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R Roy

Publications and source records attributed to R Roy.

At least 19 recordsLinked to original sources
PubMed2006

Role of the Vam3p transmembrane segment in homodimerization and SNARE complex formation.

Intracellular membrane fusion in eukaryotic cells is mediated by SNARE (soluble N-ethylmaleimide sensitive factor (NSF) attachment protein receptor) proteins and is known to involve assembly of cognate subunits to heterooligomeric complexes. For synaptic SNAREs, it has previously been shown that the transmembrane segments drive homotypic and support heterotypic interactions. Here, we demonstrate that a significant fraction of the yeast vacuolar SNARE Vam3p is a homodimer in detergent extracts of vacuolar membranes. This homodimer exists in parallel to the heterooligomeric SNARE complex. A Vam3p homodimer also formed from the isolated recombinant protein. Interestingly, homodimerization depended on the transmembrane segment. In contrast, formation of the quaternary SNARE complex from recombinant Vam3p, Nyv1p, Vti1p, and Vam7p subunits did not depend on the transmembrane segment of Vam3p nor on the transmembrane segments of its partner proteins. We conclude that Vam3p homodimerization, but not quaternary SNARE complex formation, is promoted by TMS-TMS interaction. As the transmembrane segments of Vam3p and other SNARE homologues were previously shown to be critical for membrane fusion downstream of membrane apposition, our results may shed light on the functional significance of SNARE TMS-TMS interactions.

Dimerization↗
PubMed2006

Association of polymorphisms in the bovine FASN gene with milk-fat content.

Fatty acid synthase (FASN) is a multifunctional protein that carries out the synthesis of fatty acids so it plays a central role in de novo lipogenesis in mammals. Previously, we defined the genetic structure and expression of the bovine FASN gene. Our mapping studies placed FASN on BTA19 (19q22) where several quantitative trait loci (QTL) affecting milk-fat content and related traits have been described. This study was conducted to identify polymorphisms in the bovine FASN gene and to study their association with milk-fat content. The bovine FASN gene was screened for polymorphisms in two cattle breeds. Sequence analysis revealed several single nucleotide polymorphisms (SNPs), and two of them were analysed: a G>C substitution in the untranslated exon 1 (g.763G>C), altering a potential Sp1 transcription factor-binding site, and an A>G substitution in exon 34 (g.16009A>G), which determines a non-conservative substitution of threonine by alanine. Allele-specific amplification of the SNPs in FASN revealed significant frequency differences for both polymorphisms in Holsteins with high and low breeding values for milk-fat content. The intragenic haplotypes comprising exon 1 (alleles G and C) and exon 34 (alleles A and G) polymorphisms were studied, and the existence of linkage disequilibrium between these SNPs was found (D(CG) = 0.048, P < 0.001). Our results suggest that the FASN gene polymorphisms contribute to variation in milk-fat content. We propose that the bovine FASN gene is a candidate gene for a milk-fat content QTL.

Alleles↗
PubMed2006

New developmental insights from high-throughput biological analysis in Caenorhabditis elegans.

The use of Caenorhabditis elegans as a model system for understanding animal development and human disease has long been recognized as an efficient tool of discovery. Recent developments, particularly in our understanding of RNA-mediated interference and its ability to modify gene activity, have facilitated the use of C. elegans in determining gene function via high-throughput analysis. These new strategies have provided a framework that allows investigators to analyse gene function globally at the genomic level and will likely become a prototypic model for biological analysis in the post-genome era.

Animals↗
PubMed2006

Influence of nutrient inputs, hexadecane, and temporal variations on denitrification and community composition of river biofilms.

Biofilms were cultivated on polycarbonate strips in rotating annular reactors using South Saskatchewan River water during the fall of 1999 and the fall of 2001, supplemented with carbon (glucose), nitrogen (NH4Cl), phosphorus (KH2PO4), or combined nutrients (CNP), with or without hexadecane, a model compound representing aliphatic hydrocarbons used to simulate a pollutant. In fall 1999 and fall 2001, comparable denitrification activities and catabolic potentials were observed in the biofilms, implying that denitrifying populations showed similar activity patterns and catabolic potentials during the fall from year to year in this river ecosystem, when environmental conditions were similar. Both nirS and nirK denitrification genes were detected by PCR amplification, suggesting that both denitrifying bacterial subpopulations can potentially contribute to total denitrification. Between 91.7 and 99.8% of the consumed N was emitted in the form of N2, suggesting that emission of N2O, a major potent greenhouse gas, by South Saskatchewan River biofilms is low. Denitrification was markedly stimulated by the addition of CNP, and nirS and nirK genes were predominant only in the presence of CNP. In contrast, individual nutrients had no impact on denitrification and on the occurrence of nirS and nirK genes detected by PCR amplification. Similarly, only CNP resulted in significant increases in algal and bacterial biomass relative to control biofilms. Biomass measurements indicated a linkage between autotrophic and heterotrophic populations in the fall 1999 biofilms. Correlation analyses demonstrated a significant relationship (P < or = 0.05) between the denitrification rate and the biomass of algae and heterotrophic bacteria but not cyanobacteria. At the concentration assessed (1 ppb), hexadecane partially inhibited denitrification in both years, slightly more in the fall of 2001. This study suggested that the response of the anaerobic heterotrophic biofilm community may be cyclic and predictable from year to year and that there are interactive effects between nutrients and the contaminant hexadecane.

Alkanes↗
PubMed2006

Genomic structure and an alternative transcript of bovine mitochondrial glycerol-3-phosphate acyltransferase gene (GPAM).

GPAM maps in BTA26q22, where several QTLs affecting milk production, milk fat and protein content have been mapped. On the basis of the QTL location, the GPAM gene could be considered a good candidate gene for the mentioned traits. Glycerol-3-phosphate acyltransferase mitochondrial (GPAM) is the enzyme that catalyses the initial and committed step of glycerolipid synthesis and, therefore, it is a potential site for triacylglycerol synthesis regulation. In this study, the structure of the cDNA and the genomic DNA of the bovine GPAM gene were determined and the expression of its mRNA was studied. The cDNA of the gene was cloned by RT-PCR, 5' and 3' rapid amplification of cDNA ends. The GPAM mRNA sequence contains a 2,475-bp coding region and a 3,689-bp 3' UTR. Its ORF encoded for an 825-amino acid protein and has an 89% homology with the coding regions of previously characterized mouse and human GPAM genes. The predicted amino acid sequence had an 89 and 93% similarity with mouse and human GPAM proteins, respectively. Using a 5' RACE strategy, two different 5' UTRs were cloned. Northern blot analysis confirmed the presence of two different transcripts. Adipose tissues and lung had the highest levels of GPAM mRNA expression, whereas it was barely detectable in liver. This expression pattern differs with those of non-ruminant animals where liver is one of the tissues with higher GPAM mRNA expression level.

3' Untranslated Regions↗
PubMed2006

Structural and functional characterization of the bovine solute carrier family 27 member 1 (SLC27A1) gene.

The Solute Carrier Family 27 Member 1 (SLC27A1) is an evolutionarily conserved protein involved in regulating the long chain fatty acid uptake into cells. It has been shown to be expressed in tissues undergoing rapid fatty acid metabolism such as heart, skeletal muscle and adipose tissues, but no expression is detected in liver. Here we report the molecular characterization of the bovine SLC27A1 gene and draw a comparison with orthologous genes of some monogastric species. The bovine SLC27A1 gene is organized in 13 exons and extends over more than 40 kb of genomic DNA. It codes for a protein of 646 amino acids with a predicted molecular weight of 71 kDa which has 92%, 88% and 88% similarity with the human, mouse and rat SLC27A1 proteins respectively. The bovine SLC27A1 RNA expression was high in heart, testis, nervous tissue and muscle and very low in liver. Surprisingly, adipose tissues showed very low RNA expression levels contrary to the results described for both human and mouse genes. On the other hand, discordances observed between the bovine SLC27A1 RNA and protein expression patterns suggest that complex regulation mechanisms may be involved in determining the final SLC27A1 protein levels in each tissue. Finally, we have identified an alternative transcript generated by exon skipping of exon 3 to 7 which could encode a cytosolic SLC27A1 isoform of approximately 37 kDa.

5' Untranslated Regions↗
PubMed2005

The use of denial in an ethnically diverse British cancer population: a cross-sectional study.

A total of 82 Asian and 117 randomly selected white Caucasian patients at the Leicestershire Cancer Centre were assessed using measures of coping and adaption to cancer. On the Mental Adjustment to Cancer (MAC) scale, Asian patients were more fatalistic (P < 0.0001) and had more significant hopeless/helpless scores (P = 0.007). The two ethnic groups answered the three questions thought to assess denial differently. Caucasians were more likely not to dwell on their illness (73 vs 55.5%, P < 0.0001) and agree with the statement 'I have difficulty believing this is happening to me' (73 vs 60.5%, P < 0.0001). However, Asian patients were more likely to agree with the statement 'I don't really believe I have cancer' (48.2 vs 31.3%, P = 0.019). Within both groups there was an association with denial and anxious preoccupation (P < 0.001). On the Hospital Anxiety and Depression (HAD) scale, there was no difference in anxiety scores between either sexes or between the Asian and Caucasian groups. However, Asian patients were more depressed (P = 0.001). Although denial was significantly related to the presence of both depression (P < 0.0001) and anxiety (P = 0.001) in the entire patient population, there were different predictors of denial in each subgroup. On multiple regression analysis depression was linked with denial in Caucasians, whereas Fighting Spirit (minus helplessness/hopelessness) was linked with denial in Asian patients. There are definite differences in coping styles in British cancer patients according to ethnicity. While significant numbers in both groups employ denial in some form, Caucasian patients appear to adapt to the psychological pressures of cancer more successfully than Asian patients at a particular point in time. Further work is required to elucidate longitudinal relationships between denial and adaption to cancer.

Adaptation, Psychological↗
PubMed2005

Regulation of membrane trafficking by a novel Cdc42-related protein in Caenorhabditis elegans epithelial cells.

Rho GTPases are mainly known for their implication in cytoskeleton remodeling. They have also been recently shown to regulate various aspects of membrane trafficking. Here, we report the identification and the characterization of a novel Caenorhabditis elegans Cdc42-related protein, CRP-1, that shows atypical enzymatic characteristics in vitro. Expression in mouse fibroblasts revealed that, in contrast with CDC-42, CRP-1 was unable to reorganize the actin cytoskeleton and mainly localized to trans-Golgi network and recycling endosomes. This subcellular localization, as well as its expression profile restricted to a subset of epithelial-like cells in C. elegans, suggested a potential function for this protein in polarized membrane trafficking. Consistent with this hypothesis, alteration of CRP-1 expression affected the apical trafficking of CHE-14 in vulval and rectal epithelial cells and sphingolipids (C(6)-NBD-ceramide) uptake and/or trafficking in intestinal cells. However, it did not affect basolateral trafficking of myotactin in the pharynx and the targeting of IFB-2 and AJM-1, two cytosolic apical markers of intestine epithelial cells. Hence, our data demonstrate a function for CRP-1 in the regulation of membrane trafficking in a subset of cells with epithelial characteristics.

Actins↗
PubMed2005

Regulation of membrane lipid bilayer structure during salinity adaptation: a study with the gill epithelial cell membranes of Oreochromis niloticus.

A significant variation in the membrane fluidity (as assessed by DPH-fluorescence polarisation) and membrane lipid bilayer composition is noticed in the subcellular membranes of the gill epithelial cells of Oreochromis niloticus due to exposure of the fish to 1% saline water for 1 month. Also, a 70% enhanced activity of Na(+)-K(+)-ATPase in plasma membranes and a 2.5-fold increase of glucose-6-phosphate dehydrogenase in microsomal membranes are recorded in the treated fish. The changed membrane structure and fluidity along with the changed enzymatic activity of Na(+)-K(+)-ATPase help the influx the Na(+) rather than the efflux of K(+) through the gill epithelial cells during salinity adaptation.

Animals↗
PubMed2005

Radiation hybrid and genetic linkage mapping of two genes related to fat metabolism in cattle: fatty acid synthase (FASN) and glycerol-3-phosphate acyltransferase mitochondrial (GPAM).

Fatness traits, such as fat deposition, carcass composition, fat content, and the percentage of fat in milk, are economically relevant to cattle production. Fatty acid synthase (FASN) and glycerol-3-phosphate acyltransferase mitochondrial (GPAM) are two enzymes that play a central role in de novo lipogenesis. Both could be putative candidate genes for quantitative trait loci (QTL). Several clones containing the fatty acid synthase (FASN) and glycerol-3-phosphate acyltransferase mitochondrial (GPAM) genes were isolated after screening the INRA bovine bacterial artificial chromosome (BAC) library using PCR. Five microsatellite loci were derived from the BAC clones containing the genes of interest with heterozygosity values ranging from 27 to 78%, using DNA samples from the International Bovine Reference Panel (IBRP). The newly developed markers were genotyped on the IBRP animals and on a radiation hybrid panel to compare the obtained linkage and RH maps. Radiation hybrid maps were developed for chromosome BTA19 and BTA26 regions containing FASN and GPAM genes, respectively. The two genes and their associated microsatellite markers were located on the genetic or RH maps or on both. These microsatellite markers could be useful to study the QTL effect on fat synthesis in reference population.

Animals↗
PubMed2005

Tomographic fluorescence imaging in tissue phantoms: a novel reconstruction algorithm and imaging geometry.

A novel image reconstruction algorithm has been developed and demonstrated for fluorescence-enhanced frequency-domain photon migration (FDPM) tomography from measurements of area illumination with modulated excitation light and area collection of emitted fluorescence light using a gain modulated image-intensified charge-coupled device (ICCD) camera. The image reconstruction problem was formulated as a nonlinear least-squares-type simple bounds constrained optimization problem based upon the penalty/modified barrier function (PMBF) method and the coupled diffusion equations. The simple bounds constraints are included in the objective function of the PMBF method and the gradient-based truncated Newton method with trust region is used to minimize the function for the large-scale problem (39919 unknowns, 2973 measurements). Three-dimensional (3-D) images of fluorescence absorption coefficients were reconstructed using the algorithm from experimental reflectance measurements under conditions of perfect and imperfect distribution of fluorophore within a single target. To our knowledge, this is the first time that targets have been reconstructed in three-dimensions from reflectance measurements with a clinically relevant phantom.

Algorithms↗
PubMed2005

Genomic structure and alternative transcript of bovine fatty acid synthase gene (FASN): comparative analysis of the FASN gene between monogastric and ruminant species.

Fatty acid synthesis differs considerably between monogastric and ruminant species. Fatty acid synthase (FASN) plays a central role in de novo lipogenesis in mammals. FASN has seven active sites which help to catalyse all the reaction steps in the conversion of acetyl-CoA and malonyl-CoA to palmitate. In this work, the bovine fatty acid synthase gene (FASN) was cloned, characterized and compared to the human and rat orthologs. Comparative analysis reveals evolutionarily conserved exon regions and gene flanking sequences. Analysis of the DNA sequence in the 5' flanking region of the FASN bovine gene revealed a potential TATA box, CAAT box and 5 Sp1 binding sites located in a CpG island. RT-PCR and Western blot analysis showed that FASN expression was higher in brain, testis and adipose tissue than in liver and heart. The longer form of the FASN cDNA includes a 7,542-bp sequence which encodes a protein with 2,513 amino acids. An alternative transcript was discovered in bovine and ovine tissues devoid of part of exon 9. The removal of part of exon 9 by post-transcriptional splicing causes a frameshift in the open reading frame and results in a premature termination codon. We hypothesize that in ruminants, FASN may be regulated by the ratio between the two transcripts. The small transcript is mostly produced in tissues with low fatty acid synthesis.

Alternative Splicing↗
PubMed2004

Emetine ditartrate: a possible lead for emergency contraception.

Interception of pregnancy in its initial stage is an attractive and viable approach to contraception. A chemical agent, taken within the first few days of missed menses, intercepts the conception, which is expelled with menstrual flow. The main targets of such agents are the uterus, blastocyst and the growing trophoblasts, whose nutritional requirement is inhibited. Our previous work has identified several nonsteroidal chemical entities as pregnancy interceptives in rodents and infrahuman primates. However, none reached clinical stage due to their ineffectiveness by oral route. Nevertheless, parallel to these rationally designed synthetic compounds, a program was ongoing to identify natural product(s) that can be used as interceptives. We are reporting for the first time the detailed profile of emetine ditartrate, a compound whose pregnancy interceptive efficacy has been studied in mouse, rat, hamster, guinea pig and rabbit by oral and intravaginal routes of administration. By the oral route, the compound caused 100% resorption of the fetuses in rat, hamster and guinea pig at 6.0, 5.0 and 3.0 mg/kg, respectively, on administration during peri- and early postimplantation periods of pregnancy (depending upon the day of implantation in each species). By intravaginal route, the compound was administered once in the form of a vaginal pessary on the day of implantation in respective species; interception of pregnancy was not achieved completely in rat and hamster at doses four to five times the oral dose in multi-day schedule. However, in guinea pig and rabbit it was fully effective at 7.0 and 70.0 mg/animal, respectively. The compound was devoid of estrogenic, antiestrogenic and progestational activity but possessed mild antiprogestational activity at the high dose in vivo. In in vitro assay, however, it did not show any significant binding to estrogen and progesterone receptors. The mode of action of the compound was found to be mainly on the uterus and early embryos around implantation, possibly on the trophoblasts and endometrial cells at the attachment site. The absence of 100% efficacy in rat and hamster by intravaginal route, but not by oral route, is possibly due to poor absorption of the compound through the vagina in these species. The guinea pig and rabbit, therefore, seem the better species for evaluating the efficacy of the compound administered by the vaginal route.

Administration, Intravaginal↗
PubMed2004

Anti-malarial activity of some xanthones isolated from the roots of Andrographis paniculata.

Four xanthones were isolated from the roots of Andrographis paniculata using a combination of column and thin-layer chromatographic methods. They were characterized as (i) 1,8-di-hydroxy-3,7-dimethoxy-xanthone, (ii) 4,8-dihydroxy-2,7-dimethoxy-xanthone, (iii) 1,2-dihydroxy-6,8-dimethoxy-xanthone and (iv) 3,7,8-trimethoxy-1-hydroxy xanthone by IR, MS and NMR spectroscopic methods. In vitro study revealed that compound 1,2-dihydroxy-6,8-dimethoxy-xanthone possessed substantial anti-plasmodial activity against Plasmodium falciparum with its IC(50) value of 4 microg ml(-1). Xanthones bearing hydroxyl group at 2 position demonstrated most potent activity while xanthones with hydroxyl group at 1,4 or 8 position possessed very low activity. In vivo anti-malarial sensitivity test of this compound on Swiss Albino mice with Plasmodium berghei infection using Peters' 4-day test gave substantial reduction (62%) in parasitaemia after treating the mice with 30 mg kg(-1) dose. In vitro cytotoxicity against mammalian cells revealed that 1,2-dihydroxy-6,8-dimethoxy-xanthone is non-cytotoxic with its IC(50) > 32 microg ml(-1).

Andrographis↗
PubMed2004

Metabolite pattern of Cysticercus cellulosae metacestode from different predilection sites of swine using proton magnetic resonance spectroscopy.

Cysticercosis due to Taenia solium is one of the most common public health problems in various regions of the world. We have performed prolon magnetic resonance spectroscopy (1H MRS) experiments of the fluid aspirated from cysticerci excised from skeletal muscle (n = 16) and brain (n = 9) of infected swine to compare the metabolite pattern of cysticerci in different predilection sites. Perchloric acid extract of cysticercus cysts excised from skeletal muscles (n = 16) was also prepared to ascertain water-soluble, low molecular weight metabolites using 1H MRS. Absolute quantification and statistical analysis of different metabolites was done to look for any significant differences in different locations of cysts. The metabolite pattern of cysticerci was found to be similar in the various predilection sites. Metabolites observed were leucine, valine, alanine, lysine, glycine, lipid contents, lactate, glutamate, acetate, succinate, creatine, choline, and glucose. Concentration of creatine in cysticercus fluid of cysts removed from the muscle was found to be significantly higher (p = 0.001) than the cysts located in the brain. We conclude that the metabolite pattern in the cysticerci is not influenced by the surrounding tissue location; however concentration of certain metabolites may depend upon the tissue location.

Animals↗
PubMed2004

Validation of GEANT4, an object-oriented Monte Carlo toolkit, for simulations in medical physics.

GEANT4 (GEometry ANd Tracking 4) is an object-oriented Monte Carlo simulation toolkit that has been developed by a worldwide collaboration of scientists. It simulates the passage of particles through matter. In order to validate GEANT4 for medical physics applications, different simulations are conducted. The results are compared to published results based on three Monte Carlo codes widely used in medical physics: MCNP, EGS4, and EGSnrc. When possible, the simulation results are also compared to experimental data. Different geometries are tested (multilayer and homogeneous phantoms), different sources considered (point-source and broad parallel beam), and different primary particles simulated (photons and electrons) at different energies. For the heterogeneous media, there are notable differences between the Monte Carlo codes reaching up to over 5% in relative difference. For the monoenergetic electrons in a homogeneous medium, the difference between GEANT4 and the experimental measurements is similar to the difference between EGSnrc and the experimental measurements; for the depth-dose curves, the difference expressed as a fraction of the peak dose is always smaller than 4%. We conclude that GEANT4 is a promising Monte Carlo simulation toolkit for low-energy medical applications.

Computer Simulation↗