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At least 163 records · Page 9Linked to original sources
PubMed1995

Determination of cyclic nucleotide-dependent protein kinase substrate specificity by the use of peptide libraries on cellulose paper.

An iterative approach to the a priori determination of the substrate specificity of cAMP- and cGMP-dependent protein kinases (PKA and PKG) by the use of peptide libraries on cellulose paper is described. The starting point of the investigation was an octamer library with the general structure Ac-XXX12XXX, where X represents mixtures of all 20 natural amino acids and 1 and 2 represent individual amino acid residues. The library thus contained all possible 2.56 x 10(10) octamers, divided into 400 sublibraries with defined amino acids 1 and 2 each consisting of 6.4 x 10(7) sequences. After phosphorylation with the kinases in the presence of [gamma-32P]ATP, the sublibrarys Ac-XXXRRXXX and Ac-XXXRKXXX were identified as the best substrates for PKA and PKG, respectively. The second-generation libraries had the structures Ac-XXXRR12X and Ac-XXXRK12X for PKA and PKG and resulted in the most active sequence pools Ac-XXXRRASX and Ac-XXXRKKSX. After delineation of every position in the octameric sequence and extension of the investigation to decameric peptides, the best sequences, Ac-KRAERKASIY and Ac-TQKARKKSNA, were obtained for PKA and PKG, respectively. Promising octameric and decameric peptides were assembled 5 or 10 times each and assayed in order to determine the experimental scatter inherent in the approach. The kinetic data of several octameric and decameric sequences were determined in solution and compared to data for known substrates. The recognition motif of PKA was confirmed by this approach, and a novel substrate sequence for PKG was identified.(ABSTRACT TRUNCATED AT 250 WORDS)

Adenosine Triphosphate↗
PubMed2026

Employing Metagenomics Capture targeted next-generation sequencing for the etiological diagnosis of bloodstream infections.

BACKGROUND: Bloodstream infections (BSIs) represent a significant public health concern. Metagenomic Capture targeted next-generation sequencing technology, as a newly emerging method for pathogen detection, has been applied in the etiological diagnosis of various infectious diseases and demonstrates good diagnostic efficacy. However, there is relatively limited research on the diagnostic value of this technology for the etiological diagnosis of BSIs. METHODS: A comprehensive retrospective analysis was performed on patients suspected of having BSIs who were admitted to the Affiliated Guangdong Second Provincial General Hospital of Jinan University in 2024. These patients underwent both blood culture analysis and Metagenomic Capture targeted next-generation sequencing technology for diagnostic testing, and a detailed comparison of the results was conducted. RESULTS: It was found that the Metagenomic Capture-targeted next-generation sequencing method has a shorter time to result [1.33 (1.18 - 1.69) vs 2.73 (1.89 - 3.84) days, p&#xa0;<&#xa0;0.001], more pathogenic microbial species detected, higher positive detection rate and higher sensitivity than blood culture. CONCLUSIONS: Metagenomic Capture targeted next-generation sequencing technology is a promising tool for pathogen identification in BSIs, offering substantial methodological advantages in terms of turnaround time, detection breadth, and sensitivity. These diagnostic performance characteristics support its potential utility in clinical microbiology practice.

Humans↗
PubMed1989

Computer-controlled sequencing of peptides by tandem mass spectrometry.

A fully automated computer-controlled system was used to generate series of different linked scans at constant B2E and constant neutral loss in the second field-free region. This system has been shown to be suitable for deriving the amino acid sequence of oligopeptides.

Amino Acid Sequence↗
PubMed1995

Detection of hepatitis C virus antibodies and specific hepatitis C virus ribonucleic acid sequences in cord bloods from a heterogeneous prenatal population.

OBJECTIVE: Our aim was to quantify the prevalence of at-risk pregnancies for maternal-fetal hepatitis C virus transmission in a heterogeneous prenatal population by detection of both hepatitis C virus-specific antibody and hepatitis C virus ribonucleic acid sequences in cord bloods from their deliveries. STUDY DESIGN: An anonymous serosurvey of 1432 consecutive umbilical cord blood samples were analyzed for hepatitis C virus antibodies with a second-generation enzyme immunoassay with all hepatitis C virus antibody-positive samples batched and analyzed for both human immunodeficiency virus antibodies and hepatitis C virus ribonucleic acid sequences by polymerase chain reaction. RESULTS: Forty-seven of the samples (3.2%) were positive for hepatitis C virus antibodies; seropositivity rates differed significantly by socioeconomic status but not by race. Significantly more of the antibody-positive women underwent cesarean section for delivery (31.9% vs 21.9%, p = 0.03). Three (6.4%) hepatitis C virus antibody-positive samples were also human immunodeficiency virus-antibody positive, whereas nine (19.1%) were hepatitis C virus ribonucleic acid positive. CONCLUSION: As many as 19% of hepatitis C virus antibody-positive women in this study also had hepatitis C virus ribonucleic acid isolated from their delivery cord blood samples, which may indicate an increased risk of vertical hepatitis C virus transmission in those pregnancies. Hepatitis C virus-specific antibody and ribonucleic acid detection may also be markers for other pregnancy complications that result in higher rates of cesarean section for these women.

Base Sequence↗
PubMed1984

Repeats of base oligomers as the primordial coding sequences of the primeval earth and their vestiges in modern genes.

Three outstanding properties uniquely qualify repeats of base oligomers as the primordial coding sequences of all polypeptide chains. First, when compared with randomly generated base sequences in general, they are more likely to have long open reading frames. Second, periodical polypeptide chains specified by such repeats are more likely to assume either alpha-helical or beta-sheet secondary structures than are polypeptide chains of random sequence. Third, provided that the number of bases in the oligomeric unit is not a multiple of 3, these internally repetitious coding sequences are impervious to randomly sustained base substitutions, deletions, and insertions. This is because the recurring periodicity of their polypeptide chains is given by three consecutive copies of the oligomeric unit translated in three different reading frames. Accordingly, when one reading frame is open, the other two are automatically open as well, all three being capable of coding for polypeptide chains of identical periodicity. Under this circumstance, a frame shift due to the deletion or insertion of a number of bases that is not a multiple of 3 fails to alter the down-stream amino acid sequence, and even a base change causing premature chain-termination can silence only one of the three potential coding units. Newly arisen coding sequences in modern organisms are oligomeric repeats, and most of the older genes retain various vestiges of their original internal repetitions. Some of the genes (e.g., oncogenes) have even inherited the property of being impervious to randomly sustained base changes.

Animals↗
PubMed1996

A protein class database organized with ProSite protein groups and PIR superfamilies.

A protein class (ProClass) database is developed as a "value-added" "second-generation" database organized according to family relationships. The database collects non-redundant protein sequence entries from SwissProt and PIR databases, and classifies them in families defined collectively by the ProSite protein groups and PIR superfamilies. The major objectives of the database are to maximize family information retrieval, to provide speedy family identification, and to help organizing existing protein sequence databases. The database has two sub-databases: PCFam (ProClass Family) to define protein families and provide links to ProSite patterns and PIR superfamilies, and PCSeq (ProClass Sequence) to describe sequence entries and provide links to PCFam, SwissProt, PIR, and ProSite databases. The current ProClass release has a total of 85,165 sequence entries, about half of which are classified in 3072 ProClass families; it also contains 10,431 newly established SwissProt-PIR links. The database can help reveal domain structures of related families, define new ProSite and PIR families, and provide family assignments for unclassified sequence entries. New ProSite and PIR family members are readily identified via database cross-reference, including 9437 SwissProt entries and 8522 PIR entries. False negative family members missed by both ProSite and PIR are detected using a neural network family identification system. The newly identified superfamily memberships are being incorporated into the current PIR database releases in a collaborative effort with the PIR. The ProClass database is accessible through anonymous FTP and on-line search on the World Wide Web.

Amino Acid Sequence↗
PubMed1993

Gene transfer and cardiovascular disorders.

Within the past four years, basic recombinant techniques (such as molecular cloning, sequencing, site-directed mutagenesis, PCR, and transfection) have been combined to yield a "second generation" of recombinant DNA technology with experimental potential which could barely have been envisioned only a decade ago. This review will focus upon the genesis and cardiovascular application of two recent developments in gene transfer technology: gene targeting by homologous recombination and direct in vivo gene transfer. Gene targeting evolved from transgenic mouse technology but is distinguished by its ability to precisely disrupt or "knock-out" specific genes in the murine genome. This not only provides decisive answers to functional questions, but also produces accurate models of human genetic disorders. In vivo gene transfer provides for the direct introduction of genetic information into living tissues. In vivo gene transfer not only facilitates basic research by providing a simple and direct way to analyze gene structure and function in intact animals, but may also find direct clinical application in the treatment of genetic and acquired disorders such as familial hypercholesterolemia and restenosis.

Animals↗
PubMed1997

Expression of an F1/V fusion protein in attenuated Salmonella typhimurium and protection of mice against plague.

A novel approach to making fusions of F1 and V antigens, which may be incorporated into a live recombinant vaccine for plague, was developed. The nucleotide sequences encoding Yersinia pestis V antigen (lcrV) and the mature form of F1 antigen (caf1) were amplified by PCR with primers which included tails. At the 3' end of caf1 and the 5' end of lcrV, the tails encoded one of three six- or eight-amino acid linkers or their complementary sequences. The DNA overlap in each linker region was used to prime a second PCR to generate three F1/V fusions, which were cloned into pUC18. The resulting plasmids expressed fusion proteins consisting of F1 and V antigens, separated by the linkers Gly-Ser-Ile-Glu-Gly-Arg, Ser-Ala-Pro-Gly-Thr-Pro or Ser-Ala-Pro-Gly-Thr-Pro-Ser-Arg. As shown by Western blotting of bacterial cell lysates with anti-V and anti-F1 sera, the level of expression and degree of degradation of the three fusion proteins was similar. To investigate the immunogenicity of F1/V, one of the plasmids, placFV6 which encoded the Gly-Ser-Ile-Glu-Gly-Arg linker, was electroporated into the attenuated Salmonella typhimurium strain SL3261 (aroA). Mice receiving two intravenous doses of 5 x 10(6) cfu SL3261/placFV6 developed serum anti-V and anti-F1 IgG titres, with similar IgG1:IgG2a isotype ratios, and T cell responses specific for V and F1 antigens. Six weeks after vaccination, mice were challenged subcutaneously with 7.4 x 10(2) or 7.4 x 10(4) LD50s of Y. pestis strain GB, and a significant degree of protection was demonstrated. These results demonstrate the potential of co-expressing Y. pestis antigens as fusion proteins to develop a live recombinant vaccine against plague.

Amino Acid Sequence↗
PubMed1997

Imaging of shifted stimulated echoes and multiple spin echoes.

It is shown that a repetitive pulse sequence consisting of two 90 degrees pulses and gradients in a 1:2 ratio around the second 90 degrees pulse generates interscan shifted stimulated echoes (SSTEs) and intrascan multiple spin echoes (MSEs). Separation of these two types of signals is accomplished using specific gradient crusher schemes. The intensity of the SSTEs is an order of magnitude larger than that of the MSEs and determines the signal contrast if both effects are selected simultaneously. The SSTE sequence generates improved contrast between gray and white matter, even at high field, which is explained in terms of increased inverse T1-weighting for the interscan echo. The MSE image has low signal to noise and no detectable contrast. The effect of interscan diffusion weighting is also discussed.

Animals↗
PubMed1986

Localization and DNA sequence analysis of the C gene of bacteriophage Mu, the positive regulator of Mu late transcription.

The C gene of bacteriophage Mu, required for transcription of the phage late genes, was localized by construction and analysis of a series of deleted derivatives of pKN50, a plasmid containing a 9.4 kb Mu DNA fragment which complements Mu C amber mutant phages for growth. One such deleted derivative, pWM10, containing only 0.5 kb of Mu DNA, complements C amber phages and transactivates the mom gene, one of the Mu late genes dependent on C for activation. The DNA sequence of the 0.5 kb fragment predicts a single long open reading frame coding for a 140 amino acid protein. Sequence analysis of DNA containing a C amber mutation located the base change to the second codon of this reading frame. Generation of a frameshift mutation by filling in a BglII site spanning codon 114 of this reading frame resulted in the loss of C complementation and transactivation activity. These results indicate that this open reading frame encodes the Mu C gene product. Comparison of the predicted amino acid sequence of the C protein with those of other transcriptional regulatory proteins revealed some similarity to a region highly conserved among bacterial sigma factors.

Amino Acid Sequence↗
PubMed1992

Enzyme immunoassays for anti-hepatitis C virus antibodies improved specificity and analytical sensitivity by combination of three different recombinant viral proteins in second generation tests.

The detection of hepatitis C virus infection currently relies on a "virology without a virus" approach. So far, only viral nucleic acid has been isolated and sequenced by the methods of genetic engineering. The resulting viral sequence was then used to "design" proteins for diagnostic use as antigens in enzyme immunoassays (EIA). A first-generation EIA (EIA I), which uses a non-structural hepatitis C virus protein as antigen, detected 26 (0.6%) reactive sera out of a total of 4350 blood donors. An inhibition test using recombinant hepatitis C virus antigen, and EIAs using other, both synthetic and recombinant hepatitis C virus peptides were used as a specificity enhancing measure and as confirmatory tests, respectively. Only 7 of these reactives (0.16%, inhibition test) and 5 (0.11%, peptide EIA) were confirmed positive. Of the 26 initially reactive donor sera, 5 sera (0.11%) reacted positive in a second-generation anti-hepatitis C virus antibody EIA (EIA II), which uses two different recombinant non-structural hepatitis C virus proteins and one recombinant core protein. Seventeen (77%) of 22 haemophiliacs reacted positive in EIA I, and 19 (86%) did so in EIA II. There were no false positives in this cohort. Twenty-eight (19%) out of 148 liver disease patients showed a positive reaction in EIA I, and 31 (21%) were reactive in EIA II. Based on the results of the peptide enzyme immunoassay, 1 serum of this group was false positive in EIA I, while none of the sera of this group were false positive in EIA II.(ABSTRACT TRUNCATED AT 250 WORDS)

Antigens, Viral↗
PubMed1988

Short donor site sequences inserted within the intron of beta-globin pre-mRNA serve for splicing in vitro.

We constructed SP6-human beta-globin derivative plasmids that included possible donor site (5' splice site) sequences at a specified position within the first intron. The runoff transcripts from these templates truncated in the second exon were examined for splicing in a nuclear extract from HeLa cells. In addition to the products from the authentic donor site, a corresponding set of novel products from the inserted, alternative donor site was generated. Thus, a short sequence inserted within an intron can be an active donor site signal in the presence of an authentic donor site. The active donor site sequences included a 9-nucleotide consensus sequence, 14- or 16-nucleotide sequences at the human beta-globin first or second donor, and those at simian virus 40 large T antigen or small t antigen donor. These included 3 to 8 nucleotides of an exon and 6 to 8 nucleotides of an intron. The activity of the inserted donor site relative to that of the authentic donor site depended on the donor sequence inserted. The relative activity also strongly depended on the concentrations of both KCl (40 to 100 mM) and MgCl2 (1.6 to 6.4 mM). At the higher KCl concentrations tested, all the inserted, or proximate, donor sites were more efficiently used. Under several conditions, some inserted donor sites were more active than was the authentic donor site. Our system provides an in vitro assay for donor site activity of a sequence to be tested.

Amino Acid Sequence↗
PubMed1987

The dual effector system for exocytosis in mast cells: obligatory requirement for both Ca2+ and GTP.

The secretory process is a coordinated cellular response, initiated by occupation of surface receptors and comprising an ordered sequence of biochemical steps subject to multiple controls. Conceptually we can divide the sequence into two main sections comprising early, receptor-mediated events leading to generation of intracellular second messengers, and later events leading to membrane fusion and exocytosis. With the discovery that occupation of Ca2+ mobilising receptors leads to activation of polyphosphoinositide phosphodiesterase (PPI-pde) through the mediation of a G-protein (Gp), all the early events can be ascribed to the plasma membrane. Investigation of the exocytotic stage of secretion has been simplified by the use of permeabilised cells in which the composition of the cytosol can be precisely controlled. We have used streptolysin-O, a bacterial cytolysin which generates protein-sized pores in the plasma membrane, to investigate the exocytotic mechanism of rat mast cells. We find that in addition to the activation of PPI-dpe, GTP also acts in concert with Ca2+ at, or close to, the exocytotic site. Exocytosis can occur after substantial depletion of cytosol lactate dehydrogenase and 3-phosphoglycerate kinase indicating that soluble cytosol proteins are unlikely to play any role. There is no absolute requirement for ATP or phosphorylating nucleotide in exocytosis though when present the effective affinities of the two obligatory effectors (i.e. Ca2+ and GTP) are substantially enhanced.

Animals↗
PubMed1995

Frequent patient-to-patient transmission of hepatitis C virus in a haematology ward.

Blood transfusion is a well-documented route of transmission of hepatitis C virus (HCV). However, a persisting high frequency of HCV infections was recorded in our haematology ward even after screening of blood donors had been introduced. We investigated the viral strains in 37 patients with haematological malignant diseases who had developed hepatitis C when treated in the ward during 1990-93. 17 of the patients acquired hepatitis C despite being transfused only with blood components screened by second-generation anti-HCV tests. The viral strains were characterised by PCR genotyping and nucleotide sequencing of the hypervariable region of the E2 gene. Five clusters of closely related or identical viruses were found involving 2, 3, 4, 6, and 15 patients, respectively. Blood components could be ruled out as the common source of infection because no donor had given blood to all patients sharing a specific strain, and even donors whose blood had been given to several patients were negative for HCV RNA. All patients in each cluster had been treated in the ward during overlapping periods. These findings suggest that despite strict hygienic control, HCV transmission occurred between patients treated in the same hospital setting, as has previously been reported in a smaller group of haemodialysis patients.

Adult↗
PubMed1996

An epitope chimeric antigen for the hepatitis C virus serological screening test.

The epitope chimeric antigen, CepCM, composed of the 9 selected major epitope regions (two in NS3, two each in the NS4 of two genotypes, two each in the core of two genotype, and one in the core in hepatitis C virus (HCV) polypeptide), was expressed as a fusion protein of the trpE peptide in E. coli. An ELISA test using this antigen produced the same judgements with most of the panel sera as a second generation HCV screening kit. Though discrepancies were found in twelve samples (5% of the samples), further analysis revealed that eleven samples were indeterminate sera as judged by an immunoblot test. The reactivity found in several seroconversion series sera suggested that CepCM has superior reactivity to HCV infected sera than some second generation kits. These data indicated that an epitope chimeric antigen with a man-made sequence will be a excellent tool for a diagnostic test kit.

Antigens, Viral↗
PubMed1994

Response of monkey glabrous skin mechanoreceptors to random-noise sequences: I. Temporal response characteristics.

The response of slowly adapting (SA, Merkel cell), rapidly adapting (RA, Meissner), and Pacinian corpuscle (PC) mechanoreceptors in monkey glabrous skin were recorded while being activated with a vibrotactile indenting stimulus. For one set of experiments, the stimulator was driven by an 800-point (400-msec) pseudorandom-noise (PRN) sequence, repeated 40 times. For a second set of experiments, a non-repeating-noise (NRN) sequence was used. SA impulse patterns generated with the PRN sequence were highly regular and similar for all afferents tested. RA and PC response patterns were more varied, but exhibited basic intraclass similarities. SA and RA PRN stimulus impulse patterns were often nearly indistinguishable at low to medium discharge rates. At higher discharge rates, RA and SA discharge patterns differed, primarily because of the unambiguous suprathreshold velocity sensitivity and shorter recovery periods of RA afferents. PC impulse patterns were substantially different from SA and RA patterns, being clearly dependent on the stimulus velocity at all stimulus intensities. Input-output correlation analysis, coupled with PRN stimulus-response analysis, provided a basis for hypothesizing the basic dynamic encoder function of each type of mechanoreceptor.

Afferent Pathways↗
PubMed1992

Second generation anti-MUC1 peptide monoclonal antibodies.

Second generation antibodies to mammary mucins were produced by immunizing mice with a peptide with a sequence deduced from that of the MUC1 complementary DNA sequence (PAHGVTSAPDTRPAPGSTAP). Four monoclonal antibodies (BCP7-10) were produced which gave different reactions. BCP8 was similar in tissue reactivity (by immunoperoxidase staining) to anti-breast cancer or anti-human milk fat globule membranes (HMFG) antibodies and reacted strongly with most breast cancers and a proportion of other adenocarcinomas, whether formalin fixed or fresh, and reacted less strongly with some normal tissues. The three other antibodies (BCP7, BCP9, BCP10) reacted only with fresh tissues or a single cell line (LS174T of colon cancer origin) and gave variable weak reactions. Like many anti-mucin antibodies BCP8 reacted with HMFG, but more strongly with deglycosylated HMFG; analysis with peptides by enzyme-linked immunosorbent assay indicated reactivity with an epitope contained in the amino acid motif PDTR and using the pepscan method, the minimum epitope was DTR. MAbs BCP7, BCP9, and BCP10 did not react with HMFG; substantial reactions were obtained with deglycosylated HMFG for BCP7 and weaker reactions with BCP9 and BCP10. The finding that BCP7 reacted with breast cancer tissues and deglycosylated HMFG suggested that the epitope recognized by BCP7 was masked in native form and exposed in cancer, indicating that BCP7 could be a useful agent for analyzing differences between normal and cancer mucins. The amino acid epitopes for these antibodies were VTSA (BCP7), GSTAP (BCP9), and RPAP (BCP10). For BCP8, amino acid substitution analysis of SAPDTR indicated that substitutions were poorly tolerated (except Q for T and L/Y for R), contrasting with the substitution analysis of anti-mucin antibody reactions where virtually any amino acid can be substituted for T, indicating that in the native state T (threonine) may be O-glycosylated. The use of synthetic peptides to produce antibodies similar to those produced using crude mucins or tumor extracts represents a major advance in the production of antitumor reagents.

Amino Acid Sequence↗