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  • Selected Abstracts


    Significance of Specimen Databases from Taxonomic Revisions for Estimating and Mapping the Global Species Diversity of Invertebrates and Repatriating Reliable Specimen Data

    CONSERVATION BIOLOGY, Issue 2 2004
    RUDOLF MEIER
    More specifically, we demonstrate for a specimen database assembled during a revision of the robber-fly genus Euscelidia (Asilidae, Diptera) how nonparametric species richness estimators (Chao1, incidence-based coverage estimator, second-order jackknife) can be used to (1) estimate global species diversity, (2) direct future collecting to areas that are undersampled and/or likely to be rich in new species, and (3) assess whether the plant-based global biodiversity hotspots of Myers et al. (2000) contain a significant proportion of invertebrates. During the revision of Euscelidia, the number of known species more than doubled, but estimation of species richness revealed that the true diversity of the genus was likely twice as high. The same techniques applied to subsamples of the data indicated that much of the unknown diversity will be found in the Oriental region. Assessing the validity of biodiversity hotspots for invertebrates is a formidable challenge because it is difficult to decide whether species are hotspot endemics, and lists of observed species dramatically underestimate true diversity. Lastly, conservation biologists need a specimen database analogous to GenBank for collecting specimen records. Such a database has a three-fold advantage over information obtained from digitized museum collections: (1) it is shown for Euscelidia that a large proportion of unrevised museum specimens are misidentified; (2) only the specimen lists in revisionary studies cover a wide variety of private and public collections; and (3) obtaining specimen records from revisions is cost-effective. Resumen:,Sostuvimos que los millones de registros de especimenes publicados en miles de revisiones taxonómicas en décadas anteriores son una fuente de información costo-efectiva de importancia crítica para la incorporación de invertebrados en decisiones de investigación y conservación. Más específicamente, para una base de datos de especimenes de moscas del género Euscelidia (Asilidae, Diptera) demostramos como se pueden utilizar estimadores no paramétricos de riqueza de especies (Chao 1, estimador de cobertura basado en incidencia, navaja de segundo orden) para (1) estimar la diversidad global de especies, (2) dirigir colecciones futuras a áreas que están sub-muestreadas y/o probablemente tengan especies nuevas y (3) evaluar si los sitios globales de importancia para la biodiversidad basados en plantas de Myers et al. (2000) contienen una proporción significativa de invertebrados. Durante la revisión de Euscelidia el número de especies conocidas fue más del doble, pero la estimación de riqueza de especies reveló que la diversidad real del género probablemente también era el doble. Las mismas técnicas aplicadas a las sub-muestras de datos indicaron que gran parte de la diversidad no conocida se encontrará en la Región Oriental. La evaluación de la validez de sitios de importancia para la biodiversidad de invertebrados es un reto formidable porque es difícil decidir si las especies son endémicas de esos sitios y si las listas de especies observadas subestiman dramáticamente la diversidad real. Finalmente, los biólogos de la conservación requieren de una base de datos de especimenes análoga a GenBank, para obtener registros de especimenes. Dicha base de datos tiene una triple ventaja sobre la información obtenida de colecciones de museos digitalizadas. (1) Se muestra para Euscelidia que una gran proporción de especimenes de museo no revisados están mal identificados. (2) Sólo las listas de especimenes en estudios de revisión cubren una amplia variedad de colecciones privadas y públicas. (3) La obtención de registros en revisiones es costo-efectiva. [source]


    Phylogenetic relatedness and plant invader success across two spatial scales

    DIVERSITY AND DISTRIBUTIONS, Issue 3 2009
    Marc W. Cadotte
    ABSTRACT Aim, Successful invaders often possess similar ecological traits that contribute to success in new regions, and thus under niche conservatism, invader success should be phylogenetically clustered. We asked if the degree to which non-native plant species are phylogenetically related is a predictor of invasion success at two spatial scales. Location, Australia , the whole continent and Royal National Park (south-eastern Australia). Methods, We used non-native plant species occupancy in Royal National Park, as well as estimated continental occupancy of these species from herbarium records. We then estimated phylogenetic relationships using molecular data from three gene sequences available on GenBank (matK, rbcL and ITS1). We tested for phylogenetic signals in occupancy using Blomberg's K. Results, Whereas most non-native plants were relatively scarce, there was a strong phylogenetic signal for continental occupancy, driven by the clustering of successful species in Asteraceae, Caryophyllaceae, Poaceae and Solanaceae. However, we failed to detect a phylogenetic signal at the park scale. Main Conclusions, Our results reveal that at a large spatial scale, invader success is phylogenetically clustered where ecological traits promoting success appear to be shared among close relatives, indicating that phylogenetic relationships can be useful predictors of invasion success at large spatial scales. At a smaller, landscape scale, there was no evidence of phylogenetic clustering of invasion success, and thus, relatedness plays a much reduced role in determining the relative success of invaders. [source]


    Genotype,phenotype correlation in skin fragility-ectodermal dysplasia syndrome resulting from mutations in plakophilin 1

    EXPERIMENTAL DERMATOLOGY, Issue 2 2002
    T. Hamada
    Abstract: We report a 42-year-old Japanese man with an unusual autosomal recessive genodermatosis. The clinical features comprised normal skin at birth, loss of scalp hair at 3-months of age after a febrile illness, progressive nail dystrophy during infancy, palmoplantar keratoderma starting around the age of 18 years and trauma-induced skin fragility and blisters noted from the age of 20 years. Skin biopsy of rubbed non-lesional skin revealed widening of spaces between adjacent keratinocytes from the suprabasal layer upwards. Electron microscopy demonstrated a reduced number of hypoplastic desmosomes. Immunohistochemical labeling showed a reduction in intercellular staining for the desmosome component plakophilin 1. Mutation analysis revealed a homozygous intron 11 donor splice site mutation in the plakophilin 1 gene, 2021+1 G>A (GenBank no. Z34974). RT-PCR, using RNA extracted from the skin biopsy, provided evidence for residual low levels of the full-length wild-type transcript (,8%) as well as multiple other near full-length transcripts, one of which was in frame leading to deletion of 17 amino acids from the 9th arm-repeat unit of the plakophilin 1 tail domain. Thus, the molecular findings help explain the clinical features in the patient, who has a similar but milder phenotype to previously reported patients with skin fragility-ectodermal dysplasia syndrome associated with complete ablation of plakophilin 1 (OMIM 604536). This new ,mitis' phenotype provides further clinicopathological evidence for the role of plakophilin 1 in keratinocyte cell,cell adhesion and ectodermal development. [source]


    m.6267G>A: a recurrent mutation in the human mitochondrial DNA that reduces cytochrome c oxidase activity and is associated with tumors,

    HUMAN MUTATION, Issue 6 2006
    M. Esther Gallardo
    Abstract Complete sequencing of the mitochondrial genome of 13 cell lines derived from a variety of human cancers revealed nine novel mitochondrial DNA (mtDNA) variations. One of them, m.6267G>A, is a recurrent mutation that introduces the Ala122Thr substitution in the mitochondrially encoded cytochrome c oxidase I (MT-CO1): p.MT-CO1: Ala122Thr (GenBank: NP_536845.1). Biochemical analysis of the original cell lines and the transmitochondrial cybrids generated by transferring mitochondrial DNAs to a common nuclear background, indicate that cytochrome c oxidase (COX) activity, respiration, and growth in galactose are impaired by the m.6267G>A mutation. This mutation, found twice in the cancer cell lines included in this study, has been also encountered in one out of 63 breast cancer samples, one out of 64 colon cancer samples, one out of 260 prostate cancer samples, and in one out of 15 pancreatic cancer cell lines. In all instances the m.6267G>A mutation was associated to different mtDNA haplogroups. These findings, contrast with the extremely low frequency of the m.6267G>A mutation in the normal population (1:2264) and its apparent absence in other pathologies, strongly suggesting that the m.6267G>A missense mutation is a recurrent mutation specifically associated with cancer. Hum Mutat 27(6), 575,582, 2006. © 2006 Wiley-Liss, Inc. [source]


    Molecular characterization of two novel esterase genes from carmine spider mite, Tetranychus cinnabarinus (Acarina: Tetranychidae)

    INSECT SCIENCE, Issue 2 2010
    Wei Sun
    Abstract, Two novel esterase complementary DNAs were identified and cloned from the insecticide-susceptible strain of Tetranychus cinnabarinus (Boisduval) (Acarina: Tetranychidae), which were designated as TCE1 and TCE2, respectively. The cDNA of TCE1 gene contained an open reading frame (ORF) of 1701 bp encoding 567 amino acids, and a predicted molecular weight of 62.75 kDa, the cDNA of TCE2 contained an ORF of 1680 bp encoding 560 amino acids, and a predicted molecular weight of 63.14 kDa. TCE1 and TCE2 were submitted to GenBank, accession number EU130461 and EU130462. The well-conserved sequence motif, GXSXG, used as a signature pattern in the esterase family are present in both TCE1 and TCE2 (GQSAG in TCE1, whereas GESAG in TCE2), indicating that these two genes are predicted to be esterases. Comparison of the deduced amino acid sequence with the published mite esterase sequence coming from Boophilus microplus showed that TCE1 shares 33.98% identity and TCE2 shares 33.46% identity. TCE1 and TCE2 share 46.4% identity. Quantitative real-time polymerase chain reaction revealed that expression level of the TCE2 gene was relatively higher than that of the TCE1 in all instars examined except the protonymph, and the expression level of these two esterase genes in adults of T. cinnabarinus was significantly higher than that in any other instars, respectively. T. cinnabarinus is an important agricultural mite pest and esterases are important in the metabolisms of insects and mites; the genomic information obtained in this study will contribute to esterase molecular biological study on mite pest species. [source]


    PCR-BASED TECHNIQUE FOR IDENTIFICATION AND DETECTION OF TRICHOGRAMMA SPP. (HYMENOPTERA: TRICHOGRAMMATIDAE) WITH SPECIFIC PRIMERS

    INSECT SCIENCE, Issue 3 2002
    LI Zheng-xi
    Abstract The rDNA-ITS2 regions of T. dendrolimi Matsumura and T. ostriniae Pang et Chen (Hymenoptera: Trichogrammatidae) were cloned and sequenced. The homologous sequences available in GenBank were retrieved and analyzed, and then specific primers were designed for molecular identification and detection of T. dendrolimi. Repeated screening showed that PCR amplification by the diagnostic primers enabled the differentiation of not only bulk samples and single adult (male or female), but also eggs and juveniles, which was not possible by conventional methods. The advantage of this system over morphology-based systems is that non-specialists are able to identify individuals or trace specimens efficiently. The derived molecular detection technique was then used to identify 12 specimens collected from different localities on the Chinese mainland; the results showed that this protocol could be applied to molecular monitoring of Trichogramma species in the field. Finally, 1132s of 6 geographical populations of T. dendrolimi (TdCHA, TDJL, TdXZ, TdKH, TdCZ and TdYBL) were cloned and sequenced. The multialignment analysis of intraspecific ITS2 sequences showed that the diagnostic primers have their own theoretical bases. [source]


    A survey of H2 gene sequences, including new wild-derived genes

    INTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 1 2007
    N. A. Mitchison
    Summary A comprehensive collection of mouse major histocompatibility complex (MHC) promoter and exon 2 sequences is here presented and analysed. It covers the three best known class II genes and one class I gene, and includes new wild mouse sequences from the ,w' back-cross strains and from the Jackson collection. All sequences are in GenBank, and the new exon sequences largely confirm previous typing by serology and immune function. As in human leucocyte antigen (HLA), the overall nucleotide diversity is higher in the class II genes, in keeping with their more diverse function. Diversity along the promoters is highest in the region of known transcription factor binding, most notably in and around the CRE and rCAAT sequences. This distribution parallels that of maximum single nucleotide polymorphism impact previously obtained with reporter constructs. Taking into account the low nucleotide diversity of the CIITA promoter, we conclude that MHC promoters are likely to have diversified through co-evolution with their exons, while themselves also directly subject to natural selection. The H2Ebp alleles form a distinct group, associated with their lack of the recombination hot spot located between exon 2 and exon 3. The collection is expected to prove useful in guiding functional and evolutionary studies. [source]


    Influence of long-term land application of Class B biosolids on soil bacterial diversity

    JOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2010
    H. Zerzghi
    Abstract Aim:, To evaluate the effect of long-term annual land applications of Class B biosolids on soil bacterial diversity at University of Arizona Marana Agricultural Field Center, Tucson, Arizona. Methods and Results:, Following the final of 20 consecutive years of application of Class B biosolids in March 2005, followed by cotton growth from April to November 2005 surface soil samples (0,30 cm) were collected from control (unamended) and biosolid-amended plots. Total bacterial community DNA was extracted, amplified using 16S rRNA primers, cloned, and sequenced. All 16S rRNA sequences were identified by 16S rRNA sequence analysis and comparison to known sequences in GenBank (NCBI BlastN and Ribosomal Database Project II, RDP). Results showed that the number of known genera (identifiable > 96%) increased in the high rate biosolid plots compared to control plots. Biosolids-amended soils had a broad phylogenetic diversity comprising more than four major phyla: Proteobacteria (32%), Acidobacteria (21%), Actinobacteria (16%), Firmicutes (7%), and Bacteroidetes (6%) which were typical to bacterial diversity found in the unamended arid southwestern soils. Conclusion:, Bacterial diversity was either enhanced or was not negatively impacted following 20 years of land application of Class B biosolids. Significance and Impact of the Study:, This study illustrates that long-term land application of biosolids to arid southwestern desert soils has no deleterious effect on soil microbial diversity. [source]


    Sucrose phosphorylase of the rumen bacterium Pseudobutyrivibrio ruminis strain A

    JOURNAL OF APPLIED MICROBIOLOGY, Issue 3 2009
    A. Kasperowicz
    Abstract Aims:, To verify the taxonomic affiliation of bacterium Butyrivibrio fibrisolvens strain A from our collection and to characterize its enzyme(s) responsible for digestion of sucrose. Methods and Results:, Comparison of the 16S rRNA gene of the bacterium with GenBank showed over 99% sequence identity to the species Pseudobutyrivibrio ruminis. Molecular filtration, native electrophoresis on polyacrylamide gel, zymography and thin layer chromatography were used to identify and characterize the relevant enzyme. An intracellular sucrose phosphorylase with an approximate molecular mass of 52 kDa exhibiting maximum activity at pH 6·0 and temperature 45°C was identified. The enzyme was of inducible character and catalysed the reversible conversion of sucrose to fructose and glucose-1-P. The reaction required inorganic phosphate. The Km for glucose-1-P formation and fructose release were 3·88 × 10,3 and 5·56 × 10,3 mol l,1 sucrose, respectively , while the Vmax of the reactions were ,0·579 and 0·9 ,mol mg protein,1 min,1. The enzyme also released free glucose from glucose phosphate. Conclusion:,Pseudobutyrivibrio ruminis strain A utilized sucrose by phosphorolytic cleavage. Significance and Impact of the Study:, Bacterium P. ruminis strain A probably participates in the transfer of energy from dietetary sucrose to the host animal. [source]


    Identification of Differentially Expressed Genes During Anther Abortion of Taigu Genic Male Sterile Wheat by Combining Suppression Subtractive Hybridization and cDNA Array

    JOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 11 2006
    Qing-Shan Chang
    Abstract Taigu Genic Male Sterile Wheat (TGMSW; Triticum aestivum L.), a dominant genic male sterile germplasm, is of considerable value in the genetic improvement of wheat because of its stable inherence, complete male abortion, and high cross-fertilization rate. To identify specially transcribed genes in sterile anther, a suppression subtractive hybridization (SSH) library was constructed with sterile anther as the tester and fertile anther as the driver. A total of 2 304 SSH inserts amplified by polymerase chain reaction were arrayed using robotic printing. The cDNA arrays were hybridized with 32P-labeled probes prepared from the RNA of forward- and reverse-subtracted anthers. Ninety-six clones were scored as upregulated in sterile anthers compared with the corresponding fertile anthers and some clones were selected for sequencing and analysis in GenBank. Based on their putative functions, 87 non-redundant clones were classified into the following groups: (i) eight genes involved in metabolic processes; (ii) four material transportation genes; (iii) three signal transduction-associated genes; (iv) four stress response and senescence-associated protein genes; (v) seven other functional protein genes; (vi) five genes with no known function; and (vii) another 56 genes with no match to the databases. To test the hybridization efficiency, eight genes were selected and analyzed by Northern blot. The results of the present study provide a comprehensive overview of the genes and gene products involved in anther abortion in TGMSW. (Managing editor: Li-Hui Zhao) [source]


    Construction and Characterization of a cDNA Library from the Pulp of Cara Cara Navel Orange (Citrus sinensis Osbeck)

    JOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 3 2006
    Neng-Guo Tao
    Abstract A cDNA library was constructed and characterized from the pulp of Cara Cara navel orange (Citrus sinensis Osbeck) at different stages of ripening. Tittering results revealed that approximately 5.086 × 105 independent clones were included in this library. Electrophoresis gel results of 15 randomly selected clones revealed that the size of the insertion fragments ranged from 400 bp to 2 kb, with an average size of 900 bp. Sequencing results of 150 randomly picked clones showed that the recombination rate was 94%. During subsequent sequence analysis, 41 of 139 clones failed to be identified and the amino sequence of 71 clones shared less than 30% identity with related plants in GenBank. Of 27 clones whose amino sequences shared more than 60% identity with other related plants in GenBank, 17 clones showed an 80% identity with the corresponding candidate genes of citrus. The clone recognized as the type III metallothionein-like (MT) gene was observed to occur 13 times, indicating that the protein may play an important role in fruit development and ripening. (Managing editor: Li-Hui Zhao) [source]


    Identification of a unique BK virus variant in the CNS of a patient with AIDS,

    JOURNAL OF MEDICAL VIROLOGY, Issue 1 2003
    Gunn Eli Kimo Jørgensen
    Abstract Human polyomavirus BK (BKV; GenBank or EMBL or DDBJ accession no. NC001538) is often reactivated in immunosuppressed patients. Reactivation has been associated primarily with excretion of the virus in the urine, and there have been few reports of renal and/or neurological disease caused by BKV in patients with acquired immunodeficiency syndrome (AIDS). Polymerase chain reaction, Southern blotting, and sequencing were used to detect and identify the noncoding control region (NCCR) of BKV in different tissues in an AIDS patient with meningoencephalitis, retinitis, and nephritis. An undescribed reorganized NCCR variant of the virus, completely different from the variants detected in peripheral blood leukocytes (PBLs) and urine, was identified in the cerebrospinal fluid (CSF) and CNS tissues. These results suggest that rearrangements in the NCCR of the virus have resulted in a BKV variant, which is better adapted to the host cell machinery of the cells in CNS tissue. The rearranged variant (BKV CNS) might have been involved in the initiation and/or development of the pathological lesions observed in the CNS-related tissues of this patient. J. Med. Virol. 70: 14,19, 2003. © 2003 Wiley-Liss, Inc. [source]


    Novel variants related to TT virus distributed widely in China,

    JOURNAL OF MEDICAL VIROLOGY, Issue 1 2002
    Kangxian Luo
    Abstract TTV is a DNA virus with high genetic heterogeneity. To investigate the novel isolates of the virus, blood samples were collected from subjects who lived in various parts of China and suffered from hepatitis or were asymptomatic carriers. Nested PCR was carried out to amplify a 3.2-kb fragment using primers deduced from the prototype TTV (TA278). The ten entire 3.2-kb nt sequences were aligned with isolate TA278, SANBAN, TUS01, and SENV retrieved from GenBank, and a phylogenetic tree was constructed by Neighbor-Joining method. The analysis indicated that five novel variants of the present study have not been described before, and all TTV-related isolates could be classified into three groups. The isolate TCHN-A, B and TUS01 were included in a group, and the remaining novel isolates together with SANBAN and TA278 clustered into another group, while SEN virus formed a distinct group. The genetic distances of the five novel variants were 0.5507,0.8476 to TA278, 0.4635,0.7877 to SANBAN, 0.6064,0.7834 to TUS01 and 0.6936,0.8236 to SENV. Of these novel variants, the ORF1 consisted of 426,772 aa and ORF2 of 141,156 aa. The nt identities of ORF1 and ORF2 between those variants and TA278, SANBAN, and TUS01 were 46.1,60.8 and 48.7,63.6%, and those of aa sequences were only 27.1,52.4 and 28.9,45.5%, respectively. The first 65 aa of ORF1 were rich in arginine and most conserved with homology of 56.5,70.0%. There was a hypervariable region from aa 286 to 403 with merely 17.7,27.0% of identity. Despite a low aa identity between TA278 and the variants, they have similar hydrophilicity profiles of ORF1. There were 2,10 N-glycosylation motifs found in these variants. In conclusion, despite the high divergence, sequences of all these isolates shared common genome organisation, ORF structure, hydrophilicity patterns, and some potential motifs with TTV prototype. It is suggested that various TTV and TTV-related isolates belong to a very large and complex family, which remains to be studied. J. Med. Virol. 67:118,126, 2002. © 2002 Wiley-Liss, Inc. [source]


    PHYLOGENY OF FOUR DINOPHYSIACEAN GENERA (DINOPHYCEAE, DINOPHYSIALES) BASED ON rDNA SEQUENCES FROM SINGLE CELLS AND ENVIRONMENTAL SAMPLES,

    JOURNAL OF PHYCOLOGY, Issue 5 2009
    Sara M. Handy
    Dinoflagellates are a highly diverse and environmentally important group of protists with relatively poor resolution of phylogenetic relationships, particularly among heterotrophic species. We examined the phylogeny of several dinophysiacean dinoflagellates using samples collected from four Atlantic sites. As a rule, 3.5 kb of sequence including the nuclear ribosomal genes SSU, 5.8S, LSU, plus their internal transcribed spacer (ITS) 1 and 2 regions were determined for 26 individuals, including representatives of two genera for which molecular data were previously unavailable, Ornithocercus F. Stein and Histioneis F. Stein. In addition, a clone library targeting the dinophysiacean ITS2 and LSU sequences was constructed from bulk environmental DNA from three sites. Three phylogenetic trees were inferred from the data, one using data from this study for cells identified to genus or species (3.5 kb, 28 taxa); another containing dinoflagellate SSU submissions from GenBank and the 12 new dinophysiacean sequences (1.9 kb, 56 taxa) from this study; and the third tree combing data from identified taxa, dinophysiacean GenBank submissions, and the clone libraries from this study (2.1 kb, 136 taxa). All trees were congruent and indicated a distinct division between the genera Phalacroma F. Stein and Dinophysis Ehrenb. The cyanobionts containing genera Histioneis and Ornithocercus were also monophyletic. This was the largest molecular phylogeny of dinophysoid taxa performed to date and was consistent with the view that the genus Phalacroma may not be synonymous with Dinophysis. [source]


    Generation and analysis of 5318 expressed sequence tags from the filamentous sporophyte of Porphyra haitanensis (Rhodophyta),

    JOURNAL OF PHYCOLOGY, Issue 6 2007
    Fan Xiaolei
    Porphyra haitanensis T. J. Chang et B. F. Zheng (Bangiales, Rhodophyta) is cultivated in China and widely consumed in Asia. To gain more insight into its physiological and biochemical properties, we generated 5318 expressed sequence tags (ESTs) from the sporophyte of P. haitanensis, and upon assembling into a nonredundant set, 2535 sequences were obtained, among which only 32.2% (816) shared certain similarity with published sequences (Nr and KOG). Functional classification of such ESTs revealed that most of the transcripts were related to its conservative biological metabolism, and P. haitanensis most likely possesses cyanide-resistant respiration and a C4-like carbon-fixation pathway, both of which have never been reported in a rhodophyte before. Twenty-eight percent of the nonredundant gene clusters exhibited significant similarity to those from P. yezoensis Ueda sporophytes, and 16 genes up-regulated in P. yezoensis sporophytes were also expressed abundantly in P. haitanensis. Codon usage analysis indicated that exposure to high GC pressure might occur during evolution of P. haitanensis. These findings represent the most extensive collection of ESTs from P. haitanensis to date, and all the ESTs in this study have been submitted to GenBank (accession nos. DN604790,DN608469, EG016226,EG018540). [source]


    PHYLOGENY OF AULACOSEIRA (BACILLARIOPHYTA) BASED ON MOLECULES AND MORPHOLOGY,

    JOURNAL OF PHYCOLOGY, Issue 4 2004
    Stacy M. Edgar
    The phylogeny of 67 populations representing 45 species of Aulacoseira Thwaites was estimated by maximum parsimony methods using a combination of nucleotide sequence data and qualitative and quantitative morphological characteristics of the silica cell wall gathered primarily from original observation by LM and SEM. A new type of character using continuous quantitative variables that describe the ontogenetic-allometric trajectories of cell wall characteristics over the life cycle (size range) of diatoms is introduced. In addition to the 45 Aulacoseira species, the phylogeny also incorporated one Miosira Krammer, Lange-Bertalot, and Schiller species and two outgroup species (Melosira varians Agardh and Stephanopyxis nipponica Gran & Yendo). Fifteen species, represented by 24 populations, also contained molecular data from the nuclear genome (18S rDNA), and 11 of these species (18 populations) contained data from the chloroplast genome (rbcL) as well, which were sequenced or downloaded from GenBank. The phylogeny of Aulacoseira is composed of five major clades: 1) an A. crenulata (Ehrenburg) Thwaites and A. italica (Ehrenburg) Simonsen clade, which is the most basal; 2) an A. granulata (Ehrenburg) Simonsen complex clade; 3) an A. ambigua (Grunow) Simonsen clade; 4) an A. subarctica (O. Müller) Haworth and A. distans (Ehrenburg) Simonsen clade; and 5) an A. islandica (O. Müller) Simonsen clade that also contained endemic species from Lake Baikal, Siberia and many extinct Aulacoseira taxa. Monophyly of Aulacoseira can only be achieved if Miosira is no longer given separate generic status. [source]


    Molecular Characterization of the 3,-Terminal Region of Turnip mosaic virus Isolates from Eastern China

    JOURNAL OF PHYTOPATHOLOGY, Issue 6 2007
    Y.-P. Tian
    Abstract Turnip mosaic virus (TuMV; genus Potyvirus, family Potyviridae) causes great losses to cruciferous crop production worldwide. The 3,-terminal genomic sequences of eight TuMV isolates from eastern China were compared with those of 74 other Chinese TuMV isolates of known host origin in the GenBank and isolated during the past 25 years. The reported sequences of the eight TuMV isolates are 1125 or 1126-nucleotides (nt) long excluding the poly(A) tail. They all contain one partial open reading frame of 912 nt, encoding 304 amino acids, followed by a stop codon and a non-translated region of 209,210 nt. Results of phylogenetic analyses showed that Chinese TuMV isolates clustered into three groups: basal-BR, Asian-BR and world-B. The ratios of non-synonymous and synonymous substitutions and results of amino acid alignment provided evidence for purifying or negative selection in TuMV populations of China. [source]


    Comparative Sequence Analysis of Coat Protein Gene of Iranian Citrus tristeza virus Isolates

    JOURNAL OF PHYTOPATHOLOGY, Issue 7-8 2005
    A. Barzegar
    Abstract Twenty-two isolates of Citrus tristeza virus (CTV) collected from two different geographical regions of Iran were characterized based on coat protein (CP) gene sequences. Thirteen virus isolates were collected from northern parts of Iran with high distribution of CTV infection and nine isolates were obtained from southern regions where the presence and aphid transmission of CTV was previously reported. All isolates were recovered from field trees showing varied CTV symptoms such as decline in most citrus varieties on sour orange rootstock, inverse pitting on some sour orange rootstocks below bud union, mild-to-moderate stem pitting on the trunk of some sweet orange. Isolates F, G, MB1, MB7, MB2, MB8, MB9, MB11 and MB17 were recovered from healthy looking Miyagawa Satsuma on trifoliate rootstock originally infected with CTV imported from Japan in late-1960s. The presence of virus in citrus samples was confirmed using polyclonal as well as monoclonal antibody. The CTV CP gene of all isolates was amplified by reverse transcriptase polymerase chain reaction (RT,PCR) using CP gene-specific primers yielding 672 bp amplicon. The restriction fragment length polymorphism (RFLP) profile, nucleotide and deduced amino acid sequences were analysed and compared with each other and also with some other exotic CP gene sequences of CTV isolates available in GenBank. Analysis of our data revealed that Iranian isolates have high similarity to California SY568 severe stem pitting and Japanese NUagA seedling yellows strains (up to 97%). The dendrogram generated from the deduced amino acid sequence could separate MB1, MB2, MB8, MB9, MB11 and MB17 isolates from others. However, no major dissociation between the isolates from northern and southern region could be obtained. [source]


    The Presence of Phytoplasma in Black Currant Infected with the Blackcurrant Reversion Disease

    JOURNAL OF PHYTOPATHOLOGY, Issue 11-12 2004

    Abstract A plant of black currant cv. Karl,tejnský dlouhohrozen showing symptoms of the severe Russian (R) form of the blackcurrant reversion disease (BCRD) was shown to contain phytoplasma bodies measuring 530,750 nm. Phytoplasma infection was confirmed by polymerase chain reaction (PCR) with the universal primer pair R16F1/R16R0, followed by PCR with the primer pair fU5/rU3. A comparison of the sequence of an amplification product of approximately 880 bp with sequences available in the GenBank confirmed the classification of the phytoplasma in the 16SrI (Aster yellows group). This is the first evidence of the natural occurrence of phytoplasma infection in black currant. Blackcurrant reversion virus (BRV), the cause of BCRD, was confirmed in the plant by RT-PCR. A 481 nt cDNA fragment of BRV was sequenced and compared with sequences in GenBank. Rhabdovirus-like particles were also observed in the plant by electron microscopy. [source]


    The changing face of scientific discourse: Analysis of genomic and proteomic database usage and acceptance

    JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND TECHNOLOGY, Issue 10 2003
    Cecelia Brown
    The explosion of the field of molecular biology is paralleled by the growth in usage and acceptance of Web-based genomic and proteomic databases (GPD) such as GenBank and Protein Data Bank in the scholarly communication of scientists. Surveys, case studies, analysis of bibliographic records from Medline and CAPlus, and examination of "Instructions to Authors" sections of molecular biology journals all confirm the integral role of GPD in the scientific literature cycle. Over the past 20 years the place of GPD in the culture of molecular biologists was observed to move from tacit implication to explicit knowledge. Originally journals suggested deposition of data in GDP but by the late1980s, the majority of journals mandated deposition of data for a manuscript to be accepted for publication. A surge subsequently occurred in the number of articles retrievable from Medline and CAPlus using the keyword "GenBank". GPD were not found to a new form of publication, but rather a fundamental storage and retrieval mechanism for vast amounts of molecular biology information that support the creation of scientific intellectual property. For science to continue to advance, scientists unequivocally agreed that GDP must remain free of peer-review and available at no charge to the public. The results suggest that the existing models of scientific communication should be updated to incorporate GDP data deposition into the current continuum of scientific communication. [source]


    Evaluation of PCR primers from putative transcriptional regulator genes for identification of Staphylococcus aureus

    LETTERS IN APPLIED MICROBIOLOGY, Issue 1 2005
    D. Liu
    Abstract Aims:, To examine if PCR primers derived from putative transcriptional regulator genes can be useful for Staphylococcus aureus identification. Methods and Results:,Staphylococcus aureus gene sequences that encode transcriptional regulators were retrieved from GenBank and compared with other DNA sequences via BLAST searches. Two uniquely present, putative transcriptional regulator genes (i.e. Sa0836 and Sa0856) were selected as a consequence and PCR primers (Sa0836F/R and Sa0856F/R) were then designed from these genes for evaluation. A total of 84 bacterial strains/isolates including 23 Staph. aureus, 18 nonaureus Staphylococcus and 43 other common bacterial isolates were examined. The results indicated that PCR primers from Sa0836 and Sa0856 recognized genomic DNA from Staph. aureus only, but not from other non-aureus Staphylococcus or common bacteria. Conclusions:, PCR detection of the putative transcriptional regulator genes Sa0836 and Sa0856 represents a useful means of identifying Staph. aureus from other bacteria. Significance and Impact of the Study:, The existence of species,species transcriptional regulator genes may be a common phenomenon in bacteria. Besides their value as novel diagnostic markers, further investigation on the putative transcriptional regulator genes Sa0836 and Sa0856 and their related products may shed light on the molecular mechanisms of Staph. aureus adaptation and virulence. [source]


    Field and laboratory studies in a Neotropical population of the spinose ear tick, Otobius megnini

    MEDICAL AND VETERINARY ENTOMOLOGY, Issue 1 2009
    S. NAVA
    Abstract One ear of each of five cows on a property close to Dean Funes, province of Córdoba, Argentina, was inspected monthly from December 2004 to November 2006 to determine the presence of Otobius megnini (Dugès) and to ascertain its seasonality. Ticks were collected to study the biological parameters of larvae, nymphs and adult ticks. Groups of nymphs were also maintained at three different photoperiods at 25 °C. The abundance of immature stages was greatest during January,April and August,October in the first and second years of the study, respectively. No larvae successfully moulted. Nymphs weighing < 17 mg also failed to moult, but 89% of heavier nymphs moulted into adults. Nymphs moulting to males weighed less (49.5 ± 16.09 mg) than nymphs moulting to females (98.1 ± 34.08 mg). The pre-moult period was similar for nymphs moulting to either sex and significantly longer (P < 0.01) for female nymphs maintained at 25 °C compared with nymphs kept at 27 °C. No effect of photoperiod on the pre-moult periods of nymphs was detected. Female ticks produced a mean of 7.0 ± 1.94 egg batches after a preoviposition period of 16.4 ± 8.41 days for the first batch. The mean oviposition period was 61 ± 20.8 days and the duration of oviposition for each batch varied from 1 to 6 days. The mean number of eggs per batch was 93.1 ± 87.53. The minimum incubation period for the first egg batch was 13.6 ± 2.77 days. The total number of eggs laid by each female was 651.6 ± 288.90. Parthenogenesis was not observed. The reproductive efficiency index (REI) (number of eggs laid/weight of female in mg) was 5.5 ± 1.26. Pearson's correlations showed a significant direct relationship between the weight of the female and number of eggs laid (P < 0.01) and REI (P < 0.05). Several of the biological values presented above for the tick population from the Neotropical zoogeographic region showed marked differences to equivalent values for O. megnini populations from the U.S.A. (Nearctic) and India (Oriental). Nevertheless, the only two sequences of 16S rDNA deposited in GenBank from ticks originating in Argentina and allegedly in the U.S.A. indicate that they are conspecific (99.8% agreement). We tentatively consider the biological differences among populations of this tick species to represent adaptations for survival at different conditions. [source]


    Identification of mosquito bloodmeals using mitochondrial cytochrome oxidase subunit I and cytochrome b gene sequences

    MEDICAL AND VETERINARY ENTOMOLOGY, Issue 4 2008
    J. S. TOWNZEN
    Abstract Primer pairs were designed and protocols developed to selectively amplify segments of vertebrate mitochondrial cytochrome oxidase subunit 1 (COI) and cytochrome b (Cyt b) mtDNA from the bloodmeals of mosquitoes (Diptera: Culicidae). The protocols use two pairs of nested COI primers and one pair of Cyt b primers to amplify short segments of DNA. Resultant sequences are then compared with sequences in GenBank, using the BLAST function, for putative host identification. Vertebrate DNA was amplified from 88% of our sample of 162 wild-caught, blood-fed mosquitoes from Oregon, U.S.A. and GenBank BLAST searches putatively identified 98% of the amplified sequences, including one amphibian, seven mammalian and 14 avian species. Criteria and caveats for putative identification of bloodmeals are discussed. [source]


    Universal primers and PCR of gut contents to study marine invertebrate diets

    MOLECULAR ECOLOGY, Issue 3 2005
    L. E. BLANKENSHIP
    Abstract Determining the diets of marine invertebrates by gut content analysis is problematic. Many consumed organisms become unrecognizable once partly digested, while those with hard remains (e.g. diatom skeletons) may bias the analysis. Here, we adapt DNA-based methods similar to those used for microbial diversity surveys as a novel approach to study the diets of macrophagous (the deep-sea amphipods Scopelocheirus schellenbergi and Eurythenes gryllus) and microphagous (the bivalve Lucinoma aequizonata) feeders in the deep sea. Polymerase chain reaction (PCR) in conjunction with ,universal' primers amplified portions of the mitochondrial cytochrome c oxidase I (COI) gene for animals ingested by S. schellenbergi and E. gryllus and the 18S rRNA gene for lesser eukaryotes ingested by L. aequizonata. Amplified sequences were combined with sequences from GenBank to construct phylogenetic trees of ingested organisms. Our analyses indicate that S. schellenbergi, E. gryllus and L. aequizonata diets are considerably more diverse than previously thought, casting new light on the foraging strategies of these species. Finally, we discuss the strengths and weaknesses of this technique and its potential applicability to diet analyses of other invertebrates. [source]


    DNA barcoding of stylommatophoran land snails: a test of existing sequences

    MOLECULAR ECOLOGY RESOURCES, Issue 4 2009
    ANGUS DAVISON
    Abstract DNA barcoding has attracted attention because it is a potentially simple and universal method for taxonomic assignment. One anticipated problem in applying the method to stylommatophoran land snails is that they frequently exhibit extreme divergence of mitochondrial DNA sequences, sometimes reaching 30% within species. We therefore trialled the utility of barcodes in identifying land snails, by analysing the stylommatophoran cytochrome oxidase subunit I sequences from GenBank. Two alignments of 381 and 228 base pairs were used to determine potential error rates among a test data set of 97 or 127 species, respectively. Identification success rates using neighbour-joining phylogenies were 92% for the longer sequence and 82% for the shorter sequence, indicating that a high degree of mitochondrial variation may actually be an advantage when using phylogeny-based methods for barcoding. There was, however, a large overlap between intra- and interspecific variation, with assignment failure (per cent of samples not placed with correct species) particularly associated with a low degree of mitochondrial variation (Kimura 2-parameter distance < 0.05) and a small GenBank sample size (< 25 per species). Thus, while the optimum intra/interspecific threshold value was 4%, this was associated with an overall error of 32% for the longer sequences and 44% for the shorter sequences. The high error rate necessitates that barcoding of land snails is a potentially useful method to discriminate species of land snail, but only when a baseline has first been established using conventional taxonomy and sample DNA sequences. There is no evidence for a barcoding gap, ruling out species discovery based on a threshold value alone. [source]


    Vouchering DNA-barcoded specimens: test of a nondestructive extraction protocol for terrestrial arthropods

    MOLECULAR ECOLOGY RESOURCES, Issue 6 2007
    DANIEL L. ROWLEY
    Abstract Morphology-based keys support accurate identification of many taxa. However, identification can be difficult for taxa that are either not well studied, very small, members of cryptic species complexes, or represented by immature stages. For such cases, DNA barcodes may provide diagnostic characters. Ecologists and evolutionary biologists deposit museum vouchers to document the species studied in their research. If DNA barcodes are to be used for identification, then both the DNA and the specimen from which it was extracted should be vouchered. We describe a protocol for the nondestructive extraction of DNA from terrestrial arthropods, using as examples members of the orders Acarina, Araneae, Coleoptera, Diptera, and Hymenoptera chosen to represent the ranges in size, overall sclerotization, and delicacy of key morphological characters in the group. We successfully extracted sequenceable DNA from all species after 1,4 h of immersion in extraction buffer. The extracted carcasses, processed and imaged using protocols standard for the taxon, were distinguishable from closely related species, and adequate as morphological vouchers. We provide links from the carcasses and DNA vouchers to image (MorphBank) and sequence (GenBank) databases. [source]


    Isolation of microsatellite loci in artichoke (Cynara cardunculus L. var. scolymus)

    MOLECULAR ECOLOGY RESOURCES, Issue 1 2003
    A. Acquadro
    Abstract We report the development of nine microsatellite markers in globe artichoke (Cynara cardunculus L. var. scolymus). Four markers were obtained from sequences available in GenBank and five were isolated using a biotin/streptavidin capture technique for (CA)n and (CT)n motifs directly from artichoke genomic DNA. Polymorphism was explored in 15 artichoke accessions that represent the genetic variation within cultivated varietal types. Inter-specific amplification was tested using cultivated cardoon (C. cardunculus L. var. altilis DC.) and wild cardoon (C. cardunculus L. var. sylvestris Lam.). Primers and conditions for polymerase chain reaction (PCR) amplification of detected loci are described. [source]


    Characterization of microsatellite loci in the diploid legume Medicago truncatula (barrel medic)

    MOLECULAR ECOLOGY RESOURCES, Issue 1-2 2001
    E. Baquerizo-Audiot
    Abstract We report the development of nine microsatellite markers in the diploid legume Medicago truncatula. Five markers were obtained from microsatellite-enriched genome libraries and four from sequences available in GenBank. Polymorphism was explored with plants from a natural population and cross-amplification was tested in other Medicago and three other legume genera. [source]


    Identification and quantification of differentially expressed transcripts in in vitro-produced bovine preimplantation stage embryos

    MOLECULAR REPRODUCTION & DEVELOPMENT, Issue 2 2003
    Dawit Tesfaye
    Abstract In this study, we used mRNA differential display reverse transcription polymerase chain reaction (DDRT-PCR) to analyze the mRNA expression patterns in in vitro-produced bovine 8-cell, 16-cell, morula, and blastocyst stage embryos and isolate differentially expressed amplicons. Moreover, we have used a fluorescence monitored real time quantitative PCR to quantify and analyze the expression patterns of the target differentially expressed transcripts through out the preimplantation stages from oocytes to blastocyst. For this, total RNA isolated from bovine 8-cell (n,=,188), 16-cell (n,=,94), morula (n,=,35), and blastocyst (n,=,15) were reverse transcribed and subjected to DDRT-PCR. Target differentially expressed transcripts were quantified by real time quantitative PCR. The cDNA banding pattern analysis revealed that large number of cDNA bands were conserved at 8-cell and blastocyst stage with a slight decrease at the morula stage. A total of 16 amplicons were cloned and sequenced. All expressed sequence tags (ESTs), except 1C19, showed sequence similarity with known genes or ESTs in GenBank. Sixty-two percent (10/16) of cDNA bands representing differentially expressed genes originated from 8-cell stage and the rest derived from the 16-cell, morula, or blastocyst stage. The quantitative PCR analysis has validated the expression patterns of 75% (12/16) of our transcripts to be in agreement with the results of DDRT-PCR. However, the quantitative PCR results of four transcripts showed a deviation from the pattern seen in DDRT-PCR. In conclusion, we have successfully applied mRNA DDRT-PCR to identify and isolate stage-specific expressed genes in bovine preimplantation embryos. In addition to validating the results of DDRT-PCR, quantitative real time PCR provides quantitative data on the expression of target genes. Mol. Reprod. Dev. 66: 105,114, 2003. © 2003 Wiley-Liss, Inc. [source]


    Mutational and expression analysis of CDK1, cyclinA2 and cyclinB1 in epilepsy-associated glioneuronal lesions

    NEUROPATHOLOGY & APPLIED NEUROBIOLOGY, Issue 2 2007
    V. Schick
    Gangliogliomas and focal cortical dysplasias (FCDs) constitute glioneuronal lesions, which are frequently encountered in biopsy specimens of patients with pharmacoresistant focal epilepsy and relate to impaired differentiation and migration of neural precursors. However, their molecular pathogenesis and relationship are still largely enigmatic. Recent data suggest several components of the insulin-pathway, including TSC1 and TSC2 mutated in tuberous sclerosis complex (TSC), to be altered in gangliogliomas and FCD with Taylor type balloon cells (FCDIIb). The proteins tuberin (TSC2) and hamartin (TSC1) constitute a tumour suppressor mechanism involved in cell-cycle control. Hamartin and/or tuberin were reported to colocalize and/or interact with CDK1, cyclinB1 and cyclinA2 that are critically involved in cell-size and cell-growth control. Here, we have carried out mutational and expression analyses of CDK1, cyclinB1 and cyclinA2 in gangliogliomas and FCDIIb. Mutational screening was performed by single-strand conformation polymorphism analysis in gangliogliomas (n = 20), FCDIIb (n = 35) and controls. CyclinB1 revealed a polymorphism (G to A, cDNA Position 966, GenBank: NM_031966) in exon 7 with similar frequencies in FCDIIb, gangliogliomas and control specimens (FCD n = 9/35; gangliogliomas n = 5/20; control n = 20/100). We used real-time reverse transcription polymerase chain reaction to determine expression levels of CDK1, cyclinB1 and cyclinA2 in 10 FCDIIb and nine gangliogliomas compared with unaffected adjacent control tissue of the same patients. We observed significantly lower expression of CDK1 and cyclinA2 in FCDIIb vs. controls whereas no significant expression differences were present for CDK1, cyclinB1 and cyclinA2 in gangliogliomas. Our data strongly argue against mutational events of CDK1, cyclinB1 and cyclinA2 to play a role in gangliogliomas or FCDIIb. However, a potential functional significance of lower expression for the cell-size and cell-cycle regulators CDK1 and cyclinA2 in FCDIIb composed of large dysplastic neurones and balloon cells needs to be further resolved. [source]