolved following recombination between subtypes A and J and a putative subtype G parent. In addition, we find no evidence for recombination within one of the lineages currently classified as a CRF, CRF02 -AG. Our analysis indicates that CRF02_AG was the parent of the recombinant subtype G, rather than the two having the opposite evolutionary relationship, as is currently proposed. Our results imply that the current classification of HIV-1 subtypes and CRFs is an artifact of sampling history, rather than reflecting the evolutionary history of the virus. We suggest a reanalysis of all pure subtypes and CRFs in order to better understand how high rates of recombination have influenced HIV-1 evolutionary history.</p

Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf.

Protection of populations comprising admixed genomes is a challenge under the Endangered Species Act (ESA), which is regarded as the most powerful species protection legislation ever passed in the United States but lacks specific provisions for hybrids. The eastern wolf is a newly recognized wolf-like species that is highly admixed and inhabits the Great Lakes and eastern United States, a region previously thought to be included in the geographic range of only the gray wolf. The U.S. Fish and Wildlife Service has argued that the presence of the eastern wolf, rather than the gray wolf, in this area is grounds for removing ESA protection (delisting) from the gray wolf across its geographic range. In contrast, the red wolf from the southeastern United States was one of the first species protected under the ESA and was protected despite admixture with coyotes. We use whole-genome sequence data to demonstrate a lack of unique ancestry in eastern and red wolves that would not be expected if they represented long divergent North American lineages. These results suggest that arguments for delisting the gray wolf are not valid. Our findings demonstrate how a strict designation of a species under the ESA that does not consider admixture can threaten the protection of endangered entities. We argue for a more balanced approach that focuses on the ecological context of admixture and allows for evolutionary processes to potentially restore historical patterns of genetic variation