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PubMed2001

Chromophore structure in lumirhodopsin and metarhodopsin I by time-resolved resonance Raman microchip spectroscopy.

Time-resolved resonance Raman microchip flow experiments have been performed on the lumirhodopsin (Lumi) and metarhodopsin I (Meta I) photointermediates of rhodopsin at room temperature to elucidate the structure of the chromophore in each species as well as changes in protein-chromophore interactions. Transient Raman spectra of Lumi and Meta I with delay times of 16 micros and 1 ms, respectively, are obtained by using a microprobe system to focus displaced pump and probe laser beams in a microfabricated flow channel and to detect the scattering. The fingerprint modes of both species are very similar and characteristic of an all-trans chromophore. Lumi exhibits a relatively normal hydrogen-out-of-plane (HOOP) doublet at 951/959 cm(-1), while Meta I has a single HOOP band at 957 cm(-1). These results suggest that the transitions from bathorhodopsin to Lumi and Meta I involve a relaxation of the chromophore to a more planar all-trans conformation and the elimination of the structural perturbation that uncouples the 11H and 12H wags in bathorhodopsin. Surprisingly, the protonated Schiff base C=N stretching mode in Lumi (1638 cm(-1)) is unusually low compared to those in rhodopsin and bathorhodopsin, and the C=ND stretching mode shifts down by only 7 cm(-1) in D2O buffer. This indicates that the Schiff base hydrogen bonding is dramatically weakened in the bathorhodopsin to Lumi transition. However, the C=N stretching mode in Meta I is found at 1654 cm(-1) and exhibits a normal deuteration-induced downshift of 24 cm(-1), identical to that of the all-trans protonated Schiff base. The structural relaxation of the chromophore-protein complex in the bathorhodopsin to Lumi transition thus appears to drive the Schiff base group out of its hydrogen-bonded environment near Glu113, and the hydrogen bonding recovers to a normal solvated PSB value but presumably a different hydrogen bond acceptor with the formation of Meta I.

Animals↗
PubMed1997

Regulated expression of a wheat germin gene in tobacco: oxalate oxidase activity and apoplastic localization of the heterologous protein.

Wheat (Triticum aestivum) germin is a homopentameric glycoprotein whose synthesis is allied with seed germination. Germin pentamers show an unusual resistance to dissociation and possess an oxalate oxidase (OxO) activity. In order to increase our knowledge of germin gene expression, the function(s) of germin during development and possible uses in plant genetic engineering, an in vivo expression system is required. To this end, a gene for germin, named gf-2.8, was studied by expressing either promoter-GUS fusions or the intact gene in transgenic tobacco (Nicotiana tabacum) plants. Heterologous gene transcription was monitored in vitro and in vivo by GUS or OxO activity and was found to occur in developing seeds and in seedlings. This transcription was stimulated by auxins, as would be expected because of the presence of putative auxin-responsive elements in the promoter of the gf-2.8 gene. Auxin stimulation also extended to young leaves since OxO activity could be detected in treated but not in untreated leaves. The biochemical characteristics of wheat germin were also conserved in a transgenic host: the OxO activity was present under the form of a doublet co-migrating with germin G and G' isoforms. Also, germin distributed between a soluble and an apoplastic fractions despite the fact that wheat cell wall substantially differs from tobacco cell wall. Therefore, tobacco constitutes a suitable host for in vivo studies of this monocotyledon gene.

Amino Acid Sequence↗
PubMed1995

A sequence property approach to searching protein databases.

Currently available sequence alignment programs are generally not capable of detecting functional and structural homologs in the twilight zone of sequence similarity, i.e. when the sequence identity falls below about 25%. Here we attempt to detect such weak similarities using an approach based on a notion of protein sequence similarity radically different from that used in sequential alignment. The approach defines protein sequence dissimilarity (or distance) as a weighted sum of differences of compositional properties such as singlet and doublet amino acid composition, molecular weight, isoelectric point (protein property search or PropSearch). With PropSearch, either single sequences can be used for a database query, or multiple sequences can be merged into an "average" sequence reflecting the average composition of a protein family. First, we show that members of structural protein families have a low mutual PropSearch distance when the weights are optimized to discriminate maximally between structural families. Second, we demonstrate the results of database searches using the PropSearch method. Such searches are very rapid when scanning a preprocessed database and do not require alignments. In cases in which conventional alignment tools fail to detect similarities, PropSearch can be used to generate hypotheses about possible structural or functional relationships between a new sequence and sequences in the database.

Algorithms↗
PubMed1997

Sequence and characterization of the sperm protein Sp17 from the baboon.

In this study, cDNAs encoding the sperm protein Sp17 from the baboon (Papio papio) have been cloned and sequenced. Three clones, differing in the lengths of their 3' untranslated regions, were identified, which were encoded by mRNA transcripts of 0.8-1.35 kb. The open reading frame encodes 163 amino acids with a predicted molecular mass of 18.8 kDa. The baboon Sp17 protein sequence is 97% identical to human Sp17 but differs significantly by the addition of 12 amino acids at the C-terminal, providing an additional potential protein kinase C phosphorylation site. Northern blot analysis demonstrated that the baboon Sp17 mRNA was specific to the baboon testes and was not detected in the ovary, placenta, or any of the other somatic tissues tested. Western blot analysis using anti-Sp17 antibodies demonstrated that the native baboon sperm Sp17 protein consists of a doublet with an apparent M(r) of 26.5 and 27.2 kDa. Immunocytochemical staining of baboon testis with anti-Sp17 antibodies demonstrated Sp17 in spermatocytes, spermatids, and spermatozoa within the seminiferous epithelium. No specific staining was observed on spermatogonia, Sertoli cells, Leydig cells, or other somatic cell types.

Amino Acid Sequence↗
PubMed1995

Analysis of insulin-like growth factor binding proteins in the tammar wallaby, Macropus eugenii.

The insulin-like growth factors (IGFs) are important regulators of growth and development in eutherian mammals. In this study we have analyzed circulating insulin-like growth factor binding proteins (IGFBPs) by Western ligand blotting (WLB) and neutral gel filtration, and hepatic IGFBP mRNA transcripts in the wallaby, Macropus eugenii, a marsupial in which the fetus is born at an immature stage compared to eutherian mammals. Plasma from male and female adults, lactating mothers, and pouch young contains an IGF binding species consisting of a 42- to 50-kDa doublet, 30, 28, 24, and approximately 200 kDa, as shown by WLB. This pattern of IGFBPs is very similar to that observed in human and sheep. Neutral gel filtration revealed IGF binding activity of molecular size 70-160 kDa. When electrophoresed under nonreducing, denaturing conditions, the 70- to 160-kDa IGF binding activity appeared as a 42- to 50-kDa doublet, indicating the presence of a high-molecular-weight circulating IGF binding complex. These properties are again analogous to those observed for eutherian IGFBPs. Northern analysis of total wallaby liver RNA detected transcripts of 1.8 kb for IGFBP-1 and 1.6 kb for IGFBP-2, the same as those observed in the sheep and rat. Transcripts of 3.2 kb were detected for IGFBP-4, larger than the major band of 2.6 kb observed for the sheep and rat. Transcripts representing wallaby IGFBP-3 mRNA were not detected using a rat IGFBP-3 cDNA probe. Circulating IGFBPs were analyzed in plasma from wallaby mothers and their pouch young. There were no changes in circulating IGFBPs in the wallaby mothers throughout lactation.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1999

Insulin-like growth factors and IGF-binding proteins in bovine seminal plasma.

Insulin-like growth factor-I (IGF-I) is an important factor for germ cell development and maturation of spermatozoa. Actions of IGFs are modulated by IGF-binding proteins (IGFBPs) that may, depending on their concentration and site of expression, inhibit or enhance effects of IGF-I. We characterized IGFs and IGFBPs in seminal plasma from bulls routinely used for artificial insemination (AI) and from bulls producing poor-quality semen (low mass and individual motility of spermatozoa). IGFs were measured by specific radioimmunoassay in 22 samples of seminal plasma from nine different AI bulls with high (> 76.8%), average (72.8-73.4%), or low (< 69.5%) nonreturn rate (NRR). IGF-I and IGF-II levels were 144 +/- 9 ng/ml (mean +/- SE; range, 79-238 ng/ml) and 144 +/- 10 ng/ml (range, 55-221 ng/ml), respectively, and did not correlate with NRRs. IGF-I concentrations in seminal plasma from bulls producing poor-quality semen (n = 10) were significantly (P < 0.05) greater (194 +/- 26 ng/ml; range, 94-370 ng/ml), whereas IGF-II levels were significantly (P < 0.05) lower (93 +/- 17 ng/ml; range, 38-183 ng/ml) than in AI bulls. Ligand blot analysis of seminal plasma for IGFBPs revealed the presence of a 38-/45-kDa doublet band and a 30-kDa IGFBP. These IGFBPs were identified as IGFBP-3 and IGFBP-5, respectively, by immunoprecipitation using specific antibodies. In addition, a low amount of IGFBP-4 was detected in bovine seminal plasma by immunoprecipitation. There was a marked difference in the activity of IGFBPs between individual bulls, with a relatively small within-bull variance. The differences in IGFBP activities did not correlate with the fertilization capacity of the bulls in vivo or in vitro nor with immunoreactive IGF-I and IGF-II levels in seminal plasma. Our results demonstrate the presence of IGFBPs in bovine seminal plasma. In contrast to human seminal plasma, high activity of IGFBP-3 was detected in seminal plasma of some bulls, suggesting species-specific regulation of IGFBP activity by proteases.

Animals↗
PubMed1989

Human thyrotropin receptor subunits characterized by thyrotropin affinity purification and western blotting.

We studied the subunit structure of the human TSH receptor in thyroid tissue from patients with Graves' disease and multinodular goiter by TSH affinity chromatography, immunoprecipitation with Graves' immunoglobulins (Igs), and a modified technique of Western blotting. Human TSH receptor-binding activity was purified about 1,270-fold by sequential affinity chromatography on wheat germ lectin-agarose and TSH-agarose. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of nonreduced affinity-purified receptors eluted in sodium dodecyl sulfate sample buffer revealed three noncovalently linked subunits of 70,000, 50,000, and 35,000 mol wt. When reduced, a major subunit of 25,000 mol wt was identified. When 3 mol/L NaCl was used to elute affinity-purified receptors only the 50,000 mol wt nonreduced subunit was detected. This subunit bound [125I]bovine TSH and was precipitated by Graves' Igs. Modifications to the conventional Western blotting technique enabled thyroglobulin components (approximately 220,000 mol wt), thyroid microsomal antigen (a doublet of approximately 110,000 mol wt), and putative TSH receptor subunits of 70,000 and 50,000 mol wt to be identified in thyroid particulate membranes by Graves' Igs. Blotting of affinity-purified receptors eluted in sodium dodecyl sulfate sample buffer revealed subunits of either 70,000 or 50,000 mol wt, with a minority of Graves' serum samples. We conclude that the nonreduced human TSH receptor is an oligomeric complex comprising three different subunits of 70,000, 50,000, and 35,000 mol wt. The reduced receptor exists as a single subunit of 25,000 mol wt, which may be disulfide linked to form the higher mol wt forms. The 70,000 and 50,000 mol wt subunits contain epitopes that bind Graves' Igs in modified Western blots, thus directly confirming that the human TSH receptor is a target for Graves' Igs.

Autoradiography↗
PubMed1979

Mechanisms of cellular adhesion. IV. Role of serum glycoproteins in fibroblast spreading on glass.

We have investigated the exogenous factors required for the transition from the round shape of suspended fibroblasts to the characteristic spread shape on serum-coated glass. Following the evidence of others that the transition is facilitated by adsorbed component(s) related to CIG/LETS (cold-insoluble globulin/large external transformation-sensitive) proteins, we have isolated 2 such preparations from chick serum. Their influence has been investigated on fibroblast adhesion, spreading and growth and they have been characterized by gel electrophoresis, immunological cross-reactivity, amino acid and carbohydrate residue analysis, sedimentation velocity behaviour and circular dichroism spectroscopy. The preparations have molecular weights of 225/215,000 and 140,000 Daltons respectively and are closely similar in composition and secondary structure. The 225/215 000 Dalton doublet is probably a product of limited proteolysis which almost certainly occurred in the avian circulation. For cells seeded on glass precoated in different ways and in different supplemented media we could detect no change in the extent of attachment but there were profound influences on cell shape following this initial adhesion. We confirm that prior adsorption of either CIG-related preparation to glass does indeed promote fibroblast spreading in the absence of other serum components and that CIG is the sole serum component with this type of activity. We now add 2 important qualifications: (i) the presence of substrate-adsorbed serum CIG is not essential for spreading when other serum components are present in the medium; and (ii) the adhesive organization shown by interference reflexion microscopy is incompletely formed unless the additional serum components are present in the medium. We therefore conclude that 16C fibroblasts have the ability when given the stimulus of soluble serum components other than CIG, but not otherwise, to synthesize all the components necessary for the highly organized contacts with glass, including endogenous CIG/LETS proteins.

Amino Acids↗
PubMed1987

Biosynthesis and secretion of functional protein S by a human megakaryoblastic cell line (MEG-01).

A human megakaryoblastic cell line (MEG-01) was investigated for the presence of protein S in culture medium and cell lysates using a specific enzyme-linked immunoassay (ELISA) and a functional assay. When 5 X 10(5) MEG-01 cells/mL was subcultured in RPMI 1640 medium with 10% fetal calf serum (FCS), the concentration of protein S antigen in the culture medium increased progressively with time from less than 8 ng/mL on day 0 to 105.6 +/- 6.0 ng/mL on day 13. Vitamin K2(1 microgram/mL) increased the production of functional protein S, whereas warfarin (1 microgram/mL) profoundly decreased the quantity and the specific activity of secreted protein S. By an indirect immunofluorescent technique, protein S antigen was detected in both MEG-01 cells and human bone marrow megakaryocytes. Immunoblot analysis of culture medium revealed two distinct bands (mol wt 84,000 and 78,000) that are identical to the doublets of purified plasma protein S. De novo synthesis of protein S was demonstrated by the presence of specific immunoprecipitable radioactivity in the medium after 5 hours of labeling of the cells with [35S]-methionine as a 84,000 mol wt protein. Plasma protein S levels of nine patients with severe aplastic anemia were not significantly different from those of normal controls. These results suggest that megakaryocytes produce functional protein S and contain the enzymes required for the carboxylation of selected glutamic acid residues, and that protein S synthesized by megakaryocytes does not represent a main source of plasma protein S.

Anemia, Aplastic↗
PubMed1985

Qualitative and quantitative analyses of Epstein-Barr virus early antigen diffuse component by western blotting enzyme-linked immunosorbent assay with a monoclonal antibody.

We report the use of monoclonal antibody against the early antigen diffuse component (anti-EA-D) of Epstein-Barr virus (EBV) to analyze, both qualitatively and quantitatively, the expression of EA-D in various human lymphoblastoid cell lines activated by chemical inducers. The kinetics of synthesis of EA-D in P3HR-1, B95-8, and Ramos/AW cells were similar in that they all reached the peak of synthesis on day 5 after induction. Surprisingly, no expression of EA-D was found in induced BJAB/GC, an EBV-genome-containing cell line. EBV-negative cell lines, BJAB and Ramos, were negative for EA-D. Raji cells had no detectable EA-D but responded rapidly to induction, reaching a peak on day 3. Superinfection of Raji cells also resulted in marked induction of EA-D, which reached a plateau between 8 to 12 h postinfection. Western blotting coupled with the enzyme-linked immunosorbent assay was employed to identify polypeptides representing EA-D. A family of four polypeptides with molecular weights of 46,000 (46K protein), 49,000, 52,000, and 55,000 were identified to be reactive with monoclonal anti-EA-D antiserum. The pattern of EA-D polypeptides expressed in each cell line was different. Of particular interest was the expression of a large quantity of 46K protein both in induced Raji and P3HR-1 cells, but not in superinfected Raji cells. A 49K doublet was expressed in activated p3HR-1, B95-8, and Ramos/AW cells and in superinfected Raji cells. In addition, two distinct 52K and 55K polypeptides were expressed in induced Ramos/AW and superinfected Raji cells. However, none of these EA-D polypeptides was detectable in BJAB/GC, BJAB, Ramos, and mock-infected Raji cells. To approximate relative concentrations of EA-D in cell extracts, we employed the enzyme-linked immunosorbent assay and immunoblot dot methods by using one of the purified EA-D components to construct a standard curve. Depending upon the cell lines, it was estimated that ca. 1 to 3% (determined by the enzyme-linked immunosorbent assay) and 0.8 to 1.6% (determined by immunoblot dot) of total proteins from maximally induced cells were EA-D. These results suggest that differential expression of EA-D polypeptides could be of importance in the diagnosis of state of EBV infection.

Antibodies, Monoclonal↗
PubMed1999

Submillimeter Detection of the van der Waals Stretching Vibration of the Ar-CO Complex.

With the Cologne submillimeter-wave supersonic jet spectrometer, we extended molecular jet spectroscopy with backward wave oscillators up to frequencies of about 600 GHz. For the first time, the van der Waals stretching vibration of the Ar-CO molecular complex was detected in direct absorption. We measured 13 ro-vibrational transitions (Kvstretch = 1 <-- 0, Ka = 0 <-- 0) in the frequency range from 528 to 600 GHz and additionally the two R(3) K doublet (Ka = 4 <-- 3) pure rotational transitions at 447 GHz with an accuracy of about 200 kHz. The ro-vibrational transitions were assigned and fitted within experimental accuracy to a simple Hamiltonian taking into account the Coriolis interaction between the stretching and bending states, i.e., between vstretch = 1, Ka = 0, and vbend = 1, Ka = 1. The intensity of the transitions in the van der Waals stretching mode was estimated to be a factor of 5-10 less than that in the bending mode of Ar-CO. Copyright 1999 Academic Press.

Journal Article↗
PubMed1996

Determination of the precision of spike timing in the visual cortex of anaesthetised cats.

Neuronal cortical spike trains contain precisely replicating patterns whose presence cannot be accounted for by change production. A comparison of the number of triplets of spikes present two times with the number of doublets replicated three times in the same window duration gives a frequency-insensitive measure of this type of fine temporal organisation. By varying the tolerance with which such precisely replicating patterns are detected, one can evaluate the accuracy of spike timing in spike trains. In the sample of data here analysed, it was found that replicating patterns were best seen in the precision range 0.4-1.4 ms (a result evidently at variance with a simple 'integrate and fire' model of neurons). Surprisingly, the fine temporal structure of spike trains thus evidenced was stronger at relatively low firing rate discharges and was present in both the 'spontaneous' and 'evoked' responses.

Action Potentials↗
PubMed2006

Complete nucleotide sequences of three dsRNA segments from Raphanus sativus-root cv. Yidianhong [corrected] with leaf yellow edge symptoms.

The two minor dsRNA bands, previously detected in symptomatic leaves of Raphanus sativus-root cv. Yidianhong [corrected] were subjected to further analysis. cDNA cloning and sequencing revealed that the smaller of the two dsRNA bands is actually a doublet consisting of two co-migrating dsRNA segments and the resulting three segments were designated as RasR 3, RasR 4, and RasR 5. RasR 3 was 1717 bp in length and potentially encoded a protein of about 55.3 kDa, containing all of the six conserved motifs shared by the RNA dependent RNA polymerases of members of the family Partitiviridae. RasR 4 and RasR 5, which co-migrated in the 5% polyacrylamide gel, were 1521 and 1485 bp in length and each encoded a putative protein of unknown function. Their molecular masses, as calculated from the deduced amino acid, were 38.2 and 38.8 kDa, respectively. The 5' UTRs of all three segments shared regions of high sequence similarities, but were distinct from those of the RasR 1 and RasR 2. Taken together, these results along with those described in the previous report, suggest that more than one partitivirus was co-infecting radish leaves.

5' Untranslated Regions↗
PubMed1995

GDNF: existence of a second transcript in the brain.

The detection of the glial cell-line derived neurotrophic factor (GDNF) mRNA by RT-PCR in dissociated cell culture of rat embryonic or post-natal brain allowed the amplification of a doublet. The major band corresponded to the expected size and the minor one to a shorter product. We cloned and sequenced the latter product, and thus identified a mRNA potentially encoding for an isoform of the initially described precursor protein involved in GDNF synthesis.

Animals↗
PubMed1996

Expression of ionotropic glutamate receptor subunit mRNAs by paraventricular corticotropin-releasing factor (CRF) neurons.

To determine whether paraventricular corticotropin-releasing factor (CRF) neurons express NMDA, AMPA or kainate-preferring glutamate receptors, we have colocalized, by in situ hybridization (ISH), transcripts of various glutamate receptor subunit genes with the CRF messenger RNA on doublet adjacent sections of the rat hypothalamus. We found that more than 70% of CRF-positive neurons contain the NMDA receptor subunit NR1 mRNA whereas NR2A and NR2B subunit mRNAs were not detectable in CRF cells. A significant proportion of identified CRF cells express AMPA receptor subunit GluRA (46%), GluRB (21%) as well as the kainate-preferring receptor subunit KA2 (31%) mRNAs. These results support the hypothesis that the excitatory transmitter glutamate may directly influence CRF neurons through NMDA as well as non-NMDA receptors.

Animals↗
PubMed1993

Antigenic and biological diversity among transmissible gastroenteritis virus isolates of swine.

Twenty-four field isolates of transmissible gastroenteritis virus (TGEV) were isolated and examined for antigenic and biological characteristics. Most TGEV isolates produced a typical cytopathic effect (CPE) in swine testis (ST) cell culture, which included a ballooning or lifting away of the infected cells from the cell monolayer with heavy granulation evident. Minor variations in CPE were observed with one isolate, IA-145. Protein profiles of the TGEV isolates as determined by SDS-PAGE were essentially identical, with the exception of the isolate IA-101. The TGEV isolate IA-101 presented a higher molecular mass M protein and lacked an N protein doublet that was present in all other TGEV isolates. The TGEV isolates were shown to be closely related antigenically by using hyperimmune sera in a virus neutralization (VN) test. Some antigenic diversity was detected by utilizing monoclonal antibodies (mAbs) in a VN test. Titers of the mAbs were highest with the homologous Miller TGEV, and one virus isolate, IA-156, was very poorly neutralized with the mAbs used in this study. Indirect immunofluorescence assay (IFA) results were similar to those obtained by the VN test. These studies show that some biologic and antigenic diversity exists among TGEV isolates.

Animals↗
PubMed1996

Cloning and characterization of three laccase genes from the white-rot basidiomycete Trametes villosa: genomic organization of the laccase gene family.

Three laccase genes were isolated from the white-rot basidiomycete Trametes villosa (Tv). The predicted protein products have 63-71% identity to the previously cloned Tv laccase genes lcc1 and lcc2. The genes lcc3, lcc4 and lcc5 contain 12, 10 and 11 introns, respectively. The position of several of the introns is conserved among all 5 genes. The 5 genes appear to be differentially regulated, and message has only been detected for lcc1 and lcc2. The karyotype of Tv was determined by CHEF, and 8 bands ranging in size from approximately 5.7 to 2.2 Mb were resolved of which 2 appear to be doublets. The 5 laccase genes have been mapped to specific bands resolved by CHEF. The lcc1 and lcc2 genes hybridize to a band of approximately 5.7 Mb. The lcc4 and lcc5 genes are on a chromosome of approximately 3.7 Mb, and lcc3 is on a chromosome of approximately 2.8 Mb.

Amino Acid Sequence↗
PubMed1982

Structural genes on the Y chromosome of Drosophila melanogaster.

Testis proteins of Drosophila melanogaster deficient for six different Y-chromosome regions were fractionated by means of a sodium dodecyl sulfate/polyacrylamide gel system designed to separate high molecular weight polypeptides (Mr, greater than 200,000). Analysis of the banding patterns indicates that the three regions containing fertility genes kl-2, kl-3, and kl-5 are responsible for three different high molecular weight polypeptides. Several observations indicate that these polypeptides are structural components of the sperm axoneme. They are present in seminal vesicles, which are highly enriched for mature sperm. They are first detected during development at a time when the first spermatids are elongating. Finally, deletion of either kl-5 or kl-3 leads to the absence of the outer dynein arm of the peripheral doublets of the axoneme. Although absence of the kl-2 region eliminates the third polypeptide, an associated structural defect in the axoneme has yet to be identified. The three polypeptides are in the Mr 300,000-350,000 range, and their mobilities are similar to those of dynein polypeptides from Chlamydomonas axonemes. Experiments using dosage variation and a temperature-sensitive sterile mutation in kl-5 suggest that the Y-chromosome regions contain the coding sequences for the polypeptides.

Aneuploidy↗