LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Back to previous search Search history
Advanced search

Your last searches

  1. AU="Bell, Callum J"
  2. AU="Tubiana, Mauro"

Search results

Result 1 - 10 of total 19

Search options

  1. Article ; Online: Contiguous Genome Sequence of

    Bell, Callum J / Sena, Johnny A / Gifford, Isaac S / Berry, Alison M

    Microbiology resource announcements

    2021  Volume 10, Issue 43, Page(s) e0080021

    Abstract: We report the genome sequence ... ...

    Abstract We report the genome sequence of
    Language English
    Publishing date 2021-10-28
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/MRA.00800-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  2. Article ; Online: Annotated genome sequence of a fast-growing diploid clone of red alder (Alnus rubra Bong.).

    Hixson, Kim K / Fajardo, Diego A / Devitt, Nicholas P / Sena, Johnny A / Costa, Michael A / Meng, Qingyan / Boschiero, Clarissa / Zhao, Patrick Xuechun / Baack, Eric J / Paurus, Vanessa L / Davin, Laurence B / Lewis, Norman G / Bell, Callum J

    G3 (Bethesda, Md.)

    2023  Volume 13, Issue 6

    Abstract: Red alder (Alnus rubra Bong.) is an ecologically significant and important fast-growing commercial tree species native to western coastal and riparian regions of North America, having highly desirable wood, pigment, and medicinal properties. We have ... ...

    Abstract Red alder (Alnus rubra Bong.) is an ecologically significant and important fast-growing commercial tree species native to western coastal and riparian regions of North America, having highly desirable wood, pigment, and medicinal properties. We have sequenced the genome of a rapidly growing clone. The assembly is nearly complete, containing the full complement of expected genes. This supports our objectives of identifying and studying genes and pathways involved in nitrogen-fixing symbiosis and those related to secondary metabolites that underlie red alder's many interesting defense, pigmentation, and wood quality traits. We established that this clone is most likely diploid and identified a set of SNPs that will have utility in future breeding and selection endeavors, as well as in ongoing population studies. We have added a well-characterized genome to others from the order Fagales. In particular, it improves significantly upon the only other published alder genome sequence, that of Alnus glutinosa. Our work initiated a detailed comparative analysis of members of the order Fagales and established some similarities with previous reports in this clade, suggesting a biased retention of certain gene functions in the vestiges of an ancient genome duplication when compared with more recent tandem duplications.
    MeSH term(s) Alnus/metabolism ; Diploidy ; Plant Breeding ; Symbiosis ; Trees
    Language English
    Publishing date 2023-03-25
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2629978-1
    ISSN 2160-1836 ; 2160-1836
    ISSN (online) 2160-1836
    ISSN 2160-1836
    DOI 10.1093/g3journal/jkad060
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  3. Article ; Online: Unique Molecular Identifiers reveal a novel sequencing artefact with implications for RNA-Seq based gene expression analysis.

    Sena, Johnny A / Galotto, Giulia / Devitt, Nico P / Connick, Melanie C / Jacobi, Jennifer L / Umale, Pooja E / Vidali, Luis / Bell, Callum J

    Scientific reports

    2018  Volume 8, Issue 1, Page(s) 13121

    Abstract: Attaching Unique Molecular Identifiers (UMI) to RNA molecules in the first step of sequencing library preparation establishes a distinct identity for each input molecule. This makes it possible to eliminate the effects of PCR amplification bias, which is ...

    Abstract Attaching Unique Molecular Identifiers (UMI) to RNA molecules in the first step of sequencing library preparation establishes a distinct identity for each input molecule. This makes it possible to eliminate the effects of PCR amplification bias, which is particularly important where many PCR cycles are required, for example, in single cell studies. After PCR, molecules sharing a UMI are assumed to be derived from the same input molecule. In our single cell RNA-Seq studies of Physcomitrella patens, we discovered that reads sharing a UMI, and therefore presumed to be derived from the same mRNA molecule, frequently map to different, but closely spaced locations. This behaviour occurs in all such libraries that we have produced, and in multiple other UMI-containing RNA-Seq data sets in the public domain. This apparent paradox, that reads of identical origin map to distinct genomic coordinates may be partially explained by PCR stutter, which is often seen in low-entropy templates and those containing simple tandem repeats. In the absence of UMI this artefact is undetectable. We show that the common assumption that sequence reads having different mapping coordinates are derived from different starting molecules does not hold. Unless taken into account, this artefact is likely to result in over-estimation of certain transcript abundances, depending on the counting method employed.
    MeSH term(s) Artifacts ; Bryopsida/genetics ; Chromosome Mapping ; Computational Biology/methods ; Gene Expression Regulation, Plant ; Gene Library ; Genome, Plant ; High-Throughput Nucleotide Sequencing ; Microsatellite Repeats ; RNA, Messenger/genetics ; RNA, Plant/genetics ; Sequence Analysis, RNA/methods ; Single-Cell Analysis
    Chemical Substances RNA, Messenger ; RNA, Plant
    Language English
    Publishing date 2018-09-03
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-018-31064-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  4. Article: New Insights Into Lignification via Network and Multi-Omics Analyses of Arogenate Dehydratase Knock-Out Mutants in

    Hixson, Kim K / Marques, Joaquim V / Wendler, Jason P / McDermott, Jason E / Weitz, Karl K / Clauss, Therese R / Monroe, Matthew E / Moore, Ronald J / Brown, Joseph / Lipton, Mary S / Bell, Callum J / Paša-Tolić, Ljiljana / Davin, Laurence B / Lewis, Norman G

    Frontiers in plant science

    2021  Volume 12, Page(s) 664250

    Abstract: ... ...

    Abstract Multiple
    Language English
    Publishing date 2021-05-25
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2021.664250
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  5. Article ; Online: De novo

    Zhou, Mowei / Laureanti, Joseph A / Bell, Callum J / Kwon, Mi / Meng, Qingyan / Novikova, Irina V / Thomas, Dennis G / Nicora, Carrie D / Sontag, Ryan L / Bedgar, Diana L / O'Bryon, Isabelle / Merkley, Eric D / Ginovska, Bojana / Cort, John R / Davin, Laurence B / Lewis, Norman G

    The Analyst

    2021  Volume 146, Issue 24, Page(s) 7670–7681

    Abstract: The discovery of dirigent proteins (DPs) and their functions in plant phenol biochemistry was made over two decades ago ... ...

    Abstract The discovery of dirigent proteins (DPs) and their functions in plant phenol biochemistry was made over two decades ago with
    MeSH term(s) Arabidopsis ; Forsythia ; Genome ; Humans ; Mass Spectrometry ; Plant Proteins/genetics
    Chemical Substances Plant Proteins
    Language English
    Publishing date 2021-12-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 210747-8
    ISSN 1364-5528 ; 0003-2654
    ISSN (online) 1364-5528
    ISSN 0003-2654
    DOI 10.1039/d1an01476e
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 2423: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  6. Article: Draft Genome Sequence of a

    Devitt, Nicholas P / Herman, Barrington / Luchterhand, Randi A / Costa, Michael A / Jacobi, Jennifer L / Davin, Laurence B / Lewis, Norman G / Bell, Callum J

    Genome announcements

    2017  Volume 5, Issue 39

    Abstract: ... ...

    Abstract A
    Language English
    Publishing date 2017-09-28
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2704277-7
    ISSN 2169-8287
    ISSN 2169-8287
    DOI 10.1128/genomeA.01039-17
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  7. Article: Composition, Diversity and Abundance of Gut Microbiome in Prediabetes and Type 2 Diabetes.

    Lambeth, Stacey M / Carson, Trechelle / Lowe, Janae / Ramaraj, Thiruvarangan / Leff, Jonathan W / Luo, Li / Bell, Callum J / Shah, Vallabh O

    Journal of diabetes and obesity

    2015  Volume 2, Issue 3, Page(s) 1–7

    Abstract: Association between type 2 diabetes (T2DM) and compositional changes in the gut micro biota is established, however little is known about the dysbiosis in early stages of Prediabetes (preDM). The purpose of this investigation is to elucidate the ... ...

    Abstract Association between type 2 diabetes (T2DM) and compositional changes in the gut micro biota is established, however little is known about the dysbiosis in early stages of Prediabetes (preDM). The purpose of this investigation is to elucidate the characteristics of the gut micro biome in preDM and T2DM, compared to Non-Diabetic (nonDM) subjects. Forty nine subjects were recruited for this study, 15 nonDM, 20 preDM and 14 T2DM. Bacterial community composition and diversity were investigated in fecal DNA samples using Illumina sequencing of the V4 region within the 16S rRNA gene. The five most abundant phyla identified were:
    Language English
    Publishing date 2015-12-30
    Publishing country United States
    Document type Journal Article
    ISSN 2376-0494
    ISSN 2376-0494
    DOI 10.15436/2376-0949.15.031
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  8. Article ; Online: Probing the evolution, ecology and physiology of marine protists using transcriptomics.

    Caron, David A / Alexander, Harriet / Allen, Andrew E / Archibald, John M / Armbrust, E Virginia / Bachy, Charles / Bell, Callum J / Bharti, Arvind / Dyhrman, Sonya T / Guida, Stephanie M / Heidelberg, Karla B / Kaye, Jonathan Z / Metzner, Julia / Smith, Sarah R / Worden, Alexandra Z

    Nature reviews. Microbiology

    2017  Volume 15, Issue 1, Page(s) 6–20

    Abstract: Protists, which are single-celled eukaryotes, critically influence the ecology and chemistry of marine ecosystems, but genome-based studies of these organisms have lagged behind those of other microorganisms. However, recent transcriptomic studies of ... ...

    Abstract Protists, which are single-celled eukaryotes, critically influence the ecology and chemistry of marine ecosystems, but genome-based studies of these organisms have lagged behind those of other microorganisms. However, recent transcriptomic studies of cultured species, complemented by meta-omics analyses of natural communities, have increased the amount of genetic information available for poorly represented branches on the tree of eukaryotic life. This information is providing insights into the adaptations and interactions between protists and other microorganisms and macroorganisms, but many of the genes sequenced show no similarity to sequences currently available in public databases. A better understanding of these newly discovered genes will lead to a deeper appreciation of the functional diversity and metabolic processes in the ocean. In this Review, we summarize recent developments in our understanding of the ecology, physiology and evolution of protists, derived from transcriptomic studies of cultured strains and natural communities, and discuss how these novel large-scale genetic datasets will be used in the future.
    MeSH term(s) Aquatic Organisms/genetics ; Aquatic Organisms/physiology ; Biological Evolution ; Ecosystem ; Energy Metabolism/physiology ; Eukaryota/genetics ; Eukaryota/physiology ; Transcriptome/genetics
    Language English
    Publishing date 2017
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2139054-X
    ISSN 1740-1534 ; 1740-1526
    ISSN (online) 1740-1534
    ISSN 1740-1526
    DOI 10.1038/nrmicro.2016.160
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 5865: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 74: Show issues

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  9. Article ; Online: A genome-wide linkage scan of insulin level derived traits: the Amish Family Diabetes Study.

    Hsueh, Wen-Chi / Silver, Kristi D / Pollin, Toni I / Bell, Callum J / O'Connell, Jeffrey R / Mitchell, Braxton D / Shuldiner, Alan R

    Diabetes

    2007  Volume 56, Issue 10, Page(s) 2643–2648

    Abstract: Objective: Serum insulin levels are altered in insulin resistance and insulin deficiency, states that are associated with the development of type 2 diabetes. The goal of our study was to identify chromosomal regions that are likely to harbor genetic ... ...

    Abstract Objective: Serum insulin levels are altered in insulin resistance and insulin deficiency, states that are associated with the development of type 2 diabetes. The goal of our study was to identify chromosomal regions that are likely to harbor genetic determinants of these traits.
    Research design and methods: We conducted a series of genetic analyses, including genome-wide and fine-mapping linkage studies, based on insulin levels measured during an oral glucose tolerance test (OGTT) in 552 nondiabetic participants in the Amish Family Diabetes Study. Indices of insulin secretion included the insulinogenic index and insulin at 30 min postglucose load (insulin 30), while indices of insulin resistance included homeostasis model assessment of insulin resistance (HOMA-IR) and fasting insulin. Insulin area under the curve, a measure of both insulin secretion and insulin resistance, was also examined.
    Results: All traits were modestly heritable, with heritability estimates ranging from 0.1 to 0.4 (all P < 0.05). There was significant genetic correlation between fasting insulin and HOMA-IR (rho(G) > 0.86, P < 0.05), as well as insulin 30 and insulinogenic index (rho(G) = 0.81, P < 0.0001), suggesting that common genes influence variation in these pairs of traits. Suggestive linkage signals in the genome scan were to insulin 30 on chromosome 15q23 (logarithm of odds [LOD] 2.53, P = 0.00032) and to insulinogenic index on chromosome 2p13 (LOD 2.51, P = 0.00034). Fine-mapping study further refined our signal for insulin 30 on chromosome 15 (LOD 2.38 at 68 cM).
    Conclusions: These results suggest that there may be different genes influencing variation in OGTT measures of insulin secretion and insulin resistance.
    MeSH term(s) Adult ; Blood Glucose/metabolism ; Diabetes Mellitus, Type 2/genetics ; Ethnic Groups/genetics ; Family ; Female ; Genetic Linkage ; Genome, Human ; Humans ; Insulin/blood ; Insulin/genetics ; Insulin/metabolism ; Insulin Resistance/genetics ; Insulin Secretion ; Male ; Middle Aged ; United States
    Chemical Substances Blood Glucose ; Insulin
    Language English
    Publishing date 2007-07-23
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 80085-5
    ISSN 1939-327X ; 0012-1797
    ISSN (online) 1939-327X
    ISSN 0012-1797
    DOI 10.2337/db06-1023
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Uh III Zs.175: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  10. Article ; Online: Combined DOCK8 and CLEC7A mutations causing immunodeficiency in 3 brothers with diarrhea, eczema, and infections.

    Dinwiddie, Darrell L / Kingsmore, Stephen F / Caracciolo, Sonia / Rossi, Giuseppe / Moratto, Daniele / Mazza, Cinzia / Sabelli, Cristiano / Bacchetta, Rosa / Passerini, Laura / Magri, Chiara / Bell, Callum J / Miller, Neil A / Hateley, Shannon L / Saunders, Carol J / Zhang, Lu / Schroth, Gary P / Barlati, Sergio / Badolato, Raffaele

    The Journal of allergy and clinical immunology

    2013  Volume 131, Issue 2, Page(s) 594–7.e1–3

    MeSH term(s) Adolescent ; Adult ; Diarrhea/genetics ; Diarrhea/immunology ; Eczema/genetics ; Eczema/immunology ; Guanine Nucleotide Exchange Factors/genetics ; Guanine Nucleotide Exchange Factors/immunology ; Humans ; Immunologic Deficiency Syndromes/genetics ; Infections/genetics ; Infections/immunology ; Lectins, C-Type/genetics ; Lectins, C-Type/immunology ; Male ; Mutation ; Siblings
    Chemical Substances CLEC7A protein, human ; DOCK8 protein, human ; Guanine Nucleotide Exchange Factors ; Lectins, C-Type
    Language English
    Publishing date 2013-02-02
    Publishing country United States
    Document type Case Reports ; Letter ; Research Support, N.I.H., Extramural
    ZDB-ID 121011-7
    ISSN 1097-6825 ; 1085-8725 ; 0091-6749
    ISSN (online) 1097-6825 ; 1085-8725
    ISSN 0091-6749
    DOI 10.1016/j.jaci.2012.10.062
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Uh III Zs.92: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

To top