Results 91 to 100 of about 2,805,364 (358)

Insights in bacterial genome folding

Current Opinion in Structural Biology, 2023
Chromosomes in all domains of life are well-defined structural entities with complex hierarchical organization. The regulation of this hierarchical organization and its functional interplay with gene expression or other chromosome metabolic processes such as repair, replication, or segregation is actively investigated in a variety of species, including
Yáñez-Cuna, Fares Osam, Koszul, Romain
openaire   +3 more sources

A complete bacterial genome assembled de novo using only nanopore sequencing data

Nature Methods, 2015
We have assembled de novo the Escherichia coli K-12 MG1655 chromosome in a single 4.6-Mb contig using only nanopore data. Our method has three stages: (i) overlaps are detected between reads and then corrected by a multiple-alignment process; (ii ...
N. Loman, J. Quick, J. Simpson
semanticscholar   +1 more source

Mycobacterial cell division arrest and smooth‐to‐rough envelope transition using CRISPRi‐mediated genetic repression systems

FEBS Open Bio, EarlyView.
CRISPRI‐mediated gene silencing and phenotypic exploration in nontuberculous mycobacteria. In this Research Protocol, we describe approaches to control, monitor, and quantitatively assess CRISPRI‐mediated gene silencing in M. smegmatis and M. abscessus model organisms.
Vanessa Point, Wafaa Achache, Janïs Laudouze, Eliana Sepulveda Ramos, Mickaël Maziero, Céline Crauste, Stéphane Canaan, Pierre Santucci   +7 more
wiley   +1 more source

The Janthinobacterium sp. HH01 genome encodes a homologue of the V. cholerae CqsA and L. pneumophila LqsA autoinducer synthases. [PDF]

, 2013
Janthinobacteria commonly form biofilms on eukaryotic hosts and are known to synthesize antibacterial and antifungal compounds. Janthinobacterium sp. HH01 was recently isolated from an aquatic environment and its genome sequence was established.
Blokesch, Melanie, Kirsten Jung, Bode, E., Dierking, Katja, Hinrich Schulenburg, Andreas Bonge (279782), Schmeisser, Christel, Bode, Edna, Laure Plener, Frederike S. Haack (279780), Bonge, Andreas, Haack, Frederike Svenja, Spieck, Eva, Bode, Helge Björn, Dierking, K., Edna Bode (195835), Pommerening-Roeser, Andreas, Schulenburg, Hinrich, Anja Poehlein, Andrea Pohlen, Ines Krohn-Molt, Wolfgang R Streit, Eva Spieck, Andreas Pommerening-Röser (279786), Timmermann, G., Melanie Blokesch, Kirsten Jung (256459), Bode, H., Schmidt, Martina, Katja Dierking (199184), Spieck, E., Andreas Bonge, Melanie Blokesch (106198), Helge B. Bode (195839), Streit, Wolfgang R., Claudia Hornung, Christel Schmeisser (125567), Pommerening-Röser, Andreas, Daniel, R., Plener, Laure, Katja Dierking, Andrea Pohlen (279781), Gabriele Timmermann (279784), Hornung, C., Krohn-Molt, Ines, Poehlein, Anja, Jung, Kirsten, Utpatel, C., Eva Spieck (279785), Plener, L., Utpatel, Christian, Krohn-Molt, I., Rolf Daniel (113374), Christian Utpatel, Gabriele Timmermann, Ines Krohn-Molt (279783), Schmeisser, C., Bode, Helge B., Martina Schmidt (183309), Haack, F., Schmidt, M., Bonge, A., Streit, W., Haack, Frederike S., Andreas Pommerening-Röser, Jung, K., Hornung, Claudia, Frederike S Haack, Edna Bode, Rolf Daniel, Timmermann, Gabriele, Daniel, Rolf, Hinrich Schulenburg (74712), Helge B Bode, Christian Utpatel (199158), Wolfgang R. Streit (125596), Pommerening-Roeser, A., Anja Poehlein (113372), Laure Plener (164731), Blokesch, M., Poehlein, A., Claudia Hornung (199168), Martina Schmidt, Pohlen, A., Pohlen, Andrea, Christel Schmeisser, Schulenburg, H.   +86 more
core   +1 more source

Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches.

Clinical Microbiology and Infection, 2018
BACKGROUND Whole genome sequence (WGS)-based strain typing finds increasing use in the epidemiologic analysis of bacterial pathogens in both public health as well as more localized infection control settings. AIMS This minireview describes methodologic
A. Schürch, S. Arredondo-Alonso, R. Willems, R. Goering   +3 more
semanticscholar   +1 more source

Chameleon sequences reveal structural effects in proteins representing micelle‐like distribution of hydrophobicity

FEBS Open Bio, EarlyView.
Amino acids sequence of two different proteins with the same sequence (chameleon sequence—black boxes) represent in 3D structure of the proteins different secondary structures: HHHH—helical and BBB—Beta‐structural. The chains folded in water environment adopt different III‐order structures in which the chameleon fragments appear to adopt similar status
Irena Roterman, Katarzyna Stapor, Leszek Konieczny, Krzysztof Gądek, Piotr Nowakowski   +4 more
wiley   +1 more source

A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch

Nature Communications, 2021
Whole genome sequencing data are increasingly becoming routinely available but generating actionable insights is challenging. Here, the authors describe Pathogenwatch, a web tool for genomic surveillance of S.
Silvia Argimón, Corin A. Yeats, Richard J. Goater, Khalil Abudahab, Benjamin Taylor, Anthony Underwood, Leonor Sánchez-Busó, Vanessa K. Wong, Zoe A. Dyson, Satheesh Nair, Se Eun Park, Florian Marks, Andrew J. Page, Jacqueline A. Keane, Stephen Baker, Kathryn E. Holt, Gordon Dougan, David M. Aanensen   +17 more
doaj   +1 more source

Draft Genome Sequence of Marinobacter sp. Strain P4B1, an Electrogenic Perchlorate-Reducing Strain Isolated from a Long-Term Mixed Enrichment Culture of Marine Bacteria

, 2016
The perchlorate-reducing strain Marinobacter sp. strain P4B1 was isolated from a long-term perchlorate-degrading enrichment culture seeded with marine sediment. The draft genome of Marinobacter sp. P4B1 is comprised of the bacterial chromosome (3.60 Mbp,
Roberts, Deborah J., Xiao, Yeyuan, Fox, George E., Stepanov, Victor G., Lopez, April J.   +4 more
core   +1 more source

In Silico Genome-Scale Reconstruction and Validation of the Staphylococcus aureus Metabolic Network [PDF]

, 2005
A genome-scale metabolic model of the Gram-positive, facultative anaerobic opportunistic pathogen Staphylococcus aureus N315 was constructed based on current genomic data, literature, and physiological information.
Panke, Sven, Heinemann, Matthias,, Kümmel, Anne, Ruinatscha, Reto,, Panke, Sven,, Heinemann, Matthias; id_orcid, Kümmel, Anne,, Ruinatscha, Reto, Heinemann, Matthias   +8 more
core   +1 more source

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

PLoS ONE, 2014
Advances in modern sequencing technologies allow us to generate sufficient data to analyze hundreds of bacterial genomes from a single machine in a single day.
B. J. Walker, T. Abeel, Terrance Shea, M. Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A. Cuomo, Q. Zeng, J. Wortman, Sarah K. Young, A. Earl   +10 more
semanticscholar   +1 more source