Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

In recent years, members of the protein kinase family have been discovered at an accelerated pace. Most were first described, not through the traditional biochemical approach of protein purification and enzyme assay, but as putative protein kinase amino acid sequences deduced from the nucleotide sequences of molecularly cloned genes or complementary DNAs. Phylogenetic mapping of the conserved protein kinase catalytic domains can serve as a useful first step in the functional characterization of these newly identified family members.

http://science.sciencemag.org/content/sci/241/4861/42.full.pdf

The protein kinase family: conserved features and deduced phylogeny of the catalytic domains.

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Evolution of Protein Molecules

Species distribution models (SDM) can be valuable for identifying key habitats for conservation management of threatened taxa, but anthropogenic habitat change can undermine SDM accuracy. We used data for the Red Siskin (Spinus cucullatus), a critically endangered bird and ground truthing to examine anthropogenic habitat change as a source of SDM inaccuracy. We aimed to estimate: (1) the Red Siskin's historic distribution in Venezuela; (2) the portion of this historic distribution lost to vegetation degradation; and (3) the location of key habitats or areas with both, a high probability of historic occurrence and a low probability of vegetation degradation. We ground-truthed 191 locations and used expert opinion as well as landscape characteristics to classify species' habitat suitability as excellent, good, acceptable, or poor. We fit a Random Forest model (RF) and Enhanced Vegetation Index (EVI) time series to evaluate the accuracy and precision of the expert categorization of habitat suitability. We estimated the probability of historic occurrence by fitting a MaxLike model using 88 presence records (1960-2013) and data on forest cover and aridity index. Of the entire study area, 23% (20,696 km2) had a historic probability of Red Siskin occurrence over 0.743. Furthermore, 85% of ground-truthed locations had substantial reductions in mean EVI, resulting in key habitats totaling just 976 km2, in small blocks in the western and central regions. Decline in Area of Occupancy over 15 years was between 40% and 95%, corresponding to an extinction risk category between Vulnerable and Critically Endangered. Relating key habitats with other landscape features revealed significant risks and opportunities for proposed conservation interventions, including the fact that ongoing vegetation degradation could limit the establishment of reintroduced populations in eastern areas, while the conservation of remaining key habitats on private lands could be improved with biodiversity-friendly agri- and silviculture programs.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.3628

How to deal with ground truthing affected by human‐induced habitat change?: Identifying high‐quality habitats for the Critically Endangered Red Siskin

The Red Siskin is one of Venezuela’s most endangered birds because of illegal trapping for the pet trade. Ex situ conservation of this species is an important safeguard against extinction while this threat is brought under control. However, for captive birds to be useful to a formal conservation breeding by Kathryn M. Rodríguez-Clark1,2,3, Jesús E. Maldonado2,3, David Ascanio4, Emperatriz Gamero1, Leonel Ovalle5, Jorge Pérez-Emán6, Michael Braun2

Using genetics to understand and conserve the Red Siskin ( Carduelis cucullata )

https://zslpublications.onlinelibrary.wiley.com/doi/pdf/10.1111/acv.12587

Illegal wildlife trade networks: finding creative opportunities for conservation intervention in challenging circumstances

Captive breeding for reintroduction is a conservation technique that can be important in preventing extinctions (Butchart et al. 2006, Hoffmann et al. 2010). One of the most basic factors that may influence the success of a captive breeding/reintroduction effort is obtaining appropriate founders (IUCN/ SSC 2013). Founders should ideally be representative of populations from the region to be restored,

/pdf/evaluating-a-potential-source-of-founders-for-ex-situ-59is8iwp3k.pdf

Evaluating a potential source of founders for ex situ conservation efforts: genetic differentiation between disjunct populations of the Endangered red siskin Spinus cucullatus

Michael J. Braun

Papers

How to deal with ground truthing affected by human‐induced habitat change?: Identifying high‐quality habitats for the Critically Endangered Red Siskin

Using genetics to understand and conserve the Red Siskin ( Carduelis cucullata )

Illegal wildlife trade networks: finding creative opportunities for conservation intervention in challenging circumstances

Evaluating a potential source of founders for ex situ conservation efforts: genetic differentiation between disjunct populations of the Endangered red siskin Spinus cucullatus

Erratum Correcting "Evolutionary Implications of Divergent Clines in a Manakin (;Manacus;, Aves) Hybrid Zone