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J Wojcik

Publications and source records attributed to J Wojcik.

At least 19 recordsLinked to original sources
PubMed2001

The pyrimidine ring-opened derivative of 1,N6-ethenoadenine is excised from DNA by the Escherichia coli Fpg and Nth proteins.

It was previously shown that 1,N(6)-ethenoadenine (epsilonA) in DNA rearranges into a pyrimidine ring-opened derivative of 20-fold higher mutagenic potency in Escherichia coli (AB1157 lacDeltaU169) than the parental epsilonA (Basu, A. K., Wood, M. L., Niedernhofer, L. J., Ramos, L. A., and Essigmann, J. M. (1993) Biochemistry 32, 12793-12801). We have found that at pH 7.0, the stability of the N-glycosidic bond in epsilondA is 20-fold lower than in dA. In alkaline conditions, but also at neutrality, epsilondA depurinates or converts into products: epsilondA --> B --> C --> D. Compound B is a product of water molecule addition to the C(2)-N(3) bond, which is in equilibrium with a product of N(1)-C(2) bond rupture in epsilondA. Compound C is a deformylated derivative of ring-opened compound B, which further depurinates yielding compound D. Ethenoadenine degradation products are not recognized by human N-alkylpurine-DNA glycosylase, which repairs epsilonA. Product B is excised from oligodeoxynucleotides by E. coli formamidopyrimidine-DNA glycosylase (Fpg) and endonuclease III (Nth). Repair by the Fpg protein is as efficient as that of 7,8-dihydro-8-oxoguanine when the excised base is paired with dT and dC but is less favorable when paired with dG and dA. Ethenoadenine rearrangement products are formed in oligodeoxynucleotides also at neutral pH at the rate of about 2-3% per week at 37 degrees C, and therefore they may contribute to epsilonA mutations.

Adenosine↗
PubMed2001

The protein-protein interaction map of Helicobacter pylori.

With the availability of complete DNA sequences for many prokaryotic and eukaryotic genomes, and soon for the human genome itself, it is important to develop reliable proteome-wide approaches for a better understanding of protein function. As elementary constituents of cellular protein complexes and pathways, protein-protein interactions are key determinants of protein function. Here we have built a large-scale protein-protein interaction map of the human gastric pathogen Helicobacter pylori. We have used a high-throughput strategy of the yeast two-hybrid assay to screen 261 H. pylori proteins against a highly complex library of genome-encoded polypeptides. Over 1,200 interactions were identified between H. pylori proteins, connecting 46.6% of the proteome. The determination of a reliability score for every single protein-protein interaction and the identification of the actual interacting domains permitted the assignment of unannotated proteins to biological pathways.

Amino Acid Sequence↗
PubMed2001

Protein--protein interaction maps: a lead towards cellular functions.

The availability of complete genome sequences now permits the development of tools for functional biology on a proteomic scale. Several experimental approaches or in silico algorithms aim at clustering proteins into networks with biological significance. Among those, the yeast two-hybrid system is the technology of choice to detect protein-protein interactions. Recently, optimized versions were applied at a genomic scale, leading to databases on the web. However, as with any other 'genetic' assay, yeast two-hybrid assays are prone to false positives and false negatives. Here we discuss these various technologies, their general limitations and the potential advances they make possible, especially when in combination with other functional genomics or bioinformatics analyses.

Animals↗
PubMed2001

Protein-protein interaction map inference using interacting domain profile pairs.

UNLABELLED: A number of predictive methods have been designed to predict protein interaction from sequence or expression data. On the experimental front, however, high-throughput proteomics technologies are starting to yield large volumes of protein-protein interaction data. High-quality experimental protein interaction maps constitute the natural dataset upon which to build interaction predictions. Thus the motivation to develop the first interaction-based protein interaction map prediction algorithm. A technique to predict protein-protein interaction maps across organisms is introduced, the 'interaction-domain pair profile' method. The method uses a high-quality protein interaction map with interaction domain information as input to predict an interaction map in another organism. It combines sequence similarity searches with clustering based on interaction patterns and interaction domain information. We apply this approach to the prediction of an interaction map of Escherichia coli from the recently published interaction map of the human gastric pathogen Helicobacter pylori. Results are compared with predictions of a second inference method based only on full-length protein sequence similarity - the "naive" method. The domain-based method is shown to i) eliminate a significant amount of false-positives of the naive method that are the consequences of multi-domain proteins; ii) increase the sensitivity compared to the naive method by identifying new potential interactions. AVAILABILITY: Contact the authors.

Algorithms↗
PubMed2000

Proteomic databases and software on the web.

In the wake of sequencing projects, protein function analysis is evolving fast, from the careful design of assays that address specific questions to 'large-scale' proteomics technologies that yield proteome-wide maps of protein expression or interaction. As these new technologies depend heavily on information storage, representation and analysis, existing databases and software tools are being adapted, while new resources are emerging. This paper describes the proteomics databases and software available through the World-Wide Web, focusing on their present use and applicability. As the resource situation is highly transitory, trends and probable evolutions are discussed whenever applicable.

Computational Biology↗
PubMed1999

New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification.

A bank of 13,563 loops from three to eight amino acid residues long, representing motifs between two consecutive regular secondary structures, has been derived from protein structures presenting less than 95 % sequence identity. Statistical analyses of occurrences of conformations and residues revealed length-dependent over-representations of particular amino acids (glycine, proline, asparagine, serine, and aspartate) and conformations (alphaL, epsilon, betaPregions of the Ramachandran plot). A position-dependent distribution of these occurrences was observed for N and C-terminal residues, which are correlated to the nature of the flanking regions. Loops of the same length were clustered into statistically meaningful families on the basis of their backbone structures when placed in a common reference frame, independent of the flanks. These clusters present significantly different distributions of sequence, conformations, and endpoint residue Calphadistances. On the basis of the sequence-structure correlation of this clustering, an automatic loop modeling algorithm was developed. Based on the knowledge of its sequence and of its flank backbone structures each query loop is assigned to a family and target loop supports are selected in this family. The support backbones of these target loops are then adjusted on flanking structures by partial exploration of the conformational space. Loop closure is performed by energy minimization for each support and the final model is chosen among connected supports based upon energy criteria. The quality of the prediction is evaluated by the root-mean-square deviation (rmsd) between the final model and the native loops when the whole bank is re-attributed on itself with a Jackknife test. This average rmsd ranges from 1.1 A for three-residue loops to 3.8 A for eight-residue loops. A few poorly predicted loops are inescapable, considering the high level of diversity in loops and the lack of environment data. To overcome such modeling problems, a statistical reliability score was assigned for each prediction. This score is correlated to the quality of the prediction, in terms of rmsd, and thus improves the selection accuracy of the model. The algorithm efficiency was compared to CASP3 target loop predictions. Moreover, when tested on a test loop bank, this algorithm was shown to be robust when the loops are not precisely delimited, therefore proving to be a useful tool in practice for protein modeling.

Models, Molecular↗
PubMed1999

Treatment of nonpsychotic relatives of patients with schizophrenia: four case studies.

BACKGROUND: Substantial evidence now shows that the genetic vulnerability to schizophrenia can be manifested clinically in first-degree relatives of people with schizophrenia, even without the full manifestations of the disorder. One pattern of problems observed involves the combination of negative symptoms and neuropsychological deficits. We have investigated whether a low dose of a novel antipsychotic medication, risperidone, could attenuate these clinical problems in non-psychotic, first-degree relatives, and report here findings from our first 4 cases. METHODS: Twelve adults who were first-degree relatives of patients with schizophrenia were evaluated for the presence of negative symptoms and neuropsychological deficits (in attention and working memory, long-term verbal memory and executive functions). Four subjects who met our predetermined criteria, and who did not demonstrate medical contraindications, were enrolled in a 6-week trial of risperidone. Clinical and medical measures were assessed before, during and after treatment. Doses of risperidone started at 0.25 mg and were increased to 1.0-2.0 mg/day. RESULTS: These subjects showed substantial reductions in negative symptoms, and one subject showed modest reductions. All four subjects showed substantial improvements on some tests of attention and working memory. Side effects of risperidone were temporary and mainly mild. CONCLUSIONS: These initial findings support two conclusions. First, clinical deficits in non-psychotic first-degree relatives of people with schizophrenia are identifiable, and to a significant extent, reversible. Second, risperidone may eventually serve as an effective treatment for people whose lives are impaired by similar or related problems.

Adult↗
PubMed1999

Sequence analysis identifies a ras-associating (RA)-like domain in the N-termini of band 4.1/JEF domains and in the Grb7/10/14 adapter family.

RA (RalGEF/AF6 or Ras-associating) domains are found in a wide variety of proteins, several of which are known to be Ras-GTP effectors. The three dimensional structure of the RA domain has been experimentally determined in Ral-guanine nucleotide exchange factor (Ral-GEF) and found to be similar to that of the Ras-binding domain of c-Raf1, in spite of a very low level of sequence identity. Using various approaches of sequence analysis, including automatic procedures such as BLAST2, profilescan, and hidden Markov models (HMM), as well as the bidimensional hydrophobic cluster analysis (HCA), here we found that a region with a similar structure is also present at the N-terminus of the band 4.1/JEF domain of KIAA0316 (a human cDNA open reading frame) and H09G03.2 (a related protein sequence predicted from C. elegans genome cloning), as well as in a particular class of adapter proteins including Grb7, Grb10, Grb14, MIG-10, and PRP48. Although the structural conservation of this motif does not necessarily imply a conservation of its ability to bind small GTPases of the Ras superfamily, several proteins with a band 4.1/JEF domain and adapters of the Grb7 group have close functional relationships with such small GTPases. Thus, our finding raises the intriguing possibility of a direct interaction between members of these two groups of proteins and Ras-like GTP-binding proteins.

Adaptor Proteins, Signal Transducing↗
PubMed1998

Response to interferon therapy: influence of human leucocyte antigen alleles in patients with chronic hepatitis C.

The response to interferon (IFN) therapy in patients with chronic hepatitis C is characterized by normalization of the serum alanine aminotransferase (ALT) activity during treatment, but relapse within 6 months of cessation of therapy is common. Viral characteristics, such as the genotype and viral load, may influence the patient response to IFN. The aim of this study was to examine host factors, namely the genetically determined human leucocyte antigen (HLA) class II alleles, in patients with chronic hepatitis C, and their relationship to the response to IFN therapy. Seventy white patients with chronic hepatitis C, treated with IFN-alpha for 6 months, were enrolled in the study. Serum ALT was measured at the end of treatment to assess short-term response and again 6 months post-treatment to assess sustained response. Sequence-specific primers were used in the polymerase chain reaction (PCR) to amplify genomic DNA isolated from peripheral mononuclear cells. HLA class II alleles were determined by analysis of the amplicon by gel electrophoresis and hybridization of sequence-specific oligonucleotide probes. At the end of treatment, 25 of the 70 patients (36%) had a normal ALT. By 6 months post-treatment, only six patients (9%) had a sustained normalization of ALT. The frequency of the allele DRB1*0404 was significantly higher in patients with a sustained response as compared to those lacking such a response (25.0% vs 2.3%, with a Bonferonni-corrected P-value of 0.019). There was no difference in the frequency of other class II alleles at the DRB1 and DQB1 loci in responders as compared with non-responders. Therefore, we conclude that the maintenance of a response to IFN in chronic hepatitis C may be, in part, determined by genetic factors in the host.

Alanine Transaminase↗
PubMed1998

Four contiguous amino acid substitutions, identified in patients with Laron syndrome, differently affect the binding affinity and intracellular trafficking of the growth hormone receptor.

We have analyzed the GH receptor (GHR) gene in four individuals with Laron syndrome, and a missense mutation was identified for each patient in the extracellular domain of the GHR (D152H, I153T, Q154P, and V155G). The D152H mutation was previously reported. We have reproduced the three novel mutations in the GHR complementary DNA and analyzed their consequences in human 293 transfected cells. In cells expressing the I153T and V155G mutants, binding of [125I]human GH at the cell surface was very low, whereas binding to total membrane fractions was much less affected, suggesting impaired cell surface expression. Binding assays with cells expressing the Q154P mutant revealed severe defects both at the cell surface and in total particulate membrane fractions. Immunofluorescence experiments confirmed that cell surface expression of the three mutants was altered, and colocalization studies suggested that most of the mutant receptors are retained in the endoplasmic reticulum. Endoglycosidase H resistance tests also indicated that the majority of I153T and V155G GHRs are trapped in the endoplasmic reticulum. Thus, mutations on contiguous amino acids of the GHR result in various defects. The I153T, Q154P, and V155G mutations mainly affect intracellular trafficking and binding affinity of the receptor, whereas the D152H mutation affects receptor expression, dimerization, and signaling.

Adult↗
PubMed1998

The D152H mutation found in growth hormone insensitivity syndrome impairs expression and function of human growth hormone receptor but is silent in rat receptor.

In two patients with growth hormone (GH) insensitivity syndrome (Laron syndrome), in whom the GH receptor is able to bind the hormone, the D152H mutation was identified, and lack of dimerization was proposed to explain GH resistance in these patients. To examine further the consequences of the substitution of conserved aspartate 152 on the function of the GH receptor (GHR), we reproduced the mutation in vitro on the full length GH receptor cDNA from man and rat. Effects of the mutation on expression and activity of the GHR were analyzed in 293 cells transfected with wild-type and mutant GHR cDNAs. Mutant human receptor protein was expressed at a lower level than wild-type receptor and its activity was reduced: GH-dependent signal transducer and activator of transcription 5 (Stat5)-mediated transactivation of a reporter gene was lower in 293 cells transfected with mutant GHR cDNA than in transfected cells expressing a comparable level of wild-type GHR. The membrane-bound form of the mutant and of the wild-type human GHR were able to homodimerize, as suggested by the size of the complexes detected in cross-linking experiments with 125I-human (h) GH, and also by the activity in the functional test. With the soluble GHR resulting from proteolysis of the wild-type membrane form, no dimeric complexes could be detected. However, when a soluble receptor lacking the transmembrane and cytoplasmic domains of the receptor was expressed, wild-type and not mutant GH binding protein (GHBP) was able to form dimers in the presence of hGH. The amino acid substitution has no effect on either expression or function of the rat receptor. Structural modeling of D152H soluble human and rat GHR (GHBP) supports the species-specific functional consequences of the mutation. Evaluation of the functional importance of the mutation strongly suggests that impairment in expression and activity of the mutant receptor, rather than complete lack of dimerization, explains the GH resistance of the patients.

Animals↗
PubMed1995

Thrombolysis with recombinant unglycosylated single-chain urokinase-type plasminogen activator (saruplase) in acute myocardial infarction: influence of heparin on early patency rate (LIMITS study). Liquemin in Myocardial Infarction During Thrombolysis With Saruplase.

OBJECTIVES: The Liquemin in Myocardial Infarction During Thrombolysis With Saruplase (LIMITS) study was instituted to evaluate and characterize the effect of a prethrombolytic heparin bolus (5,000 IU) on the efficacy and safety of saruplase in patients with acute myocardial infarction. BACKGROUND: Heparin has been used after thrombolytic therapy for acute myocardial infarction to prevent reocclusion of the infarct-related artery. METHODS: The study was designed as a randomized, parallel-group, double-blind, multicenter trial. Patients were treated within 6 h of onset of symptoms with either a bolus of 5,000 IU of heparin (Liquemin) (n = 56, HSH group) or placebo (n = 62, PSH group) before thrombolytic treatment with saruplase given as a 20-mg bolus followed by an infusion of 60 mg over 60 min. Thirty minutes after completion of thrombolysis, an intravenous heparin infusion was administered for 5 days. Before coronary angiography was performed at 6 to 12 h after start of lysis, an additional bolus of 5,000 IU heparin was given to all patients. End points studied were patency of the infarct-related artery, changes in the hemostatic system and bleeding complications. RESULTS: In the HSH group (heparin-saruplase-heparin), 78.6% of patients had an open infarct-related vessel (Thrombolysis in Myocardial Infarction [TIMI] flow grade 2 or 3) compared with 56.5% in the PSH group (placebo-saruplase-heparin) (intention-to-treat analysis, p = 0.01). No significant difference was observed between the two groups with regard to changes in fibrinogen and fibrin/fibrinogen degradation products. A total of eight bleeding complications (14.3%) were observed in the HSH group and five (8.1%) in the PSH group; no cerebrovascular event occurred, and no allergic reaction was reported. A total of 12 patients died during the hospital stay, 3 in the HSH group (5.4%) and 9 in the PSH group (14.5%). CONCLUSIONS: In acute myocardial infarction, the administration of a heparin bolus before thrombolytic therapy with saruplase is associated with a significantly higher patency at angiography 6 to 12 h after the start of thrombolysis without any appreciable increase in risk of bleeding.

Adult↗
PubMed1995

Expression of feline immunodeficiency virus (FIV) gag gene in vaccinia virus vector.

The selected part of gag gene (nucleotide sequences at position 618 to 1724) coding for P24 and P15 proteins of feline immunodeficiency virus (FIV) was expressed in vaccinia virus vector under control of 7.5 kDa vaccinia virus transtriptional signal (p 7.5 vaccinia virus early/late promoter). The vaccinia virus recombinant (denoted VV-G(1)) was generated by homologous recombination following CV-1 cells transfection with a newly prepared vaccinia virus insertion vector -- pWKr75.

Animals↗
PubMed1994

Risky PHOs' winning bet.

Integrated delivery systems are bearing much of the risk under capitation, and some would like to accept even more. Becoming an insurer, however, brings questions of regulation and access to patients. Many PHOs will find the move too big a gamble.

Capitation Fee↗
PubMed1993

Temperature elevation in focused Gaussian ultrasonic beams at various insonation times.

Transient solution of the thermal conductivity equation for the three-dimensional case of the Gaussian ultrasonic focused beam was derived and applied for cases relevant to medical ultrasonography. Quantitative results for the case of a homogeneous medium with constant values of thermal coefficients and constant absorption as well as for the two-layer tissue model used in obstetrics were presented for various diagnostic probes used in ultrasonography. The possible effects of perfusion and nonlinear propagation were neglected. The results obtained are in agreement with results of other authors when considering the steady-state and the infinitely short insonation time. The computations show the influence of the insonation time on the temperature elevation, thus making it possible to introduce its value as a factor in limiting the possible harmful effects in ultrasonography. This has been shown in diagrams presenting the temperature distribution along the beam axis of 6 different diagnostic probes for various insonation times and demonstrating the corresponding temperature decrease when limiting the insonation time to 5 and 1 min. For instance, the highest temperature elevation (for probe number 1, see Table 1) decreases 2.6 and 5 times with respect to the steady-state temperature when the insonation time equals 5 and 1 min, respectively.

Absorption↗
PubMed1992

Frequency of complications of cardiopulmonary resuscitation after thrombolysis during acute myocardial infarction.

Prolonged external cardiac massage is often regarded as a contraindication for thrombolytic therapy because of the risk of fatal hemorrhage. The influence of cardiopulmonary resuscitation on complications of thrombolytic bleeding was assessed analyzing data of all patients with myocardial infarction admitted to our clinic during the 10-year period between 1978 and 1987. From the total of 2,147 patients with acute myocardial infarction, 590 received thrombolytic therapy (intracoronary in 229, intravenous in 400). Of these, 43 patients underwent prolonged cardiopulmonary resuscitation and received thrombolysis within a time interval of less than 24 hours. In 21 patients, resuscitation was performed within a short period of time (5 minutes to 20 hours) after thrombolysis (10 intracoronary, 10 intravenous, 1 intravenous + intracoronary) had been initiated; 9 of these patients survived (43%). In the other 22 patients, thrombolytic therapy was initiated during ongoing resuscitation (n = 6: intravenous in 5, intravenous + intracoronary in 1) or in the early phase (10 to 120 minutes) after successful resuscitation (n = 16: intracoronary in 10, intravenous in 4, intravenous + intracoronary in 2). From this group, 14 patients survived (in-hospital mortality 36%). The mean duration of cardiopulmonary resuscitation was 36 +/- 32 minutes (range 4 to 120). Autopsy studies were performed in 16 of 20 decreased patients. Bleeding complications occurred in 8 of 43 patients. No case of bleeding was directly related to cardiocompression despite the often traumatic procedure with rib fractures verified in 17 patients.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed1992

Pharmacokinetics and fibrin specificity of alteplase during accelerated infusions in acute myocardial infarction.

Pharmacokinetics and fibrin specificity of alteplase (recombinant tissue-type plasminogen activator) were determined in 10 patients with acute myocardial infarction undergoing an accelerated infusion regimen during the alteplase/anistreplase patency study (TAPS). Fifteen milligrams of alteplase was administered as an intravenous bolus injection, followed by infusions of 50 mg over 30 min and 35 mg over a further 60 min. Mean steady state plasma concentrations of alteplase during the initial 30 min were 3.2 +/- 0.84 micrograms/ml, measured immunochemically, and 2.1 +/- 0.23 micrograms/ml, measured using a functional activity assay. These values were 45% and 51% higher, respectively, than those during the standard infusion schedule (p less than 0.01). However, the predominant plasma half-life determined by model fitting based on either assay (3.3 to 3.5 min) was unaltered compared with the standard regimen. Maximal concentrations of fibrin and fibrinogen degradation products were 5.1 +/- 2.2 and 1.9 +/- 1.1 micrograms/ml, respectively. Plasminogen decreased to 70% and alpha 2-antiplasmin to 35% of values before infusion. The results indicate that 1) improved coronary patency rates during "front-loaded" infusions can be rationalized in terms of higher plasma concentrations of both free and immunoreactive alteplase, 2) kinetic variables are comparable with those of other dosing strategies, and 3) fibrin specificity is not diminished relative to that of the standard infusion regimen.

Aged↗