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PubMed2001

Toward high-throughput genotyping: dynamic and automatic software for manipulating large-scale genotype data using fluorescently labeled dinucleotide markers.

To efficiently manipulate large amounts of genotype data generated with fluorescently labeled dinucleotide markers, we developed a Microsoft database management system, named. offers several advantages. First, it accommodates the dynamic nature of the accumulations of genotype data during the genotyping process; some data need to be confirmed or replaced by repeat lab procedures. By using, the raw genotype data can be imported easily and continuously and incorporated into the database during the genotyping process that may continue over an extended period of time in large projects. Second, almost all of the procedures are automatic, including autocomparison of the raw data read by different technicians from the same gel, autoadjustment among the allele fragment-size data from cross-runs or cross-platforms, autobinning of alleles, and autocompilation of genotype data for suitable programs to perform inheritance check in pedigrees. Third, provides functions to track electrophoresis gel files to locate gel or sample sources for any resultant genotype data, which is extremely helpful for double-checking consistency of raw and final data and for directing repeat experiments. In addition, the user-friendly graphic interface of renders processing of large amounts of data much less labor-intensive. Furthermore, has built-in mechanisms to detect some genotyping errors and to assess the quality of genotype data that then are summarized in the statistic reports automatically generated by. The can easily handle >500,000 genotype data entries, a number more than sufficient for typical whole-genome linkage studies. The modules and programs we developed for the can be extended to other database platforms, such as Microsoft SQL server, if the capability to handle still greater quantities of genotype data simultaneously is desired.

Alleles↗

PubMed1995

Cellular and humoral immune responses to recombinant antigens in sheep infected with Toxoplasma gondii.

Immune responses to recombinant fragments of the Toxoplasma gondii antigens ROP2 and GRA2 were investigated in sheep naturally and experimentally infected with T. gondii oocysts. Specific serum antibodies to C-terminal fragments were detected by ELISA. Cell-mediated responses in peripheral blood mononuclear cells were demonstrated by proliferation and interferon-gamma production following in vitro stimulation with the ROP2 fragment. This data indicates the presence of epitopes for sheep B cells in the recombinant GRA2 fragment and for both B and T cells in the ROP2 fragment.

Animals↗

PubMed1988

Low pH-induced release of diphtheria toxin A-fragment in Vero cells. Biochemical evidence for transfer to the cytosol.

When Vero cells with surface-bound 125I-labeled, nicked diphtheria toxin were exposed to pH 4.5, two polypeptides of Mr 20,000 and 25,000 became protected against externally applied Pronase E. The 20-kDa polypeptide appears to be the toxin A-fragment, whereas the 25-kDa polypeptide must be derived from the B-fragment. Permeabilization of the cells with saponin allowed efflux of the 20-kDa fragment to occur, whereas most of the 25-kDa polypeptide remained associated with the cells. A number of compounds and conditions which protect cells against diphtheria toxin prevented the protection against Pronase E. Protection of the 25-kDa polypeptide occurred even when the transmembrane proton gradient (delta pH) was dissipated by acidification of the cytosol, whereas protection and release of the A-fragment were prevented under these conditions. Electrical depolarization and ATP depletion of the cells did not inhibit protection and release of the A-fragment. The data indicate that delta pH is required for the transfer of the A-fragment to the cytosol, whereas the insertion of part of the B-fragment into the membrane occurs at low pH, even in the absence of a delta pH.

Adenosine Diphosphate Ribose↗

PubMed2002

Insights into recently fragmented vole populations from combined genetic and demographic data.

We combined demographic and genetic data to evaluate the effects of habitat fragmentation on the population structure of the California red-backed vole (Clethrionomys californicus). We analysed variation in the mitochondrial DNA (mtDNA) control region and five nuclear microsatellite loci in small samples collected from two forest fragments and an unfragmented control site in 1990-91. We intensively sampled the same forest fragments and two different control sites in 1998 and 1999. Vole abundances fluctuated greatly at sizes below 50 individuals per fragment. Fragment populations had significantly lower mtDNA allelic diversity than controls, but not nuclear heterozygosity or numbers of alleles. The use of only trapping and/or mtDNA marker data would imply that fragment populations are at least partially isolated and vulnerable to inbreeding depression. In contrast, the abundance estimates combined with microsatellite data show that small fragment populations must be linked to nearby forests by high rates of migration. These results provide evidence for the usefulness of combining genetic and demographic data to understand nonequilibrium population structure in recently fragmented habitats.

Animals↗

PubMed1997

Activated protein C cleavage of factor Va leads to dissociation of the A2 domain.

The products of cleavage of bovine factor Va by activated protein C (APC) in the presence and absence of phospholipid (25% phosphatidylserine, 75% phosphatidylcholine, PCPS) were evaluated using sedimentation velocity/equilibrium methods in the analytical ultracentrifuge and by immunoprecipitation using an antibody directed against the light chain of the factor Va molecule. The molecular weight and sedimentation coefficient of the associated heavy and light chains of factor Va, 173,000 (7.9 S) is reduced to 132,000 (7.1 S) by APC cleavage at Arg505 and Arg662. Complete cleavage of the factor Va heavy chain (with APC-PCPS) at Arg505, Arg662 and Arg306 results in a drastic change in the molecular weight observed for the product. Two products are resolved with sedimentation coefficients of 3.3 and 6.3 S with estimated molecular weights of 48,000 and 114,000, respectively. Immunoprecipitation studies showed that the products of factor Va cleavage at Arg505 and Arg662 (A1A2N.A2C.LC) are mostly noncovalently associated and consequently immunoprecipitated with an antibody directed against the light chain of the factor Va molecule. In contrast, for factor Va cleaved at Arg505, Arg662, and Arg306 the precipitated complex consisted of the A1 domain (residues 1-306) and the light chain (residues 1537-2183) of factor Va (A1.LC). The fragments corresponding to residues 307-505 (A2N) and 506-662 (A2C) are found in the supernatant. The combined mass of these two products (48,000) is similar to the estimated mass of the 3.3 S fragment estimated from sedimentation velocity/equilibrium studies; while the combined mass of the 1-306 + 1537-2183 products corresponds to 114,000, the estimated mass of the 6.3 S fragment. These data lead to the conclusion that cleavages at Arg306, Arg505, and Arg662 of the factor Va molecule resulted in the dissociation of the entire A2 domain as two noncovalently associated fragments (A2N.A2C). Enzyme kinetic and light scattering data suggest that the complete inactivation of the factor Va molecule involves not only cleavage at Arg306 but also the dissociation of the A2 domain. These data also suggest that the complete APC inactivation of the factor Va molecule is analogous to the spontaneous inactivation of factor VIIIa, which occurs via the dissociation of the A2 domain.

Animals↗

PubMed1999

The in situ spatial arrangement of the influenza A virus matrix protein M1 assessed by tritium bombardment.

Intact influenza A virions were bombarded with thermally activated tritium atoms, and the intramolecular distribution of the label in the matrix protein M1 was analyzed to determine the in situ accessibility of its tryptic fragments. These data were combined with the previously reported x-ray crystal structure of the M1 fragment 2-158 [Sha, B. & Luo, M. (1997) Nat. Struct. Biol. 4, 239-244] and the predicted topology of the C domain (159-252) to propose a model of M1 arrangement in the virus particle.

Animals↗

PubMed2005

[A study of DNA depolyploidization and depolytenization of the heterochromatized gonosomal chromatin bodies in the secondary giant trophoblast cells of the field vole Microtus rossiaemeridionalis using cytophotometry].

A study was made of the distribution of the heterochromatized gonosomal chromatin bodies (GCB) material in the course of nuclear fragmentation of secondary giant trophoblast cells resulting in polykaryocyte formation at the late stage of their differentiation. A simultaneous DNA cytophotometry in GCBs and nuclear fragments showed a progressive GCB DNA content decrease proportional to that of DNA content in nuclear fragments. DNA contents in the nuclear fragments corresponded to 2c, 4c and 8c. In most cases 1-2 GCBs were found in the nuclear fragments of different ploidy levels. Both the total DNA content in GCBs and the DNA content in separate GCBs well correlated with the ploidy levels of fragments. The data obtained demonstrate a regular, whole-genome distribution of chromosomal materials into the nuclear fragments exemplified by sex chromosome distribution in compliance with the ploidy of nuclear fragments. We discuss a possible mechanism of nuclear fragmentation that may ensure substantially a balanced genome of nuclear fragments without leading to mitotic cycle renewal in the giant trophoblast cell population.

Animals↗

PubMed2002

Copper speciation in the alpha and beta domains of recombinant human metallothionein by electrospray ionization mass spectrometry.

ESI-MS data are reported for Cu(I) binding to the metal-free and cadmium-alpha and beta domains of recombinant human metallothionein. These data provide information on the stoichiometric ratios of copper and cadmium that bind to the 11 thiolate sulfurs in the alpha fragment and the nine thiolate sulfurs in the beta fragment. The data show the effects of the existing three-dimensional structure on the formation of different Cu(I)-thiolate clusters. Charge-state spectra are reported for a range of Cu(I) binding at low and neutral pH to the isolated alpha and beta domains. There is an uneven distribution of charge states that show that changes in the three-dimensional structure take place as a function of Cu(I) loading. Metallation of the alpha domain at low pH takes place in a series of steps with the Cu7 species dominating until at higher levels of Cu(I) the clusters become unstable resulting in increased concentrations of the metal-free being detected. We interpret this behavior as being the result of the expansion of the Cu-S domain structure to accommodate digonal co-ordination for the increased Cu(I) loading. This larger structure is unstable in the mass spectrometer and demetallation takes place. Metallation of the beta domain at low pH proceeds in steps that involve initial formation of a Cu5S9 cluster, followed by the Cu6S9 at higher concentrations of Cu(I). The charge state spectra indicate a significant change in exposure of protonatable amino acids between Cu5S9 and Cu6S9 clusters, which indicates a change in peptide conformation when the Cu6S9 cluster forms. Metallation at neutral pH follows this same trend, namely, a much greater range of copper species is found during titrations of the Cd4S11-alpha fragment compared with the number of species that form when Cu(I) is added to Cd3S9-beta. The mass spectral data indicate that at neutral pH, the presence of the tetrahedral geometry of the Cd(II) facilitates formation of mixed trigonal and digonal geometries for the incoming Cu(I) so that the most prominent species in the beta fragment is Cd1Cu5S9 which transforms into Cu7S9 at higher concentrations of Cu(I), and finally to Cu9S9 at saturation, all species involving a number of Cu(I) in digonal geometries. The observation that the metallation patterns of the alpha and beta clusters follow different pathways at both low and neutral pH's, suggests that the structures in the two domains are quite different, in agreement with previous proposals

Amino Acid Sequence↗

PubMed1992

Analysis of chimerism after bone marrow transplantation using specific oligonucleotide probes.

DNA hybridization with synthetic oligonucleotide probes was used to follow 18 leukemia patients who received bone marrow transplantation from HLA-identical siblings. Five oligomers complementary to the tandem repetitive sequences of different hypervariable regions of human DNA were designed to produce simple restriction fragment length polymorphism patterns. Each probe hybridized to one or two bands in Hinf I-digested genomic DNA. Combined use of these probes enabled us to distinguish all sibling pairs. DNA analysis early post-transplant (15 days) detected donor-specific fragments in 14 of 18 subjects; two patients had a combination of recipient and donor fragments. Later post-transplant, (102-15 days), one of these two showed only recipient-specific fragments, and the other donor-specific fragments. These data are in accord with other markers of engraftment including cytogenetics and red blood cell phenotyping.

Adolescent↗

PubMed1989

Linkage studies of HLA and insulin gene restriction fragment length polymorphisms in families with IDDM.

Linkage analysis of HLA DR antigen as well as DR and DQ restriction fragment length polymorphism (RFLP) data using the LIPED computer program and various three-allele disease locus models showed very close linkage to an insulin-dependent diabetes mellitus (IDDM)-susceptibility locus. RFLP data alone were equal or superior to conventional HLA antigen typing in the linkage analysis. Insulin gene restriction fragment data were analyzed for evidence of either a susceptibility locus linked to the insulin gene or an effect of alleles at the insulin locus on the HLA-linked susceptibility gene. No evidence was found of any effect of the insulin gene, and it is suggested that alternative explanations of the reported population associations between the insulin gene and IDDM should be considered.

Computer Simulation↗

PubMed1991

Molecular structure of a functional rat gene for manganese-containing superoxide dismutase.

The manganese-containing superoxide dismutase (MnSOD) constitutes one of the major cellular defense mechanisms against the toxic effects of superoxide radical. The development of tolerance in adult rats to lethal exposure of O2 (100%) after pre-exposing them to a sublethal concentration of O2 (85%) was found to be closely associated with the increased activity of this enzyme in the lungs. Further experiments have shown that the transcriptional rate of the gene coding for MnSOD in rat lungs is increased at day 3 of 85% O2 exposure. To elucidate the nature of this transcriptional activation during hyperoxic insults, we chose to first understand the structure of the rat MnSOD gene. Three overlapping rat genomic fragments were isolated, and the DNA sequence containing the whole MnSOD gene was completely determined. The rat MnSOD gene contains at least five exons and is located in one piece of 16.4-kb EcoRI genomic DNA fragment. However, Southern blot analysis of total rat genomic DNA probed with MnSOD cDNA revealed an additional hybridizing 8.6-kb EcoRI genomic fragment besides the 16.4-kb one. To clarify the origin of this unexpected hybridizing genomic fragment, three unique genomic sequences derived from the promoter, intron 2, and the 3' untranslated region of the genomic clones were used to rehybridize the same Southern blot filter and were found to only hybridize to the 16.4-kb but not 8.5-kb EcoRI genomic fragment. These data suggest: (1) two MnSOD genes are present per haploid rat genome, and (2) all three cloned genomic fragments are derived from the MnSOD gene, which is located in the 16.4-kb EcoRI genomic fragment.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

PubMed1993

Processing of the beta-amyloid precursor protein carrying the familial, Dutch-type, and a novel recombinant C-terminal mutation.

Mutations within the beta-amyloid precursor protein (beta-APP) gene that cosegregate with early onset familial Alzheimer's disease (FAD) and hereditary cerebral hemorrhage with amyloidosis of the Dutch-type (HCHWA-D) have been reported. The effects of these mutations on the products of both the non-amyloidogenic and potentially amyloidogenic processing pathways of the beta-APP protein were examined in stably transfected cells. Processing of these mutants appeared to be the same as wild-type. These results contrasted sharply to those observed with a mutation near the amino terminus of the beta-protein domain of beta-APP. This mutation resulted in a two-fold decrease of a potentially amyloidogenic 11 kDa peptide fragment. The data suggest that the FAD and HCHWA-D mutations have no effect on the formation of potentially amyloidogenic fragments in this cell system, possibly implicating an alternative mechanism for their effects.

Alzheimer Disease↗

PubMedDate not supplied

Cleaving proteins for the immune system.

Proteasomes are enzymes in eukaryotic cells which cut proteins marked for degradation into fragments. In mammals some of these fragments are used by the immune system to detect proteins of foreign, e.g. viral, origin. Hence reproducing, predicting and possibly understanding the cleaving patterns of proteasomes is an interesting theoretical problem and its solution would be beneficial for vaccine design. The equations connecting cut probabilities, fragment frequencies and so-called cut strengths are derived. A simple model for the time course of protein digestion is used to explain the problem of fragment competition and the possible deviation of in vitro fragment frequencies from those that can be expected in vivo. A family of neural network proteasome models for the reproduction and prediction of cleavage patterns is described in detail together with the webtool PAProC. The first model is based on the experimentally observed cleavage pattern, an intermediate model on the distinction between weak and strong cuts, and the most elaborate model uses quantitative data, i.e., fragment frequencies.

Amino Acid Sequence↗

PubMed2004

Normative data on the familiarity and difficulty of 196 Spanish word fragments.

In this article, normative data on the familiarity and difficulty of 196 single-solution Spanish word fragments are presented. The database includes the following indices: difficulty, familiarity, frequency, number of meanings, number of letters given in the fragment, first and/or last letters given, and ratio of letters to blanks. A factor analysis was performed on difficulty, and two factors were obtained. Frequency, familiarity, and number of meanings loaded highly on the first factor, which we consider to measure lexical processes, whereas number of letters in the fragment, first and/or last letters given, and ratio of letters to blanks loaded highly on the second factor, which we judge to be determined by perceptual information. Regression analyses using factor scores as predictors showed that both factors accounted for a significant part of the completion probability scores. The full set of these norms may be downloaded from the Psychonomic Society Web archive at www.psychonomic.org/archive/.

Adolescent↗

PubMed1988

An interactive computer program for the analysis of HLA class II restriction fragment patterns.

There is considerable current interest in the application of Southern blotting and hybridization, with locus-specific HLA class II probes, to HLA typing. The work of several laboratories has shown that, under suitable conditions, restriction fragment patterns that correlate with DR and DQ serology and with DP cellular reactivities can be obtained from homozygous cell lines. Although the identification of class II specificities from restriction fragment patterns is relatively straightforward in homozygotes, the increased complexity of the patterns obtained from heterozygotes makes the interpretation considerably more difficult; this difficulty is compounded by even slight variation between and within gels. We have developed an interactive computer program that allows HLA-DR and DQ typing by the visual matching of restriction fragment pattern data with standard data derived from a panel of well-characterized homozygous cell lines. The program also uses a simple algorithm (after Southern) to estimate the fragment sizes in the unknown track. The screen display can be printed out to give a convenient record of the match; a numerical measure is also given of the goodness of fit of the new data.

Algorithms↗

PubMed2006

Calculation of stopping power ratios for carbon ion dosimetry.

Water-to-air stopping power ratio calculations for the ionization chamber dosimetry of clinical carbon ion beams with initial energies from 50 to 450 MeV/u have been performed using the Monte Carlo technique. To simulate the transport of a particle in water the computer code SHIELD-HIT v2 was used, which is a newly developed version where substantial modifications were implemented on its predecessor SHIELD-HIT v1 (Gudowska et al 2004 Phys. Med. Biol. 49 1933-58). The code was completely rewritten replacing formerly used single precision variables with double precision variables. The lowest particle transport specific energy was decreased from 1 MeV/u down to 10 keV/u by modifying the Bethe-Bloch formula, thus widening its range for medical dosimetry applications. In addition, the code includes optionally MSTAR and ICRU-73 stopping power data. The fragmentation model was verified and its parameters were also adjusted. The present code version shows excellent agreement with experimental data. It has been used to compute the physical quantities needed for the calculation of stopping power ratios, s(water,air), of carbon beams. Compared with the recommended constant value given in the IAEA Code of Practice, the differences found in the present investigations varied between 0.5% and 1% at the plateau region, respectively for 400 MeV/u and 50 MeV/u beams, and up to 2.3% in the vicinity of the Bragg peak for 50 MeV/u.

Carbon Radioisotopes↗

PubMed1996

[Phenotypic expression of the Ca2+-dependence trait in recombinant cells of Yersinia pestis (Lehmann, Neumann)].

A conceptual model of the Yersinia pestis Ca(2+)-dependence mechanism is proposed. The model is based on data from analyses of peculiarities of recombinant cells of this plague-causing agent carrying the cloned first Bg/II fragment of the Ca(2+)-dependence plasmid (pCaD) and a combination of this fragment and other plasmid pCaD fragments. The data obtained also allowed a revision of the role of the lcr GVH locus of pCaD in this phenomenon.

Calcium↗

PubMed2006

A dynamic programming algorithm for binning microbial community profiles.

MOTIVATION: A number of community profiling approaches have been widely used to study the microbial community composition and its variations in environmental ecology. Automated Ribosomal Intergenic Spacer Analysis (ARISA) is one such technique. ARISA has been used to study microbial communities using 16S-23S rRNA intergenic spacer length heterogeneity at different times and places. Owing to errors in sampling, random mutations in PCR amplification, and probably mostly variations in readings from the equipment used to analyze fragment sizes, the data read directly from the fragment analyzer should not be used for down stream statistical analysis. No optimal data preprocessing methods are available. A commonly used approach is to bin the reading lengths of the 16S-23S intergenic spacer. We have developed a dynamic programming algorithm based binning method for ARISA data analysis which minimizes the overall differences between replicates from the same sampling location and time. RESULTS: In a test example from an ocean time series sampling program, data preprocessing identified several outliers which upon re-examination were found to be because of systematic errors. Clustering analysis of the ARISA from different times based on the dynamic programming algorithm binned data revealed important features of the biodiversity of the microbial communities.

Algorithms↗