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At least 1,783 records · Page 99Linked to original sources
PubMed1987

Evidence for prokaryotic transcription and translation control regions in the human factor IX gene.

A human factor IX cDNA clone isolated from a liver cDNA library constructed in phage lambda gt11 vector was shown to express factor IX protein in Escherichia coli. A factor IX immunospecific protein of 46.8 kDa was expressed, but was not a beta-galactosidase-factor IX fusion protein. Expression was seen when the factor IX cDNA was cloned into two different vector systems, lambda gt11 and pUC9, in both orientations with respect to the vector lacZ promoter. The expression of factor IX was not under control of the lacZ promoter of either vector system. In addition, when the factor IX cDNA fragment was subcloned in both orientations into a promoterless cloning vector (p CPP3), the factor IX cDNA fragment demonstrated promoter activity when inserted in only one orientation resulting in expression of chloramphenicol acetyl transferase in E. coli and Bacillus subtilis. A DNA computer search of the N-terminal sequences of the factor IX gene revealed prokaryotic-like promoter and ribosome-binding site (RBS) sequences with strong homology to the E. coli consensus sequences. The predicted sites homologous with prokaryotic promoter and RBS consensus sequences are followed by an in-frame methionine which could correspond to the translation start codon of the expressed factor IX. This report provides the first evidence that a eukaryotic gene encodes the information necessary for both transcription and translation to control gene expression in a prokaryotic host.

Bacteriophage lambda↗
PubMed2004

An improved prediction of chloroplast proteins reveals diversities and commonalities in the chloroplast proteomes of Arabidopsis and rice.

Proteins that form part of the chloroplast proteome can be identified by computational prediction of the N-terminal presequences (chloroplast transit peptides, cTPs) of their cytoplasmic precursor proteins. The accuracy of four different cTP predictors has been evaluated on a test set of 4500 proteins whose subcellular localization is known, and was found to be substantially lower than previously reported. A combination of cTP prediction programs was superior to any one of the predictors alone. This combination was employed to estimate the size and composition of the chloroplast proteomes of Arabidopsis and rice, and about 2100 (Arabidopsis thaliana) and 4800 (Oryza sativa) different chloroplast proteins with a cTP are predicted to be encoded by their nuclear genomes. A subset of around 900 chloroplast proteins, predominantly derived from the cyanobacterial endosymbiont and with functions mostly related to metabolism, energy and transcription, is shared by the two species. This points to the existence of both conserved nucleus-encoded chloroplast proteins that are predominantly of prokaryotic origin, and a large fraction of taxon-specific chloroplast-targeted proteins, in flowering plants.

Arabidopsis↗
PubMed1998

A novel bacteriocin with a YGNGV motif from vegetable-associated Enterococcus mundtii: full characterization and interaction with target organisms.

A novel broad-spectrum antimicrobial peptide produced by vegetable-associated Enterococcus mundtii was purified and characterized, and designated mundticin. To our knowledge, this is the first report on bacteriocin production by this organism. The elucidation of the full primary amino acid sequence of mundticin (KYYGNGVSCNKKGCSVDWGKAIGIIGNNSAANLATGGAAGWSK) revealed that this antimicrobial peptide belongs to the class IIa bacteriocins of lactic acid bacteria which share a highly conserved N-terminal 'YGNGV' motif. Data obtained by computer modelling indicated an oblique orientation of the alpha-helical regions of mundticin and homologous class IIa bacteriocins at a hydrophobic-hydrophilic interface, which may play a role in the destabilization of phospholipid bilayers. The average mass of mundticin, as determined by electron spray mass spectrometry, was found to be 4287.21+/-0.59 Da. With respect to its biological activity, mundticin was shown to inhibit the growth of Listeria monocytogenes, Clostridium botulinum and a variety of lactic acid bacteria. Moreover, it was demonstrated to have a bactericidal effect on L. monocytogenes as a result of the dissipation of the membrane potential, and a loss of intracellular ATP in absence of ATP leakage. Its good solubility in water, and its stability over a wide pH and temperature range indicate the potential of this broad spectrum bacteriocin as a natural preservation agent for foods.

Amino Acid Sequence↗
PubMed1986

L-aspartate ammonia-lyase and fumarate hydratase share extensive sequence homology.

Based on our recent determinations of the nucleotide sequences of the L-aspartate ammonia-lyase genes from Escherichia coli and Pseudomonas fluorescens, primary structures of the two L-aspartate ammonia-lyases and fumarate hydratases from Bacillus subtilis and E. coli (N-terminal partial sequence) were compared by computer analysis. These four enzymes exhibited a significant homology of at least 37%, implying that L-aspartate ammonia-lyase and fumarate hydratase share a common evolutionary origin. To authors' knowledge, this feature appears to be the first example showing that two kinds of enzymes catalyzing different types of reactions, albeit similar, share such a high degree of sequence homology.

Amino Acid Sequence↗
PubMed2000

Structure-function studies on Taiwan cobra long neurotoxin homolog.

A novel long neurotoxin homolog was purified from Naja naja atra (Taiwan cobra) venom using the combination of ion exchange chromatography and reverse phase high performance liquid chromatography. The determined protein sequence was essentially the same as that deduced from the cDNA amplified by reverse transcriptase-polymerase chain reaction. The long neurotoxin homolog exhibited an activity that inhibited acetylcholine-induced muscle contractions, as with N. naja atra cobrotoxin. The degree of inhibition caused by the addition of long neurotoxin homolog was approximately 70% of that observed with the addition of cobrotoxin. Unlike the well-known short and long neurotoxins, this neurotoxin homolog contained two additional cysteine residues forming a disulfide linkage in the N-terminal region. Circular dichroism measurement and computer models of the neurotoxin reveal that its secondary structure was not abundant in beta-sheet as noted with short and long neurotoxins. This less ordered structure may be associated with the lower activity noted with the long neurotoxin homolog. Together with the finding that the known long neurotoxin homologs exclusively appear in the venoms of the Naja and Bungarus genera, the long neurotoxin homologs should represent an evolutionary branch from the long and short neurotoxins in the Elapidae family.

Amino Acid Sequence↗
PubMed2002

Proteomics reveals protein profile changes in doxorubicin--treated MCF-7 human breast cancer cells.

MCF-7 cells are extensively used as a cell model to investigate human breast tumors and the cellular mechanism of antitumor drugs such as doxorubicin (DOX), an anthracycline antitumor drug widely used in clinical chemotherapy. To understand the effects of DOX on the protein expression, we perform a comprehensive proteomics to survey global changes in proteins after DOX treatment in MCF-7 cells. Exposure of MCF-7 cells to 0.1 microM DOX for 2 days induced a differentiation-like phenotype with prominent perinuclear autocatalytic vacuoles, abundant filamentous material, and irregular microvilli at the cell surface. In this study, we also present a proteome reference map of MCF-7 cells with 21 identified protein spots via analysis of N-terminal sequencing, mass spectrometry, immunoblot and/or computer matching with protein database. Based on the proteome map, we found that DOX causes a markedly decrease in the levels of three isoforms of heat shock protein 27 (HSP27) whereas the levels of other stress associated proteins including HSP60, calreticulin, and protein disulfide isomerase were not significantly altered in DOX-treated MCF-7 cells. Taken together, we suggest that that action of DOX on breast tumor cells may be partly related to dysregulation of HSP27 expression. Modulation of HSP27 levels may be a clinically useful potential target for design of antitumor drugs and controlling breast tumor growth.

Antineoplastic Agents↗
PubMed2004

Neocognitron capable of incremental learning.

This paper proposes a new neocognitron that accepts incremental learning, without giving a severe damage to old memories or reducing learning speed. The new neocognitron uses a competitive learning, and the learning of all stages of the hierarchical network progresses simultaneously. To increase the learning speed, conventional neocognitrons of recent versions sacrificed the ability of incremental learning, and used a technique of sequential construction of layers, by which the learning of a layer started after the learning of the preceding layers had completely finished. If the learning speed is simply set high for the conventional neocognitron, simultaneous construction of layers produces many garbage cells, which become always silent after having finished the learning. The proposed neocognitron with a new learning method can prevent the generation of such garbage cells even with a high learning speed, allowing incremental learning.

Cognition↗
PubMed2002

Viral RNA-polymerases -- a predicted 2'-O-ribose methyltransferase domain shared by all Mononegavirales.

The Mononegavirales virus group comprises several major human pathogens, including measles, rabies and Ebola viruses. This article reports a computational analysis of the C-terminal region of RNA-dependent RNA-polymerases from Mononegavirales. Using a combination of sequence similarity and threading analysis, a 2'-O-ribose methyltransferase domain was identified that is involved in the capping of viral mRNAs.

Amino Acid Sequence↗
PubMed2001

Switching devices based on interlocked molecules.

An architectural rationale and an experimental program aimed at the development of molecular electronics switching devices for memory and computing applications are discussed. Two-terminal molecular switch tunnel junctions are identified as the critical device components of molecular electronics-based circuitry. They can be tiled in two dimensions and are tolerant of manufacturing defects. Singly and multiply configurable solid-state switching devices that are based upon electrochemically switchable molecular and supramolecular systems are discussed in terms of both the synthesis of the molecular components and the fabrication and performance of the devices.

Electrochemistry↗
PubMed2002

Interaction of influenza A virus M1 matrix protein with caspases.

In this investigation, an ability of influenza A virus M1 matrix protein to bind intracellular caspases, the key enzymes of cell apoptosis, has been examined. Protein-protein binding on polystyrene plates and polyvinyl pyrrolidone membrane was employed for this purpose. Under a comparative study of caspases-3, -6, -7, -8 influenza virus M1 protein specifically bound caspase-8 and weakly bound caspase-7. Using a computer analysis of the N-terminal region of M1 protein, a site similar to the anti-caspase site of baculovirus p35 protein, which inhibits caspases and displays antiapoptotic activity, was identified. These results are in good agreement with the supposition that influenza virus M1 protein is involved in a caspase-8-mediated apoptosis pathway in influenza virus infected cells.

Amino Acid Sequence↗
PubMed1999

Gambling and the Health of the Public: Adopting a Public Health Perspective.

During the last decade there has been an unprecedented expansion of legalized gambling throughout North America. Three primary forces appear to be motivating this growth: (1) the desire of governments to identify new sources of revenue without invoking new or higher taxes; (2) tourism entrepreneurs developing new destinations for entertainment and leisure; and (3) the rise of new technologies and forms of gambling (e.g., video lottery terminals, powerball mega-lotteries, and computer offshore gambling). Associated with this phenomenon, there has been an increase in the prevalence of problem and pathological gambling among the general adult population, as well as a sustained high level of gambling-related problems among youth. To date there has been little dialogue within the public health sector in particular, or among health care practitioners in general, about the potential health impact of gambling or gambling-related problems. This article encourages the adoption of a public health perspective towards gambling. More specifically, this discussion has four primary objectives:1. Create awareness among health professionals about gambling, its rapid expansion and its relationship with the health care system;2. Place gambling within a public health framework by examining it from several perspectives, including population health, human ecology and addictive behaviors;3. Outline the major public health issues about how gambling can affect individuals, families and communities;4. Propose an agenda for strengthening policy, prevention and treatment practices through greater public health involvement, using the framework of The Ottawa Charter for Health Promotion as a guide.By understanding gambling and its potential impacts on the public's health, policy makers and health practitioners can minimize gambling's negative impacts and appreciate its potential benefits.

Journal Article↗
PubMed1986

Nucleic acid secondary structure prediction and display.

A set of programs has been developed for the prediction and display of nucleic acid secondary structures. Information from experimental data can be used to restrict or enforce secondary structural elements. The predictions can be displayed either on normal line printers or on graphic devices like plotters or graphic terminals.

Animals↗
PubMed1990

Nucleotide sequence of the gene encoding the spike glycoprotein of human coronavirus HCV 229E.

The gene encoding the spike glycoprotein of the human coronavirus HCV 229E has been cloned and sequenced. This analysis predicts an S polypeptide of 1173 amino acids with an Mr of 128,600. The polypeptide has 30 potential N-glycosylation sites. A number of structural features typical of coronavirus S proteins can be recognized, including a signal sequence, a membrane anchor, heptad repeat structures and a carboxy-terminal cysteine cluster. A detailed, computer-aided comparison with the S proteins of infectious bronchitis virus, feline infectious peritonitis virus, transmissible gastroenteritis virus and murine hepatitis virus, strain JHM is presented. We have also done a Northern blot analysis of viral RNAs in HCV 229E-infected cells using synthetic oligonucleotides. On the basis of this analysis, and by analogy to the replication strategy of other coronaviruses, we are able to propose a model for the organization and expression of the HCV 229E genome.

Amino Acid Sequence↗
PubMed1994

Sequence analysis and location of capsid proteins within RNA 2 of strawberry latent ringspot virus.

The nucleotide sequence of the RNA 2 of a strawberry isolate (H) of strawberry latent ringspot virus (SLRSV) comprised 3824 nucleotides and contained one long open reading frame with a theoretical coding capacity of 890 amino acids equivalent to a protein of 98.8K. The N-terminal amino acid sequences of virion-derived proteins were determined by Edman degradation allowing the capsid coding regions to be located and serine/glycine cleavage sites to be identified within the polyprotein. The amino acid sequence in the capsid coding region of an isolate of SLRSV from flowering cherry in New Zealand was 97% identical to that of SLRSV-H. Except in the 3' and 5' terminal non-coding sequences, computer-based alignment and comparison algorithms did not reveal any substantial homologies between RNA 2 of SLRSV-H and the equivalent genomic segments in the nepoviruses arabis mosaic, cherry leaf roll, grapevine fanleaf, raspberry ringspot, grapevine hungarian chrome mosaic, tomato blackring, tomato ringspot, tobacco ringspot, or in the comoviruses cowpea mosaic and red clover mottle. Despite the similarities in overall genome organization, data from RNA 2 remain insufficient for unambiguous positioning of SLRSV in relation to species/genera in the Comoviridae.

Amino Acid Sequence↗
PubMed2006

Dynamics of yeast prion aggregates in single living cells.

Prions are propagating proteins that are ordered protein aggregates, in which the phenotypic trait is retained in the altered protein conformers. To understand the dynamics of the prion aggregates in living cells, we directly monitored the fate of the aggregates using an on-chip single-cell cultivation system as well as fluorescence correlation spectroscopy (FCS). Single-cell imaging revealed that the visible foci of yeast prion Sup35 fused with GFP are dispersed throughout the cytoplasm during cell growth, but retain the prion phenotype. FCS showed that [PSI+] cells, irrespective of the presence of foci, contain diffuse oligomers, which are transmitted to their daughter cells. Single-cell observations of the oligomer-based transmission provide a link between previous in vivo and in vitro analyses of the prion and shed light on the relationship between the protein conformation and the phenotype.

Cell Survival↗
PubMed1997

Molecular cloning of the hamster CMP-sialic acid transporter.

Chinese hamster ovary (CHO) glycosylation mutants of the Lec2 complementation group are unable to express sialylated glycoproteins and glycolipids due to a defect in the Golgi CMP-sialic acid transporter (CMP-Sia-Tr). Using an expression cloning strategy, we isolated a cDNA encoding the hamster CMP-Sia-Tr which complements the Lec2 phenotype. The deduced amino acid sequence of the cloned cDNA shows 95% identity to the recently cloned murine CMP-Sia-Tr. The expression of a hamster CMP-Sia-Tr fusion protein with an N-terminal MDYKDDDDK (FLAG) sequence revealed Golgi localisation of the transporter. Amino acid sequence comparison revealed strong similarity (44.6% identity and 19.3% similarity) of CMP-Sia-Tr to the recently cloned human UDP-galactose transporter (UDP-Gal-Tr). In contrast, sequence similarities to the yeast UDP-N-acetylglucosamine transporter (UDP-GlcNAc-Tr) and the GDP-mannose transporter (GDP-Man-Tr) of Leishmania donovani are restricted to a region encoding the two most C-terminally located transmembrane helices. A computer-based structural analysis of CMP-Sia-Tr proposes an eight transmembrane helix model with the N- and C-termini located on the cytosolic side of the Golgi membrane.

Amino Acid Sequence↗
PubMed2001

Compartmentalized and binary behavior of terminal dendrites in hippocampal pyramidal neurons.

The dendritic arbor of pyramidal neurons is not a monolithic structure. We show here that the excitability of terminal apical dendrites differs from that of the apical trunk. In response to fluorescence-guided focal photolysis of caged glutamate, individual terminal apical dendrites generated cadmium-sensitive all-or-none responses that were subthreshold for somatic action potentials. Calcium transients produced by all-or-none responses were not restricted to the sites of photolysis, but occurred throughout individual distal dendritic compartments, indicating that electrogenesis is mediated primarily by voltage-gated calcium channels. Compartmentalized and binary behavior of parallel-connected terminal dendrites can greatly expand the computational power of a single neuron.

2-Amino-5-phosphonovalerate↗
PubMed1993

The ams-1 and rne-3071 temperature-sensitive mutations in the ams gene are in close proximity to each other and cause substitutions within a domain that resembles a product of the Escherichia coli mre locus.

Two temperature-sensitive mutations, ams-1 and rne-3071, in the ams (altered mRNA stability) gene have been used extensively to investigate the processing and decay of RNA in Escherichia coli. We have sequenced these temperature-sensitive alleles and found that the mutations are separated by only 6 nucleotides and cause conservative amino acid substitutions next to a possible nucleotide-binding site within the N-terminal domain of the Ams protein. Computer analysis revealed that the region altered by the mutations has extensive sequence similarity to a predicted gene product from the mre (murein pathway cluster e) locus of E. coli, which has been implicated previously in determining bacterial cell shape.

Adenosine Triphosphate↗