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  • American Physical Society  (39,774)
  • Oxford University Press  (22,957)
  • American Society of Hematology  (9,981)
  • 2005-2009  (33,403)
  • 2000-2004  (19,889)
  • 1990-1994  (19,420)
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  • 1
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    Oxford University Press
    In:  Handbook of Avian Hybrids of the World vol. 76, 1, pp. 59-61
    Publication Date: 2024-01-12
    Keywords: book review ; geographic distribution ; hybridisation ; birds
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/review
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  • 2
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    Oxford University Press
    Publication Date: 2022-07-11
    Type: Book , NonPeerReviewed
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  • 3
    Publication Date: 2022-05-26
    Description: © The Author 2006. This article is posted here by permission of Oxford University Press. The definitive version was published in Nucleic Acids Research 34 (2006): 1-9, doi:10.1093/nar/gkj405.
    Description: The goal of this group project has been to coordinate and bring up-to-date information on all genes of Escherichia coli K-12. Annotation of the genome of an organism entails identification of genes, the boundaries of genes in terms of precise start and end sites, and description of the gene products. Known and predicted functions were assigned to each gene product on the basis of experimental evidence or sequence analysis. Since both kinds of evidence are constantly expanding, no annotation is complete at any moment in time. This is a snapshot analysis based on the most recent genome sequences of two E.coli K-12 bacteria. An accurate and up-to-date description of E.coli K-12 genes is of particular importance to the scientific community because experimentally determined properties of its gene products provide fundamental information for annotation of innumerable genes of other organisms. Availability of the complete genome sequence of two K-12 strains allows comparison of their genotypes and mutant status of alleles.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 4
    Publication Date: 2022-05-25
    Description: © 2007 The Author et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Nucleic Acids Research 35 (2007): 2107-2115, doi:10.1093/nar/gkm049.
    Description: Trypanosomatids contain an unusual DNA base J (ß-D-glucosylhydroxymethyluracil), which replaces a fraction of thymine in telomeric and other DNA repeats. To determine the function of base J, we have searched for enzymes that catalyze J biosynthesis. We present evidence that a protein that binds to J in DNA, the J-binding protein 1 (JBP1), may also catalyze the first step in J biosynthesis, the conversion of thymine in DNA into hydroxymethyluracil. We show that JBP1 belongs to the family of Fe2+ and 2-oxoglutarate-dependent dioxygenases and that replacement of conserved residues putatively involved in Fe2+ and 2-oxoglutarate-binding inactivates the ability of JBP1 to contribute to J synthesis without affecting its ability to bind to J-DNA. We propose that JBP1 is a thymidine hydroxylase responsible for the local amplification of J inserted by JBP2, another putative thymidine hydroxylase.
    Description: This work was funded by a grant from the Netherlands Organization for Scientific Research and Chemical Sciences (NWO-CW) to P.B., NIH grant A1063523 to R.S. and NIH grant GM063584 to R.P.H.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 5
    Publication Date: 2022-05-25
    Description: © 2007 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Nucleic Acids Research 36 (2008): D607-D611, doi:10.1093/nar/gkm941.
    Description: The starlet sea anemone, Nematostella vectensis, is a basal metazoan organism that has recently emerged as an important model system in developmental biology and evolutionary genomics. StellaBase, the Nematostella Genomics Database (http://stellabase.org), was developed in 2005 as a resource to support the Nematostella research community. Recently, it has become apparent that Nematostella may be a particularly useful system for studying (i) microevolutionary variation in natural populations, and (ii) the functional evolution of human disease genes. We have developed two new databases that will foster such studies: StellaBase Disease (http://stellabase.org/disease) is a relational database that houses 155 904 invertebrate homologous isoforms of human disease genes from four leading genomic model systems (fly, worm, yeast and Nematostella), including 14 874 predicted genes from the sea anemone itself. StellaBase SNP (http://stellabase.org/SNP) is a relational database that describes the location and underlying type of mutation for 20 063 single nucleotide polymorphisms.
    Description: This work was supported by NSF grant FP-91656101-0 to J.C.S. and J.R.F. and EPA Grant F5E11155 to A.R.M. and J.R.F. and by a Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by The Beacon Institute for Rivers and Estuaries, and the J. Seward Johnson Fund to A.M.R.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 6
    Publication Date: 2022-05-25
    Description: © 2007 The Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Bioinformatics 23 (2007): 1434-1436, doi:10.1093/bioinformatics/btm109.
    Description: Web content syndication through standard formats such as RSS and ATOM has become an increasingly popular mechanism for publishers, news sources, and blogs to disseminate regularly updated content. These standardized syndication formats deliver content directly to the subscriber, allowing them to locally aggregate content from a variety of sources instead of having to find the information on multiple websites. The uBioRSS application is a "taxonomically intelligent" service customized for the biological sciences. It aggregates syndicated content from academic publishers and science news feeds, then uses a taxonomic name entity recognition algorithm to identify and index taxonomic names within those data streams. The resulting name index is cross-referenced to current global taxonomic datasets to provide context for browsing the publications by taxonomic group. This process, called taxonomic indexing, draws upon services developed specifically for biological sciences, collectively referred to as "taxonomic intelligence." Such value-added enhancements can provide biologists with accelerated and improved access to current biological content.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 7
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    Oxford University Press
    In:  Integrative and Comparative Biology, 47 (4). pp. 645-655.
    Publication Date: 2021-09-03
    Description: Mechanisms that affect thermal tolerance of ectothermic organisms have recently received much interest, mainly due to global warming and climate-change debates in both the public and in the scientific community. In physiological terms, thermal tolerance of several marine ectothermic taxa can be linked to oxygen availability, with capacity limitations in ventilatory and circulatory systems contributing to oxygen limitation at extreme temperatures. The present review briefly summarizes the processes that define thermal tolerance in a model cephalopod organism, the cuttlefish Sepia officinalis, with a focus on the contribution of the cephalopod oxygen-carrying blood pigment, hemocyanin. When acutely exposed to either extremely high or low temperatures, cuttlefish display a gradual transition to an anaerobic mode of energy production in key muscle tissues once critical temperatures (Tcrit) are reached. At high temperatures, stagnating metabolic rates and a developing hypoxemia can be correlated with a progressive failure of the circulatory system, well before Tcrit is reached. However, at low temperatures, declining metabolic rates cannot be related to ventilatory or circulatory failure. Rather, we propose a role for hemocyanin functional characteristics as a major limiting factor preventing proper tissue oxygenation. Using information on the oxygen binding characteristics of cephalopod hemocyanins, we argue that high oxygen affinities (= low P50 values), as found at low temperatures, allow efficient oxygen shuttling only at very low venous oxygen partial pressures. Low venous PO2s limit rates of oxygen diffusion into cells, thus eventually causing the observed transition to anaerobic metabolism. On the basis of existing blood physiological, molecular, and crystallographical data, the potential to resolve the role of hemocyanin isoforms in thermal adaptation by an integrated molecular physiological approach is discussed.
    Type: Article , PeerReviewed
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  • 8
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    Oxford University Press
    In:  Journal of Molluscan Studies, 73 (3). pp. 287-289.
    Publication Date: 2021-08-31
    Type: Article , PeerReviewed
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  • 9
    Publication Date: 2021-08-23
    Description: Recent molecular studies investigating higher-level phylogenetics of coleoid cephalopods (octopuses, squids and cuttlefishes) have produced conflicting results. A wide range of sequence alignment and analysis methods are used in cephalopod phylogenetic studies. The present study investigated the effect of commonly used alignment and analysis methods on higher-level cephalopod phylogenetics. Two sequence homology methods: (1) eye alignment, (2) implied alignment, and three analysis methods: (1) parsimony, (2) maximum likelihood, (3) Bayesian methodologies, were employed on the longest sequence dataset available for the coleoid cephalopods, comprising three mitochondrial and six nuclear loci. The data were also tested for base composition heterogeneity, which was detected in three genes and resolved using RY coding. The Octopoda, Argonautoidea, Oegopsida and Ommastrephidae are monophyletic in the phylogenies resulting from each of the alignment and analysis combinations. Furthermore, the Bathyteuthidae are the sister taxon of the Oegopsida in each case. However many relationships within the Coleoidea differed depending upon the alignment and analysis method used. This study demonstrates how differences in alignment and analysis methods commonly used in cephalopod phylogenetics can lead to different, but often highly supported, relationships.
    Type: Article , PeerReviewed
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  • 10
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    Oxford University Press
    In:  Zoological Journal of the Linnean Society, 139 (1). pp. 93-127.
    Publication Date: 2021-07-15
    Description: The systematics and distribution of the cirrate octopod genus Grimpoteuthis in the north-east Atlantic are reviewed. Three new species are described and Grimpoteuthis wuelkeri (Grimpe, 1920) is redescribed. A new generic diagnosis is proposed. Five species of Grimpoteuthis are recognized in the north-east Atlantic. The type species, G. umbellata (Fisher, 1883) is known only from the type specimen, which is in such poor condition that comparison with recently captured material was not possible. G. wuelkeri is a large, slope species, caught between 1600 m and 2200 m in the north-east and north-west Atlantic. Of the three new species, both G. boylei and G. challengeri are large abyssal species. G. boylei is found in the north-east Atlantic at the Porcupine Abyssal Plain (PAP) and the Madeira Abyssal Plain and may be found at abyssal depths throughout the north-east Atlantic. G. challengeri is known from the PAP, with a single specimen from the north-west Atlantic. G. discoveryi is a small, lower slope and abyssal species found in the north-east Atlantic. The Grimpoteuthis species can be separated based on shell form, presence of a radula and posterior salivary glands, arrangement of suckers and cirri and gill morphology. Two species, G. megaptera Verrill and G. plena Verrill, have been described from the north-west Atlantic, but the types are either lost (G. megaptera) or in poor condition (G. plena), hindering comparisons. Material examined from the north-west Atlantic included G. wuelkeri, G. challengeri and at least two other species.
    Type: Article , PeerReviewed
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