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Accession Number (accession + number)
Kinds of Accession Number Selected AbstractsIdentification of mariner elements from house flies (Musca domestica) and German cockroaches (Blattella germanica)INSECT MOLECULAR BIOLOGY, Issue 4 2004N. Liu Abstract Full-length mariner elements were isolated and sequenced from house flies (Musca domestica) and German cockroaches (Blattella germanica). The amino acid sequence of the house fly mariner element (accession number: AF373028) showed 99.5% identity with Mos1 and peach elements, whereas the German cockroach mariner element (accession number: AF355143) showed 98.8% and 99.8% identity, respectively. Sequence analysis revealed that the mariner elements in house flies and German cockroaches differed from the active Mos1 mariner element by seven and 15 nucleotides, respectively. Four essential nucleotide substitutions at positions 64, 154, 305, and 1203, which have been proposed to contribute to the loss of activity of the inactive elements, were detected in the German cockroach mariner element. In contrast, although the mariner element in house flies contained substitutions at positions 64, 154, and 305, it retained T at position 1203, identical to active mariner elements. Mariner is present in approximately eight copies in the German cockroach genome. [source] Identification and functional analysis of a human homologue of the monkey replication origin ors8JOURNAL OF CELLULAR BIOCHEMISTRY, Issue 6 2006Mario Callejo Abstract We previously isolated from African green monkey (CV-1) cells a replication origin, ors8, that is active at the onset of S-phase. Here, its homologous sequence (hors8, accession number: DQ230978) was amplified from human cells, using the monkey-ors8-specific primers. Sequence alignment between the monkey and the human fragment revealed a 92% identity. Nascent DNA abundance analysis, involving quantification by real-time PCR, indicated that hors8 is an active replication origin, as the abundance of nascent DNA from a genomic region containing it was 97-fold higher relative to a non-origin region in the same locus. Furthermore, the data showed that the hors8 fragment is capable of supporting the episomal replication of its plasmid, when cloned into pBlueScript (pBS), as assayed by the DpnI resistance assay after transfection of HeLa cells. A quantitative chromatin immunoprecipitation (ChIP) assay, using antibodies against Ku, Orc2, and Cdc6, showed that these DNA replication initiator proteins were associated in vivo with the human ors8 (hors8). Finally, nascent DNA abundance experiments from human cells synchronized at different phases of the cell cycle revealed that hors8 is a late-firing origin of DNA replication, having the highest activity 8 h after release from late G1. J. Cell. Biochem. 99: 1606,1615, 2006. © 2006 Wiley-Liss, Inc. [source] A New Farnesyl Diphosphate Synthase Gene from Taxus media Rehder: Cloning, Characterization and Functional ComplementationJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 6 2006Zhi-Hua Liao Abstract Farnesyl diphosphate synthase (FPS; EC 2.5.1.10) catalyzes the production of 15-carbon farnesyl diphosphate which is a branch-point intermediate for many terpenoids. This reaction is considered to be a rate-limiting step in terpenoid biosynthesis. Here we report for the first time the cloning of a new full-length cDNA encoding farnesyl diphosphate synthase from a gymnosperm plant species, Taxus media Rehder, designated as TmFPS1. The full-length cDNA of TmFPS1 (GenBank accession number: AY461811) was 1 464 bp with a 1 056-bp open reading frame encoding a 351-amino acid polypeptide with a calculated molecular weight of 40.3 kDa and a theoretical pI of 5.07. Bioinformatic analysis revealed that TmFPS1 contained all five conserved domains of prenyltransferases, and showed homology to other FPSs of plant origin. Phylogenetic analysis showed that farnesyl diphosphate synthases can be divided into two groups: one of prokaryotic origin and the other of eukaryotic origin. TmFPS1 was grouped with FPSs of plant origin. Homology-based structural modeling showed that TmFPS1 had the typical spatial structure of FPS, whose most prominent structural feature is the arrangement of 13 core helices around a large central cavity in which the catalytic reaction takes place. Our bioinformatic analysis strongly suggests that TmFPS1 is a functional gene. Southern blot analysis revealed that TmFPS1 belongs to a small FPS gene family in T. media. Northern blot analysis indicated that TmFPS1 is expressed in all tested tissues, including the needles, stems and roots of T. media. Subsequently, functional complementation with TmFPS1 in a FPS-deficient mutant yeast demonstrated that TmFPS1 did encode farnesyl diphosphate synthase, which rescued the yeast mutant. This study will be helpful in future investigations aiming at understanding the detailed role of FPS in terpenoid biosynthesis flux control at the molecular genetic level. (Managing editor: Wei Wang) [source] OsEF3, a homologous gene of Arabidopsis ELF3, has pleiotropic effects in ricePLANT BIOLOGY, Issue 5 2009C. Fu Abstract Heading date is an important agronomic trait in rice. A rice mutant with a late heading date and no photoperiodic sensitivity in long or short day conditions was obtained from rice T-DNA insertion mutants in Zhonghua11 (ZH11). Through isolation and analysis of the flanking sequence of the T-NDA insertion site, the target sequence of insertion was obtained and found to locate in AP003296, the sequence accession number of rice chromosome 1 of RGP (http://rgp.dna.affrc.go.jp). The putative amino acid sequences of this target gene are homologous to the Arabidopsis protein ELF3 encoded by an early flowering gene. The rice target gene orthologous to Arabidopsis ELF3 is named OsEF3; this encodes a putative nematode responsive protein-like protein. OsEF3 has pleiotropic effects in rice that differ from the effects of Arabidopsis ELF3, which only affects biological rhythms. OsEF3 regulates heading date by influencing the BVG stage and does not affect photoperiodic sensitivity, which suggests that the OsEF3 gene may be involved in an autonomous pathway in rice. OsEF3 may affect root development and kilo-grain weight by delaying cell division or cell elongation. [source] Evaluations of lactic acid bacteria as probiotics for juvenile seabass Lates calcariferAQUACULTURE RESEARCH, Issue 2 2008Sirirat Rengpipat Abstract Lactic acid bacteria (LAB) were isolated from adult, wild-caught and farmed seabass (Lates calcarifer) intestines for evaluation as possible probiotics using the well agar diffusion method. Five LAB isolates (designated as LAB-1,5) were found to inhibit Aeromonas hydrophila, a known seabass pathogen. Median lethal concentrations (LC50) of A. hydrophila on juvenile seabass were measured in aquaria. Median lethal concentration values of 7.76, 7.47 and 7.26 log10 CFU mL,1 for 72, 96 and 120 h, respectively, were found. Juvenile seabass (0.6±0.2 g) were cultured in aquaria and fed individual LAB-1,5 fortified feeds with 7 log10 CFU g,1 LAB. Seabass fed LAB-4 fortified feed had significantly greater growth (P<0.05) than fish fed other feeds. Seabass fed LAB-4 also had greater survival, but this was non-significant (P<0.05). Challenge tests of LAB-4 fed seabass with A. hydrophila at ,7 log10CFU mL,1 yielded significantly greater survival compared with control seabass (P<0.05). Aeromonas hydrophila infections in seabass were confirmed by observing disease manifestation and by immunohistochemistry techniques. LAB-4 was preliminarily identified using lactic acid analysis, biochemical and physical characteristics. It was further identified using 16S rDNA sequencing. LAB-4 was identified as Weissella confusa (identity of 99%). GenBank accession number for the 16S rDNA sequence for LAB-4 was AB023241. [source] Molecular characterization of two novel deltamethrin-inducible P450 genes from Liposcelis bostrychophila Badonnel (Psocoptera: Liposcelididae)ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY (ELECTRONIC), Issue 1 2010Hong-Bo Jiang Abstract Two novel P450 genes, CYP6CE1 and CYP6CE2 (GenBank accession number: EF421245 and EF421246), were cloned and characterized from psocid, Liposcelis bostrychophila. CYP6CE1 and CYP6CE2 contain open reading frames of 1,581 and 1,563 nucleotides that encode 527 and 521 amino acid residues, respectively. The putative proteins of CYP6CE1 and CYP6CE2 show predicted molecular weights of 60.76 and 59.83,kDa with a theoretical pI of 8.58 and 8.78, respectively. CYP6CE1 and CYP6CE2 share 74% identity with each other, and the deduced proteins are typical microsomal P450s sharing signature sequences with other insect CYP6 P450s. Both CYP6CE1 and CYP6CE2 share the closest identities with Hodotermopsis sjoestedti CYP6AM1 at 48% among the published sequences. Phylogenetic analysis showed a closer relationship of CYP6CE1 and CYP6CE2 with CYP6 members of other insects than with those from other families. Quantitative real-time RT-PCR showed that both CYP6CE1 and CYP6CE2 are expressed at all developmental stages tested. Interestingly, CYP6CE2 transcripts decreased from the highest in 1st nymph to the lowest in adults, which seemed to suggest developmental regulation. However, neither CYP6CE1 nor CYP6CE2 were stage specific. The CYP6CE1 and CYP6CE2 transcripts in adults increased significantly after deltamethrin exposure. Recombinant protein expression studies are needed to determine the real functions of these proteins. © 2010 Wiley Periodicals, Inc. [source] Molecular characterization of two nicotinic acetylcholine receptor subunits from Liposcelis bostrychophila Badonnel (Psocoptera: Liposcelididae)ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY (ELECTRONIC), Issue 1 2009Pei-An Tang Abstract Two nicotinic acetylcholine receptor (nAChR) subunit genes, Lb,1 and Lb,8, were isolated and characterized from psocid, Liposcelis bostrychophila Badonnel, using the rapid amplification of cDNA ends (RACE) technique. They are the first two nAChR family members isolated from the insect order of Psocoptera. The full-length cDNAs of Lb,1 (GenBank accession number: EU871527) and Lb,8 (EU871526) consist of 2,025 and 1,763 nucleotides, respectively, and an open reading frame of 1,644 and 1,608,bp encoding 547 and 535 amino acid proteins, respectively. Both genes have typical features of nAChR family members, though they share only 56% identity in amino acid sequence. The dendrogram generated by the MEGA 3.1 program shows that the protein deduced by Lb,1 had the closest phylogenetic relationship to Agam,1 from Anopheles gambiae and Amel,1 from Apis mellifera, and Lb,8 shares the highest identity with Agam,8 from An. gambiae and Amel,8 from A. mellifera. Quantitative real-time PCR analysis showed that Lb,1 was expressed 2.03,6.54-fold higher than Lb,8 at the different developmental stages of L. bostrychophila. The highest expression levels of Lb,1 and Lb,8 were both detected at adult stage and the lowest were at the third and fourth nymphal stages, respectively. There was a stable and relatively low expression level for Lb,1, whereas there was a descending expression pattern for Lb,8 in the 1st through the 4th nymphal stadia. © 2009 Wiley Periodicals Inc. [source] Contribution to the knowledge of the Flora of the Mongolian AltaiFEDDES REPERTORIUM, Issue 5-6 2003B. Neuffer Apl. During a German-Mongolian expedition to the Mongolian Altai in July/August 2000, 404 specimens of vascular plants were collected. They are deposited in the Herbarium of the University of Osnabrück (OSBU). 381 specimens could be determined conclusively. The collected material comprises 300 species, 156 genera, and 44 families. Six of these species were first records for Mongolia, six species had not been recorded so far for the region Mongolian Altai, five are new for the region Khobdo, and 19 species new records for both regions, Mongolian Altai and Khobdo, Western Mongolia. A list of the collected plants with accession numbers and provenances is presented. Beitrag zur Kenntnis der Flora des Mongolischen Altais Auf einer deutsch-mongolischen Expedition in den Mongolischen Altai im Juli/August 2000 konnten wir 404 Herbarbelege von Gefäßpflanzen sammeln. Diese werden im Herbarium der Universität Osnabrück (OSBU) aufbewahrt. 381 Belege konnten endgültig bestimmt werden. Das gesammelte Material umfasst 300 Arten aus 156 Gattungen und 44 Familien. Sechs Arten sind neu für die Mongolei, sechs Arten sind neu für die Region Mongolischer Altai, fünf für die Region Khobdo und 19 für beide Provinzen, Mongolischer Altai und Khobdo der westlichen Mongolei. Die gesammelten Belege werden in alphabetischer Reihenfolge mit Angabe der Akzessionsnummern und Herkünfte tabellarisch aufgelistet. [source] Two-dimensional reference map for the basic proteome of the human dorsolateral prefrontal cortex (dlPFC) of the prefrontal lobe region of the brainPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 13 2010Ciara A. McManus Abstract We describe a 2-DE proteomic reference map containing 227 basic proteins in the dorsolateral prefrontal cortex region of the human brain. Proteins were separated in the first dimension on pH 6,11 IPG strips using paper-bridge loading and on 12% SDS-PAGE in the second dimension. Proteins were subsequently identified by MS and spectra were analyzed using an in-house proteomics data analysis platform, Proline. The 2-DE reference map is available via the UCD 2-DE Proteome Database (http://proteomics-portal.ucd.ie:8082) and can also be accessed via the WORLD-2DPAGE Portal (http://www.expasy.ch/world-2dpage/). The associated protein identification data have been submitted to the PRIDE database (accession numbers 10018,10033). Separation of proteins in the basic region resolves more membrane associated proteins relevant to the synaptic pathology central to many neurological disorders. The 2-DE reference map will aid with further characterisation of neurological disorders such as bipolar and schizophrenia. [source] Proteomic analysis of spore wall proteins and identification of two spore wall proteins from Nosema bombycis (Microsporidia)PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 12 2008Zhengli Wu Abstract Microsporidia are fungal-like unicellular eukaryotes which develop as obligate intracellular parasites. They differentiate into resistant spores that are protected by a thick spore wall composed of a glycoprotein-rich outer layer or exospore and a chitin-rich inner layer or endospore. In this study performed on the silkworm pathogen Nosema bombycis, we analyzed the spore wall proteins (SWPs) by proteomic-based approaches, MALDI-TOF MS and LC-MS/MS, and 14 hypothetical spore wall proteins (HSWPs) or peptides were obtained in total. Furthermore, we have examined the SWPs by SDS-PAGE and three main spore wall peptides were detected with molecular weights of 32.7,kDa (SWP32), 30.4,kDa (SWP30), and 25.3,kDa (SWP25), respectively. By N-terminal amino acid residue sequencing, and searching the genomic DNA shotgun database of N. bombycis, the complete ORFs of SWP30 and SWP32 were obtained, which encode for a 278- and a 316-amino acid peptide, respectively. Mouse polyclonal antibodies were raised against SWP30 and SWP32 recombinant proteins produced in Escherichia coli, and the results of indirect immunofluorescence assay (IFA) and immunoelectron microscopy (IEM) analyses indicated SWP30 to be an endosporal protein while SWP32 was shown to be an exosporal protein. Both SWP30 and SWP32 are included in the 14 HSWPs identified by MS, confirming the results of the proteomic-based approaches. (GenBankÔ, EMBL and DDBJ accession numbers: NbHSWP1,NbHSWP12, accession no. EF683101,EF683112. NbHSWP13 and NbHSWP14, accession no. EU179719 and EU179720). [source] Genetic structure of native circumpolar populations based on autosomal, mitochondrial, and Y chromosome DNA markersAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 1 2010Rohina Rubicz Abstract This study investigates the genetic structure of the present-day inhabitants of Beringia in order to answer questions concerning their origins and evolution. According to recent studies, the ancestors of Native Americans paused for a time in Beringia, during which they differentiated genetically from other Asians before peopling the New World. Furthermore, the Koryaks of Kamchatka share a "ubiquitous" allele (D9S1120) with Native Americans, indicating they may have descended from the same ancestral Beringian population that gave rise to the New World founders. Our results show that a genetic barrier exists between Kamchatkans (Koryaks and Even) and Bering Island inhabitants (Aleuts, mixed Aleuts, and Russians), based on Analysis of Molecular Variance (AMOVA) and structure analysis of nine autosomal short tandem repeats (STRs). This is supported by mitochondrial DNA evidence, but not by analysis of Y chromosome markers, as recent non-native male admixture into the region appears to have partially obscured ancient population relationships. Our study indicates that while Aleuts are descended from the original New World founders, the Koryaks are unlikely to represent a Beringian remnant of the ancestral population that gave rise to Native Americans. They are instead, like the Even, more recent arrivals to Kamchatka from interior Siberia, and the "ubiquitous" allele in Koryaks may result from recent gene flow from Chukotka. Genbank accession numbers for mtDNA sequences: GQ922935-GQ922973. Am J Phys Anthropol 143:62,74, 2010. © 2010 Wiley-Liss, Inc. [source] | |||||||||||||