Automated, longitudinal measures of drinking behavior provide insights into the social hierarchy in dairy cows.

Dairy cows compete for feed and water access on commercial farms. In this study we used EloSteepness to assess the summed Elo winning probabilities (i.e.

Automated monitoring of brush use in dairy cattle.

Access to brushes allows for natural scratching behaviors in cattle, especially in confined indoor settings. Cattle are motivated to use brushes, but brush use varies with multiple factors including social hierarchy and health. Brush use might serve an indicator of cow health or welfare, but practical application of these measures requires accurate and automated monitoring tools.

Effects of group size on agonistic interactions in dairy cows: a descriptive study.

Group-housed cattle may engage in agonistic interactions over resources such as feed, which can negatively affect aspects of welfare. Little is known about how contextual factors such as group size influence agonistic behaviour. We explored the frequency of agonistic interactions at the feeder when cattle were housed in different-sized groups.

The Effect of Placement and Group Size on the Use of an Automated Brush by Groups of Lactating Dairy Cattle.

Mechanical brushes are often provided on dairy farms to facilitate grooming. However, current brush designs do not provide data on their use, and thus little is known about the effects of group size and placement of brushes within the pen. The objectives of this study were to automatically detect brush use in cow groups and to investigate the influence of (1) group size and the corresponding cow-to-brush ratio and (2) brush placement in relation to the lying stalls and the feeding and drinking areas.

Invited review: Social dominance in dairy cattle: A critical review with guidelines for future research.

Cattle are gregarious animals able to form social relationships. Dominance is one of the most widely studied social behaviors of dairy cattle, especially cows confined indoors. However, much of the past dairy cattle research has used an unstandardized approach, differing in definitions and conceptual understanding of dominance, as well as their methods of data collection and dominance calculation.

The effects of cow dominance on the use of a mechanical brush.

An animal's social position within a group can influence its ability to perform important behaviours like eating and resting, but little is known about how social position affects the ability to express what are arguably less important but still rewarding behaviors, such as grooming. We set out to assess if dominance measured at the feeder is associated with increased use of a mechanical brush. Over a 2-year period, 161 dry cows were enrolled in a dynamically changing group of 20 individuals with access to a mechanical brush.

Structure of human ADAM-8 catalytic domain complexed with batimastat.

The role of ADAM-8 in cancer and inflammatory diseases such as allergy, arthritis and asthma makes it an attractive target for drug development. Therefore, the catalytic domain of human ADAM-8 was expressed, purified and crystallized in complex with a hydroxamic acid inhibitor, batimastat. The crystal structure of the enzyme-inhibitor complex was refined to 2.

Dissecting the substrate recognition of 3-O-sulfotransferase for the biosynthesis of anticoagulant heparin.

Heparin is a polysaccharide-based natural product that is used clinically as an anticoagulant drug. Heparan sulfate 3-O-sulfotransferase (3-OST) is an enzyme that transfers a sulfo group to the 3-OH position of a glucosamine unit. 3-OST is present in multiple isoforms, and the polysaccharides modified by these different isoforms perform distinct biological functions.

Conformational dependence of 13C shielding and coupling constants for methionine methyl groups.

Methionine residues fulfill a broad range of roles in protein function related to conformational plasticity, ligand binding, and sensing/mediating the effects of oxidative stress. A high degree of internal mobility, intrinsic detection sensitivity of the methyl group, and low copy number have made methionine labeling a popular approach for NMR investigation of selectively labeled protein macromolecules. However, selective labeling approaches are subject to more limited information content.

Der p 5 crystal structure provides insight into the group 5 dust mite allergens.

Group 5 allergens from house dust mites elicit strong IgE antibody binding in mite-allergic patients. The structure of Der p 5 was determined by x-ray crystallography to better understand the IgE epitopes, to investigate the biologic function in mites, and to compare with the conflicting published Blo t 5 structures, designated 2JMH and 2JRK in the Protein Data Bank. Der p 5 is a three-helical bundle similar to Blo t 5, but the interactions of the helices are more similar to 2JMH than 2JRK.

A 5' cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs.

A single regulatory protein can control the fate of many mRNAs with related functions. The Puf3 protein of Saccharomyces cerevisiae is exemplary, as it binds and regulates more than 100 mRNAs that encode proteins with mitochondrial function. Here we elucidate the structural basis of that specificity.

Template strand scrunching during DNA gap repair synthesis by human polymerase lambda.

Family X polymerases such as DNA polymerase lambda (Pol lambda) are well suited for filling short gaps during DNA repair because they simultaneously bind both the 5' and 3' ends of short gaps. DNA binding and gap filling are well characterized for 1-nucleotide (nt) gaps, but the location of yet-to-be-copied template nucleotides in longer gaps is unknown. Here we present crystal structures revealing that, when bound to a 2-nt gap, Pol lambda scrunches the template strand and binds the additional uncopied template base in an extrahelical position within a binding pocket that comprises three conserved amino acids.

Slow conformational dynamics at C2'-endo nucleotides in RNA.

RNA molecules undergo local conformational dynamics on timescales spanning picoseconds to minutes. Slower local motions have the greater potential to govern RNA folding, ligand recognition, and ribonucleoprotein assembly reactions but are difficult to detect in large RNAs with complex structures. RNA SHAPE chemistry employs acylation of the ribose 2'-hydroxyl position to measure local nucleotide flexibility in RNA and is well-characterized by a mechanism in which each nucleotide samples unreactive (closed) and reactive (open) states.

Crystal structure of a type II dihydrofolate reductase catalytic ternary complex.

Type II dihydrofolate reductase (DHFR) is a plasmid-encoded enzyme that confers resistance to bacterial DHFR-targeted antifolate drugs. It forms a symmetric homotetramer with a central pore which functions as the active site. Its unusual structure, which results in a promiscuous binding surface that accommodates either the dihydrofolate (DHF) substrate or the NADPH cofactor, has constituted a significant limitation to efforts to understand its substrate specificity and reaction mechanism.

Role of the catalytic metal during polymerization by DNA polymerase lambda.

The incorporation of dNMPs into DNA by polymerases involves a phosphoryl transfer reaction hypothesized to require two divalent metal ions. Here we investigate this hypothesis using as a model human DNA polymerase lambda (Pol lambda), an enzyme suggested to be activated in vivo by manganese. We report the crystal structures of four complexes of human Pol lambda.

Identification and functional characterization of polymorphisms in human cyclooxygenase-1 (PTGS1).

Objective: Cyclooxygenase-1 (COX-1, PTGS1) catalyzes the conversion of arachidonic acid to prostaglandin H2, which is subsequently metabolized to various biologically active prostaglandins. We sought to identify and characterize the functional relevance of genetic polymorphisms in PTGS1.

Methods: Sequence variations in human PTGS1 were identified by resequencing 92 healthy individuals (24 African, 24 Asian, 24 European/Caucasian, and 20 anonymous).

Magnesium-induced assembly of a complete DNA polymerase catalytic complex.

The molecular details of the nucleotidyl transferase reaction have remained speculative, as strategies to trap catalytic intermediates for structure determination utilize substrates lacking the primer terminus 3'-OH and catalytic Mg2+, resulting in an incomplete and distorted active site geometry. Since the geometric arrangement of these essential atoms will impact chemistry, structural insight into fidelity strategies has been hampered. Here, we present a crystal structure of a precatalytic complex of a DNA polymerase with bound substrates that include the primer 3'-OH and catalytic Mg2+.

Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase.

Insertions and deletions in coding sequences can alter the reading frame of genes and have profound biological consequences. In 1966, Streisinger proposed that these mutations result from strand slippage, which in repetitive sequences generates misaligned intermediates stabilized by correct base pairing that support polymerization. We report here crystal structures of human DNA polymerase lambda, which frequently generates deletion mutations, bound to such intermediates.

Crystal structures, reactivity and inferred acylation transition states for 2'-amine substituted RNA.

Ribose 2'-amine substitutions are broadly useful as structural probes in nucleic acids. In addition, structure-selective chemical reaction at 2'-amine groups is a robust technology for interrogating local nucleotide flexibility and conformational changes in RNA and DNA. We analyzed crystal structures for several RNA duplexes containing 2'-amino cytidine (C(N)) residues that form either C(N)-G base pairs or C(N)-A mismatches.

Structural insight into the DNA polymerase beta deoxyribose phosphate lyase mechanism.

A large number of biochemical and genetic studies have demonstrated the involvement of DNA polymerase beta (Pol beta) in mammalian base excision repair (BER). Pol beta participates in BER sub-pathways by contributing gap filling DNA synthesis and lyase removal of the 5'-deoxyribose phosphate (dRP) group from the cleaved abasic site. To better understand the mechanism of the dRP lyase reaction at an atomic level, we determined a crystal structure of Pol beta complexed with 5'-phosphorylated abasic sugar analogs in nicked DNA.

Evolution from DNA to RNA recognition by the bI3 LAGLIDADG maturase.

LAGLIDADG endonucleases bind across adjacent major grooves via a saddle-shaped surface and catalyze DNA cleavage. Some LAGLIDADG proteins, called maturases, facilitate splicing by group I introns, raising the issue of how a DNA-binding protein and an RNA have evolved to function together. In this report, crystallographic analysis shows that the global architecture of the bI3 maturase is unchanged from its DNA-binding homologs; in contrast, the endonuclease active site, dispensable for splicing facilitation, is efficiently compromised by a lysine residue replacing essential catalytic groups.

A closed conformation for the Pol lambda catalytic cycle.

Pol lambda is a family X member believed to fill short gaps during DNA repair. Here we report crystal structures of Pol lambda representing three steps in filling a single-nucleotide gap. These structures indicate that, unlike other DNA polymerases, Pol lambda does not undergo large subdomain movements during catalysis, and they provide a clear characterization of the geometry and stereochemistry of the in-line nucleotidyl transfer reaction.