The central domain is required to target and anchor perilipin A to lipid droplets

The perilipins are the most abundant proteins coating the surfaces of lipid droplets in adipocytes and are found at lower levels surrounding lipid droplets in steroidogenic cells. Perilipins drive triacylglycerol storage in adipocytes by regulating the rate of basal lipolysis and are also required to maximize hormonally stimulated lipolysis. To map the domains that target and anchor perilipin A to lipid droplets, we stably expressed fragments of perilipin A in 3T3-L1 fibroblasts. Immunofluorescence microscopy and immunoblotting of proteins from isolated lipid droplets revealed that neither the amino nor the carboxyl terminus is required to target perilipin A to lipid droplets; however, there are multiple, partially redundant targeting signals within a central domain including 25% of the primary amino acid sequence. A peptide composed of the central domain of perilipin A directed a fused green fluorescent protein to the surfaces of lipid droplets. Full-length perilipin A associates with lipid droplets via hydrophobic interactions, as shown by the persistence of perilipins on lipid droplets after centrifugation through an alkaline carbonate solution. Results of the mutagenesis studies indicate that the sequences responsible for anchoring perilipin A to lipid droplets are most likely domains of moderately hydrophobic amino acids located within the central 25% of the protein. Thus, we conclude that the central 25% of the perilipin A sequence contains all of the amino acids necessary to target and anchor the protein to lipid droplets.     

Differentiation potential of intestinal mesenchyme and its interaction with epithelial cells: a study using beta-galactosidase-expressing fibroblast lines

Rat intestinal fibroblast lines (F1:G9 and A1:F1) differing in their potential to support intestinal mucosal development were marked with reporter genes to investigate their differentiation potential. The fibroblasts were transfected with plasmids expressing either beta-galactosidase (with or without a nuclear localisation signal) or green fluorescent protein (GFP). Transfection using Tfx50 or Fugene was more efficient than electroporation. The expression of beta-galactosidase was more stable and stronger than GFP. Cells were optimally labelled using the plasmid pL27B-GAL, and sub-clones with a strong and uniform nuclear expression of beta-galactosidase were isolated. These clones expressed beta-galactosidase even after prolonged passage in the absence of selection. The beta-galactosidase tagged lines (F1:G9gal and A1:F1gal) retained the morphological characteristics, viability and differentiation properties of the parental non-transfected lines. In co-culture with a colorectal tumour cell line Caco-2, the F1:G9gal and A1:F1gal cells differed in their morphological organisation but this did not change their expression of smooth muscle alpha-actin.     

MRD: a microsatellite repeats database for prokaryotic and eukaryotic genomes

MRD is a database system to access the microsatellite repeats information of genomes such as archea, eubacteria, and other eukaryotic genomes whose sequence information is available in public domains. MRD stores information about simple tandemly repeated k-mer sequences where k= 1 to 6, i.e. monomer to hexamer. The web interface allows the users to search for the repeat of their interest and to know about the association of the repeat with genes and genomic regions in the specific organism. The data contains the abundance and distribution of microsatellites in the coding and non-coding regions of the genome. The exact location of repeats with respect to genomic regions of interest (such as UTR, exon, intron or intergenic regions) whichever is applicable to organism is highlighted. MRD is available on the World Wide Web at and/or . The database is designed as an open-ended system to accommodate the microsatellite repeats information of other genomes whose complete sequences will be available in future through public domain.     

Ab initio structure of human seminal plasma prostatic inhibin gives significant insight into its biological functions

Human seminal plasma prostatic inhibin (HSPI) is a protein isolated from the human prostate gland. Despite its profound biomedical and biotechnological importance, the 3D structure of this protein of 94 amino acids remains undeciphered. The difficulties in extracting it in pure form and crystallizing it have restrained the determination of its structure experimentally. The homology-based computational methods are also not applicable, as HSPI lacks sufficient sequence homology with known structures in the protein data banks. We have predicted the structure of HSPI by a knowledge-based method using nonparametric multivariate statistical techniques. Stereochemical and other standard validation tests confirm this to be a well-refined structure. The biophysical properties exhibited by this structure are in good agreement with the NMR experimental observations. Docking and other computational studies on this structure provide significant explanation and insight into its binding activities and related biological and immunogenic functions and offer new directions for its potential applications.     

Harlequin (hlq) and short blue root (sbr), two Arabidopsis mutants that ectopically express an abscisic acid- and auxin-inducible transgenic carrot promoter and have pleiotropic effects on morphogenesis

Plant growth and development is regulated by complex interactions among different hormonal, developmental and environmental signalling pathways. Isolation of mutants in these processes is a powerful approach to dissect unknown mechanisms in regulatory networks. The plant hormones abscisic acid (ABA) and auxin are involved in vegetative, developmental and environmental growth responses, including cell division and elongation, vascular tissue differentiation and stress adaptation. The uidA (-glucuronidase; GUS) reporter gene driven by the carrot (Daucus carota) late embryogenesis-abundant Dc3 promoter in transgenic Arabidopsis thaliana seedlings is ABA-inducible in the root zone of elongation and vasculature. We show here that the ABA-insensitive2-1 mutation (abi2) reduces ABA-inducible Dc3-GUS expression in these root tissues. Dc3-GUS expression is also induced in root cortex cells by indole-3-acetic acid. We mutagenized, with ethyl methane sulfonate, 5100 M₁ abi2/abi2 homozygous plants of a line that carries two independent Dc3-GUS reporter genes and screened M₂ clonal lines for ABA-inducible Dc3-GUS expression in roots. We isolated two novel single-gene nuclear mutants, harlequin (hlq) and short blue root (sbr), that ectopically express Dc3-GUS in roots and have pleiotropic effects on morphogenesis. The hlq mutant expresses Dc3-GUS in a checkered pattern in epidermis of roots and hypocotyls, accumulates callose and has deformed and collapsed epidermal cells and abnormal and reduced root hairs and leaf trichomes. It (hlq) is also dwarfed, skotomorphogenic and sterile. The sbr mutant is a seedling-lethal dwarf that over-expresses Dc3-GUS in the root and has radially swollen epidermal cells in the root and hypocotyl, supernumerary cell number in the root cortex and epidermis, abnormal vasculature, and abnormal epidermal cell patterning in cotyledons and leaves. It (sbr) also exhibits a semidominant root phenotype of reduced growth and lateral root initiation. The hlq and sbr mutants are not rescued by exogenous application of plant growth regulators. The hlqand sbr mutants do not require the abi2-1 mutant gene for their phenotypes and map to chromosome III and I, respectively. Further characterization of the hlq and sbr phenotypes and genes may provide insights into the relationship of hormone- and stress-regulated gene expression to morphogenesis and plant growth.     

Identification of key concepts in biomedical literature using a modified Markov heuristic

MOTIVATION: The recent explosion of interest in mining the biomedical literature for associations between defined entities such as genes, diseases and drugs has made apparent the need for robust methods of identifying occurrences of these entities in biomedical text. Such concept-based indexing is strongly dependent on the availability of a comprehensive ontology or lexicon of biomedical terms. However, such ontologies are very difficult and expensive to construct, and often require extensive manual curation to render them suitable for use by automatic indexing programs. Furthermore, the use of statistically salient noun phrases as surrogates for curated terminology is not without difficulties, due to the lack of high-quality part-of-speech taggers specific to medical nomenclature. RESULTS: We describe a method of improving the quality of automatically extracted noun phrases by employing prior knowledge during the HMM training procedure for the tagger. This enhancement, when combined with appropriate training data, can greatly improve the quality and relevance of the extracted phrases, thereby enabling greater accuracy in downstream literature mining tasks.     

Radioprotective property of polysaccharide in Tinospora cordifolia

Radioprotective activity of a polysaccharide preparation from the Indian medicinal plant. Tinospora cordifolia Miers has been established using Saccharomyces cerevisiae X2180 strain as the in vivo test model. The entire activity could be attributed to the radical scavenging capacity of the preparation, as it did not enhance the expression of the protective enzymes, catalase and superoxide dismutase in the yeast cells.     

Multiple transporters associated with malaria parasite responses to chloroquine and quinine

Mutations and/or overexpression of various transporters are known to confer drug resistance in a variety of organisms. In the malaria parasite Plasmodium falciparum, a homologue of P-glycoprotein, PfMDR1, has been implicated in responses to chloroquine (CQ), quinine (QN) and other drugs, and a putative transporter, PfCRT, was recently demonstrated to be the key molecule in CQ resistance. However, other unknown molecules are probably involved, as different parasite clones carrying the same pfcrt and pfmdr1 alleles show a wide range of quantitative responses to CQ and QN. Such molecules may contribute to increasing incidences of QN treatment failure, the molecular basis of which is not understood. To identify additional genes involved in parasite CQ and QN responses, we assayed the in vitro susceptibilities of 97 culture-adapted cloned isolates to CQ and QN and searched for single nucleotide polymorphisms (SNPs) in DNA encoding 49 putative transporters (total 113 kb) and in 39 housekeeping genes that acted as negative controls. SNPs in 11 of the putative transporter genes, including pfcrt and pfmdr1, showed significant associations with decreased sensitivity to CQ and/or QN in P. falciparum. Significant linkage disequilibria within and between these genes were also detected, suggesting interactions among the transporter genes. This study provides specific leads for better understanding of complex drug resistances in malaria parasites.     

Melanosomal proteins promote melanin polymerization

In melanocytes, enzymes involved in the generation of melanin monomers are present and active in coated vesicles which are known to be acidic. Melanin polymerization however, occurs only in melanosomes. In vitro, it is not possible to generate melanin at the acidic pH of melanosomes using 3,4-dihydroxyphenylalanine (DOPA) and tyrosinase alone whereas melanin readily forms at higher pH with these reagents. Dimerization and elongation of the melanin polymer is known to require deprotonation. We have hypothesized that the amino acid side chains of melanosomal proteins act as proton acceptors to initiate polymerization and that the protonated basic groups serve to attract the negatively charged oligomers thus aiding polymerization and binding to proteins. We show that basic model proteins and basic premelanosomal proteins promote polymerization at an acidic pH and that positively charged surfaces allow binding of the growing melanin polymer. With progressive polymerization and exhaustion of the proton abstracting ability of melanosomal proteins, melanosomal pH drops further, which, we argue, is an additional controlling step that limits tyrosinase activity and melanin polymerization.