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At least 1,405 records · Page 78Linked to original sources
PubMed1999

Methylmalonyl-CoA mutase encoding gene of Sinorhizobium meliloti.

A cluster of genes on megaplasmid pRmeSU47b, bhbA-D, is required for growth on the polyhydroxyalkanoate degradation pathway intermediates 3-hydroxybutyrate and acetoacetate as sole carbon source. DNA sequence analysis of the bhbA gene indicated that it encoded a protein of 712 amino acids (aa) (78kDa) which appeared to be a homodimeric methylmalonyl-CoA mutase enzyme (EC 5.4.99.2). Cell-free extract of a bhbA::Tn5 mutant was devoid of methylmalonyl-CoA mutase activity, thus confirming the identity of the bhbA-encoded enzyme. The reason for the requirement of methylmalonyl-CoA mutase activity for operation of the polyhydroxyalkanoate degradation pathway is not immediately apparent. Situated immediately upstream of bhbA, in the same orientation, is a gene which is predicted to encode a protein that exhibits remarkable sequence similarity to the alpha subunit of propionyl-CoA carboxylase (EC 6.4.1.3). A mutation in this gene did not affect ability to grow on 3-hydroxybutyrate as sole carbon source. Downstream of, and oriented towards bhbA, was identified a member of the GNTR class of transcriptional regulator-encoding genes. It is not yet known whether this regulatory protein is directly involved in modulation of bhbA expression.

3-Hydroxybutyric Acid↗
PubMed2000

Identification of the gene encoding BmpB, a 30 kDa outer envelope lipoprotein of Brachyspira (Serpulina) hyodysenteriae, and immunogenicity of recombinant BmpB in mice and pigs.

A gene encoding a 30kDa outer envelope protein of the intestinal spirochaete Brachyspira (Serpulina) hyodysenteriae, was cloned and expressed in Escherichia coli strain XLOLR. Five phagemids containing DNA inserts encoding the protein were established and one clone (pSHA) was sequenced. An 816bp hypothetical open reading frame (ORF) was identified, with a potential ribosome binding site (AGGAG), and putative -10 (TATAAT) and -35 (TTGAAA) promoter regions upstream from the ATG start of the ORF. A 12bp inverted repeat sequence, possibly serving as a transcription terminator, was identified downstream from the TAA stop codon. Analysis of the amino acid sequence identified a 19 residue hydrophobic signal peptide, incorporating a potential signal peptidase cleavage site and membrane lipoprotein lipid attachment site. Further analysis of the amino acid usage of this lipoprotein, designated BmpB, showed its possible outer membrane localisation. Comparison of the gene encoding the lipoprotein, bmpB, with GenBank nucleotide sequences showed that it has homology with the gene (plp3) encoding Plp3, an outer membrane lipoprotein of Pasteurella haemolytica (54% identity in 735bp). Comparison of the deduced amino acid sequence with the SWISS-PROT amino acid database revealed greatest homology with the outer membrane lipoproteins (Plp1, 2, 3) of P. haemolytica (34% identity in 242 aa, 37% identity in 250 aa, and 39% identity in 272 aa, respectively), and lipoproteins (rcsF and lipoprotein-28) of E. coli (40% identity in 267 aa and 36% identity in 263 aa, respectively). Three of the recombinant E. coli clones (pSHA, pSHD, and pSHE) were formalinised and used to immunise mice. A bacterin preparation of one recombinant E. coli clone (pSHA) was used to immunise pigs. Sera from these mice and pigs recognised the 30kDa lipoprotein in outer membrane preparations of B. hyodysenteriae, indicating the immunogenicity of recombinant BmpB. Sera from pigs naturally infected with B. hyodysenteriae also reacted with recombinant BmpB expressed in E. coli.

Amino Acid Sequence↗
PubMed2001

The SEF14 fimbrial antigen of Salmonella enterica serovar Enteritidis is encoded within a pathogenicity islet.

The DNA sequence of the chromosomal gene cluster encoding the SEF14 fimbriae of Salmonella enterica serovar Enteritidis was determined. Five contiguous open reading frames, sefABCDE, were identified. The sefE gene shared significant homology with araC-like positive regulators. Serovar-associated virulence plasmid (SAP) genes orf7,8,9 and pefI were identified immediately adjacent to the sef operon. The pefI gene encoded a putative regulator of the Plasmid-encoded fimbrial antigen (PEF) expression. The entire sef--pef region, flanked by two IS-like elements, was inserted adjacent to leuX that encoded a transfer RNA molecule. The organisation of this region was suggestive of a classic pathogenicity islet. Southern hybridisation confirmed two copies of the SAP derived orf7,8,9 and pefI region in S. Enteritidis, one in the chromosome and one on the SAP. Of other group D Salmonella, only S. Blegdam and S. Moscow harboured both chromosomal and plasmid copies of pefI--orf9 region although polymorphism was evident.

Antigens, Bacterial↗
PubMed2002

The Salmonella enterica subspecies I specific centisome 7 genomic island encodes novel protein families present in bacteria living in close contact with eukaryotic cells.

We have determined the genetic structure of the Salmonella enterica centisome 7 genomic island (SCI) located at the aspV loci in S. enterica subspecies I strains. The 47-kb long genomic island encodes 37 putative proteins, including the previously described saf fimbrial operon and the sinR transcriptional regulator. Other open reading frames (designated sci A to Z) in the island encode putative proteins with homologies to virulence-associated proteins in a number of gram-negative bacteria such as Pseudomonas aeruginosa, Yersinia pestis and enterohemorrhagic Escherichia coli, bacteria that have the ability to interact with and manipulate eukaryotic cells. The Sci proteins have putative cytoplasmic, periplasmic and outer membrane localizations pointing to a role in extracellular processes such as secretion or organelle biosynthesis. The genes encoding Sci-like proteins are clustered in all sequenced bacterial genomes available in the databases and a core set can be defined by the presence of genes encoding proteins with similarity to the SciB, C, G, H, I, O proteins. The SCI genomic island DNA sequences are restricted to Salmonella strains belonging to S. enterica subspecies I and deletion of the entire island affects the ability of the organisms to enter eukaryotic cells.

Animals↗
PubMed1997

Expression of mtDNA and nDNA encoded respiratory chain proteins in chemically and genetically-derived Rho0 human fibroblasts: a comparison of subunit proteins in normal fibroblasts treated with ethidium bromide and fibroblasts from a patient with mtDNA depletion syndrome.

Although much progress has been made in identifying genetic defects associated with mitochondrial diseases, the protein expression patterns of most disorders are poorly understood. Here we use immunochemical techniques to describe subunit expression patterns of respiratory chain enzyme complexes II (succinate dehydrogenase: SD) and IV (cytochrome c oxidase: COX) in cultured cells lacking mtDNA (Rho0 cells) derived either chemically by exposure of normal cells to ethidium bromide, or genetically in cells derived from a patient with mtDNA depletion syndrome. Both control cells and early passage patient-derived cells express a normal complement of SD and COX subunit proteins. Ethidium bromide treatment of normal cells and in vitro cell proliferation of patient-derived cells caused both populations to acquire identical Rho0 phenotypes. As expected, they lack mtDNA-encoded subunits COX-I and COX-II. In contrast, nDNA-encoded subunits are affected differentially, with some (COX-VIc) lacking and others (COX-IV, COX-Va, SD 30 and SD 70) maintained at somewhat reduced levels. We suggest that the differential stability of nDNA-encoded subunits in the absence of intact enzyme complexes is due to the ability of some, but not all, subunits to associate as partial complexes in the absence of mtDNA-encoded subunits.

Cells, Cultured↗
PubMed2002

Nobox is a homeobox-encoding gene preferentially expressed in primordial and growing oocytes.

To identify novel genes involved in early mammalian folliculogenesis, we used the Unigene collection of mouse cDNA libraries to identify unique expressed sequence tags in a newborn mouse ovary cDNA library. Nobox (newborn ovary homeobox-encoding gene) was one of several genes identified by in silico (electronic database) subtraction. We cloned the mouse Nobox cDNA and characterized its genomic organization. The gene spans 14kb and is encoded by eight exons. The Nobox gene maps to proximal chromosome 6 in the mouse, and we identified a portion of the human gene encoding a NOBOX homolog which resides at a syntenic position on chromosome 7q35. Reverse transcriptase polymerase chain reaction and Northern blot analyses show that Nobox is preferentially expressed in the ovary at high levels. In situ hybridization analysis demonstrates that Nobox mRNA is present in primordial and growing oocytes. Nobox is one of the first homeobox-encoding genes preferentially expressed during mammalian folliculogenesis.

Amino Acid Sequence↗
PubMed2001

Event related brain potentials and illusory memories: the effects of differential encoding.

This study investigates event related potentials (ERP) elicited by true and false recognition using words from different semantic categories. In Experiment 1, ERPs for true and false recognition were more positive than for correctly rejected NEW words starting around 300 ms after test word presentation (old/new ERP effects). ERP waveforms for true and false recognition revealed equal early (300-500 ms) fronto-medial old/new ERP effects, reflecting similar familiarity processes, but smaller parietal old/new ERP effects (500-700 ms) for false relative to true recognition, suggesting less active recollection. Interestingly, a subsequent performance based group comparison showed equivalent old/new ERP effects for true and false recognition for participants with high rates of false recognition. In contrast, false recognition failed to elicit an old/new ERP effect in a group with low false recognition rates. To examine whether this between group difference was driven by the differential use of information that studied words and semantically related non studied test words (LURE) have in common (conceptual similarity), we manipulated encoding strategy in Experiment 2. When encoding focused on conceptual similarity, comparable ERP-effects for true and false recognition were obtained, suggesting that both forms of recognition were equally based on familiarity and recollection processes. Conversely, when encoding was focused on item specific features, differences in brain activity for true and false recognition were obtained. The ERP data indicate that, in addition to the false recognition rate, strategic processes during encoding, such as processing conceptual features, are an important factor in determining electrophysiological differences between true and false recognition.

Adult↗
PubMed2001

Attention and successful episodic encoding: an event-related potential study.

Event-related potentials (ERPs) were used to delineate the cerebral processes occurring when information is encoded into episodic memory and to determine how these processes are affected by divided attention. ERPs were recorded during encoding under focused or divided attention, and were selectively averaged on the basis of their retrieval during later free recall and recognition tests (with remember-know judgments). Items retrieved with conscious recollection of the encoding episode (remembered, recalled) were distinguished at encoding from later missed items by an enhanced left fronto-temporal negative wave (N340), a negative posterior sustained potential and a positive frontal sustained potential. These effects occurred independently of the level of attention. Items later retrieved on the basis of familiarity (known) elicited a larger N340 than missed items, but did not demonstrate the increased sustained potentials. We suggest that item-specific conceptual processing (N340) is sufficient to produce familiarity-based recognition, but additional elaborative processing (sustained interaction of frontal and posterior regions) is necessary for conscious recollection. The effect of divided attention on these processes was related to the difficulty of the secondary task, with the more difficult task causing greater and earlier interference.

Adult↗
PubMed2001

Encoding and retrieval related cerebral activation in continuous verbal recognition.

The differential neuronal activation related to encoding of novel and recognition of previously studied items and the effect of retrieval effort on neuronal activation were assessed in a event-related functional magnetic resonance imaging experiment. A verbal continuous recognition task with two repetitions of the target items was used. The interpretation of the results was focused on brain areas that have been previously reported to be involved in explicit memory. Encoding of novel words in comparison with the first repetition was associated with a stronger activation in the left parahippocampal and inferior frontal gyrus. Encoding of novel words compared to the second repetition was related to a greater bifrontal activation. Recognition of studied items was associated with greater activation in the medial and bilateral inferior parietal lobe at first repetition and in the medial and left inferior parietal lobe at second repetition in comparison with encoding of the novel items. Recognition at first repetition compared to recognition at second repetition was associated with greater bilateral frontal activation. The results are discussed in relation to current concepts of spatial differentiation of memory function and findings from event-related potentials studies of continuous recognition.

Adult↗
PubMed2003

Item-related versus task-related activity during encoding and retrieval in verbal and non-verbal episodic memory: an event-related potential study.

In the past 10 years, functional neuroimaging studies have elucidated the role of the prefrontal cortex in memory encoding and retrieval. However, it is still unclear whether these activations reflect item- or task-related activities. In the present study, Event-Related Potentials (ERPs) were used to distinguish item-related activity from task-related activity in both encoding and retrieval processes. This activity was assessed with both verbal and non-verbal material. A recognition paradigm with words or random shapes was administered to 12 young participants. Memory elicited ERPs were compared to those evoked by control tasks that used similar material. The distribution of the N400 was found to be larger on left frontal than right frontal areas for verbal material, however, this was the case in the control and memory conditions as well. This finding likely reflects the sensitivity of this component to processing verbal material. The LPC amplitude was greater in the non-verbal encoding than the non-verbal control condition, whereas in retrieval it was larger than the control condition for both verbal and non-verbal material. Thus, item-related activity is determined by an interaction between properties of the material and the task instructions. Task-related activity was found for non-verbal material: compared to the control condition, the memory condition of non-verbal material elicited bilateral and right frontal activity in encoding and retrieval processes. No task-related effect was reported with the verbal material. Material differences in eliciting task-related effects are discussed in terms of their relation to elaborative and effortful processes.

Adult↗
PubMed1997

Encoding behavioral context in recurrent networks of the fronto-striatal system: a simulation study.

This research addresses the hypothesis that behavioral context is encoded in recurrent networks of the fronto-striatal system. Behavioral context influences the processing of subsequent brain events, including responses to sensory inputs, thus providing a basis for context-dependent behavior. We define context-dependent behavior as the adaptive ability to produce the appropriate response to a given stimulus, dependent upon the context in which it appears. Behavioral context can change with a time-scale on the order of seconds to tens of seconds or more. This suggests a flexible mechanism that encodes context via an ensemble of neural activation that will appropriately influence the processing of subsequent sensory stimuli. We present a functional model of context encoding in recurrent connections of the fronto-striatal system with simulation results that correspond closely to empirical data. Neuronal activity in monkeys that perform a context-dependent task indicate that the prefrontal cortex and striatum participate differentially in this kind of context encoding. Likewise, simulated neurons in our model of the fronto-striatal system, which performs the context-dependent task, display task-related activity remarkably similar to that found in monkey frontal cortex and striatum, supporting our hypothesis.

Adaptation, Psychological↗
PubMed2003

Flow encoded NMR spectroscopy for quantification of metabolite flow in intact plants.

An NMR flow quantification technique applicable to metabolite flow in plants is presented. It combines flow sensitive magnetization preparation with slice selective spectroscopy. Flow encoded NMR spectroscopy is described to quantify, for the first time, flow velocities of metabolites in plants non-invasively. Flow sensitivity is introduced by magnetization preparation based on a stimulated echo experiment, prior to slice selective spectroscopy. For flow quantification eight different flow-weighted spectra are collected. With this flow preparation very slow flow velocities down to 0.1mm/s can be detected and small amounts of flowing metabolites can be observed despite the large background signal of stationary and flowing water. Important sequence optimization steps include appropriate choice of experimental parameters used for flow encoding as well as complete balancing of eddy currents from the flow encoding gradients. The method was validated in phantom experiments and applied in vivo. Examples of quantitative flow measurements of water and metabolites in phantoms and plants are provided to demonstrate the reliability and the performance of flow encoded spectroscopy.

Magnetic Resonance Spectroscopy↗
PubMed2002

Molecular cloning and expression of a cDNA encoding the luciferase from the firefly, Hotaria unmunsana.

We have cloned and characterized a cDNA encoding the luciferase from the firefly, Hotaria unmunsana. The cDNA encoding the luciferase of H. unmunsana was isolated by RT-PCR with a gene-specific primer set. The cDNA encoding the luciferase of H. unmunsana is 1644 base pairs long with an open reading frame of 548 amino acid residues. The deduced amino acid sequence of the luciferase gene of H. unmunsana showed 98.0 and 96.8% identity to H. parvula and Luciola mingrelica, respectively. Phylogenetic analysis further confirmed that the deduced amino acid sequences of the H. unmunsana luciferase gene belonged to the same subfamily, Luciolinae. Southern blot analysis of genomic DNA suggested the presence of the H. unmunsana luciferase gene as a single copy and Northern blot analysis confirmed light organ-specific expression at the transcriptional level. The cDNA encoding the luciferase of H. unmunsana was expressed as a 61-kDa band in the baculovirus-infected insect cells and the extracts of the recombinant baculovirus-infected cells emitted luminescence in the luciferase activity assay.

Amino Acid Sequence↗
PubMed2003

Cloning and expression of a cDNA encoding a matrix peptide associated with calcification in the exoskeleton of the crayfish.

Calcification-associated peptide (CAP)-1 isolated from the exoskeleton of the crayfish, Procambarus clarkii, has anti-calcification activity and chitin-binding ability and is, therefore, considered to be associated with calcification. In this study, a cDNA encoding CAP-1 was cloned and characterized. An open reading frame encoded a pre-propeptide of 99 amino acid residues, which was composed of a signal peptide, a CAP-1 precursor and two-basic amino acid residues at the C-terminus. The dibasic residues were not observed in the natural CAP-1. Expression analyses using Northern blot and RT-PCR revealed that the mRNA encoding CAP-1 was strongly expressed in the epidermal tissue during the postmolt stage, where and when the calcification takes place. These results support that CAP-1 may play an important role in the calcification of the exoskeleton. Based on the nucleotide sequence of the cDNA encoding CAP-1, a recombinant CAP-1 and that carrying the basic residues at the C-terminus were expressed in Escherichia coli. Anti-calcification assay showed that these recombinant peptides were less active than natural CAP-1, indicating that the phosphate group at the 70th residue, Ser, in natural CAP-1 is important for inhibitory activity and that the paired basic residues have some contribution to the elevation of inhibitory activity.

Amino Acid Sequence↗
PubMed2002

Characterization of the human gene encoding alpha-aminoadipate aminotransferase (AADAT).

In mammals, the conversion of alpha-aminoadipate to alpha-ketoadipate by alpha-aminoadipate aminotransferase (AADAT) is an intermediate step in lysine degradation. A gene encoding for alpha-aminoadipate aminotransferase and kynurenine aminotransferase activities had been previously identified in the rat (KAT/AadAT). We identified the human gene (AADAT) encoding for AADAT. It has a 2329 bp cDNA, a 1278 bp open-reading frame, and is predicted to encode 425 amino acids with a mitochondrial cleavage signal and a pyridoxal-phosphate binding site. AADAT is 73% and 72% identical to the mouse and rat orthologs, respectively. The genomic structure spans 30 kb and consists of 13 exons. FISH studies localized the gene to 4q32.2. Two transcripts (approximately 2.9 and approximately 4.7 kb) were identified, with expression highest in liver. Bacterial expression studies confirm that the gene encodes for AADAT activity. The availability of the DNA sequence and enzyme assay will allow further evaluation of individuals suspected to have defects in this enzyme.

2-Aminoadipate Transaminase↗
PubMed2001

Solutions for library encoding to create collections of discrete compounds.

The ability to design, produce, analyze, and manage high quality combinatorial libraries depends on the encoding strategy applied. Several recent advances in encoding technology have extended the range of library design parameters. Enhancements of established techniques have made them more robust and versatile, while additional new and creative encoding concepts have been introduced. With better options now available, combinatorial chemists can more easily select an encoding technique to match resources, library design, and compound management criteria.

Combinatorial Chemistry Techniques↗
PubMed2004

Cloning of a novel tyrosinase-encoding gene (melB) from Aspergillus oryzae and its overexpression in solid-state culture (Rice Koji).

We have cloned a novel tyrosinase-encoding gene (melB) specifically expressed in solid-state culture of Aspergillus oryzae. A tyrosinase-encoding gene (melO) from A. oryzae was already cloned and the protein structures of its catalytic and copper binding domains were investigated. However, our recent results revealed that the melO gene was highly expressed in submerged culture but not in solid-state culture. Because tyrosinase activity was also detected in solid-state culture, we assumed that another tyrosinase gene other than melO is expressed in solid-state culture. Another tyrosinase gene was screened using the expressed sequence tag (EST) library. One redundant cDNA clone homologous with the tyrosinase gene was found in the collection of wheat bran culture. Northern blot analysis revealed that the gene corresponding to the cDNA clone was specifically expressed in solid-state culture (koji making), but not in submerged culture. Molecular cloning showed that the gene carried six exons interrupted by five introns and had an open reading frame encoding 616 amino acid residues. This gene was designated as melB. The deduced amino acid sequence of the gene had weak homology (24%-33%) with MelO and other fungal tyrosinases but the sequences of the copper binding domains were highly conserved. When the melB gene was expressed under the control of the glaB promoter in solid-state culture, tyrosinase activity was markedly enhanced and the culture mass was browned with the melanization by MelB tyrosinase. These results indicated that the melB gene encodes a novel tyrosinase associated with melanization in solid-state culture.

Journal Article↗
PubMed2004

Isolation and characterization of a novel gene encoding alpha-L-arabinofuranosidase from Aspergillus oryzae.

We cloned and characterized a novel gene (abfA) encoding alpha-L-arabinofuranosidase (alpha-L-AFase) from Aspergillus oryzae. One clone homologous to the alpha-L-AFase gene of Thermotoga maritima was found in an expressed sequence tag (EST) library of A. oryzae and a corresponding gene was isolated. Molecular analysis showed that the abfA gene carried six exons interrupted by five introns and had an open reading frame encoding 481 amino acid residues. The amino acid sequence similarity at active sites to the alpha-L-AFases from other organisms indicated that the alpha-L-AFase encoded by abfA was classified as a family 51 glycoside hydrolase. When the abfA was overexpressed in the homologous hyperexpression system of A. oryzae, a large amount of alpha-L-AFase was produced as intracellular protein. The apparent molecular mass of the purified enzyme was estimated to be 228,000 by gel filtration and that of its subunit as 55,000 by SDS-PAGE, suggesting that the enzyme is a tetramer. The enzyme hydrolyzed p-nitrophenyl-alpha-L-arabinofuranoside but not other p-nitrophenyl glycosides. These results demonstrated that the abfA gene encodes a functional alpha-L-AFase.

Journal Article↗