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At least 991 records · Page 55Linked to original sources
PubMed1995

Induction of a primary human cytotoxic T-lymphocyte response against a novel conserved epitope in a functional sequence of HIV-1 reverse transcriptase.

OBJECTIVE: To identify novel major histocompatibility complex (MHC) class I-restricted cytotoxic T-lymphocyte (CTL) epitopes conserved in HIV-1. METHODS: Potential conserved CTL epitopes were selected using a predictive computer algorithm based on a human leukocyte antigen (HLA)-A*0201 peptide-binding motif and tested for actual binding to the human processing defective cell line 174.CEM T2 (T2). Hence, the amino-acid sequences of 14 full-length sequenced HIV-1 strains were analysed. An in vitro primary peptide-specific human CTL response was induced with responding lymphocytes of an HIV-1-seronegative donor. Responding T cells were cloned by limiting dilution and tested for their ability to recognize naturally processed antigen in a 51Cr-release assay using recombinant vaccinia-HIV protein-infected B-lymphoblastoid cells (B-LCL) as target cells. RESULTS: The analysis of peptides bearing the HLA-A*0201 motif for conservation resulted in one peptide of Env, three of Gag and 12 of Pol. Only Gag340-348, Pol83-92, Pol267-277 and Pol960-968 showed binding properties to T2 comparable with those of known CTL epitopes Gag76-84 SLYNTVATL and Pol468-476 ILKEPVHGV. A successful primary MHC class I-restricted CTL response was induced against Pol468-476 and Pol267-277 VLDVGDAYFSV, a peptide in a functional sequence of reverse transcriptase (RT). The resulting CD8+ CTL clones were peptide-specific and able to specifically lyse recombinant vaccinia-HIV-1 RT-infected HLA-A*0201-matched B-LCL. CONCLUSION: The method used to screen proteins sequences for potential CTL epitopes, test selected peptides for binding to MHC class I and induction of an in vitro primary response against optimal binding peptides resulted in the identification of at least one novel conserved CTL epitope. The novel epitope is located in an area crucial for RT activity. This study demonstrates the feasibility of identifying highly conserved HIV-1-derived peptides capable of eliciting novel anti-HIV-1 CTL responses.

Amino Acid Sequence↗
PubMed1993

Molecular characterization of a xyloglucan-specific endo-(1-->4)-beta-D-glucanase (xyloglucan endo-transglycosylase) from nasturtium seeds.

A novel xyloglucan-specific endo-(1-->4)-beta-D-glucanase, involved in the post-germinative mobilization of xyloglucan storage reserves, has previously been isolated from nasturtium (Tropaeolum majus L.) seed. Its mode of action has been shown, in vitro, to be one of transglycosylation except at low substrate (glycosylacceptor) concentrations when hydrolysis predominates. Here it is shown that this nasturtium seed xyloglucan endo-transglycosylase is encoded by a single gene which is transcribed and processed to a 1.5 kb mRNA. The isolation and DNA sequence analysis of a cDNA copy of the nasturtium xyloglucan endo-transglycosylase transcript is described. The cDNA encodes a 33.5 kDa precursor polypeptide which is subsequently processed to a 31 kDa mature protein. The precursor incorporates an N-terminal signal sequence which probably contains information relevant to the targeting of the enzyme to the cell wall. The computer-predicted isoelectric point (5.14) and low (approximately 0%) alpha-helix content of the deduced mature protein are in excellent agreement with the experimental data obtained using the purified enzyme. The deduced protein sequence lacks homology with known plant endo-(1-->4)-beta-D-glucanases, consistent with the unique properties of the enzyme. Database searches have revealed that a Brassica protein (meri-5) of previously unknown function, but abundantly expressed in expanding tissue, shares structural identity with the nasturtium xyloglucan endo-transglycosylase. The expression of a xyloglucan endo-transglycosylase in expanding tissue would be consistent with the contention that enzymes of this type are involved in cell wall loosening.

Amino Acid Sequence↗
PubMed1996

Anthropometric equations for estimating abdominal adipose tissue distribution in women.

OBJECTIVES: (1) to develop multiple regression equations for predicting computed tomography (CT) derived intra-abdominal (IAF), subcutaneous (SCF) and total (TOTF = IAF + SCF) abdominal adipose tissue areas from anthropometric measures and (2) to validate the equations. DESIGN: Cross-sectional study. SUBJECTS: 204 healthy Caucasian females subjects with a large range of age (17-76 years) and percentage body fat (8.8%-48.1%). Fifty-one subjects served as an independent sub-sample for the validation of the equations. MEASUREMENTS: Various fatness and fat distribution parameters (hydrodensitometry, single CT scan, skinfold and circumference measures). RESULTS: Multiple regression equations were developed to estimate IAF, SCF and TOTF. R2 for IAF, SCF and TOTF was 0.75, 0.81 and 0.85, respectively. The equations were validated on an independent sub-sample of 51 subjects. All three equations met validation criteria with R2 validations of 0.79, 0.71 and 0.84 for IAF, SCF and TOTF, respectively. CONCLUSION: These equations might be used as an inexpensive estimation of IAF, SCF and TOTF in adult Caucasian females varying greatly in age and percentage body fat.

Abdomen↗
PubMed1996

Structure-function analysis of the Escherichia coli GrpE heat shock protein.

We have isolated various missense mutations in the essential grpE gene of Escherichia coli based on the inability to propagate bacteriophage lambda. To better understand the biochemical mechanisms of GrpE action in various biological processes, six mutant proteins were overexpressed and purified. All of them, GrpE103, GrpE66, GrpE2/280, GrpE17, GrpE13a and GrpE25, have single amino acid substitutions located in highly conserved regions throughout the GrpE sequence. The biochemical defects of each mutant GrpE protein were identified by examining their abilities to: (i) support in vitro lambda DNA replication; (ii) stimulate the weak ATPase activity of DnaK; (iii) dimerize and oligomerize, as judged by glutaraldehyde crosslinking and HPLC size chromatography; (iv) interact with wild-type DnaK protein using either an ELISA assay, glutaraldehyde crosslinking or HPLC size chromatography. Our results suggest that GrpE can exist in a dimeric or oligomeric form, depending on its relative concentration, and that it dimerizes/oligomerizes through its N-terminal region, most likely through a computer predicted coiled-coil region. Analysis of several mutant GrpE proteins indicates that an oligomer of GrpE is the most active form that interacts stably with DnaK and that the interaction is vital for GrpE biological function. Our results also demonstrate that both the N-terminal and C-terminal regions are important for GrpE function in lambda DNA replication and its co-chaperone activity with DnaK.

Adenosine Triphosphatases↗
PubMed1997

Minimal templates directing accurate initiation of subgenomic RNA synthesis in vitro by the brome mosaic virus RNA-dependent RNA polymerase.

Short regions of (-)-strand brome mosaic virus (BMV) RNA3, proscripts, were shown to direct accurate in vitro synthesis of (+)-strand subgenomic RNA by the BMV RNA-dependent RNA polymerase (RdRp), facilitating characterization of the sequences and/or structures directing subgenomic RNA synthesis. Proscripts retaining fewer than 8-nt of an 18-nt polyuridylate tract located just upstream of the core promoter sequence (French R, Ahlquist P, 1988, J Virol 62:2411-2420; Marsh LE, Dreher TW, Hall TC, 1988, Nucleic Acids Res 16:981-995) directed dramatically less synthesis of 26-nt or longer products. Original levels of RNA synthesis were not restored by replacement of the 3' polyuridylate tract with polyadenylate, polycytidylate, or polyguanylate tracts, or by movement of the polyuridylate tract to the 5' end of the proscript. The polyuridylate tract presumably binds some component(s) required for RdRp activity because the addition of poly(U) [but not poly(C)] RNA to RdRp reactions decreased RNA synthesis significantly. Quite surprisingly, deletions of the polyuridylate tract in proscripts directing synthesis of 24-nt or shorter products had little or no detrimental effect on subgenomic RNA synthesis, correlated with their inability to form a computer-predicted stem-loop present in longer proscripts requiring the polyuridylate tract. Successive 3' and 5' deletions demonstrated that the minimal elements required for accurate initiation of subgenomic RNA synthesis are within a proscript of 22-nt.

Bromovirus↗
PubMed1997

Secondary structure of the 5'-noncoding region of border disease virus genome RNAs.

The computer predicted secondary structures from the 5'-NC genome region of four border disease virus (BDV) strains collected from sheep in England and Scotland over a period 1976-1986 were prepared. The FOLD program from GCG sequence analysis software package was used for the analysis of a 243 bp RNA fragment. Two typical shapes of secondary structures were observed which contained multiple imperfect stem-loop motifs. The shape of those structures exactly fit with the grouping of BDV strains to two phylogenetic groups. Secondary structures are typical only of BDV strains and they are different from the structures prepared for NADL (BVDV) and Alfort (CSFV) strains.

Animals↗
PubMed1995

Evaluation of immunodominant epitopes of human T-lymphotropic virus type 1 (HTLV-I) using synthetic peptides.

Human T-lymphotropic virus type 1 (HTLV-I) causes adult T-cell leukemia/lymphoma (ATLL) and has been associated with a variety of immunologically-mediated diseases. Recently, the immunodominant epitopes of HTLV-I have begun to be defined through the utilization of synthetic peptides and recombinant proteins. Strategies to define the conformational features of immunogenic peptides and design chimeric and multivalent constructs that mimic native viral proteins have provided the opportunity to create an effective synthetic vaccine against HTLV-I infection. An ideal peptide vaccine to be universally immunogenic must incorporate rationally designed antigenic determinants that accurately mimic the corresponding structural architecture found in native proteins and elicit relevant components of the immune system. We have recently designed and tested chimeric and beta-sheet template constructs containing HTLV-I immunodominant peptide motifs that elicit neutralizing antibody responses and overcome genetically restricted immune responses. To further illustrate putative vaccine candidates, HTLV-I env and tax proteins were analyzed using various computer-predicted correlates of protein antigenicity, secondary structural predictions, and major histocompatibility complex class I binding motifs. These approaches provide the opportunity to design synthetic peptide vaccines against HTLV-I infection that are based on structurally defined criteria, as well as test the influence of glycosylation on peptide conformation and immunogenicity.

Amino Acid Sequence↗
PubMed1997

Epitope analysis of the CS3 fimbrial subunit of human enterotoxigenic Escherichia coli and the construction of novel CS3::ST and CS3::LT-B immunogens.

Enterotoxigenic E. coli (ETEC) are the major cause of traveler's diarrhoea and the CS3 fimbriae/fibrillae are expressed by most strains bearing the colonization factor CFA/II. The cstAH gene cluster determining CS3 biosynthesis has been previously cloned and sequenced and it has been shown that cstH encodes the major fimbrial subunit and cstA-G encode an assembly cassette. In the work described here we have sought to define the surface exposed domains on CS3 and to manipulate them so that CS3 can be used as a means of expressing foreign antigenic determinants on the bacterial surface. Using a panel of 21 monoclonal antibodies, which we have used in western blotting, immunofluorescence microscopy and colony blotting, together with computer predictions, we have identified three domains within CstH. Two of these sites were permissive for insertion and we have introduced, in-frame, either an epitope from the B subunit of LT (heat labile toxin) or the entire coding sequence of mature ST (heat stable toxin) to construct hybrid proteins. These proteins could be assembled into hybrid fimbriae which could be recognized by antibodies to both CS3 and the foreign epitope as shown by immunofluorescence microscopy and colony blotting. The immunogenicity of the constructs has been evaluated following both oral and intraperitoneal immunization of mice with the attenuated Salmonella typhimurium strain G30 harbouring the hybrid cst operons. Although plasmid stability is currently a problem, these experiments showed that antibodies to both the carrier and the foreign epitope were generated.

Amino Acid Sequence↗
PubMed1998

Nucleotide sequence and genetic analysis of the leader region of Canadian, American and European equine arteritis virus isolates.

The extreme 5' end, the entire leader sequence of the Arvac vaccine strain, and 10 equine arteritis virus (EAV) isolates, including the ATCC Bucyrus reference strain and 5 Canadian field isolates, were determined and compared at the primary nucleotide and secondary structure levels. The leader sequence of eight EAV isolates, including the Bucyrus reference strain, and the leader sequence of the Arvac vaccine strain was determined to be 206 nt in length (not including the putative 5' cap structure-associated nucleotide) whereas those of the 86AB-A1 and 86NY-A1 isolates were found to be 205 and 207 nt in length, respectively. The sequence identity of the leader sequences, between the different isolates and the Bucyrus reference strain, ranged from 94.2 to 98.5%. Phylogenetic analysis and estimation of genetic distances, based on the leader nucleic acid sequences, showed that all EAV isolates/strains are likely to represent a large phylogenetically-related group. An AUG start codon found at position 14 in all EAV isolates/strains could initiate an open reading frame (ORF) that could produce a polypeptide of 37 amino acids, except for the 86NY-A1 isolate where the intraleader polypeptide would contain 54 amino acids. Computer-predicted RNA secondary structures were identified in the 11 EAV leader regions analyzed. All EAV isolates/strains showed 3 conserved stem-loops (designated A, B and C). An additional conserved stem-loop (D) was observed in 7 EAV isolates, including the Bucyrus reference strain. The leader region distal to stem-loop D did not contain conserved sequences or stem-loop structures common to the EAV isolates/strains.

Animals↗
PubMed1999

T cell epitopes of a lipocalin allergen colocalize with the conserved regions of the molecule.

In this study we characterized the human T cell-reactive sites of the major cow dander allergen, Bos d 2, a member of the lipocalin protein family. We showed that Bos d 2 contains only a limited number of epitopes. This is in contrast to many other allergens, which usually contain multiple T cell epitopes throughout the molecule. The epitopes of Bos d 2 were primarily concentrated in the conserved regions of the molecule. One of the epitopes was recognized by all the cow-asthmatic individuals regardless of their HLA phenotype. Computer-predicted T cell epitopes on Bos d 2, other lipocalin allergens, and human endogenous lipocalins were situated in similar locations on these molecules and corresponded to experimentally identified epitopes on Bos d 2. The results suggest that human endogenous lipocalins could be involved in the modulation of immune responses against exogenous lipocalin allergens. In addition, our findings are likely to facilitate the development of new forms of immunotherapy against allergies induced by the important group of lipocalin allergens.

Allergens↗
PubMed2004

Comparison of calcium scores from thick- and thin image slice-computed tomography scanning in predicting future coronary events.

Computed tomographic image slices between 2.5 and 3.0 mm are commonly used for coronary calcium scanning. To evaluate the comparative accuracy of thicker image slices (5 to 6 mm) for predicting coronary events, we acquired both types of scans in 280 research participants and clinically followed them up for 7 years. We found that thick-slice image scanning and image assessment ranked calcium scores similarly and that measurements from both scanning methods predicted coronary heart disease events equally.

Calcinosis↗
PubMed2004

Computational methods for prediction of T-cell epitopes--a framework for modelling, testing, and applications.

Computational models complement laboratory experimentation for efficient identification of MHC-binding peptides and T-cell epitopes. Methods for prediction of MHC-binding peptides include binding motifs, quantitative matrices, artificial neural networks, hidden Markov models, and molecular modelling. Models derived by these methods have been successfully used for prediction of T-cell epitopes in cancer, autoimmunity, infectious disease, and allergy. For maximum benefit, the use of computer models must be treated as experiments analogous to standard laboratory procedures and performed according to strict standards. This requires careful selection of data for model building, and adequate testing and validation. A range of web-based databases and MHC-binding prediction programs are available. Although some available prediction programs for particular MHC alleles have reasonable accuracy, there is no guarantee that all models produce good quality predictions. In this article, we present and discuss a framework for modelling, testing, and applications of computational methods used in predictions of T-cell epitopes.

Animals↗
PubMed2005

A new polymorph of 5-fluorouracil found following computational crystal structure predictions.

A new polymorph of 5-fluorouracil has been obtained following a manual polymorph screen inspired by a computational crystal structure prediction search. It corresponds to the structure that was predicted to be the global minimum in lattice energy. The difficulty of crystallizing this simple structure with a rational hydrogen-bonding motif can be rationalized from the differential solvation of the functional groups.

Antimetabolites, Antineoplastic↗
PubMed2005

Computer-aided rodent carcinogenicity prediction.

The potential of the computer program PASS (Prediction Activity Spectra for Substances) to predict rodent carcinogenicity for chemical compounds was studied. PASS predicts carcinogenicity of chemical compounds on the basis of their structural formula and of structure-activity relationship analysis of known carcinogens and non-carcinogens. The data on structures and experimental results of 2-year carcinogenicity assays for 412 chemicals from the NTP (National Toxicological Program) and 1190 chemicals from the CPDB (Carcinogenic Potency Database) were used in our study. The predictions take into consideration information about species and sex of animals. For evaluation of the predictive accuracy we used two procedures: leave-one-out cross-validation (LOO CV) and leave-20%-out cross-validation. In the last case we randomly divided the studied data set 20 times into two subsets. The data from the first subset, containing 80% of the compounds, were added to the PASS training set (which includes about 46,000 compounds with about 1500 biological activity types collected during the last 20 years to predict biological activity spectra), the second subset with 20% of the compounds was used as an evaluation set. The mean accuracy of prediction calculated by LOO CV is about 73% for NTP compounds in the 'equivocal' category of carcinogenic activity and 80% for NTP compounds in the 'evidence' category of carcinogenicity. The mean accuracy of prediction for the CPDB database is 89.9% calculated by LOO CV and 63.4% calculated by leave-20%-out cross-validation. Influence of incorporation of species and sex data on the accuracy of carcinogenicity prediction was also investigated. It was shown that the accuracy was increased only for data on male animals.

Animals↗
PubMed2006

Computational approaches for predicting protein-protein interactions: a survey.

Discovery of the protein interactions that take place within a cell can provide a starting point for understanding biological regulatory pathways. Global interaction patterns among proteins, for example, can suggest new drug targets and aid the design of new drugs by providing a clearer picture of the biological pathways in the neighborhoods of the drug targets. High-throughput experimental screens have been developed to detect protein-protein interactions, however, they show high rates of errors in terms of false positives and false negatives. Many computational approaches have been proposed to tackle the problem of protein-protein interaction prediction. They range from comparative genomics based methods to data integration based approaches. Challenging properties of protein-protein interaction data have to be addressed appropriately before a higher quality interaction map with better coverage can be achieved. This paper presents a survey of major works in computational prediction of protein-protein interactions, explaining their assumptions, main ideas, and limitations.

Humans↗
PubMed2004

A combined computational-experimental approach predicts human microRNA targets.

A new paradigm of gene expression regulation has emerged recently with the discovery of microRNAs (miRNAs). Most, if not all, miRNAs are thought to control gene expression, mostly by base pairing with miRNA-recognition elements (MREs) found in their messenger RNA (mRNA) targets. Although a large number of human miRNAs have been reported, many of their mRNA targets remain unknown. Here we used a combined bioinformatics and experimental approach to identify important rules governing miRNA-MRE recognition that allow prediction of human miRNA targets. We describe a computational program, "DIANA-microT", that identifies mRNA targets for animal miRNAs and predicts mRNA targets, bearing single MREs, for human and mouse miRNAs.

Animals↗
PubMed2005

A computational model to predict aortic wall stresses in patients with systolic arterial hypertension.

Computational cardiovascular mechanics has allowed scientists to create complex 3D models for the simulation of cardiovascular problems. Mechanical stress plays a crucial role in the function of the cardiovascular system; stress analysis is a useful tool for the understanding of vascular pathophysiology. By using the spiral CT imaging and computational structural analysis, we present a noninvasive method of wall stress analysis in the normal aorta. The aortic segment was extended from the origin of the inferior mesenteric artery to the aortic bifurcation. The length of this segment was 12 cm, while the maximum transverse diameter was 2.075+/-0.129 cm. A 3D aortic model was constructed based on the CT scan images. The aorta was assumed to have a uniform wall thickness of 1.5mm. The generated unstructured grid, which was used for the structural analysis, consisted of 14,440 hexahedral elements. The wall material was assumed to be hyperelastic, homogeneous, isotropic and nearly incompressible (Poisson ratio=0.45). According to experimental studies, the Young modulus of aortic wall was set equal to 4.66 MPa. The shear stress induced by the blood flow was neglected. A finite-element static structural analysis was performed. Three different cases were examined applying constant intraluminal systolic blood pressures of 120, 180 and 240 mmHg, respectively. The von Mises stress distribution and the displacements of the aortic wall were calculated. Peak wall stress for the normal load case of 120 mmHg was 22.5 N/cm2, while the max displacement was 0.44 mm. The case with the intraluminal pressure of 180 mmHg resulted into peak wall stress of 32 N/cm2 with max displacement 0.59 mm, while for 240 mmHg was 40.6N/cm2, max displacement 0.72 mm. The rise in blood pressure caused all stresses to increase. The pattern of stress distribution and the orientation of the stress were similar for all test cases. A quantitative evaluation of the aortic wall stresses under systolic hypertension is presented. The calculated values of peak wall stress are far lower to those of failure strength of healthy aortic wall specimens estimated by ex vivo mechanical testing (121.0 N/cm2). Our values are consistent with prior stress values predicted by experimental studies. The described methodology offers a significant advancement in incorporating biomechanical principles in the clinical assessment of hypertensive patients with normal or aneurysmatic aortas and can be applied in a patient-specific basis in both conditions in order to detect the vulnerable high stressed regions and the resultant risk of aortic dissection or rupture. We hypothesize that this could assist in deciding the timing of surgical intervention, especially in high-risk patients with abdominal aortic aneurysms.

Aorta↗
PubMed2005

Computational models for prediction of IVF/ICSI outcomes with surgically retrieved spermatozoa.

IVF/intracytoplasmic sperm injection (ICSI) using surgically retrieved spermatozoa (SRS) is a key option in the treatment of severe male infertility. It was aimed to develop a computational model for the prediction of this modality's outcome. A dataset of 113 exemplars, derived from patients who underwent IVF/ICSI with SRS, was retrospectively analysed. The dataset, containing input features maternal age, sperm retrieval technique, type of spermatozoa used, type of male factor and output intrauterine pregnancy, was randomized into a modelling ('training') set of 83 and cross-validation ('test') set of 30. neUROn++, a set of C++ programs, was used to model the dataset using linear and quadratic discriminant function analysis, logistic regression, and neural computation. A 4-hidden node neural network was found to have the highest accuracy, with a test set receiver operator characteristic (ROC) curve area of 0.783. Reverse regression of this neural network showed maternal age to be the most significant feature in predicting pregnancy (P = 0.025), followed by sperm type (P = 0.076). Type of male factor (P = 0.47) and sperm retrieval technique (P = 0.88) did not predict outcome. In summary, a neural network of clinical relevance was found to be superior in terms of IVF/ICSI outcome prediction. Future media deployment is planned.

Adult↗