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Regulated expression of the X. tropicalis connexin43 promoter.

The spatio-temporal expression pattern of the connexin43 gene during Xenopus development has been described (Van der Heyden et al. 2001). To further investigate the regulation and function of connexin43 (Cx43) in amphibians, we have isolated the gene from Xenopus tropicalis (Xt) and determined its structure. The X. tropicalis Cx43 gene displays the typical two exon-one intron connexin configuration, where the first exon is non-coding. The predicted amino acid sequence of the XtCx43 protein is highly homologous to that of X. laevis, chicken and mammals. Expression of XtCx43 cDNA in N2A cells results in gap-junction plaque formation. Promoter activity of a 3.5 kb upstream region of the X. tropicalis Cx43 gene, including exon 1, mimics endogenous timing of expression after injection of reporter constructs in X. laevis embryos.

Amino Acid Sequence↗

Verbal recoding of visual stimuli impairs mental image transformations.

Two experiments were carried out to test the hypothesis that verbal recoding of visual stimuli in short-term memory influences long-term memory encoding and impairs subsequent mental image operations. Easy and difficult-to-name stimuli were used. When rotated 90 degrees counterclockwise, each stimulus revealed a new pattern consisting of two capital letters joined together. In both experiments, subjects first learned a short series of stimuli and were then asked to rotate mental images of the stimuli in order to detect the hidden letters. In Experiment 1, articulatory suppression was used to prevent subjects from subvocal rehearsal when learning the stimuli, whereas in Experiment 2, verbal labels were presented with each stimulus during learning to encourage a reliance on the verbal code. As predicted, performance in the imagery task was significantly improved by suppression when the stimuli were easy to name (Experiment 1) but was severely disrupted by labeling when the stimuli were difficult to name (Experiment 2). We concluded that verbal recoding of stimuli in short-term memory during learning disrupts the ability to generate veridical mental images from long-term memory.

Attention↗

Automatic prediction of trauma registry procedure codes from emergency room dictations.

Current natural language processing techniques for recognition of concepts in the electronic medical record have been insufficient to allow their broad use for coding information automatically. We have undertaken a preliminary investigation into the use of machine learning methods to recognize procedure codes from emergency room dictations for a trauma registry. Our preliminary results indicate moderate success, and we believe future enhancements with additional learning techniques and selected natural language processing approaches will be fruitful.

Artificial Intelligence↗

Cloning, sequencing, and expression of the hepatitis E virus (HEV) nonstructural open reading frame 1 (ORF1).

Hepatitis E virus (HEV) causes enterically transmitted epidemic and sporadic viral hepatitis affecting millions of people in the developing world. Different geographical isolates of HEV show a high degree of homology at the nucleotide and amino acid levels. The approximately 7.2 kb RNA genome has three open reading frames of which ORF1 is predicted to code for the viral nonstructural polyprotein. The expression, processing and properties of the nonstructural ORF1 polyprotein have not been reported so far. In this study, the complete HEV ORF1 was reconstructed from overlapping fragments amplified by polymerase chain reaction (PCR) of total RNA isolated from the bile fluid of a rhesus monkey experimentally infected with HEV isolate from an epidemic. The complete assembled ORF1 was sequenced using HEV specific primers. The ORF1 polyprotein was expressed in E. coli, in a cell free translation system and in HepG2 cells, and was characterized by western blotting and immunoprecipitation using acute phase patient serum as well as polyclonal antibodies raised against defined parts of the ORF1 polyprotein. The nonstructural polyprotein of HEV was expressed as a 186 kDa protein. No processing was observed into discrete units, either in-vitro based on a kinetic analysis, or in HepG2 cells based on immunoprecipitation.

Animals↗

Identification of a novel breast- and salivary gland-specific, mucin-like gene strongly expressed in normal and tumor human mammary epithelium.

Expression profiling using the public expressed sequence tag (EST) and serial analysis of gene expression (SAGE) databases resulted in the identification of a putative breast-specific mRNA that we have termed small breast epithelial mucin (SBEM). Hybridization analysis performed on 43 normal human tissues revealed that the SBEM gene was only expressed in mammary and salivary glands. Further reverse-transcription PCR analyses confirmed SBEM expression in most of established human breast epithelial cell lines analyzed (7 of 8) but not in cell lines of non-breast origin (0 of 6). SBEM mRNA expression was detected in >90% of invasive ductal carcinomas and correlated with the expression of a previously characterized breast-specific gene, mammaglobin-1 (n = 54; Spearman r = 0.34, P = 0.011). Interestingly, a higher SBEM:mammaglobin-1 ratio was observed in primary tumors with axillary lymph node metastasis than in node-negative tumors (n = 46; Mann-Whitney, P = 0.04). In a subset of 20 primary breast tumors and their matched axillary lymph nodes, a high concordance (Fisher's exact test, P < 0.001) was seen between PCR detection of SBEM mRNA in lymph node tissue and their histopathological status, indicating that SBEM mRNA expression is conserved in nodal metastasis. The SBEM gene is predicted to code for a putative low molecular weight, secreted sialoglycoprotein, potentially useful for the diagnosis of metastatic breast cancer.

Biomarkers, Tumor↗

Isolation, expression, and mutation of a rabbit skeletal muscle cDNA clone for troponin I. The role of the NH2 terminus of fast skeletal muscle troponin I in its biological activity.

A cDNA for rabbit fast skeletal muscle troponin I (TnI) was isolated and sequenced. The clone contains a coding sequence predicting a 182-amino-acid protein with a molecular mass of 21,162 daltons. The translated sequence is different from that reported by Wilkinson and Grand (Wilkinson, J. M., and Grand, R. J. A. (1978) Nature 271, 31-35) in that Arg-153, Asp-154, and Leu-155 must be inserted into their original sequence. Amino acid sequencing of adult rabbit TnI confirmed this result. In order to investigate the role of the NH2 terminus of TnI in its biological activity, we have expressed a recombinant deletion mutant (TnId57), which lacks residues 1-57, in a bacterial expression system. Both wild type TnI (WTnI) and TnId57 inhibited acto-S1-ATPase activity and this inhibition could be fully reversed by troponin C (TnC) in the presence of Ca2+. Additionally both WTnI and TnId57 bound to an actin affinity column. Thus, both inhibitory actin binding and Ca(2+)-dependent neutralization by TnC were retained in TnId57. TnC affinity chromatography was used to compare the binding of TnI and TnId57 to TnC. Using this method, two types of interaction between TnC and TnI were observed: 1) one which is metal independent (or structural) and 2) one dependent on Ca2+ or Mg2+ binding to the Ca(2+)-Mg2+ sites of TnC. The same experiments with TnId57 demonstrated that the type 1 interaction was weakened, and type 2 binding was lost. This method also revealed an interaction between TnC and TnI which is dependent upon Ca2+ binding to the Ca(2+)-specific sites of TnC and which is retained in TnId57. Taken together, these results suggest that the NH2 terminus of TnI may constitute a Ca(2+)-Mg(2+)-dependent interaction site between TnC and TnI and play, in part, a structural role in maintaining the stability of the troponin complex while the COOH terminus of TnI contains a Ca(2+)-specific site-dependent interaction site for TnC as well as the previously demonstrated Ca(2+)-sensitive inhibitory and actin binding activities.

Actins↗

Comparative analysis of the genomes of cyanobacteria and plants.

Chloroplast genome originates from the genome of ancestral cyanobacterial endosymbiont. The comparison of the genomes of cyanobacteria and plants has been made possible by the advance in genome sequencing. I report here current results of our computational efforts to compare the genomes of cyanobacteria and plants and to trace the process of evolution of cyanobacteria, chloroplasts and plants. Cyanobacteria form a clearly defined monophyletic clade with reasonable level of diversity and are ideal for testing various approaches of genome comparison. Analysis of short sequence features such as genome signature was found to be useful in characterizing cyanobacterial genomes. Comparison of genome contents was performed by homology grouping of predicted protein coding sequences, rather than orthologue-based comparison, to minimize effects of multi-domain proteins and large protein families, both of which are important in cyanobacterial genomes. Comparison of the genomes of six species of cyanobacteria suggests that there are a number of species-specific additions of protein genes, and this information is useful in reconstructing phylogenetic relationship. The homology groups in cyanobacteria were used as a reference to compare plants and non-photosynthetic organisms. The results suggest that 238 groups that are common to all organisms analyzed may define a minimal set of gene groups. In addition, only 80 groups are identified as the gene groups that could not have been acquired by plants without cyanobacterial endosymbiosis. Further study is needed to identify plant genes of cyanobacterial origin.

Cyanobacteria↗

[Molecular cloning and sequencing of Dendrolimus punctatus Wenshanensis cytoplasmic polyhedrosis virus (DpwCPV) NS5 protein gene].

DpwCPV were purified from infected Dendrolimus punctatus Wenshanensis larvae by density gradient centrifugation. The genomic dsRNA segments were subsequently extracted directly from the purified polyhedra by SDS treatmen, phenol/chloroform extraction and ethanol precipitation. Defferent segments of genomic dsRNA were separated by low melting point agarose electrophoresis, and S9 dsRNA was purified after being excised from the gel. S9 RNA was denaturalized in high temperature. The primers was designed on the basis of the RNA sequence of S9 in BmCPV-1 (H strain). After RT-PCR, the amplified cDNA was cloned into the pMD18-T Vector. The NS5 protein gene of DpwCPV is found to be 977 nucleotides in length with one open reading frame in one strand. It can code a predicted protein of 320 residues (35560).

Amino Acid Sequence↗

[InterPro as a new tool for whole genome analysis. A comparative analysis of Mycobacterium tuberculosis, Bacillus subtilis and Escherichia coli as a case study].

InterPro was developed as a new integrated documentation resource for protein families, domains and functional sites to rationalize the complementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects and has applications in computational functional classification of newly determined sequences lacking biochemical characterization and in comparative genome analysis. InterPro contains over 3500 entries, with more than 1000000 hits in SWISS-PROT and TrEMBL. The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/. InterPro was used for whole proteome analysis of the pathogenic microorganism, Mycobacterium tuberculosis, and comparison with the predicted protein coding sequences of the complete genomes of Bacillus subtilis and Escherichia coli. 64.8% of the M. tuberculosis proteins in the proteome matched InterPro entries, and these could be classified according to function. The comparison with B. subtilis and E. coli provided information on the most common protein families and domains, and the most highly represented families in each organism. InterPro thus provides a useful tool for global views of whole proteomes and their compositions.

Bacillus subtilis↗

Bacillus subtilis alkaline phosphatases III and IV. Cloning, sequencing, and comparisons of deduced amino acid sequence with Escherichia coli alkaline phosphatase three-dimensional structure.

Bacillus subtilis has an alkaline phosphatase multigene family. Two members of this gene family, phoAIII and phoAIV, were cloned, taking advantage of in vitro constructed strains containing a plasmid insertion within one or the other of the structural genes. The DNA sequences of the two genes showed approximately 64% identity at the DNA level and 63% identity in the deduced primary amino acid sequences. The phoAIII and phoAIV genes code for predicted proteins of 47,149 and 45,935 Da, respectively. Comparison of the deduced primary amino acid sequence of the mature proteins with other sequenced alkaline phosphatases from Escherichia coli, yeast, and humans shows 25-30% identity. Based on the refined crystal structure of E. coli alkaline phosphatase, it appears that the active site and the core of the structure are retained in both Bacillus alkaline phosphatases. However, both proteins are truncated at the amino terminus compared with other mature alkaline phosphatases, three sizable surface loops of E. coli are deleted, and a minidomain is replaced with a larger domain in the model. Neither Bacillus alkaline phosphatase sequenced contains any cysteine residues, an amino acid implicated in intrachain disulfide bond formation in other alkaline phosphatases.

Alkaline Phosphatase↗

Single amino acid substitution defines a naturally occurring genetic variant of human thymidylate synthase.

Previously, we identified an altered structural form of thymidylate synthase (TS) in a human colonic tumor cell line. This form, which is encoded by a variant structural gene, renders cells relatively resistant to 5-fluoro-2'-deoxyuridine as a result of the reduced affinity of the enzyme for the active metabolite 5-fluoro-2'-deoxyuridylic acid. We have isolated a cDNA clone specific to the altered TS and have determined its sequence. Two point mutations distinguish the normal from the altered TS mRNAs. One, a (A----G) change, is located within the 3'-untranslated region; the other, a T----C change within the amino acid-coding region, predicts replacement of tyrosine by histidine at residue 33 of the polypeptide. This sequence change was confirmed by direct analysis of cDNA amplified by the polymerase chain reaction and was further verified using allele-specific oligonucleotides as probes in Northern blots. These results, along with studies by other laboratories showing Tyr33 to be evolutionarily conserved, suggest that this residue plays an important role in TS function.

Amino Acid Sequence↗

Bovine alpha 1----3-galactosyltransferase: isolation and characterization of a cDNA clone. Identification of homologous sequences in human genomic DNA.

We have isolated, by immunological screening of a lambda gt11 expression library, a cDNA clone that represents the complete coding sequence for bovine alpha 1----3-galactosyltransferase. The coding sequence predicts a membrane-bound protein with three distinct structural features: a large, potentially glycosylated COOH-terminal domain (346 amino acids), a single transmembrane domain (16 amino acids), and a short NH2-terminal domain (6 amino acids). Thus, the domain structure for this transferase is similar to that deduced for beta 1----4-galactosyltransferase (Shaper, N. L., Hollis, G. F., Douglas, J. G., Kirsch, I. R., and Shaper, J. H. (1988) J. Biol. Chem. 263, 10420-10428) and alpha 2----6-sialyltransferase (Weinstein, J., Lee, E. V., McEntee, K., Lai, P.-H., and Paulson, J. C. (1987) J. Biol. Chem. 262, 17735-17743). S1 analysis demonstrates that two sets of mRNAs, which are heterogeneous at their 5' ends, are transcribed. Because both sets initiate upstream of the translational start site, only one protein is encoded by this gene. alpha 1----3-Galactosyltransferase is widely expressed in different mammalian species, with the notable exception of man and Old World monkeys (Galili, U., Shohet, S. B., Kobrin, E., Stults, C.L.M., and Macher, B. A. (1988) J. Biol. Chem. 263, 17755-17762). By Northern blot analysis we were indeed unable to detect transcripts for this enzyme in various human and Old World monkey cell lines; transcripts were readily detected in other mammalian species. However, by Southern blot analysis, homologous sequences for alpha 1----3-galactosyltransferase were identified in human genomic DNA. This suggests that the gene, although present in the human genome, is normally not expressed. These observations have potential medical implications. Because many humans have high levels of circulating antibodies directed against the enzymatic product of alpha 1----3-galactosyltransferase (Gal alpha 1----3Gal beta 1----4GlcN Ac) (Galili, U., Clark, M. R., Shohet, S. B., Buehler, J., and Macher, B. A. (1987) Proc. Natl. Acad. Sci. U. S. A. 84, 1369-1373), it has been suggested that activation of this normally silent gene may play a role in autoimmune disease in man (Etienne-Decerf, J., Malaise, M., Mahieu, P., and Winand, R. (1987) Acta Endocrinol. 115, 67-74).

Amino Acid Sequence↗

cDNA and gene sequence of Manduca sexta arylphorin, an aromatic amino acid-rich larval serum protein. Homology to arthropod hemocyanins.

The serum (storage) proteins produced by insect larvae at the end of the feeding cycle are hexameric blood proteins with one or more type of subunits. The cDNA and gene structure of the aromatic amino acid-rich larval serum protein arylphorin from the tobacco hornworm, Manduca sexta, has been determined. In M. sexta arylphorin there are two subunits alpha and beta, which have 686 and 687 amino acids, respectively, and whose amino acid sequences are 68% identical. The two genes, separated by 7.1 kilobases of chromosomal DNA, are transcribed in the same direction. Based on the alignment of the amino acid sequence, the rate of nucleotide substitution between the two coding regions predicts that the two genes diverged about 100 million years ago. Both genes contain 5 exons and the upstream region contains a sequence, TGATAAA, which is similar to a sequence found in all other storage protein genes for which information is available. When the National Biomedical Research Foundation protein sequence data base was searched, it was found that the arylphorin subunits showed significant similarity to the arthropod hemocyanins, which are hexameric oxygen-carrying proteins. Based on the alignment of the sequence of M. sexta arylphorin and the hemocyanin from the spiny lobster (Panulirus interruptus), for which a 3.2 A structure has been determined, it was observed that the highest concentration of conserved residues were found in those regions of the sequence which are involved in subunit interactions in the hexameric protein. It is suggested that the insect storage proteins and the arthropod hemocyanins have evolved from a common ancestor.

Amino Acid Sequence↗

Hepatocyte growth factor (HGF), keratinocyte growth factor (KGF), and their receptors in human breast cells and tissues: alternative receptors.

We sought to determine whether the hepatocyte growth factor/scatter factor (HGF/SF)- and keratinocyte growth factor-receptor systems were expressed in normal breast cells, breast carcinoma cell lines, normal breast tissues, and breast cancer tissues. Reverse transcriptase-polymerase chain reaction and hot blotting were used to detect HGF, HGF/SF (met) receptor, KGF, and KGF receptor mRNAs in human mammary epithelial (HME) and stromal (HMS) cells. We also examined breast carcinoma (MDA-MB-157, SCC 38, and SCC 70) and spontaneously immortalized breast epithelial (HMT 3522) cell lines, as well as normal breast and breast carcinoma tissues. PCR products were also confirmed by nucleic acid sequencing. The effects of HGF and KGF, compared to EGF and heparin-binding EGF, on the proliferation of normal human mammary epithelial cells in serum-free defined medium was determined by cell counting. HGF and KGF mRNAs were detected in HMS cells, but not HME cells. KGF receptor mRNA was detected in HME cells, but not HMS cells. HGF/SF receptor mRNA was detected in both HME and HMS cells. mRNAs were also detected in normal breast and breast carcinoma tissues, as well as breast carcinoma and transformed breast epithelial cell lines. Alternative cDNA sequences that are predicted to code for a soluble KGF receptor and a membrane bound, truncated HGF/SF receptor were detected in breast epithelial cells and breast tissues. HGF and KGF maintained viability and stimulated proliferation of HME cells.

Adult↗

Cloning of the NCX2 isoform of the plasma membrane Na(+)-Ca2+ exchanger.

The Na(+)-Ca2+ exchanger is an important regulator of cellular Ca2+ levels, and one isoform of this transporter, NCX1, has been cloned previously (Nicoll, D.A., Longoni, S., and Philipson, K.D. (1990) Science 250, 562-565). We now report the cloning of a second isoform (NCX2) of the Na(+)-Ca2+ exchanger which was present in a rat brain cDNA library. NCX2 is predicted to code for a protein of 921 amino acids. NCX1 and NCX2 are 61 and 65% identical at the nucleotide and amino acid levels, respectively, and are the products of different genes. The genes for NCX1 and NCX2 are located on human chromosomes 2 and 14, respectively. Hydropathy profiles of the two exchangers are very similar. Transcripts of NCX2 are detected in brain and skeletal muscle. NCX2 was expressed in Xenopus oocytes and Na(+)-Ca2+ exchange activity was analyzed electrophysiologically by the giant inside-out, excised patch technique. Outward currents were evoked by the application of Na+ with the exchanger operating in the reversed mode (extracellular Ca2+ exchanging for intracellular Na+). The affinity for Na+ (30 mM) and the current-voltage relationship of NCX2 are similar to those for NCX1. Like NCX1, NCX2 is secondarily regulated by intracellular Ca2+, but the affinity of NCX2 for regulatory Ca2+ (1.5 microM) upon initial application of Na+ is lower than that of NCX1 (0.3 microM). The existence of multiple Na(+)-Ca2+ exchanger isoforms may provide flexibility for regulation and expression.

Amino Acid Sequence↗

Functional expression cloning of the canalicular sulfate transport system of rat hepatocytes.

We have cloned a single cDNA encoding the canalicular sulfate transporter of rat liver using Xenopus laevis oocytes as a functional expression system. The cloned cDNA sulfate anion transporter-1 (sat-1) expresses saturable Na(+)-independent sulfate uptake (Km approximately 0.14 mM) that can be inhibited by 4,4'-diisothiocyano-2,2'-disulfonic acid stilbene (DIDS, IC50 = 28 microM) and oxalate, but not by succinate or cholate. These properties are very similar to sulfate uptake expressed in oocytes injected with total rat liver mRNA and to the bicarbonate/sulfate exchange system previously characterized in canalicular rat liver plasma membrane vesicles. The cloned sat-1 cDNA has a total length of 3726 base pairs (bp) with an open reading frame encompassing 2109 bp, a 5'-untranslated region of 367 bp, and a 3'-untranslated region of 1250 bp. The coding region predicts a protein of 703 amino acids with a calculated molecular mass of 75.4 kDa. Computer-based hydrophobicity analysis suggests the presence of 12 putative transmembrane spanning domains. Furthermore, three potential glycosylation sites are detected (Asn-158, Asn-163, Asn-587). Northern blot analysis indicates that similar sulfate anion transporters are also present in the kidney, muscle, and brain of rat and in the liver of the mouse. Using antisense oligonucleotides the mRNA-species of the sat-1 analogue in rat kidney has been characterized by hybrid depletion experiments (Markovich, D., Bissig, M., Sorribas, V., Hagenbuch, B., Meier, P. J., and Murer, H. (1994) J. Biol. Chem. 269, 3022-3026).

Amino Acid Sequence↗

Tnk1: a novel intracellular tyrosine kinase gene isolated from human umbilical cord blood CD34+/Lin-/CD38- stem/progenitor cells.

Degenerate PCR was employed to identify novel tyrosine kinase genes from an enriched population of human umbilical cord blood hematopoietic stem/progenitor cells. One novel tyrosine kinase gene, designated Tnk1, was cloned. The sequence of the complete Tnk1 coding region predicts a 72 kD protein. Comparison of Tnk1 to available sequences in protein databases reveals that it is most homologous to Ack, an intracellular tyrosine kinase which associates with the GTP-bound form of p21cdc42Hs. Like Ack, Tnk1 consists of an N-terminal kinase domain, a putative SH3 domain immediately C-terminal to the kinase domain, and a proline-rich C-terminal region. Analysis of Tnk1 mRNA expression demonstrates that Tnk1 is expressed in all cord blood, bone marrow and adult blood sub-populations, as well as in most of the leukemia cell lines examined (16 of 20). Hybridization to fetal multi-tissue Northern blots detected several different Tnk1 transcripts in all fetal tissues examined. In contrast, a single Tnk1 transcript was detected in only five of 16 adult tissues examined (prostate, testis, ovary, small intestine and colon). Fluorescence in situ hybridization (FISH) analysis of metaphase chromosomes localized the Tnk1 gene to the short arm of chromosome 17 (17p13.1), near the p53 locus. Thus, Tnk1 is a novel tyrosine kinase that may be involved in signalling pathways utilized broadly during fetal development, more selectively in adult tissues and in cell of the lymphohematopoietic system.

ADP-ribosyl Cyclase↗

Comparative genomics of mycoplasmas.

The mycoplasmas are the smallest and simplest self-replicating organisms. The goal of defining in molecular terms the entire machinery of a living cell by using mycoplasmas as models was put forward by Harold Morowitz in 1984. The recent complete sequencing of the genomes of the human pathogens Mycoplasma genitalium and Mycoplasma pneumoniae brings us much closer to achieving this goal. The M. genitalium genome contains only 479 predicted protein coding sequences (genes) and that of M. pneumoniae 677, as compared with 1703 in Haemophilus influenzae and about 4000 in E. coli. Thus, M. genitalium is apparently the simplest organism capable of independent life with a minimal set of genes. The drastic economization in genetic information must have been associated with the parasitic mode of life of the mycoplasmas. During their reductive evolution from Gram-positive bacteria the mycoplasmas have lost the cell wall and many biosynthetic systems involved in synthesis of macromolecule building blocks provided by their host. Thus, the M. genitalium and M. pneumoniae genomes do not carry any gene involved in amino acid biosynthesis, and very few genes for vitamin, nucleic acid precursor and fatty acid biosynthesis. The mycoplasma genomes carry a minimal set of energy metabolism genes, being content with a restricted supply of ATP needed for their parasitic mode of life. Nevertheless, these minimal organisms carry the essential genes for DNA replication, transcription and translation, but even here gene saving is expressed by a minimal number of rRNA and tRNA genes. A genomic price had been paid to maintain parasitism, so that a significant number of mycoplasmal genes is devoted to adhesins, attachment organelles and variable membrane surface antigens directed towards evasion of the host immune system.

Animals↗