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Article ; Online: Towards a post-pandemic future for global pathogen genome sequencing.

Ladner, Jason T / Sahl, Jason W

2023 Volume 21, Issue 8, Page(s) e3002225

Abstract: Pathogen genome sequencing has become a routine part of our response to active outbreaks of infectious disease and should be an important part of our preparations for future epidemics. In this Essay, we discuss the innovations that have enabled routine ... ...

Abstract	Pathogen genome sequencing has become a routine part of our response to active outbreaks of infectious disease and should be an important part of our preparations for future epidemics. In this Essay, we discuss the innovations that have enabled routine pathogen genome sequencing, as well as how genome sequences can be used to understand and control the spread of infectious disease. We also explore the impact of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic on the field of pathogen genomics and outline the challenges we must address to further improve the utility of pathogen genome sequencing in the future.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19/epidemiology ; Pandemics ; Disease Outbreaks ; Chromosome Mapping
Language	English
Publishing date	2023-08-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.3002225
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Article ; Online: Genomic signatures for predicting the zoonotic potential of novel viruses.

Ladner, Jason T

PLoS biology

2021 Volume 19, Issue 9, Page(s) e3001403

Abstract: Powered by metagenomics, viral discovery is outpacing our capacity for the downstream characterization needed to fully assess zoonotic potential. A study published in PLOS Biology uses machine learning to prioritize novel viruses based only on genomic ... ...

Abstract	Powered by metagenomics, viral discovery is outpacing our capacity for the downstream characterization needed to fully assess zoonotic potential. A study published in PLOS Biology uses machine learning to prioritize novel viruses based only on genomic signatures.
MeSH term(s)	Genome, Viral/genetics ; Machine Learning ; Metagenomics ; Viruses/genetics
Language	English
Publishing date	2021-09-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.3001403
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Article ; Online: Genomic signatures for predicting the zoonotic potential of novel viruses.

Jason T Ladner

PLoS Biology, Vol 19, Iss 9, p e

2021 Volume 3001403

Abstract	Powered by metagenomics, viral discovery is outpacing our capacity for the downstream characterization needed to fully assess zoonotic potential. A study published in PLOS Biology uses machine learning to prioritize novel viruses based only on genomic signatures.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Recurrent SARS-CoV-2 mutations at Spike D796 evade antibodies from pre-Omicron convalescent and vaccinated subjects.

Elko, Evan A / Mead, Heather L / Nelson, Georgia A / Zaia, John A / Ladner, Jason T / Altin, John A

Microbiology spectrum

2024 Volume 12, Issue 2, Page(s) e0329123

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages of the Omicron variant rapidly became dominant in early 2022 and frequently cause human infections despite vaccination or prior infection with other variants. In addition to antibody- ... ...

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages of the Omicron variant rapidly became dominant in early 2022 and frequently cause human infections despite vaccination or prior infection with other variants. In addition to antibody-evading mutations in the receptor-binding domain, Omicron features amino acid mutations elsewhere in the Spike protein; however, their effects generally remain ill defined. The Spike D796Y substitution is present in all Omicron sub-variants and occurs at the same site as a mutation (D796H) selected during viral evolution in a chronically infected patient. Here, we map antibody reactivity to a linear epitope in the Spike protein overlapping position 796. We show that antibodies binding this region arise in pre-Omicron SARS-CoV-2 convalescent and vaccinated subjects but that both D796Y and D796H abrogate their binding. These results suggest that D796Y contributes to the fitness of Omicron in hosts with pre-existing immunity to other variants of SARS-CoV-2 by evading antibodies targeting this site.IMPORTANCESevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved substantially through the coronavirus disease 2019 (COVID-19) pandemic: understanding the drivers and consequences of this evolution is essential for projecting the course of the pandemic and developing new countermeasures. Here, we study the immunological effects of a particular mutation present in the Spike protein of all Omicron strains and find that it prevents the efficient binding of a class of antibodies raised by pre-Omicron vaccination and infection. These findings reveal a novel consequence of a poorly understood Omicron mutation and shed light on the drivers and effects of SARS-CoV-2 evolution.
MeSH term(s)	Humans ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; COVID-19 ; Mutation ; Antibodies, Viral ; Antibodies, Neutralizing
Chemical Substances	Spike Glycoprotein, Coronavirus ; Antibodies, Viral ; Antibodies, Neutralizing ; spike protein, SARS-CoV-2
Language	English
Publishing date	2024-01-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.03291-23
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Global phylogenomic diversity of

Janke, Nicolette R / Williamson, Charles H D / Drees, Kevin P / Suárez-Esquivel, Marcela / Allen, Adrian R / Ladner, Jason T / Quance, Christine R / Robbe-Austerman, Suelee / O'Callaghan, David / Whatmore, Adrian M / Foster, Jeffrey T

Frontiers in microbiology

2023 Volume 14, Page(s) 1287046

Abstract: ... Brucella ... ...

Abstract	Brucella abortus
Language	English
Publishing date	2023-11-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2023.1287046
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Article ; Online: Precision epidemiology for infectious disease control.

Ladner, Jason T / Grubaugh, Nathan D / Pybus, Oliver G / Andersen, Kristian G

Nature medicine

2019 Volume 25, Issue 2, Page(s) 206–211

Abstract: Advances in genomics and computing are transforming the capacity for the characterization of biological systems, and researchers are now poised for a precision-focused transformation in the way they prepare for, and respond to, infectious diseases. This ... ...

Abstract	Advances in genomics and computing are transforming the capacity for the characterization of biological systems, and researchers are now poised for a precision-focused transformation in the way they prepare for, and respond to, infectious diseases. This includes the use of genome-based approaches to inform molecular diagnosis and individual-level treatment regimens. In addition, advances in the speed and granularity of pathogen genome generation have improved the capability to track and understand pathogen transmission, leading to potential improvements in the design and implementation of population-level public health interventions. In this Perspective, we outline several trends that are driving the development of precision epidemiology of infectious disease and their implications for scientists' ability to respond to outbreaks.
MeSH term(s)	Communicable Disease Control/statistics & numerical data ; Communicable Diseases/epidemiology ; Disease Outbreaks ; Genomics ; Humans
Keywords	covid19
Language	English
Publishing date	2019-02-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1220066-9
ISSN	1546-170X ; 1078-8956
ISSN (online)	1546-170X
ISSN	1078-8956
DOI	10.1038/s41591-019-0345-2
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Zs.A 4212: 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)
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Article ; Online: Virome-wide detection of natural infection events and the associated antibody dynamics using longitudinal highly-multiplexed serology.

Kelley, Erin J / Henson, Sierra N / Rahee, Fatima / Boyle, Annalee S / Engelbrektson, Anna L / Nelson, Georgia A / Mead, Heather L / Anderson, N Leigh / Razavi, Morteza / Yip, Richard / Ladner, Jason T / Scriba, Thomas J / Altin, John A

Nature communications

2023 Volume 14, Issue 1, Page(s) 1783

Abstract: Current methods for detecting infections either require a sample collected from an actively infected site, are limited in the number of agents they can query, and/or yield no information on the immune response. Here we present an approach that uses ... ...

Abstract	Current methods for detecting infections either require a sample collected from an actively infected site, are limited in the number of agents they can query, and/or yield no information on the immune response. Here we present an approach that uses temporally coordinated changes in highly-multiplexed antibody measurements from longitudinal blood samples to monitor infection events at sub-species resolution across the human virome. In a longitudinally-sampled cohort of South African adolescents representing >100 person-years, we identify >650 events across 48 virus species and observe strong epidemic effects, including high-incidence waves of Aichivirus A and the D68 subtype of Enterovirus D earlier than their widespread circulation was appreciated. In separate cohorts of adults who were sampled at higher frequency using self-collected dried blood spots, we show that such events temporally correlate with symptoms and transient inflammatory biomarker elevations, and observe the responding antibodies to persist for periods ranging from ≤1 week to >5 years. Our approach generates a rich view of viral/host dynamics, supporting novel studies in immunology and epidemiology.
MeSH term(s)	Adult ; Adolescent ; Humans ; Virome ; Viruses ; Enterovirus D, Human ; Antibodies, Viral ; Epidemics ; Enterovirus Infections
Chemical Substances	Antibodies, Viral
Language	English
Publishing date	2023-03-30
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-37378-z
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The population genetics of the causative agent of snake fungal disease indicate recent introductions to the USA.

Ladner, Jason T / Palmer, Jonathan M / Ettinger, Cassandra L / Stajich, Jason E / Farrell, Terence M / Glorioso, Brad M / Lawson, Becki / Price, Steven J / Stengle, Anne G / Grear, Daniel A / Lorch, Jeffrey M

PLoS biology

2022 Volume 20, Issue 6, Page(s) e3001676

Abstract: Snake fungal disease (SFD; ophidiomycosis), caused by the pathogen Ophidiomyces ophiodiicola (Oo), has been documented in wild snakes in North America and Eurasia, and is considered an emerging disease in the eastern United States of America. However, a ... ...

Abstract	Snake fungal disease (SFD; ophidiomycosis), caused by the pathogen Ophidiomyces ophiodiicola (Oo), has been documented in wild snakes in North America and Eurasia, and is considered an emerging disease in the eastern United States of America. However, a lack of historical disease data has made it challenging to determine whether Oo is a recent arrival to the USA or whether SFD emergence is due to other factors. Here, we examined the genomes of 82 Oo strains to determine the pathogen's history in the eastern USA. Oo strains from the USA formed a clade (Clade II) distinct from European strains (Clade I), and molecular dating indicated that these clades diverged too recently (approximately 2,000 years ago) for transcontinental dispersal of Oo to have occurred via natural snake movements across Beringia. A lack of nonrecombinant intermediates between clonal lineages in Clade II indicates that Oo has actually been introduced multiple times to North America from an unsampled source population, and molecular dating indicates that several of these introductions occurred within the last few hundred years. Molecular dating also indicated that the most common Clade II clonal lineages have expanded recently in the USA, with time of most recent common ancestor mean estimates ranging from 1985 to 2007 CE. The presence of Clade II in captive snakes worldwide demonstrates a potential mechanism of introduction and highlights that additional incursions are likely unless action is taken to reduce the risk of pathogen translocation and spillover into wild snake populations.
MeSH term(s)	Animals ; Dermatomycoses/epidemiology ; Dermatomycoses/microbiology ; Genetics, Population ; Onygenales ; Snakes/genetics ; United States
Language	English
Publishing date	2022-06-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.3001676
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Book ; Online: PepSIRF + QIIME 2

Brown, Annabelle M. / Bolyen, Evan / Raspet, Isaiah / Altin, John A. / Ladner, Jason T.

software tools for automated, reproducible analysis of highly-multiplexed serology data

2022

Abstract: PepSIRF is a command-line, module-based open-source software package that facilitates the analysis of data from highly-multiplexed serology assays (e.g., PepSeq or PhIP-Seq). It has nine separate modules in its current release (v1.5.0): demux, info, ... ...

Abstract	PepSIRF is a command-line, module-based open-source software package that facilitates the analysis of data from highly-multiplexed serology assays (e.g., PepSeq or PhIP-Seq). It has nine separate modules in its current release (v1.5.0): demux, info, subjoin, norm, bin, zscore, enrich, link, and deconv. These modules can be used together to conduct analyses ranging from demultiplexing raw high-throughput sequencing data to the identification of enriched peptides. QIIME 2 is an open-source, community-developed and plugin-based bioinformatics platform that focuses on data and analytical transparency. QIIME 2's features include integrated and automatic tracking of data provenance, a semantic type system, and built-in support for many types of user interfaces. Here, we describe three new QIIME 2 plugins that allow users to conduct PepSIRF analyses within the QIIME 2 environment and extend the core functionality of PepSIRF in two key ways: 1) enabling generation of interactive visualizations and 2) enabling automation of analysis pipelines that include multiple PepSIRF modules. Comment: 9 pages, 6 figures, software announcement
Keywords	Quantitative Biology - Quantitative Methods
Subject code	004
Publishing date	2022-07-23
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Genome Sequence of Weissella ceti NC36, an Emerging Pathogen of Farmed Rainbow Trout in the United States

Ladner, Jason T

Genome Announcements. 2013, v. 1, no. 1

2013

Abstract: Novel Weissella sp. bacteria have recently been reported associated with disease outbreaks in cultured rainbow trout (Oncorhynchus mykiss) at commercial farms in China, Brazil and the United States. Here we present the first genome sequence of this novel ...

Abstract	Novel Weissella sp. bacteria have recently been reported associated with disease outbreaks in cultured rainbow trout (Oncorhynchus mykiss) at commercial farms in China, Brazil and the United States. Here we present the first genome sequence of this novel Weissella species isolated from the Southeastern United States.
Keywords	Oncorhynchus mykiss ; Weissella ; animal pathogenic bacteria ; disease outbreaks ; farmed fish ; genome ; nucleotide sequences ; Southeastern United States
Language	English
Size	p. 1-2.
Document type	Article
Database	NAL-Catalogue (AGRICOLA)

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