PubMed Health⌕ Search

Biomedical subjects

S Garde

Publications and source records attributed to S Garde.

30 records · Page 2Linked to original sources

Conformational equilibria of alkanes in aqueous solution: relationship to water structure near hydrophobic solutes.

Conformational free energies of butane, pentane, and hexane in water are calculated from molecular simulations with explicit waters and from a simple molecular theory in which the local hydration structure is estimated based on a proximity approximation. This proximity approximation uses only the two nearest carbon atoms on the alkane to predict the local water density at a given point in space. Conformational free energies of hydration are subsequently calculated using a free energy perturbation method. Quantitative agreement is found between the free energies obtained from simulations and theory. Moreover, free energy calculations using this proximity approximation are approximately four orders of magnitude faster than those based on explicit water simulations. Our results demonstrate the accuracy and utility of the proximity approximation for predicting water structure as the basis for a quantitative description of n-alkane conformational equilibria in water. In addition, the proximity approximation provides a molecular foundation for extending predictions of water structure and hydration thermodynamic properties of simple hydrophobic solutes to larger clusters or assemblies of hydrophobic solutes.

Alkanes↗

PCR amplification of the gene acmA differentiates Lactococcus lactis subsp. lactis and L. lactis subsp. cremoris.

The occurrence of the acmA gene, encoding the lactococcal N-acetylmuramidase in new lactococcal isolates from raw milk cheeses, has been determined. Isolates were genotypically identified to the subspecies level with a PCR technique. On the basis of PCR amplification of the acmA gene, the presence or absence of an additional amplicon of approximately 700 bp correlated with Lactococcus lactis subspecies. L. lactis subsp. lactis exhibits both the expected 1,131-bp product and the additional amplicon, whereas L. lactis subsp. cremoris exhibits a single 1,131-bp fragment.

Animals↗

The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins.

Proteins can be denatured by pressures of a few hundred MPa. This finding apparently contradicts the most widely used model of protein stability, where the formation of a hydrophobic core drives protein folding. The pressure denaturation puzzle is resolved by focusing on the pressure-dependent transfer of water into the protein interior, in contrast to the transfer of nonpolar residues into water, the approach commonly taken in models of protein unfolding. Pressure denaturation of proteins can then be explained by the pressure destabilization of hydrophobic aggregates by using an information theory model of hydrophobic interactions. Pressure-denatured proteins, unlike heat-denatured proteins, retain a compact structure with water molecules penetrating their core. Activation volumes for hydrophobic contributions to protein folding and unfolding kinetics are positive. Clathrate hydrates are predicted to form by virtually the same mechanism that drives pressure denaturation of proteins.

Hydrostatic Pressure↗

Molecular cloning and gene expression analysis of PSP94 (prostate secretory protein of 94 amino acids) in primates.

Prostate secretory protein of 94 amino acids (PSP94) has shown the potential to be a diagnostic biomarker and a therapeutic agent for prostate cancer. Primates have been the main animal models for studying the biology of this molecule. We have cloned and analyzed the cDNA and promoter region of PSP94 from baboon (Papio anubis). Sequence divergence among baboon, monkey, pig, and human, in both the exons and 5'-flanking region indicates rapid evolution of the PSP94 gene. There are conserved steroid hormone response elements (SHRE) in the promoter region of all three primate species. Multiple, alternative transcripts starting near these SHREs and upstream to the TATA box were identified by reverse transcriptase polymerase chain reaction (RT-PCR) and rapid amplification of 5'-cDNA ends (5' RACE) in primate prostatic tissues. This differential transcription initiation may be linked to androgen regulation of PSP94 gene expression. PSP94 transcripts were detected by RT-PCR in a wide variety of mucus-secreting tissues. However, the alternative transcripts were found only in the prostate. The distribution of the PSP94 protein in baboon secretory tissues was also examined by Western blot analysis using a polyclonal antibody against the human homolog. A positive immunoreactive band was detected, but it was weak, due probably to epitope divergence between the two species. In all young, healthy primate animals tested, the level of immunoreactive PSP94 in prostate tissues was lower than expected. In addition, RT-PCR combined with Southern blot analysis on prostate tissues in these animals failed to detect the PSP57 mRNA produced by alternative splicing of PSP94 primary transcript. These observations can be explained by the sexual immaturity and incomplete prostate development in these young primates. This explanation was supported by histological examination of their prostate during PSP94 immunohistochemistry.

Amino Acid Sequence↗

Analysis of epitope structure of PSP94 (prostate secretory protein of 94 amino acids): (I). Immuno-dominant and immuno-recessive area.

PSP94 is a potential biomarker for evaluating patients with prostate carcinoma. We have systematically studied the epitope structure of PSP94 by using a polyclonal antibody against human PSP94. Results of peptide mapping and ELISA tests of dose response to rabbit antiserum against human PSP94 protein showed that only the N-terminal peptides (N30 and M23) are immunoreactive while all the synthetic peptides (C28, C10) located closer to the C-terminus are completely devoid of antigenic activity with the polyclonal antibody. These results were confirmed by analysis of reciprocal competitive binding of PSP94 polyclonal antibody by the N-terminal peptides (N30 and M23) v. either recombinant GST-PSP94 fusion protein, purified recombinant PSP94, or natural PSP94 protein. To further delineate the antigenic activity of the N- and C-termini, we have also expressed N- and C-terminal half of the whole PSP94 (each 47 peptides) using the E. coli GST expression system. The recombinant N47/C47 peptides were released by thrombin cleavage from the GST fusion protein and characterized by Western blotting experiments. Dose response of the recombinant GST-PSP-N47 and -C47 peptides to PSP94 polyclonal antibody showed differential binding activities. Competitive binding of these recombinant N47/C47 proteins against the GST-PSP94 protein demonstrates that the polyclonal antibody has a higher affinity for the N47 peptide than the C47 peptide. Based on the immunological studies of both synthetic peptides and recombinant PSP94- N/C terminal proteins, we propose an epitope structure of human PSP94 with an immuno-dominant N-terminus and an immuno-recessive C-terminus.

Amino Acid Sequence↗

An information theory model of hydrophobic interactions.

A molecular model of poorly understood hydrophobic effects is heuristically developed using the methods of information theory. Because primitive hydrophobic effects can be tied to the probability of observing a molecular-sized cavity in the solvent, the probability distribution of the number of solvent centers in a cavity volume is modeled on the basis of the two moments available from the density and radial distribution of oxygen atoms in liquid water. The modeled distribution then yields the probability that no solvent centers are found in the cavity volume. This model is shown to account quantitatively for the central hydrophobic phenomena of cavity formation and association of inert gas solutes. The connection of information theory to statistical thermodynamics provides a basis for clarification of hydrophobic effects. The simplicity and flexibility of the approach suggest that it should permit applications to conformational equilibria of nonpolar solutes and hydrophobic residues in biopolymers.

Journal Article↗

Mesoderm enhancing effect of human seminal plasma inhibin and its synthetic C-terminal nonapeptide fragment in the chick embryo.

Isomers of fibroblast growth factor and members of the transforming growth factor beta family have been identified as potent mesoderm inducing factors, particularly in amphibians. Activins belonging to the latter group are capable of inducing all types of mesoderm. Inhibins, also belonging to the same family of proteins have an exactly opposite biological action than activins in the adult organism. We have examined the effects of human seminal plasma inhibin on the early development of the chick embryo, where also activins appear to be important in mesoderm induction. Contrary to expectations, inhibin brought about stimulation of development of somites and heart, structures of mesodermal origin, and increase in the body length in more than 50% of the treated chick blastoderms. A synthetic fragment of human seminal plasma inhibin, a nonapeptide fragment of C-terminal end, also exhibited similar effects. In some cases the treatments resulted in completely abnormal development while in some increase in the number of somites was associated with abnormality in the anterior region. Our results demonstrate that human seminal plasma inhibin does not act as an inhibitor of mesoderm induction in the chick embryo but in amniotes inhibin-related molecules may have a role as mesoderm enhancers.

Amino Acid Sequence↗

Effect of prostatic inhibin peptide (PIP) on prostate cancer cell growth in vitro and in vivo.

Prostatic inhibin peptide (PIP), is a 94 amino acid protein which is secreted by the prostate gland in an androgen-independent manner. Previously, it has been demonstrated that PIP appears to inhibit follicle-stimulating-hormone (FSH) secretion by the pituitary and prostate glands. In vitro, the Dunning R3327 rat prostate cancer cell line MAT-LyLu (MLL) cells and the human prostate cancer cell line PC-3, are stimulated to grow in response to exogenous FSH and these effects are blocked by PIP. In vivo, PIP inhibits the growth of the highly metastatic MLL prostate cancer cell line. A comparison of hormone levels in control and PIP-treated rats demonstrates a significant inhibition of FSH in treated animals. It appears that, in vivo, PIP may inhibit prostate cancer growth by inhibiting FSH. PIP may represent a novel hormonal treatment for prostate cancer.

Adenocarcinoma↗

Gonadal function in prepubertal boys following treatment for Hodgkin's disease.

PURPOSE: Gonadal functions were evaluated in 26 male patients with Hodgkin's disease (HD), who were in continuous unmaintained remission following combination chemotherapy consisting of COPP/MOPP. MATERIALS AND METHODS: These patients had received chemotherapy during the prepubertal phase. The median duration after termination of chemotherapy was 72 months. RESULTS: Semen analysis of 18 patients showed azoospermia. Hormonal analysis showed elevated mean levels follicle-stimulating hormone (FSH) and inhibin as compared to age-matched controls, whereas luteinizing hormone levels were only marginally elevated. CONCLUSIONS: These results suggest that COPP/MOPP causes severe damage to germinal epithelium even when given during prepubertal age. Sertoli cells, which are responsible for secretion of inhibin, are resistant to these cytotoxic agents. Our data emphasize the lack of gross dysfunction of Leydig cells. It is possible that an alternative chemotherapy protocol (ABVD) may be used in young patients to minimize the gonadal damage.

Adolescent↗

DNA probes for detection of copper resistance genes in Xanthomonas campestris pv. vesicatoria.

The copper resistance (Cur) genes encoded on pXV10A, a 190-kb plasmid in Xanthomonas campestris pv. vesicatoria XV10, were isolated on a 44-kb cosmid clone designated pCuR1. Tn5 mutagenesis of pCuR1 indicated that a 4.0-kb region was required for copper resistance. Three restriction fragments located within the 4.0-kb region demonstrated high specificity for the Cur genes present in X. campestris pv. vesicatoria and will be useful in monitoring the presence of these genes in the environment.

Blotting, Southern↗