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PubMed1976

Isolation and characterization of tryptic fragments of the adenosine triphosphatase of sarcoplasmic reticulum.

Exposure of sarcoplasmic reticulum to trypsin in the presence of 1 M sucrose results in degradation of the Mr = 102,000 ATPase enzyme to two fragments of Mr = 55,000 and 45,000 with subsequent appearance of fragments of Mr = 30,000 and 20,000. These fragments were purified by column chromatography in sodium dodecyl sulfate. Antibodies were raised against the ATPase and the Mr = 55,000, 45,000, and 20,000 fragments. There was no antigenic cross-reactivity between the Mr = 55,000 and 45,000 fragments, indicating that they were derived from a single linear cleavage of the larger enzyme. There was antigenic cross-reactivity between the Mr = 20,000 and 55,000 fragments, indicating an origin of the Mr = 20,000 fragment in the Mr = 55,000 fragment. None of the antibodies inhibited (Ca2+ + Mg2+)-dependent ATPase or Ca2+ transport. The Mr = 20,000 fragment and the Mr = 55,000 fragment were active in Ca2+ ionophore assays. The active site of ATP hydrolysis was labeled with [gamma-32P]ATP and the site of ATP binding was labeled with tritiated N-ethylmaleimide. In both cases radioactivity was found in the intact ATPase and in the Mr = 55,000 and 30,000 fragments, indicating that the Mr = 30,000 fragment was also derived from the Mr = 55,000 fragment. Amino acid composition data showed that the Mr = 45,000 fragment contained about 60% nonpolar and 40% polar amino acids, while the Mr = 55,000 fragment and the Mr = 20,0000 fragment contained about equal amounts of polar and nonpolar amino acids. Studies of the reaction of various antibodies at the external surface of sarcoplasmic reticulum vesicles showed that the ATPase was exposed, whereas calsequestrin and the high affinity Ca2+-binding protein were not. The use of antibodies against the various fragments indicated that the Mr = 55,000 fragment was in large part exposed, whereas the Mr = 20,000 and the 45,000 fragments were only poorly exposed. It is probable that the site of ATP hydrolysis in the Mr = 55,000 fragment is external, whereas the ionophore site is only partially exposed and the Mr = 45,000 fragment is largely buried within the membrane.

Adenosine Triphosphatases↗

PubMed1991

Recognition of peptides that are immunopathogenic but cryptic. Mechanisms that allow lymphocytes sensitized against cryptic peptides to initiate pathogenic autoimmune processes.

Interphotoreceptor retinoid binding protein (IRBP) is a glycoprotein that localizes in the retina and induces inflammatory changes in this tissue in immunized animals. Certain IRBP-derived peptide determinants are also immunopathogenic, and we have previously shown that these determinants could be either immunodominant or cryptic. Lymphocytes sensitized against the cryptic peptides do not recognize whole IRBP in vitro, and yet these lymphocytes must recognize the protein in vivo to initiate the autoimmune pathogenic process. We have examined here two hypothetical explanations for this dissociation: 1) It is possible that when IRBP is processed in vitro, immunodominant peptide determinants compete with the cryptic ones and inhibit their interaction with the MHC molecules on the APC. This explanation was ruled out here by the finding that the immunodominant peptide 1179-1191 ("W10") did not inhibit the response to a cryptic one, 1158-1180 ("R4"), when added at equivalent and even moderately higher concentrations. 2) The second hypothesis proposes that the cryptic antigenic sites are not generated from IRBP by the APC in vitro, whereas enzymes in the retina digest the protein to yield fragments that generate these antigenic sites upon processing by the APC. In line with this hypothesis, we have found that cleavage of IRBP by certain endoproteinases (Asp-N, Glu-C, or V-8) produced molecules that were recognized in culture by lymphocytes sensitized to the immunopathogenic but cryptic peptide R4. This study, therefore, describes a putative Ag processing mechanism that results in IRBP recognition and, consequently, the initiation of an autoimmune process by lymphocytes sensitized against a cryptic peptide. Furthermore, experiments with R4 and other cryptic peptides have shown that cleavage fragments of up to 38 residues in length can be presented by APC, to stimulate lymphocytes sensitized against these peptides. No responses were stimulated, however, by fragments of 75 or more residues. The data thus provide new insights into the processing and presentation of cryptic peptide determinants by APC.

Amino Acid Sequence↗

PubMedDate not supplied

[Fibrin fragment beta 15-118. Inhibitory and complex-forming properties].

Peptide beta 15-118 isolated from desAABB-NDSK preserves fibrin polymerization active site "B", inhibits polymerization process at 12 degrees C, eliminates the inhibitory properties of plasmin D-D-fragment but does not influence inhibitory properties of a D-monomer fragment. Complex formation between peptide beta 15-118 and both D- and D-D fragments was electrophoretically demonstrated. Peptide beta 15-118 forms more stable complex with the D-D fragment which does not dissociate in the medium of polymerizing fibrin as the complex of the peptide with monomer D fragment does. Gel filtration data confirm dimerization of D-monomer fragments after their complexing with beta 15-118. This phenomenon suggests that mutual affinity of D-domains in fibrin increases after loci interactions of the "B"-"b" type.

Antifibrinolytic Agents↗

PubMed1976

Structure of the heavy chain from strain 13 guinea pig immunoglobulin G1: isolation of cyanogen bromide fragments.

Guinea pig serum contains two isotypes of immunoglobulin G: IgG1 and IgG2. These immunoglobulins are antigentically distinct from each other and they mediate different biologic processes in the same guinea pig, although they share the ability to bind the same antigen. An attempt was made to study the primary structure of the gamma1 heavy chain from IgG1 in comparison with the largely known primary structure of the gamma-heavy chain from IgG2, with the aim of demarcating the structural differences between these molecules. IgG1 was isolated from the serum of immune strain 13 guinea pigs. Both IgG1 and the gamma1 chain were digested with CNBr. Nine fragments were isolated from both digests by gel filtration procedures before and after reductive cleavage of disulfide bonds. These fragments appear to account for the entire approximately 444 residues in the gamma1 chain. Amino acid composition data of CNBr fragments suggest that at least the amino terminal approximately 182 residues of the gamma1 and gamma2 chains are very similar. Two of the fragments which have been isolated have amino acid compositions suggesting their derivation from the "hinge" region and carboxyl terminus of the gamma1 chain.

Amino Acids↗

PubMed1989

Toward a physical map of the Xq28 region in man: linking color vision, G6PD, and coagulation factor VIII genes to an X-Y homology region.

We are using pulsed-field gel electrophoresis (PFGE) to establish a physical map of the human Xq28 region. We have identified a new probe 35.239 (DXYS64), localized in Xq28 by somatic hybrid mapping and belonging to a region of greater than 99% homology between the X and the Y chromosomes. PFGE data show that probes 35.239 and the polymorphic locus DXS115 (probe 767) map within a common 300-kb BssHII fragment. Both probes, in addition, hybridize to 575-kb BssHII and 590-kb ClaI fragments that contain the gene coding for coagulation factor VIII (F8C). The order F8C-DXS115-DXYS64 could be determined. Our results also provide evidence for linkage between the red/green color vision locus (RCP,GCP) and probes MD13 and T1.7 (GdX, DXS254) within a 750-kb ClaI fragment. Although the latter two probes are located within 50 kb of the 3' end of the G6PD gene, a G6PD cDNA probe did not hybridize to this fragment. G6PD, on the other hand, could be linked to F8C on a 290-kb BssHII fragment. All these data allow us to propose the order (RCP,GCP)-MD13-GdX-G6PD-F8C-DXS115-DXYS 64. We also linked probes St14 (DXS52), MN12 (DXS33), and DX13 (DXS15) to a member of a small family of X-linked dispersed sequences (DNF22S3) within a 575-kb BssHII fragment. The preliminary physical map presented here should be useful for further fine mapping of disease genes in the Xq28 region and should be helpful in orientating efforts toward the cloning of sequences close to the fragile X syndrome.

Animals↗

PubMed1994

NUCFRG2: a semiempirical nuclear fragmentation model.

The semiempirical abrasion/ablation model has been successful in generating a large nuclear data base for use in the study of high charge and energy (HZE) ion beams, radiation physics and galactic cosmic ray shielding. The cross sections generated agree with the measured HZE fragmentation data to the degree that different experimental groups agree among themselves. Several improvements in the model have been made including a Coulomb trajectory correction, an improved treatment of nuclear attenuation factors, an improved second order correction to the spectator fragment excitation spectrum, a pre-equilibrium emission process, and competitive equilibrium emission of additional hydrogen and helium isotope fragments.

Carbon↗

PubMed1996

The fragmentation of 510 MeV/nucleon iron-56 in polyethylene. II. Comparisons between data and a model.

The results of a Monte Carlo model for calculating fragment fluences and LET spectra are compared to data taken with 600 MeV/nucleon iron ions incident on an accelerator beamline configured for irradiation of biological samples, with no target and with 2, 5 and 8 cm of polyethylene. The model uses a multi-generation nuclear fragmentation code, coupled with a formulation of ionization energy loss based on the Bethe-Bloch equation. In the region where the data are reliable and the experimental acceptance is well understood, many of the features of the experimental spectra are well replicated by the model. To obtain good agreement with the experimental data, the model must allow for at least two generations of fragment production in the target.

Algorithms↗

PubMed1999

Evaluation of the facioscapulohumeral muscular dystrophy (FSHD1) phenotype in correlation to the concurrence of 4q35 and 10q26 fragments.

Probe p13E-11 (locus D4F104S1) detects two highly homologous polymorphic loci on chromosomes 4q35 and 10q26. Previous reports in the literature have described a correlation of shortened 4q35-specific fragments and facioscapulohumeral muscular dystrophy (FSHD1). We have identified 30 FSHDI families (46 patients) carrying one short 4q35 and one short 10q26 fragment. The clinical data of these patients were compared with those of 47 families (131 patients) showing a single short 4q35 fragment, in order to evaluate a potentially modifying influence of shortened 10q26 fragments on the phenotype. According to our results, the polymorphic locus on 10q26 does not modify the FSHDI phenotype. The normal population (14%) and our FSHDI population (13%) did not significantly differ in the overall frequency of short polymorphic 10q26 fragments. The specificity of the p13E-11/EcoRI-BlnI test for FSHD1 was 100%.

Chromosomes, Human, Pair 10↗

PubMed1983

Domain characteristics of the cyanogen bromide fragment 121-316 of thermolysin.

The molecule of thermolysin was shown by X-ray crystallography to be composed of two structural domains of equal size comprising residues 1-157 and 158-316. In order to explore the possibility that these domains correspond to globular fragments able to refold autonomously, we have investigated the conformational and stability properties of fragment 121-316, which was obtained by limited chemical cleavage of thermolysin with cyanogen bromide. As judged by far-ultraviolet circular dichroism measurements, in aqueous solution under neutral conditions the fragment maintains a relative amount of helical structure which is comparable to that exhibited by the corresponding region in native thermolysin. The secondary structure attained by the fragment appears remarkably stable to the denaturing action of heat. By measuring the temperature dependence of the dichroic signal at 220 nm a Tm near 74 degrees was obtained. Immunodiffusion analyses indicated that the fragment recognizes and precipitates antibodies raised in rabbits using native thermolysin as immunogen. The overall conformational and immunochemical data indicate that fragment 121-316 of thermolysin is able to refold into a stable structure of native-like characteristics independently of the rest of the molecule. The results of this study complement those previously reported for fragment 206-316 (Vita, C., Fontana, A., Seeman, J.R. & Chaiken, I.M. (1979) Biochemistry 18, 3023-3031).

Amino Acids↗

PubMed1993

The 47-kD fragment of talin is a substrate for protein kinase P.

This laboratory has been characterizing protein serine/threonine kinase reactions of hematopoietic tissues, whose most distinguishing characteristics in vitro are stimulation with vesicular phosphatidyl glycerol, and the ability to function using Mn2+ as the sole divalent cation. The major protein substrates are a 73-kD protein and a protein migrating near ovalbumin on sodium dodecyl sulfate polyacrylamide gel electrophoresis. The 47-kD protein was partially purified from cells harvested by leukapheresis from a patient with acute myelogenous leukemia, using ammonium sulfate precipitation and ion exchange chromatography. This partially purified ion-exchange fraction contained an endogenous kinase activity with characteristics similar to those we previously described of protein kinase P (protein kinase, phospholipid-stimulable: PK-P), but not typical of any form of protein kinase C (PK-C). With longer phosphorylation, the 47-kD band showed increasingly lower mobility demonstrable both by Coomassie blue staining and autoradiography, suggesting both that it was multiply phosphorylated, and that the excisable band was pure. The protein was thus eluted from preparative gel slices and digested with endoproteinase lys C. Sequence data from the fragments identified the protein as the 47-kD calpain fragment of talin, a protein found in focal adhesion plaques and some cell-cell contacts. PK-C phosphorylated the 47-kD protein, as has been reported previously, and phosphopeptide mapping disclosed a similar pattern of phosphorylation using either PK-C or the endogenous activity. The 47-kD protein labeled with the endogenous kinase contained predominantly phosphoserine, with some phosphothreonine and a trace of phosphotyrosine. Intact, purified talin was also phosphorylated by PK-P in a phospholipid-stimulable manner, but at 1/20 the rate of the 47-kD fragment.

Amino Acid Sequence↗

PubMedDate not supplied

Measurement of apoptotic fragments in growing hair follicles following gamma-ray irradiation in mice.

The usefulness of apoptotic fragments assay for investigating radiation response of hair follicles was examined. Frequency was defined as the ratio of the total number of apoptotic fragments to the number of hair follicles per section examined. The curve of dose-effect relationship for the data of apoptotic fragments was obtained by fitting the linear-quadratic model y= a+bD+cD2. When plotting on a linear scale against radiation dose, the line of best fit was y= 0.549 +/- 1.775) + 3.578 +/- 1.236)D + (-0.124 +/- 0.139)D2. The dose-response curves were linear-quadratic and a significant relationship was found between the frequency of apoptotic fragments and dose. The morphological findings of the irradiated groups were typical apoptotic fragments in the matrix region of hair follicles, but the spontaneous occurrence of apoptotic fragments was not observed. Since the apoptotic fragments was not observed. Since the apoptotic fragment assay is simple and reproducible in the whole body irradiation range of 0.5 to 8 Gy, it may be a good tool for evaluating the dose response of low dose radiation in vivo and provide a potentially valuable biological dosimeter for dose distribution determinations following accidental exposure.

Animals↗

PubMed1994

Identification of a partition region carried by the plasmid QpH1 of Coxiella burnetii.

Coxiella burnetii is an intracellular bacterial pathogen which causes Q fever in humans and other animals. Most of the isolates found carry plasmids which share considerable homology. Unfortunately all of these plasmids remain cryptic. Initial attempts to look for secreted or membrane proteins encoded by these plasmids using TnphoA mutagenesis revealed an open reading frame on the EcoRI-fragment C of the plasmid QpH1. Upstream DNA sequencing of the TnphoA insertions revealed a deduced peptide sequence with homology to the SopA protein which is encoded by the F plasmid in Escherichia coli. Maxicell analysis showed that fragment C encoded two proteins: one was 43.5 kDa in size and designated QsopA, and a second was 38 kDa in size. These proteins are similar in molecular weight to the SopA and SopB proteins, which are essential components of the partition mechanism of the F plasmid. The region appears to be conserved in plasmids QpRS, QpDV, and QpDG, but is absent in a plasmidless isolate in which plasmid sequences have integrated into the chromosomal DNA. Complementation studies demonstrated that fragment C has a plasmid partitioning function and can restore maintenance stability of the partition-defective mini-F plasmid. These data suggest that fragment C carries the plasmid partition region of the plasmid QpH1.

Amino Acid Sequence↗

PubMed2002

Human papillomavirus and blastocyst apoptosis.

PURPOSE: The effect of human papillomavirus (HPV) DNA from the E6-E7 region on the integrity of DNA in blastocyst stage embryonic cells was studied. The study design paralleled the event whereby HPV DNA from the infecting virus would target host cell DNA. The objectives were (a) to determine if the DNA of blastocysts were disrupted by the presence of HPV DNA and (b) to determine if the intensity of DNA damage was associated with the type of HPV. METHODS: This study involved superovulating female mice, mating, collecting one-cell embryos, and culturing to the expanded blastocyst stage. The blastocysts were infected with PCR-synthesized DNA fragments from either HPV type 16, 18, 31, or 33. The blastocyst DNA were analyzed by comet assay after 24 h of incubation. The fluorescent images were digitized and the pixel intensity of each blastocyst was measured. RESULTS: Only the DNA of HPV type 16 was associated with significant DNA fragmentation in comparison with the other HPV types. There was no relationship between HPV DNA fragment size and the intensity of DNA fragmentation. CONCLUSIONS: The data suggested that one mode of action of HPV type 16 was to initiate apoptosis of embryonic cells through DNA fragmentation. The effect of HPV 16 occurred rapidly within 24 h. The intensity of DNA damage was not linked to the specific type of HPV. However, the results do not rule out the other HPV types affecting embryos under conditions different from this study.

Animals↗

PubMed1995

Pharmacokinetics of 111In-labelled monoclonal antibody ZCE-025 and fragments in tumour-bearing mice.

Radiolabelled anti-tumour antibodies, their fragments and derivatives hold promise for imaging and therapeutics in oncology. A better understanding of the pharmacokinetics of these entities is therefore important for clinical applications and management. In the present study, the in vivo behaviour of 111Indium-labelled monoclonal anti-CEA antibody ZCE-025 and its F(ab')2 and Fab' fragments and a Fab' derivative are compared in the nude mouse-human tumour model. The object of the derivative was to improve the tumour uptake of the fragment yet reduce its high renal uptake while continuing to achieve desirable kinetics in the normal tissues. Uptake of the derivative in the tumour was comparable to that of the intact antibody and exceeded that of the underivatized fragments. Moreover, uptake in non-target tissues was lower with the derivative than with the intact entity. The renal uptake of the derivative was dramatically lower than for the fragments. The modelling data strongly suggest that the derivatives will be advantageous for clinical use compared with the underivatized whole antibodies or their fragments.

Animals↗

PubMed2006

Assessment of linkage disequilibrium in potato genome with single nucleotide polymorphism markers.

The extent of linkage disequilibrium (LD) is an important factor in designing association mapping experiments. Unlike other plant species that have been analyzed so far for the extent of LD, cultivated potato (Solanum tuberosum L.), an outcrossing species, is a highly heterozygous autotetraploid. The favored genotypes of modern cultivars are maintained by vegetative propagation through tubers. As a first step in the LD analysis, we surveyed both coding and noncoding regions of 66 DNA fragments from 47 accessions for single nucleotide polymorphism (SNP). In the process, we combined information from the potato SNP database with experimental SNP detection. The total length of all analyzed fragments was >25 kb, and the number of screened sequence bases reached almost 1.4 million. Average nucleotide polymorphism (=11.5x10(-3)) and diversity (pi=14.6x10(-3)) was high compared to the other plant species. The overall Tajima's D value (0.5) was not significant, but indicates a deficit of low-frequency alleles relative to expectation. To eliminate the possibility that an elevated D value occurs due to population subdivision, we assessed the population structure with probabilistic statistics. The analysis did not reveal any significant subdivision, indicating a relatively homogenous population structure. However, the analysis of individual fragments revealed the presence of subgroups in the fragment closely linked to the R1 resistance gene. Data pooled from all fragments show relatively fast decay of LD in the short range (r2=0.208 at 1 kb) but slow decay afterward (r2=0.137 at approximately 70 kb). The estimate from our data indicates that LD in potato declines below 0.10 at a distance of approximately 10 cM. We speculate that two conflicting factors play a vital role in shaping LD in potato: the outcrossing mating type and the very limited number of meiotic generations.

Alleles↗

PubMed1983

Characterization of protease-resistant fragments of laminin mediating attachment and spreading of rat hepatocytes.

In attempts to identify cell binding domains in the basement membrane protein laminin (Mr = 900,000), responsible for the substrate attachment mediating activity of the protein, proteolytic fragments were isolated and compared with respect to their biological activity. The fragments analyzed were generated by digestion of the protein with elastase or pepsin and included the previously described fragments 1 to 4 and three additional fragments, 5, 6, and 7 with molecular weights of 30,000 to 50,000. Fragments 1, 5, and 6 promoted substrate attachment of rat hepatocytes. Fragment 5, and to a lesser extent also fragment 6, but not fragment 1, induced spreading of the cells. Other fragments including the heparin-binding domain were inactive. Structural and immunological analyses indicated that fragment 1 is distinctly different from the other cell-binding fragments, whereas fragment 5 and 6 are similar but not identical. Furthermore, the active fragments were localized to different regions of the three short arms of the cross-shaped laminin molecule. Thus, the data suggest that fragments 1, 5, and 6 represent three separate domains with cell binding capacity. Attachment of hepatocytes to the fragments but not to intact laminin could be inhibited by specific antibodies indicating that the intact protein may contain an additional cell-binding site.

Amino Acids↗

PubMed1988

Porcine thyroid peroxidase: relationship between the native enzyme and an active, highly purified tryptic fragment.

We previously described the preparation of highly purified porcine thyroid peroxidase by a procedure that involved initial solubilization of the enzyme with trypsin plus detergent. Recently, the complete amino acid sequence of porcine thyroid peroxidase (TPO) was determined by cDNA cloning, and it became of interest to compare the structure of the purified trypsin-solubilized enzyme with that of the native enzyme. For this purpose we employed antibodies to the purified enzyme and to two synthetic peptides representing defined regions of the protein. We also obtained N-terminal amino acid sequence data on TPO fragments separated by gel electrophoresis. Trypsin cleavage sites in the purified enzyme were observed after arg residues 109 and 561, and also at two undetermined sites close to the putative membrane spanning region at the carboxyl end. Major fragments of approximately 60, 32, and 29 kilodaltons were observed when the purified enzyme was subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis under reducing conditions. This observation is explained by assuming that the cleavage site after arg residue 561 occurred within a disulfide loop. The Mr of the trypsin-solubilized enzyme is approximately 88,000 compared to approximately 106,000 for the native enzyme. The difference can be accounted for by the loss of approximately 90 residues from the amino terminus and of at least 80 residues from the carboxyl end. Despite the loss of these fragments totaling approximately 18 kilodaltons and cleavage of the peptide bond after arg residue 561, the purified trypsin-solubilized TPO appears to retain full enzyme activity.

Amino Acid Sequence↗

PubMed2006

MobileMed: a PDA-based mobile clinical information system.

Patient clinical data are distributed and often fragmented in heterogeneous systems, and therefore the need for information integration is a key to reliable patient care. Once the patient data are orderly integrated and readily available, the problems in accessing the distributed patient clinical data, the well-known difficulties of adopting a mobile health information system, are resolved. This paper proposes a mobile clinical information system (MobileMed), which integrates the distributed and fragmented patient data across heterogeneous sources and makes them accessible through mobile devices. The system consists of four main components: a smart interface, an HL7 message server (HMS), a central clinical database (CCDB), and a web server. The smart interface and the HMS work in concert to generate HL7 messages from the existing legacy systems, which essentially send the patient data in HL7 messages to the CCDB to be stored and maintained. The CCDB and the web server enable the physicians to access the integrated up-to-date patient data. By proposing the smart interface approach, we provide a means for effortless implementation and deployment of such systems. Through a performance study, we show that the HMS is reliable yet fast enough to be able to support efficient clinical data communication.

Computer Communication Networks↗