Effects of frequent machine milking and suckling in early lactation on blood plasma ion homoeostasis in high-yielding dairy cows

SUMMARY Groups of nine or ten cows were assigned, after calving, to treatments in which they were (i) machine milked three times daily (M3), (ii) machine milked six times daily (M6) or (iii) suckled three times daily in addition to being machine milked three times daily (S). Treatments were administered during the first 6 weeks postpartum. On one day, at weeks 1 and 6 postpartum, blood samples were collected from all cows at 30-min intervals between 06.00 and 13.00 h and these were analysed for plasma osmolality and plasma concentrations of Na + , K + and Cl − . Milk yield was significantly higher in suckled cows than in cows milked six times daily, but significantly lower in cows milked three times daily. In cows milked six times daily, and to a greater extent in suckled cows, there was a reduction in plasma osmolality and monovalent ion concentrations (Na + , K + and Cl − ), which could increase the susceptibility of the cows to water intoxication. Moreover, suckling or milking the cows six times daily was associated with increased fluctuations in plasma osmolality and plasma Cl − concentrations. The decrease in plasma osmolality and ion concentration and the increased variation in plasma osmolality and Cl − were probably related to increased water intake and may be indicative of a severe challenge to homoeostasis regulation

PDBe: Protein Data Bank in Europe

The Protein Data Bank in Europe (PDBe) (http://www.ebi.ac.uk/pdbe/) is actively working with its Worldwide Protein Data Bank partners to enhance the quality and consistency of the international archive of bio-macromolecular structure data, the Protein Data Bank (PDB). PDBe also works closely with its collaborators at the European Bioinformatics Institute and the scientific community around the world to enhance its databases and services by adding curated and actively maintained derived data to the existing structural data in the PDB. We have developed a new database infrastructure based on the remediated PDB archive data and a specially designed database for storing information on interactions between proteins and bound molecules. The group has developed new services that allow users to carry out simple textual queries or more complex 3D structure-based queries. The newly designed ‘PDBeView Atlas pages’ provide an overview of an individual PDB entry in a user-friendly layout and serve as a starting point to further explore the information available in the PDBe database. PDBe’s active involvement with the X-ray crystallography, Nuclear Magnetic Resonance spectroscopy and cryo-Electron Microscopy communities have resulted in improved tools for structure deposition and analysis

TOMOBFLOW: feature-preserving noise filtering for electron tomography

<p>Abstract</p> <p>Background</p> <p>Noise filtering techniques are needed in electron tomography to allow proper interpretation of datasets. The standard linear filtering techniques are characterized by a tradeoff between the amount of reduced noise and the blurring of the features of interest. On the other hand, sophisticated anisotropic nonlinear filtering techniques allow noise reduction with good preservation of structures. However, these techniques are computationally intensive and are difficult to be tuned to the problem at hand.</p> <p>Results</p> <p>TOMOBFLOW is a program for noise filtering with capabilities of preservation of biologically relevant information. It is an efficient implementation of the Beltrami flow, a nonlinear filtering method that locally tunes the strength of the smoothing according to an edge indicator based on geometry properties. The fact that this method does not have free parameters hard to be tuned makes TOMOBFLOW a user-friendly filtering program equipped with the power of diffusion-based filtering methods. Furthermore, TOMOBFLOW is provided with abilities to deal with different types and formats of images in order to make it useful for electron tomography in particular and bioimaging in general.</p> <p>Conclusion</p> <p>TOMOBFLOW allows efficient noise filtering of bioimaging datasets with preservation of the features of interest, thereby yielding data better suited for post-processing, visualization and interpretation. It is available at the web site <url>http://www.ual.es/%7ejjfdez/SW/tomobflow.html</url>.</p

Integrating sequence and structural biology with DAS.

BACKGROUND: The Distributed Annotation System (DAS) is a network protocol for exchanging biological data. It is frequently used to share annotations of genomes and protein sequence. RESULTS: Here we present several extensions to the current DAS 1.5 protocol. These provide new commands to share alignments, three dimensional molecular structure data, add the possibility for registration and discovery of DAS servers, and provide a convention how to provide different types of data plots. We present examples of web sites and applications that use the new extensions. We operate a public registry of DAS sources, which now includes entries for more than 250 distinct sources. CONCLUSION: Our DAS extensions are essential for the management of the growing number of services and exchange of diverse biological data sets. In addition the extensions allow new types of applications to be developed and scientific questions to be addressed. The registry of DAS sources is available at http://www.dasregistry.org.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Portal drained visceral flux, hepatic metabolism, and mammary uptake of free and peptide-bound amino acids and milk amino acid output in dairy cows fed diets containing corn grain steam flaked at 360 orsteam rolled at 490 g/L.

Objectives were to measure net fluxes of free (FAA) and peptide bound amino acids (AA) (PBAA) across portal-drained viscera (PDV), liver, splanchnic, and mammary tissues, and of milk AA output of lactating Holstein cows (n = 6, 109 +/- 9 d in milk) as influenced by flaking density of corn grain. Cows were fed alfalfa-based total mixed ration (TMR) containing 40% steam-flaked (SFC) or steam-rolled corn (SRC) grain. The TMR were offered at 12-h intervals in a crossover design. Six sets of blood samples were obtained from indwelling catheters in portal, hepatic, and mammary veins and mesenteric or costoabdominal arteries every 2 h from each cow and diet. Intake of dry matter (18.4 +/- 0.4 kg/d), N, and net energy for lactation were not altered by corn processing. Milk and milk crude protein yields (kg/12-h sampling) were 14.2 vs. 13.5 and 0.43 vs. 0.39 for cows fed SFC or SRC, respectively. The PDV flux of total essential FAA was greater (571.2 vs. 366.4 g/12 h, SEM 51.4) in cows fed SFC. The PDV flux of total essential PBAA was 69.3 +/- 10.8 and 51.5 +/- 13.2 g/12 h for cows fed SFC and SRC, respectively, and differed from zero, but fluxes of individual PBAA rarely differed between treatments. Liver flux of essential FAA was greater in cows fed SRC, but only the PBAA flux in cows fed SRC differed from zero. Splanchnic flux of FAA and PBAA followed the pattern of PDV flux, but variation was greater. Mammary uptake (g/12 h) of total essential FAA was greater in cows fed SFC than SRC (224.6 vs. 198.3, SEM 7.03). Mammary uptake of essential PBAA was 25.0 vs. 15.1, SEM 5.2, g/12 h for cows fed SFC or SRC, respectively, and differed from zero in half of the PBAA. Milk output of EAA was 187.8 vs 175.4, SEM 4.4 g/12 h in cows fed SFC and SRC, respectively, and output of most essential AA consistently tended to be greater in cows fed SFC. It is apparent that PBAA comprise a portion of total AA flux across PDV and are affected by grain processing. Further, this pool supplies an important component of AA taken up by the mammary gland. Quantifying the contribution of PBAA may improve diet formulation with respect to intestinal absorption and mammary uptake of AA

A 3D cellular context for the macromolecular world

We report the outcomes of the discussion initiated at the workshop entitled A 3D Cellular Context for the Macromolecular World and propose how data from emerging three-dimensional (3D) cellular imaging techniques—such as electron tomography, 3D scanning electron microscopy and soft X-ray tomography—should be archived, curated, validated and disseminated, to enable their interpretation and reuse by the biomedical community

Intrinsically Disordered Proteins Display No Preference for Chaperone Binding In Vivo

Intrinsically disordered/unstructured proteins (IDPs) are extremely sensitive to proteolysis in vitro, but show no enhanced degradation rates in vivo. Their existence and functioning may be explained if IDPs are preferentially associated with chaperones in the cell, which may offer protection against degradation by proteases. To test this inference, we took pairwise interaction data from high-throughput interaction studies and analyzed to see if predicted disorder correlates with the tendency of chaperone binding by proteins. Our major finding is that disorder predicted by the IUPred algorithm actually shows negative correlation with chaperone binding in E. coli, S. cerevisiae, and metazoa species. Since predicted disorder positively correlates with the tendency of partner binding in the interactome, the difference between the disorder of chaperone-binding and non-binding proteins is even more pronounced if normalized to their overall tendency to be involved in pairwise protein–protein interactions. We argue that chaperone binding is primarily required for folding of globular proteins, as reflected in an increased preference for chaperones of proteins in which at least one Pfam domain exists. In terms of the functional consequences of chaperone binding of mostly disordered proteins, we suggest that its primary reason is not the assistance of folding, but promotion of assembly with partners. In support of this conclusion, we show that IDPs that bind chaperones also tend to bind other proteins

Structural similarity-based predictions of protein interactions between HIV-1 and Homo sapiens

Abstract Background In the course of infection, viruses such as HIV-1 must enter a cell, travel to sites where they can hijack host machinery to transcribe their genes and translate their proteins, assemble, and then leave the cell again, all while evading the host immune system. Thus, successful infection depends on the pathogen's ability to manipulate the biological pathways and processes of the organism it infects. Interactions between HIV-encoded and human proteins provide one means by which HIV-1 can connect into cellular pathways to carry out these survival processes. Results We developed and applied a computational approach to predict interactions between HIV and human proteins based on structural similarity of 9 HIV-1 proteins to human proteins having known interactions. Using functional data from RNAi studies as a filter, we generated over 2000 interaction predictions between HIV proteins and 406 unique human proteins. Additional filtering based on Gene Ontology cellular component annotation reduced the number of predictions to 502 interactions involving 137 human proteins. We find numerous known interactions as well as novel interactions showing significant functional relevance based on supporting Gene Ontology and literature evidence. Conclusions Understanding the interplay between HIV-1 and its human host will help in understanding the viral lifecycle and the ways in which this virus is able to manipulate its host. The results shown here provide a potential set of interactions that are amenable to further experimental manipulation as well as potential targets for therapeutic intervention

EMDataBank.org: unified data resource for CryoEM

Cryo-electron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. EMDataBank.org, a joint effort of the Protein Data Bank in Europe (PDBe), the Research Collaboratory for Structural Bioinformatics (RCSB) and the National Center for Macromolecular Imaging (NCMI), is a global ‘one-stop shop’ resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular complexes by the wider scientific community

Mapping Protein Interactions between Dengue Virus and Its Human and Insect Hosts

Dengue virus (DENV) represents a major disease burden in tropical and subtropical regions of the world, and has shown an increase in the number of cases in recent years. DENV is transmitted to humans through the bite of an infected mosquito, typically Aedes aegypti, after which it begins the infection and replication lifecycle within human cells. To perform the molecular functions required for invasion, replication, and spread of the virus, proteins encoded by DENV must interact with and alter the behavior of protein networks in both of these hosts. In this work, we used a computational method based on protein structures to predict interactions between DENV and its human and insect hosts. We predict numerous interactions, with many involved in known cell death, stress, and immune system pathways. Further investigation of these predicted protein-protein interactions should provide targets to combat the clinical manifestations of this disease in humans as well as points of intervention focused within the mosquito vector