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D Thomas

Publications and source records attributed to D Thomas.

At least 271 records · Page 15Linked to original sources
PubMed1998

Prediction of functional residues in water channels and related proteins.

In this paper, we present an updated classification of the ubiquitous MIP (Major Intrinsic Protein) family proteins, including 153 fully or partially sequenced members available in public databases. Presently, about 30 of these proteins have been functionally characterized, exhibiting essentially two distinct types of channel properties: (1) specific water transport by the aquaporins, and (2) small neutral solutes transport, such as glycerol by the glycerol facilitators. Sequence alignments were used to predict amino acids and motifs discriminant in channel specificity. The protein sequences were also analyzed using statistical tools (comparisons of means and correspondence analysis). Five key positions were clearly identified where the residues are specific for each functional subgroup and exhibit high dissimilar physico-chemical properties. Moreover, we have found that the putative channels for small neutral solutes clearly differ from the aquaporins by the amino acid content and the length of predicted loop regions, suggesting a substrate filter function for these loops. From these results, we propose a signature pattern for water transport.

Animals↗
PubMed1998

Mechanism of activation of the GM-CSF, IL-3, and IL-5 family of receptors.

The process of ligand binding leading to receptor activation is an ordered and sequential one. High-affinity binding of GM-CSF, interleukin 3 (IL-3), and IL-5 to their receptors induces a number of key events at the cell surface and within the cytoplasm that are necessary for receptor activation. These include receptor oligomerization, activation of tyrosine kinase activity, phosphorylation of the receptor, and the recruitment of SH2 (src-homology) and PTB (phosphotyrosine binding) domain proteins to the receptor. Such a sequence of events represents a recurrent theme among cytokine, growth factor, and hormone receptors; however, a number of very recent and interesting findings have identified unique features in this receptor system in terms of: A) how GM-CSF/IL-3/IL-5 bind, oligomerize, and activate their cognate receptors; B) how multiple biological responses such as proliferation, survival, and differentiation can be transduced from activated GM-CSF, IL-3, or IL-5 receptors, and C) how the presence of novel phosphotyrosine-independent signaling motifs within a specific cytoplasmic domain of betaC may be important for mediating survival and differentiation by these cytokines. This review does not attempt to be all-encompassing but rather to focus on the most recent and significant discoveries that distinguish the GM-CSF/IL-3/IL-5 receptor subfamily from other cytokine receptors.

Animals↗
PubMed1998

Further evidence for hexagonal organization of HIV gag protein in prebudding assemblies and immature virus-like particles.

The fullerene-like model for the organization of HIV gag encoded precursor pr55gag was based on the study of prebudding assemblies at the plasma membrane of cells infected with a recombinant baculovirus expressing HIV-1 gag protein. The objective of the present study was to support the model by image processing of virus-like particles (VLP). In this work we used VLP purified by density gradient centrifugation, which caused partial or occasionally complete loss of the lipid bilayer in some VLP without the use of detergent. In addition more plasma membrane-associated pr55gag protein assemblies were processed. Image processing of negatively stained specimens revealed the presence of threefold symmetry and a hexagonal network of rings with a resolution of 29 A in VLP and better than 25 A in membrane associated assemblies. The center-to-center spacing of the rings was 67 A in VLP and 70 A in membrane assemblies. Patches of gag protein oligomers at the plasma membrane were usually round and varying in size, but some of them were triangular. Indication of triangular-shaped gag protein assemblies was also seen in partly dissociated VLP. Since the hexagonal network is formed by the uncleaved gag polyprotein, we conclude that the threefold symmetry applies to all domains including p24gag. The presence of threefold symmetry and the hexagonal network in VLP are consistent with the hypothesis that immature HIV particles possess icosahedral symmetry.

Animals↗
PubMed1998

Antibody catalysis based on functional mimicry.

Approaches aiming at eliciting antibodies (Abs) that catalyze specific chemical transformations are numerous. Most of the developed methods are based on the chemical steps of the reaction catalyzed rather than on the structure of known enzyme active sites. The authors have developed an approach that rests on the mimicry properties of the idiotypic network of immune regulation. Recent results, together with the existence of natural catalytic Abs in autoimmune diseases, indicate the need to better understand the regulation properties of immune response, in order to improve the efficiency of tailor-made catalytic Abs.

Animals↗
PubMed1998

Tonoplast intrinsic proteins from cauliflower (Brassica oleracea L. var. botrytis): immunological analysis, cDNA cloning and evidence for expression in meristematic tissues.

The vacuolar membrane (tonoplast) of plant cells contains aquaporins, protein channels that facilitate the selective transport of water. These tonoplast intrinsic proteins (TIPs) of 23-29 kDa belong to the ancient major intrinsic protein (MIP) family. A monospecific polyclonal antiserum directed against a 26 kDa intrinsic protein from the tonoplast of meristematic cells from cauliflower (Brassica oleracea L. var. botrytis) was used to screen a cDNA library. Two distinct cDNAs have been isolated. Both clones, c26-1 and c26-2, encode closely related TIPs. The c26-1 insert, consisting of 933 bp upstream of the poly(A) tail, is a full-length cDNA with an open reading frame encoding a protein of 251 amino acids with a calculated M(r) of 25,500. The c26-2 insert is a 5' truncated cDNA. The two cDNAs share 90.5% sequence identity within their overlapping coding regions but only 35% sequence identity in the 3' untranslated regions, indicating that highly related TIP-encoding genes are expressed in meristematic cells. Although TIPs have previously been found in a variety of cell types, they have not been found in meristems. The derived amino acid sequences (BobTIP26-1 and BobTIP26-2, respectively) closely resemble the aquaporin gamma-TIP from Arabidopsis thaliana. Northern blot analysis and in situ hybridization show that BobTIP26 mRNAs preferentially accumulate in highly meristematic cells, mostly before and during cell enlargement, and in the living cells of the xylem. This differential pattern of expression is also found by immunodetection of BobTIP26 polypeptides. The gene expression patterns are discussed with respect to the probable function of the gene products.

Amino Acid Sequence↗
PubMed1998

Proliferation and MHC-unrestricted bystander lysis by virus-specific cytotoxic T cells following antigen self-presentation.

Cytotoxic T cells (CTL) not only act as effector cells, but can also serve as antigen-presenting cells (APC) for other CTL due to their expression of major histocompatibility complex (MHC) class I molecules. In the present study we show that independently derived CTL lines (CTLL) with specificity for an L(d)-presented nonapeptide corresponding to amino acids 168-176 of the immediate-early 1 (IE1) protein of murine cytomegalovirus not only lyse syngeneic but also allogeneic target cells, if the peptide is present during the cytolytic assay. Whereas a short peptide pulse is sufficient to render syngeneic cells susceptible to lysis, continued presence of soluble peptide is mandatory for the lysis of allogeneic target cells. This indicates a difference in the mechanisms involved. Syngeneic BALB/c B cell blasts (K(d)D(d)L(d)) and mutant BALB/c-H-2dm2 B cell blasts lacking the restricting Ld molecules (K(d)D(d)0) were lysed to a similar extent in the absence of the IE1 nonapeptide, provided that the IE1-specific CTL had been pre-incubated with the peptide before the cytolytic assay. Since the mutant cells cannot present the IE1 peptide, their lysis indicates an MHC-unrestricted, peptide-independent mode of recognition by the CTLL. In addition, proliferation of the CTLL takes place after incubation with the cognate peptide, even in the absence of professional APC. These data indicate inter-CTL antigen self-presentation, resulting in activation of the lytic machinery leading to peptide-independent bystander lysis of allogeneic as well as syngeneic target cells.

Animals↗
PubMed1998

Effects of cisapride on QT interval in children.

Recent reports of torsade de pointes and heart block associated with prolonged QT interval in children receiving cisapride raise questions about its safety. We prospectively examined the effects of cisapride on the QT interval in children. Electrocardiography was performed on 30 children before and after cisapride was administered. An additional 71 children underwent electrocardiography only after starting cisapride. The incidence of a corrected QT (QTc) interval > 440 msec or a marked abnormality in T wave morphology was determined in all 101 children. Cisapride significantly lengthened the QTc with a mean increase of 15.5 +/- 4.6 msec (mean +/- SEM, p = 0.002 in the 30 children with baseline electrocardiographs. Twelve of the 101 patients were found to have a QTc > 440 msec, and one had a new prominent notched T wave in all leads. In these 13 (13%) patients with repolarization abnormalities, other factors that might contribute to a long QT were noted in 11 (85%) patients. We conclude that cisapride use in children is associated with a modest increase in QT interval. The incidence of QTc > 440 msec is low. Most children with long QTc have other factors that could compound the effects of cisapride.

Child↗
PubMed1998

Are we detecting and operating on high risk patients in the asymptomatic carotid surgery trial? The Asymptomatic Carotid Surgery Trial Collaborators.

OBJECTIVE: This study aims to determine whether asymptomatic carotid surgery trial (ACST) centres have entered and can identify high risk patients using duplex. DESIGN: Retrospective study. MATERIALS AND METHODS: Eighty-six vascular laboratories collaborating in ACST were studied, Equipment, operator experience, methodology and interpretation criteria were assessed. The ACST randomisation data were examined to determine whether patients believed to be at higher risk of stroke because of tight stenosis, contralateral occlusion or echolucent plaque were randomised. RESULTS: Laboratories (92%) had colour duplex and 62% of all operators had > 3 years experience in carotid evaluation. The Doppler angle used to obtain peak velocity was 30-60 degrees in 65%, 60 degrees in 28% and 60-80 degrees in 6% of laboratories. Sixty-two per cent reported diameter reduction, 27% area reduction, and 11% used both methods. One-third of 1657 randomised patients were reported to have ipsilateral echolucent plaque. Median ipsilateral stenosis was 80%, 8% had contralateral occlusion and 8.5% had bilateral > 80% stenosis. CONCLUSIONS: Centres in ACST use experienced operators, high quality equipment and conscientious data recording. Variations in methods of determining carotid stenosis exist, but can be smoothed by simple data collection. Patients at higher perceived risk of stroke are being entered and with continued recruitment it should be possible to determine whether surgery improves disabling stroke-free survival.

Angiography↗
PubMed1998

A novel human WD protein, h-beta TrCp, that interacts with HIV-1 Vpu connects CD4 to the ER degradation pathway through an F-box motif.

HIV-1 Vpu interacts with CD4 in the endoplasmic reticulum and triggers CD4 degradation, presumably by proteasomes. Human beta TrCP identified by interaction with Vpu connects CD4 to this proteolytic machinery, and CD4-Vpu-beta TrCP ternary complexes have been detected by coimmunoprecipitation. beta TrCP binding to Vpu and its recruitment to membranes require two phosphoserine residues in Vpu essential for CD4 degradation. In beta TrCP, WD repeats at the C terminus mediate binding to Vpu, and an F box near the N terminus is involved in interaction with Skp1p, a targeting factor for ubiquitin-mediated proteolysis. An F-box deletion mutant of beta TrCP had a dominant-negative effect on Vpu-mediated CD4 degradation. These data suggest that beta TrCP and Skp1p represent components of a novel ER-associated protein degradation pathway that mediates CD4 proteolysis.

Binding Sites↗
PubMed1998

Missense mutations in disease genes: a Bayesian approach to evaluate causality.

The problem of interpreting missense mutations of disease-causing genes is an increasingly important one. Because these point mutations result in alteration of only a single amino acid of the protein product, it is often unclear whether this change alone is sufficient to cause disease. We propose a Bayesian approach that utilizes genetic information on affected relatives in families ascertained through known missense-mutation carriers. This method is useful in evaluating known disease genes for common disease phenotypes, such as breast cancer or colorectal cancer. The posterior probability that a missense mutation is disease causing is conditioned on the relationship of the relatives to the proband, the population frequency of the mutation, and the phenocopy rate of the disease. The approach is demonstrated in two cancer data sets: BRCA1 R841W and APC I1307K. In both examples, this method helps establish that these mutations are likely to be disease causing, with Bayes factors in favor of causality of 5.09 and 66.97, respectively, and posterior probabilities of .836 and .985. We also develop a simple approximation for rare alleles and consider the case of unknown penetrance and allele frequency.

Adenomatous Polyposis Coli↗
PubMed1998

Functional mimicry: elicitation of a monoclonal anti-idiotypic antibody hydrolizing beta-lactams.

Antigen mimicry by anti-idiotypic antibodies is investigated as a reliable strategy to achieve molecular imprinting of an enzymatic activity. A monoclonal anti-idiotypic antibody (Ab2-9G4H9) was elicited by using a monoclonal antibody (Ab1-7AF9) specific for the beta-lactamase active site. Catalytic features of Ab2 were characterized with beta-lactamase substrates. The antibody combining site appeared to have retained a part of the catalytic specificity. The relevance of the idiotypic mimicry concept for the generation of catalytic antibodies was further demonstrated by eliciting a third generation antibody (Ab3), which was shown to recognize beta-lactamase: the complete internal image properties of Ab2 9G4H9, including binding and catalytic properties, were thus checked.

Animals↗
PubMed1998

Comparison of the effects of enucleation and orbital reconstruction using free-fat grafts, dermis grafts, and porous polyethylene implants in infant rabbits.

Twenty-nine infant rabbits from four litters were randomly assigned to three groups. No surgery was performed on left eyes. All right eyes were enucleated. Group 1, the control group, had no right-socket reconstruction. Group 2 had reconstruction using free-fat and dermis grafts. Group 3 had reconstruction using porous polyethylene implants. On attaining adult size, rabbits were killed, decapitated, and prepared for measurements. Orbital volume measurements were performed twice and orbital entrance areas were determined once. No significant differences were noted between first and second measurements of orbital volumes. Right orbital volumes were significantly smaller than left orbits in all groups except for the second measurement of the polyethylene implant group. Right orbital entrance areas were significantly smaller than left areas in the control and the free-fat and dermis graft groups. Right orbital entrance areas of the polyethylene group were not significantly smaller than the corresponding left orbital entrance areas. The use of free-fat and dermis grafts for orbital reconstruction in anophthalmic infant rabbits did not significantly stimulate orbital bone growth. In one trial, the polyethylene implant group displayed right orbital volumes and orbital entrance areas that were not significantly smaller than controls.

Adipose Tissue↗
PubMed1998

Sucrose is a nonaccumulated osmoprotectant in Sinorhizobium meliloti.

Intracellular accumulation of sucrose in response to lowered water activity seems to occur only in photosynthetic organisms. Here we demonstrate, for the first time, the potent ability of this common sugar, supplied exogenously, to reduce growth inhibition of Sinorhizobium meliloti cells in media of inhibitory osmolarity. Independently of the nature of the growth substrates and the osmotic agent, sucrose appears particularly efficient in promoting the recovery of cytoplasmic volume after plasmolysis. Surprisingly, sucrose is not accumulated by the bacteria at an osmotically efficient level. Instead, it strongly stimulates the accumulation of the main endogenous osmolytes glutamate and N-acetylglutaminylglutamine amide (NAGGN). Examining cell volume changes during the hyperosmotic treatment, we found a close correlation between the enhancement of the osmotically active solute pool and the increase in cell volume. Sucrose shares several features with ectoine, another nonaccumulated osmoprotectant for S. meliloti. Overall, osmoregulation in S. meliloti appears to be strongly divergent from that in most bacteria.

Betaine↗
PubMed1998

Control of cytomegalovirus in bone marrow transplantation chimeras lacking the prevailing antigen-presenting molecule in recipient tissues rests primarily on recipient-derived CD8 T cells.

Cytomegalovirus (CMV) infection during the transient immunodeficiency after bone marrow transplantation (BMT) develops into disease unless antiviral CD8 T cells are restored in due course. Histoincompatibility between donor and recipient is associated with increased risk. Complications may include a rejection response against the foreign major histocompatibility complex (MHC) antigens and a lack of antiviral control resulting from a misfit between donor-derived T cells and the antigenic viral peptides presented in recipient tissues. Here we have established a murine model of CMV disease after experimental BMT performed across a single MHC class I disparity. Specifically, BALB/c bone marrow cells expressing the prevailing antigen-presenting molecule Ld were transplanted into the Ld gene deletion mutant BALB/c-H-2(dm2), an experimental setting that entails a selective risk of host-versus-graft but not graft-versus-host response. The reconstituted T-cell population proved to be chimeric in that it consisted of Ld-positive donor-derived and Ld-negative recipient-derived cells. Pulmonary infiltrates did not include cytolytic T cells directed against Ld. This finding implies that the infection did not trigger a host-versus-graft response. Notably, upon adoptive transfer, donor-derived CD8 T cells preferentially protected tissues of donor genotype, whereas recipient-derived CD8 T cells protected tissues of either genotype. We infer from these data that the focus on immunodominant antigens presented by Ld within the donor cell population distracted the donor T cells from protecting recipient tissues and that protection in the chimeras was therefore primarily based on recipient T cells. As a consequence, T-cell chimerism after BMT should give a positive prognosis with respect to control of CMV.

Animals↗