Nucleic acid sequence ≈ Nucleic acid sequence
View article
The establishment of reference sequence for SARS‐CoV‐2 and variation analysis Open
Starting around December 2019, an epidemic of pneumonia, which was named COVID‐19 by the World Health Organization, broke out in Wuhan, China, and is spreading throughout the world. A new coronavirus, named severe acute respiratory syndrom…
View article
PLSDB: a resource of complete bacterial plasmids Open
The study of bacterial isolates or communities requires the analysis of the therein included plasmids in order to provide an extensive characterization of the organisms. Plasmids harboring resistance and virulence factors are of especial i…
View article
The international nucleotide sequence database collaboration Open
The International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org/) has been the core infrastructure for collecting and providing nucleotide sequence data and metadata for >30 years. Three partner organizations, the…
View article
MeCP2 recognizes cytosine methylated tri-nucleotide and di-nucleotide sequences to tune transcription in the mammalian brain Open
Mutations in the gene encoding the methyl-CG binding protein MeCP2 cause several neurological disorders including Rett syndrome. The di-nucleotide methyl-CG (mCG) is the classical MeCP2 DNA recognition sequence, but additional methylated s…
View article
Highly parallel direct RNA sequencing on an array of nanopores Open
Ribonucleic acid sequencing can allow us to monitor the RNAs present in a sample. This enables us to detect the presence and nucleotide sequence of viruses, or to build a picture of how active transcriptional processes are changing – infor…
View article
The European Nucleotide Archive in 2019 Open
The European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena) at the European Molecular Biology Laboratory’s European Bioinformatics Institute provides open and freely available data deposition and access services across the spectrum of…
View article
A nucleotide-sensing endonuclease from the Gabija bacterial defense system Open
The arms race between bacteria and phages has led to the development of exquisite bacterial defense systems including a number of uncharacterized systems distinct from the well-known restriction-modification and CRISPR/Cas systems. Here, w…
View article
Systematic investigation of sequence requirements for DNA i-motif formation Open
The formation of intercalated motifs (iMs) - secondary DNA structures based on hemiprotonated C.C+ pairs in suitable cytosine-rich DNA sequences, is reflected by typical changes in CD and UV absorption spectra. By means of spectroscopic me…
View article
Complete Nucleotide Sequence of an IncI2 Plasmid Coharboring <i>bla</i> <sub>CTX-M-55</sub> and <i>mcr-1</i> Open
We report the complete nucleotide sequence of a plasmid, pA31-12, carrying bla CTX-M-55 and mcr-1 from a chicken Escherichia coli isolate. pA31-12 has an IncI2 replicon that displays extensive sequence similarity with pHN1122-1-borne bla C…
View article
Citrus leprosis virus N: A New Dichorhavirus Causing Citrus Leprosis Disease Open
Citrus leprosis (CL) is a viral disease endemic to the Western Hemisphere that produces local necrotic and chlorotic lesions on leaves, branches, and fruit and causes serious yield reduction in citrus orchards. Samples of sweet orange (Cit…
View article
A <i>gapA</i> PCR-sequencing Assay for Identifying the <i>Dickeya</i> and <i>Pectobacterium</i> Potato Pathogens Open
Several pectinolytic Pectobacterium and Dickeya species and subspecies are causative agents of blackleg and soft rot diseases on potato plants and tubers. Rapid and accurate identification of these taxa is a crucial issue for the productio…
View article
Description of a Novel Monopartite Geminivirus and Its Defective Subviral Genome in Grapevine Open
A novel virus was detected in grapevines by Illumina sequencing during the screening of two table grape (Vitis vinifera) accessions, cultivars Black Beet and Nagano Purple, from South Korea. The monopartite circular ssDNA genome sequence w…
View article
Sequencing by avidity enables high accuracy with low reagent consumption Open
We present avidity sequencing, a sequencing chemistry that separately optimizes the processes of stepping along a DNA template and that of identifying each nucleotide within the template. Nucleotide identification uses multivalent nucleoti…
View article
Diverse functions of homologous actin isoforms are defined by their nucleotide, rather than their amino acid sequence Open
β‐ and γ‐cytoplasmic actin are nearly indistinguishable in their amino acid sequence, but are encoded by different genes that play non‐redundant biological roles. The key determinants that drive their functional distinction are unknown. He…
View article
A massively parallel 3′ UTR reporter assay reveals relationships between nucleotide content, sequence conservation, and mRNA destabilization Open
Compared to coding sequences, untranslated regions of the transcriptome are not well conserved, and functional annotation of these sequences is challenging. Global relationships between nucleotide composition of 3′ UTR sequences and their …
View article
The dsRNA Virus Papaya Meleira Virus and an ssRNA Virus Are Associated with Papaya Sticky Disease Open
Papaya sticky disease, or "meleira", is one of the major diseases of papaya in Brazil and Mexico, capable of causing complete crop loss. The causal agent of sticky disease was identified as an isometric virus with a double stranded RNA (ds…
View article
Semi-automated fact-checking of nucleotide sequence reagents in biomedical research publications: The Seek & Blastn tool Open
Nucleotide sequence reagents are verifiable experimental reagents in biomedical publications, because their sequence identities can be independently verified and compared with associated text descriptors. We have previously reported that i…
View article
Characterisation of the nicotianamine aminotransferase and deoxymugineic acid synthase genes essential to Strategy II iron uptake in bread wheat (Triticum aestivum L.) Open
Iron (Fe) uptake in graminaceous plant species occurs via the release and uptake of Fe-chelating compounds known as mugineic acid family phytosiderophores (MAs). In the MAs biosynthetic pathway, nicotianamine aminotransferase (NAAT) and de…
View article
RNase H sequence preferences influence antisense oligonucleotide efficiency Open
RNase H cleaves RNA in RNA-DNA duplexes. It is present in all domains of life as well as in multiple viruses and is essential for mammalian development and for human immunodeficiency virus replication. Here, we developed a sequencing-based…
View article
Ultrasensitive version of nucleic acid sequence-based amplification (NASBA) utilizing a nicking and extension chain reaction system Open
An ultrasensitive version of nucleic acid sequence-based amplification (NASBA) utilizing a nicking and extension chain reaction system, termed nicking and extension chain reaction system-based amplification (NESBA), was developed.
View article
The prediction of virus mutation using neural networks and rough set techniques Open
Viral evolution remains to be a main obstacle in the effectiveness of antiviral treatments. The ability to predict this evolution will help in the early detection of drug-resistant strains and will potentially facilitate the design of more…
View article
Identification and Characterization of Wheat Yellow Striate Virus, a Novel Leafhopper-Transmitted Nucleorhabdovirus Infecting Wheat Open
A new wheat viral disease was found in China. Bullet-shaped viral particles within the nucleus of the infected wheat leave cells, which possessed 180-210 nm length and 35-40 nm width, were observed under transmission electron microscopy. A…
View article
Essential nucleotide- and protein-dependent functions of<i>Actb</i>/β-actin Open
Significance Actin is required for many general and specialized cellular functions. Two isoforms, β-actin and γ-actin, are ubiquitously expressed and 99% identical in amino acid sequence, yet previous studies indicated only β-actin is indi…
View article
Identification, Characterization and Full-Length Sequence Analysis of a Novel Polerovirus Associated with Wheat Leaf Yellowing Disease Open
To identify the pathogens responsible for leaf yellowing symptoms on wheat samples collected from Jinan, China, we tested for the presence of three known barley/wheat yellow dwarf viruses (BYDV-GAV, -PAV, WYDV-GPV) (most likely pathogens) …
View article
Complete Nucleotide Sequence of an <i>Escherichia coli</i> Sequence Type 410 Strain Carrying <i>bla</i> <sub>NDM-5</sub> on an IncF Multidrug Resistance Plasmid and <i>bla</i> <sub>OXA-181</sub> on an IncX3 Plasmid Open
Using Nanopore sequencing, we describe here the circular genome of an Escherichia coli sequence type 410 (ST410) strain with five closed plasmids. A large 111-kb incompatibility group F (IncF) plasmid harbored bla NDM-5 and 16 other resist…
View article
Mutational analysis of the<i>Potyviridae</i>transcriptional slippage site utilized for expression of the P3N-PIPO and P1N-PISPO proteins Open
The Potyviridae comprise the largest and most important family of RNA plant viruses. An essential overlapping ORF, termed pipo, resides in an internal region of the main polyprotein ORF. Recently, expression of pipo was shown to depend on …
View article
Complete Nucleotide Sequences of <i>mcr-4.3</i> -Carrying Plasmids in Acinetobacter baumannii Sequence Type 345 of Human and Food Origin from the Czech Republic, the First Case in Europe Open
Here, we describe two plasmids carrying mcr-4.3 in two Acinetobacter baumannii strains isolated from imported food and a clinical sample. The comparative analysis of these plasmids, with two other plasmids reported in the NCBI database, hi…
View article
StructMAn: annotation of single-nucleotide polymorphisms in the structural context Open
The next generation sequencing technologies produce unprecedented amounts of data on the genetic sequence of individual organisms. These sequences carry a substantial amount of variation that may or may be not related to a phenotype. Pheno…
View article
A Novel Astrovirus-Like RNA Virus Detected in Human Stool Open
Several novel clades of astroviruses have recently been identified in human faecal samples. Here, we describe a novel astrovirus-like RNA virus detected in human stools, which we have tentatively named bastrovirus. The genome of this novel…
View article
Ruminococcus bovis sp. nov., a novel species of amylolytic Ruminococcus isolated from the rumen of a dairy cow Open
This study describes JE7A12 T (=ATCC TSD-225 T =NCTC 14479 T ), an isolate from the ruminal content of a dairy cow. Phenotypic and genotypic traits of the isolate were explored. JE7A12 T was found to be a strictly anaerobic, catalase-negat…