Isofunctional Clustering and Conformational Analysis of the Arsenate Reductase Superfamily Reveals Nine Distinct Clusters.

Arsenate reductase (ArsC) is a superfamily of enzymes that reduce arsenate. Due to active site similarities, some ArsC can function as low-molecular weight protein tyrosine phosphatases (LMW-PTPs). Broad superfamily classifications align with redox partners (Trx- or Grx-linked).

Development and Implementation of a National Center of Excellence in Dairy Production Medicine Education for Veterinary Students: Description of the Effort and Lessons Learned.

The need for consortial programs to provide advanced education in food animal veterinary production medicine has been recognized and lauded for nearly three decades. This article describes one effort to create a dairy production medicine curriculum funded by a United States Department of Agriculture (USDA) Higher Education Challenge Grant. This National Center of Excellence in Dairy Production Medicine Education for Veterinarians is housed at the Dairy Education Center of the University of Minnesota and the project was a collaboration of the University of Minnesota, the University of Illinois, the University of Georgia, and Kansas State University.

Methods Used to Assess Student Performance and Course Outcomes at the National Center of Excellence in Dairy Production Medicine Education for Veterinarians.

Between 2012 and 2014, three cohorts of senior veterinary students participated in an 8-week dairy production medicine course created by the National Center of Excellence in Dairy Production Medicine Education for Veterinarians. One goal of this course is to better prepare veterinary students to serve the increasingly complex needs of the dairy industry. In this article, we describe the assessment methods and student performance outcomes of those first three cohorts.

Effects of an 8-Week Dairy Production Medicine Course on Veterinary Student Self-Confidence and Perceptions of Knowledge and Skills Used by Dairy Veterinarians.

The 8-week dairy production medicine course at the National Center of Excellence in Dairy Production Medicine Education for Veterinarians is designed to equip senior veterinary students with the knowledge and skills needed to serve the dairy industry. Course developers identified 59 topics of importance for dairy production medicine veterinarians. Students ( = 50) were surveyed before and after the course to determine their perceptions of (a) the importance of the 59 topics for their intended positions and (b) their knowledge and skill in those areas.

Prior Experience, Career Intentions, and Post-Graduate Positions of Veterinary Students Who Participated in an 8-week Dairy Production Medicine Course.

Three cohorts of senior veterinary students ( = 50) from seven United States (US) colleges of veterinary medicine took an 8-week dairy production medicine course at the Dairy Center of Excellence in Production Medicine Education for Veterinarians (DCE) between 2012 and 2014. Participants completed a questionnaire before and after the course and 1 to 2 years after graduation. Objectives were to determine the prior academic training and livestock experience of course participants, to compare students' career aspirations before and after taking the course, and to identify factors associated with post-graduate position.

Identification of Transcriptional and Receptor Networks That Control Root Responses to Ethylene.

Transcriptomic analyses with high temporal resolution provide substantial new insight into hormonal response networks. This study identified the kinetics of genome-wide transcript abundance changes in response to elevated levels of the plant hormone ethylene in roots from light-grown Arabidopsis () seedlings, which were overlaid on time-matched developmental changes. Functional annotation of clusters of transcripts with similar temporal patterns revealed rapidly induced clusters with known ethylene function and more slowly regulated clusters with novel predicted functions linked to root development.

An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins.

Peroxiredoxins (Prxs or Prdxs) are a large protein superfamily of antioxidant enzymes that rapidly detoxify damaging peroxides and/or affect signal transduction and, thus, have roles in proliferation, differentiation, and apoptosis. Prx superfamily members are widespread across phylogeny and multiple methods have been developed to classify them. Here we present an updated atlas of the Prx superfamily identified using a novel method called MISST (Multi-level Iterative Sequence Searching Technique).

An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences.

Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification-amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants.

DASP3: identification of protein sequences belonging to functionally relevant groups.

Background: Development of automatable processes for clustering proteins into functionally relevant groups is a critical hurdle as an increasing number of sequences are deposited into databases. Experimental function determination is exceptionally time-consuming and can't keep pace with the identification of protein sequences. A tool, DASP (Deacon Active Site Profiler), was previously developed to identify protein sequences with active site similarity to a query set.

Impact of the Type I Interferon Receptor on the Global Gene Expression Program During the Course of Dendritic Cell Maturation Induced by Polyinosinic Polycytidylic Acid.

Dendritic cell (DC) maturation involves widespread changes in cellular function and gene expression. The regulatory role of IFNAR in the program of DC maturation remains incompletely defined. Thus, the time evolution impact of IFNAR on this process was evaluated.

Mutating a Highly Conserved Residue in Diverse Cytochrome P450s Facilitates Diastereoselective Olefin Cyclopropanation.

Cytochrome P450s and other heme-containing proteins have recently been shown to have promiscuous activity for the cyclopropanation of olefins using diazoacetate reagents. Despite the progress made thus far, engineering selective catalysts for all possible stereoisomers for the cyclopropanation reaction remains a considerable challenge. Previous investigations of a model P450 (P450BM3 ) revealed that mutation of a conserved active site threonine (Thr268) to alanine transformed the enzyme into a highly active and selective cyclopropanation catalyst.

Effect of feeding heat-treated colostrum on risk for infection with Mycobacterium avium ssp. paratuberculosis, milk production, and longevity in Holstein dairy cows.

In summer 2007, a randomized controlled field trial was initiated on 6 large Midwest commercial dairy farms to investigate the effect of feeding heat-treated (HT) colostrum on transmission of Mycobacterium avium ssp. paratuberculosis (MAP) and on future milk production and longevity within the herd. On each farm, colostrum was collected daily from fresh cows, pooled, divided into 2 aliquots, and then 1 aliquot was heat-treated in a commercial batch pasteurizer at 60°C for 60min.

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity.

The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information.

Integration of gene expression data with network-based analysis to identify signaling and metabolic pathways regulated during the development of osteoarthritis.

Osteoarthritis (OA) is characterized by remodeling and degradation of joint tissues. Microarray studies have led to a better understanding of the molecular changes that occur in tissues affected by conditions such as OA; however, such analyses are limited to the identification of a list of genes with altered transcript expression, usually at a single time point during disease progression. While these lists have identified many novel genes that are altered during the disease process, they are unable to identify perturbed relationships between genes and gene products.

Broad phenotypic changes associated with gain of radiation resistance in head and neck squamous cell cancer.

Aims: The central issue of resistance to radiation remains a significant challenge in the treatment of cancer despite improvements in treatment modality and emergence of new therapies. To facilitate the identification of molecular factors that elicit protection against ionizing radiation, we developed a matched model of radiation resistance for head and neck squamous cell cancer (HNSCC) and characterized its properties using quantitative mass spectrometry and complementary assays.

Results: Functional network analysis of proteomics data identified DNA replication and base excision repair, extracellular matrix-receptor interaction, cell cycle, focal adhesion, and regulation of actin cytoskeleton as significantly up- or downregulated networks in resistant (rSCC-61) HNSCC cells.

A kinetic analysis of the auxin transcriptome reveals cell wall remodeling proteins that modulate lateral root development in Arabidopsis.

To identify gene products that participate in auxin-dependent lateral root formation, a high temporal resolution, genome-wide transcript abundance analysis was performed with auxin-treated Arabidopsis thaliana roots. Data analysis identified 1246 transcripts that were consistently regulated by indole-3-acetic acid (IAA), partitioning into 60 clusters with distinct response kinetics. We identified rapidly induced clusters containing auxin-response functional annotations and clusters exhibiting delayed induction linked to cell division temporally correlated with lateral root induction.

Effects of weekly regrouping of prepartum dairy cows on metabolic, health, reproductive, and productive parameters.

The objectives of the current experiment were to determine the effect of 2 prepartum grouping strategies on the health, metabolic, reproductive, and productive parameters of dairy cows. Jersey cows enrolled in the experiment at 253±3 d of gestation (d 0=calving) were balanced for parity and projected 305-d mature equivalent and assigned to 1 of 2 treatments. Cows assigned to the traditional (TRD; n=6 replicates with a total of 308 cows) treatment were moved to the study pen as a group of 44 cows and weekly thereafter groups of 2 to 15 cows were moved to the study pen to reestablish stocking density.

Disease progression and phasic changes in gene expression in a mouse model of osteoarthritis.

Osteoarthritis (OA) is the most common form of arthritis and has multiple risk factors including joint injury. The purpose of this study was to characterize the histologic development of OA in a mouse model where OA is induced by destabilization of the medial meniscus (DMM model) and to identify genes regulated during different stages of the disease, using RNA isolated from the joint "organ" and analyzed using microarrays. Histologic changes seen in OA, including articular cartilage lesions and osteophytes, were present in the medial tibial plateaus of the DMM knees beginning at the earliest (2 week) time point and became progressively more severe by 16 weeks.

Electrostatics of cysteine residues in proteins: parameterization and validation of a simple model.

One of the most popular and simple models for the calculation of pK(a) s from a protein structure is the semi-macroscopic electrostatic model MEAD. This model requires empirical parameters for each residue to calculate pK(a) s. Analysis of current, widely used empirical parameters for cysteine residues showed that they did not reproduce expected cysteine pK(a) s; thus, we set out to identify parameters consistent with the CHARMM27 force field that capture both the behavior of typical cysteines in proteins and the behavior of cysteines which have perturbed pK(a) s.

Heat-treated colostrum and reduced morbidity in preweaned dairy calves: results of a randomized trial and examination of mechanisms of effectiveness.

A randomized controlled clinical trial was conducted using 1,071 newborn calves from 6 commercial dairy farms in Minnesota and Wisconsin, with the primary objective being to describe the effects of feeding heat-treated colostrum on serum immunoglobulin G concentration and health in the preweaning period. A secondary objective was to complete a path analysis to identify intermediate factors that may explain how feeding heat-treated colostrum reduced the risk for illness. On each farm, colostrum was collected each day, pooled, and divided into 2 aliquots; then, one aliquot was heat-treated in a commercial batch pasteurizer at 60°C for 60 min.

Heat treatment of colostrum on commercial dairy farms decreases colostrum microbial counts while maintaining colostrum immunoglobulin G concentrations.

This study was conducted on 6 commercial dairy farms in Minnesota and Wisconsin to describe the effect of heat treatment (at 60°C for 60 min) on colostrum, on colostrum bacteria counts, and immunoglobulin G concentrations. First-milking colostrum was collected each day, pooled, divided into 2 aliquots, and then 1 aliquot was heat treated in a commercial batch pasteurizer at 60°C for 60 min. Frozen samples of pre- and post- heat-treated colostrum were submitted for standard microbial culture (total plate count and total coliform count, cfu/mL) and testing for immunoglobulin G concentrations (mg/mL).

Structural and electrostatic asymmetry at the active site in typical and atypical peroxiredoxin dimers.

The peroxiredoxins (Prx) are ubiquitous peroxidases involved in important biological processes; however, details of their enzymatic mechanism remain elusive. To probe potential dynamics-function relationships, molecular dynamics simulations and electrostatic calculations were performed on the atypical 2-cysteine thiol peroxidase (Tpx) from Streptococcus pneumoniae and results compared to a previous study of a typical 2-cysteine Prx from Trypanosoma cruzi. The analyses indicate a commonality between both typical and atypical Prx: dynamic asymmetry.

Effects of resynchronization strategies for lactating Holstein cows on pattern of reinsemination, fertility, and economic outcome.

The objectives were to evaluate the pattern of re-insemination, pregnancy outcomes to re-insemination in estrus and at fixed time, and economic outcomes of lactating Holstein cows submitted to three resynchronization protocols. Cows were enrolled in the Experiment at 32 ± 3 d after pre-enrollment Artificial Insemination (AI), 7 d before pregnancy diagnosis, and randomly assigned to three resynchronization protocols. All cows diagnosed not pregnant at 39 ± 3 d after pre-enrollment AI were submitted to the Cosynch72 (Day 0 GnRH, Day 7 prostaglandin F(2α), and Day 10 GnRH and fixed time AI).