An isotope dilution model for partitioning of phenylalanine and tyrosine uptake by the liver of lactating dairy cows

An isotope dilution model to describe the partitioning of phenylalanine (PHE) and tyrosine (TYR) in the bovine liver was developed. The model comprises four intracellular and six extracellular pools and various flows connecting these pools and external blood. Conservation of mass principles were applied to generate the fundamental equations describing the behaviour of the system in the steady state. The model was applied to datasets from multi-catheterised dairy cattle during a constant infusion of [1-13C] phenylalanine and [2,3,5,6-2H] tyrosine tracers. Model solutions described the extraction of PHE and TYR from the liver via the portal vein and hepatic artery. In addition, the exchange of free PHE and TYR between extracellular and intracellular pools was explained and the hydroxylation of PHE to TYR was estimated. The model was effective in providing information about the fates of PHE and TYR in the liver and could be used as part of a more complex system describing amino acid metabolism in the whole animal

Skema Penyembunyian Teks Terkompresi Adaptive Huffman pada Citra Digital Menggunakan Kuantisasi Berbasis Graf

Jaringan komputer dan internet semakin banyak digunakan untuk aktivitas pengiriman data. Namun, tidak ada jaminan bahwa jaringan komputer dan internet yang digunakan sebagai media pengiriman data ini aman dari pihak ketiga yang tidak memiliki hak akses terhadap data tersebut [1]. Berbagai teknik telah dikembangkan untuk melindungi data dari pengaksesan secara ilegal. Salah satu diantaranya yaitu dengan menyisipkan/ menyembunyikan data tersebut ke dalam media cover. Pada penelitian ini, implementasi penyembunyian data memanfaatkan kuantisasi berbasis graf, yaitu menggunakan Vector Quantization (VQ) dan pewarnaan graf dengan menggunakan Genetic Algorithm. Untuk meningkatkan kapasitas penyisipan, data dikompres terlebih dahulu dengan menggunakan Adaptive Huffman sebelum penyisipan dilakukan. Hasil pengujian menunjukkan bahwa skema ini dapat menghasilkan kapasitas penyisipan sebanyak 9000 bit atau sekitar 1800 karakter, dengan nilai PSNR 27,5054 db. Keywords: Penyembunyian Data, Kuantisasi Berbasis Graf, Vector Quantization, Pewarnaan Graf, Adaptive Huffman, Genetic Algorith

E-MSD: improving data deposition and structure quality

The Macromolecular Structure Database (MSD) () [H. Boutselakis, D. Dimitropoulos, J. Fillon, A. Golovin, K. Henrick, A. Hussain, J. Ionides, M. John, P. A. Keller, E. Krissinel et al. (2003) E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. Nucleic Acids Res., 31, 458–462.] group is one of the three partners in the worldwide Protein DataBank (wwPDB), the consortium entrusted with the collation, maintenance and distribution of the global repository of macromolecular structure data [H. Berman, K. Henrick and H. Nakamura (2003) Announcing the worldwide Protein Data Bank. Nature Struct. Biol., 10, 980.]. Since its inception, the MSD group has worked with partners around the world to improve the quality of PDB data, through a clean up programme that addresses inconsistencies and inaccuracies in the legacy archive. The improvements in data quality in the legacy archive have been achieved largely through the creation of a unified data archive, in the form of a relational database that stores all of the data in the wwPDB. The three partners are working towards improving the tools and methods for the deposition of new data by the community at large. The implementation of the MSD database, together with the parallel development of improved tools and methodologies for data harvesting, validation and archival, has lead to significant improvements in the quality of data that enters the archive. Through this and related projects in the NMR and EM realms the MSD continues to improve the quality of publicly available structural data

CentrosomeDB: a human centrosomal proteins database

Active research on the biology of the centrosome during the past decades has allowed the identification and characterization of many centrosomal proteins. Unfortunately, the accumulated data is still dispersed among heterogeneous sources of information. Here we present centrosome:db, which intends to compile and integrate relevant information related to the human centrosome. We have compiled a set of 383 likely human centrosomal genes and recorded the associated supporting evidences. Centrosome:db offers several perspectives to study the human centrosome including evolution, function and structure. The database contains information on the orthology relationships with other species, including fungi, nematodes, arthropods, urochordates and vertebrates. Predictions of the domain organization of centrosome:db proteins are graphically represented at different sections of the database, including sets of alternative protein isoforms, interacting proteins, groups of orthologs and the homologs identified with blast. Centrosome:db also contains information related to function, gene–disease associations, SNPs and the 3D structure of proteins. Apart from important differences in the coverage of the set of centrosomal genes, our database differentiates from other similar initiatives in the way information is treated and analyzed. Centrosome:db is publicly available at http://centrosome.dacya.ucm.es

Building bridges between cellular and molecular structural biology

The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.Peer reviewe

Conventions and workflows for using Situs

Recent developments of the Situs software suite for multi-scale modeling are reviewed. Typical workflows and conventions encountered during processing of biophysical data from electron microscopy, tomography or small-angle X-ray scattering are described

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

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

Circulating 5-hydroxytryptamine concentrations in preterm newborns

Alterations in circulating 5-hydroxytryptamine (5-HT) concentrations play a role in the pathophysiology of respiratory failure in adults. We undertook a study to develop a micromethod and measure circulating free 5-HT concentrations in preterm newborns with and without respiratory distress. Forty-six samples of platelet-poor plasma were obtained from 29 preterm newborns with varying degrees of respiratory distress. Samples were taken on days 2–3 and 6–7 of life. For measuring 5-HT concentrations we used a precolumn sample enhancement technique followed by ion exchange HPLC with electrochemical detection. The assay allowed detection of extremely small (50 pg) amounts of 5-HT from small (0.2 ml) amounts of blood. The mean 5-HT concentration on days 2–3 was 1.77 ± 0.74 ng/ml (mean ± 95% confidence limits) and on days 6–7 was 0.69 ± 0 23 ng/ml. This represented a significant fall in 5-HT concentrations (P = 0.01). All of 16 paired serial samples fell with time (P = 0.006). We conclude that platelet-poor plasma 5-HT concentrations in premature newborns are low, that there is a significant decline in these values over the first week of life, and that, in contrast with adults, the presence of respiratory failure is not associated with increased free 5-HT concentrations. The low 5-HT concentrations seen in newborns may reflect the ability to increase pulmonary uptake. Pediatr Pulmonol 1987; 3:117–122 .Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/38593/1/1950030214_ftp.pd