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Biomedical subjects

A Naim

Publications and source records attributed to A Naim.

11 recordsLinked to original sources
PubMed2003

E-MSD: the European Bioinformatics Institute Macromolecular Structure Database.

The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool.

Animals↗
PubMed2001

From molecular activities and processes to biological function.

This paper describes how biological function can be represented in terms of molecular activities and processes. It presents several key features of a data model that is based on a conceptual description of the network of interactions between molecular entities within the cell and between cells. This model is implemented in the aMAZE database that presently deals with information on metabolic pathways, gene regulation, sub- or supracellular locations, and transport. It is shown that this model constitutes a useful generalisation of data representations currently implemented in metabolic pathway databases, and that it can furthermore include multiple schemes for categorising and classifying molecular entities, activities, processes and localisations. In particular, we highlight the flexibility offered by our system in representing multiple molecular activities and their control, in viewing biological function at different levels of resolution and in updating this view as our knowledge evolves.

Animals↗
PubMed1995

Masking as a mechanism for evaporative loss of trace analyte, especially after solid-phase extraction.

Using a Pasteur pipette plugged with silanized glass wool and packed with C18-silica particles, we attempted to remove K2CO3 from an aqueous acetonitrile solution. In spite of extensive washing of the column with water after the sample was applied, elution with acetonitrile followed by evaporation gave a visible, white residue. It was found that the residue was derived from both the sample and the packing, including particles from the latter. Substitution of a plastic column/polyethylene frit for the Pasteur pipette/glass wool gave a more consistent residue, apparently because this improved the retention of particles. Subsequent experiments were conducted in the plastic hardware. The amount of the residue was observed to vary as much as 19-fold when C18-silica particles were tested from different manufacturers, and the residue could be reduced in amount as much as 9-fold when a column was prepared in the laboratory vs. the use of a comparable, pre-packed column. The water itself contributed some of the residue: even the "purest" water routinely available left a visible residue when 1.0 ml was appropriately evaporated (e.g. on Saran Wrap in a microwave oven). The recovery of an arbitrary trace analyte and internal standard (pentafluorobenzylated nucleobases at the low pg level) was 32% less when they were evaporated in acetonitrile that had been passed through an acetonitrile and water-washed cartridge containing C18-Si vs. evaporation in untreated acetonitrile. Collectively these results reveal that an evaporation can risk some loss of an analyte from masking by even subtle solvent contaminants.(ABSTRACT TRUNCATED AT 250 WORDS)

Acetonitriles↗
PubMed1995

Non-invasive approach for body composition measurement: differential buoyancy method and correction for water loss.

The Differential Buoyancy method uses Archimedes' principle to non-invasively determine body fat percentage by measuring the subject's weight in breathable high and low densities atmospheres. We currently use both air and helium/oxygen mixtures in our experiments[1]. When the method was tested on rats, an anomaly was observed. As helium/oxygen mixture was admitted to the weighing chamber, while the atmospheric density monotonically decreased, the rat's weight first increased but then after several minutes decreased. Water loss from the rat's body was found to be the main cause of this anomaly. Therefore it was necessary to compensate for this water loss. Consistent with experimental findings the water loss was modeled as a constant rate process, and determined experimentally from weight measurements at the beginning and at the end of the experiment. Making these corrections allowed for accurate predictions of the rat's volume and body fat percentage.

Adipose Tissue↗
PubMed1994

Bioengineering approach to non-invasive measurement of body composition.

Measurement of body fat percentage is essential for medical care and research. The "gold standard" method for humans is underwater weighing, which is clearly inappropriate for infants, sick people and non-human animals. The corresponding criterion method for animals is comminution of the carcass followed by extraction of the fat with a volatile solvent such as ether. Our goal has been to develop a method for body composition (fat percentage) for use in animals and humans which is non-invasive and minimally intrusive, independent of variation in body conformation and fat distribution, and reasonable in cost. In one variant, our approach to this problem has been to move Archimedes' principle "on to dry land." The subject's volume is determined by measuring the differential buoyancy in comfortably breathable light (low density) and heavy atmospheres. In another, we use "structured light," in which a pattern of illumination is cast on the patient. The image is acquired using a video camera and the geometrical spatial coordinates of a large number of points on the surface of the subject are acquired. This permits the computation of the surface area and volume of the subject; which, combined with the weight, determines the fat percentage.

Adipose Tissue↗
PubMedDate not supplied

Long-term correction of albumin levels in the Nagase analbuminemic rat: repopulation of the liver by transplanted normal hepatocytes under a regeneration response.

Numerous studies have reported successful transplantation of hepatocytes with demonstration of function. However, none have shown long-term correction of a liver-related metabolic defect. Male Nagase analbuminemic rats, immunosuppressed with cyclosporin-A, were transplanted with normal hepatocytes (2 x 10(7) cells/rat) isolated from allogeneic male Sprague-Dawley rat donors. Hepatocytes were selectively transplanted via the portal vein tributary into the posterior liver lobes of Nagase analbuminemic rats. Following 2 wk, to allow engraftment, selected transplanted rats (Group I) were reoperated and the portal venous branch supplying the anterior liver lobes was permanently ligated, resulting in their atrophy and induction of regeneration in the residual transplant-bearing lobes. Control rats consisted of: Group II-transplanted with normal hepatocytes without portal branch ligation; Group III-transplanted with analbuminemic hepatocytes with portal branch ligation; and Group IV-nontransplanted analbuminemic rats with portal branch ligation. The experimental period extended to 3 mo posttransplantation. All rats transplanted with normal hepatocytes demonstrated a significant elevation in serum albumin levels (ELISA). Group I rats had dramatic elevations in serum albumin to near normal levels (1.78 +/- 0.20 g/dl), and maintained these levels until the end of the experiment. Albumin levels in Group II rats reached 0.26 +/- 0.07 g/dl (p < 0.001), whereas Group III and IV rats showed no changes in serum albumin levels throughout the experiment. Immunohistology of liver tissue obtained from Group I rats, demonstrated large numbers (22.6 +/- 7.5%) of albumin-positive hepatocytes populating the recipient liver. This is the first report of near-total and sustained correction of a genetic defect in liver function in an experimental animal model following allogeneic hepatocyte transplantation.

Acetylglucosaminidase↗
PubMedDate not supplied

Representing and analysing molecular and cellular function using the computer.

Determining the biological function of a myriad of genes, and understanding how they interact to yield a living cell, is the major challenge of the post genome-sequencing era. The complexity of biological systems is such that this cannot be envisaged without the help of powerful computer systems capable of representing and analysing the intricate networks of physical and functional interactions between the different cellular components. In this review we try to provide the reader with an appreciation of where we stand in this regard. We discuss some of the inherent problems in describing the different facets of biological function, give an overview of how information on function is currently represented in the major biological databases, and describe different systems for organising and categorising the functions of gene products. In a second part, we present a new general data model, currently under development, which describes information on molecular function and cellular processes in a rigorous manner. The model is capable of representing a large variety of biochemical processes, including metabolic pathways, regulation of gene expression and signal transduction. It also incorporates taxonomies for categorising molecular entities, interactions and processes, and it offers means of viewing the information at different levels of resolution, and dealing with incomplete knowledge. The data model has been implemented in the database on protein function and cellular processes 'aMAZE' (http://www.ebi.ac.uk/research/pfbp/), which presently covers metabolic pathways and their regulation. Several tools for querying, displaying, and performing analyses on such pathways are briefly described in order to illustrate the practical applications enabled by the model.

Cell Physiological Phenomena↗