Escherichia coli C is a commonly used strain in the bioprocessing industry, but despite its utility, the publicly available sequence of the E. coli C genome has gaps and 4,180 ambiguous base calls. Here, we present an updated, high-quality, unambiguous genome sequence with no assembly gaps.
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http://dx.doi.org/10.1128/MRA.00890-18 | DOI Listing |
Integr Zool
December 2024
School of Natural Sciences, Canterbury, Kent, UK.
Bird eggs can be spherical, ellipsoid, ovoid, or pear-shaped (pyriform), the latter being the most complex. There is however no unambiguous evolutionary/adaptive explanation for this final, exotic shape. We hypothesized that pyriform eggs have a larger surface area-to-volume ratio (S/V) that may be a criterion for increased embryo metabolism.
View Article and Find Full Text PDFGenome Med
December 2024
Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
Background: The Human Genome Variation Society (HGVS) Nomenclature is the global standard for describing and communicating variants in DNA, RNA, and protein sequences in clinical and research genomics. This manuscript details recent updates to the HGVS Nomenclature, highlighting improvements in governance, community engagement, website functionality, and underlying implementation of the standard.
Methods: The HGVS Variant Nomenclature Committee (HVNC) now operates under the Human Genome Organization (HUGO), facilitating broader community feedback and collaboration with related standards organizations.
Cell Rep Methods
December 2024
German National Reference Centre for Borrelia, Oberschleissheim, Germany; Bavarian Health and Food Safety Authority, Oberschleissheim, Germany.
Multi-locus sequence typing (MLST) based on eight genes has become the method of choice for Borrelia typing and is extensively used for population studies. Whole-genome sequencing enables studies to scale up to genomic levels but necessitates extended schemes. We have developed a 639-loci core genome MLST (cgMLST) scheme for Borrelia burgdorferi sensu lato (s.
View Article and Find Full Text PDFFront Genome Ed
December 2024
Department of Horticultural Sciences, Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States.
STAR Protoc
December 2024
Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. Electronic address:
Small noncoding RNAs (sncRNAs) can regulate gene expression by guiding the RNA-induced silencing complex (RISC) to targeted transcripts for translational repression and/or target destabilization. Here, we present a robust benchtop protocol, termed CIMERA-seq, for the unambiguous profiling of sncRNA:target RNA interactions in a genome-wide and cell-type-selective manner. We describe steps for in vivo crosslinking and harvesting tissue, immunoprecipitation and covalent ligation of sncRNAs to target RNAs within the RISC, and sequencing of the resulting chimeric sncRNA:target RNA interactions.
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