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Article ; Online: Historical biomonitoring of pollution trends in the North Pacific using archived samples from the Continuous Plankton Recorder Survey.

Li, Kefeng / Naviaux, Jane C / Lingampelly, Sai Sachin / Wang, Lin / Monk, Jonathan M / Taylor, Claire M / Ostle, Clare / Batten, Sonia / Naviaux, Robert K

The Science of the total environment

2022 Volume 865, Page(s) 161222

Abstract: First started in 1931, the Continuous Plankton Recorder (CPR) Survey is the longest-running and most geographically extensive marine plankton sampling program in the world. This pilot study investigates the feasibility of biomonitoring the spatiotemporal ...

Abstract	First started in 1931, the Continuous Plankton Recorder (CPR) Survey is the longest-running and most geographically extensive marine plankton sampling program in the world. This pilot study investigates the feasibility of biomonitoring the spatiotemporal trends of marine pollution using archived CPR samples from the North Pacific. We selected specimens collected from three different locations (British Columbia Shelf, Northern Gulf of Alaska, and Aleutian Shelf) in the North Pacific between 2002 and 2020. Comprehensive profiling of the plankton chemical exposome was conducted using liquid and gas chromatography coupled with tandem mass spectrometry (LC-MS/MS and GC-MS/MS). Our results show that phthalates, plasticizers, persistent organic pollutants (POPs), pesticides, pharmaceuticals, and personal care products were present in the plankton exposome, and that many of these pollutants have decreased in amount over the last two decades, which was most pronounced for tri-n-butyl phosphate. In addition, the plankton exposome differed significantly by regional human activities, with the most polluted samples coming from the nearshore area. Exposome-wide association analysis revealed that bioaccumulation of environmental pollutants was highly correlated with the biomass of different plankton taxa. Overall, this study demonstrates that exposomic analysis of archived samples from the CPR Survey is effective for long-term biomonitoring of the spatial and temporal trends of environmental pollutants in the marine environment.
MeSH term(s)	Humans ; Plankton ; Biological Monitoring ; Tandem Mass Spectrometry ; Chromatography, Liquid ; Pilot Projects ; Gas Chromatography-Mass Spectrometry ; Environmental Monitoring ; Environmental Pollutants
Chemical Substances	Environmental Pollutants
Language	English
Publishing date	2022-12-28
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2022.161222
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Article ; Online: Full genome sequence analysis of African swine fever virus isolates from Cameroon.

Goatley, Lynnette C / Freimanis, Graham / Tennakoon, Chandana / Foster, Thomas J / Quershi, Mehnaz / Dixon, Linda K / Batten, Carrie / Forth, Jan Hendrik / Wade, Abel / Netherton, Christopher

PloS one

2024 Volume 19, Issue 3, Page(s) e0293049

Abstract: African swine fever (ASF) is a devastating disease of domestic pigs that has spread across the globe since its introduction into Georgia in 2007. The etiological agent is a large double-stranded DNA virus with a genome of 170 to 180 kb in length ... ...

Abstract	African swine fever (ASF) is a devastating disease of domestic pigs that has spread across the globe since its introduction into Georgia in 2007. The etiological agent is a large double-stranded DNA virus with a genome of 170 to 180 kb in length depending on the isolate. Much of the differences in genome length between isolates are due to variations in the copy number of five different multigene families that are encoded in repetitive regions that are towards the termini of the covalently closed ends of the genome. Molecular epidemiology of African swine fever virus (ASFV) is primarily based on Sanger sequencing of a few conserved and variable regions, but due to the stability of the dsDNA genome changes in the variable regions occur relatively slowly. Observations in Europe and Asia have shown that changes in other genetic loci can occur and that this could be useful in molecular tracking. ASFV has been circulating in Western Africa for at least forty years. It is therefore reasonable to assume that changes may have accumulated in regions of the genome other than the standard targets over the years. At present only one full genome sequence is available for an isolate from Western Africa, that of a highly virulent isolate collected from Benin during an outbreak in 1997. In Cameroon, ASFV was first reported in 1981 and outbreaks have been reported to the present day and is considered endemic. Here we report three full genome sequences from Cameroon isolates of 1982, 1994 and 2018 outbreaks and identify novel single nucleotide polymorphisms and insertion-deletions that may prove useful for molecular epidemiology studies in Western Africa and beyond.
MeSH term(s)	Swine ; Animals ; African Swine Fever Virus ; African Swine Fever/epidemiology ; Cameroon/epidemiology ; Sus scrofa/genetics ; Sequence Analysis ; Sequence Analysis, DNA
Language	English
Publishing date	2024-03-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0293049
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Article ; Online: Full genome sequence analysis of African swine fever virus isolates from Cameroon

Goatley, Lynnette C. / Freimanis, Graham / Tennakoon, Chandana / Foster, Thomas J. / Quershi, Mehnaz / Dixon, Linda K. / Batten, Carrie / Forth, Jan Hendrik / Wade, Abel / Netherton, Christopher

2024

Abstract	African swine fever (ASF) is a devastating disease of domestic pigs that has spread across the globe since its introduction into Georgia in 2007. The etiological agent is a large double-stranded DNA virus with a genome of 170 to 180 kb in length depending on the isolate. Much of the differences in genome length between isolates are due to variations in the copy number of five different multigene families that are encoded in repetitive regions that are towards the termini of the covalently closed ends of the genome. Molecular epidemiology of African swine fever virus (ASFV) is primarily based on Sanger sequencing of a few conserved and variable regions, but due to the stability of the dsDNA genome changes in the variable regions occur relatively slowly. Observations in Europe and Asia have shown that changes in other genetic loci can occur and that this could be useful in molecular tracking. ASFV has been circulating in Western Africa for at least forty years. It is therefore reasonable to assume that changes may have accumulated in regions of the genome other than the standard targets over the years. At present only one full genome sequence is available for an isolate from Western Africa, that of a highly virulent isolate collected from Benin during an outbreak in 1997. In Cameroon, ASFV was first reported in 1981 and outbreaks have been reported to the present day and is considered endemic. Here we report three full genome sequences from Cameroon isolates of 1982, 1994 and 2018 outbreaks and identify novel single nucleotide polymorphisms and insertion-deletions that may prove useful for molecular epidemiology studies in Western Africa and beyond.
Keywords	article ; Text ; ddc:570 ; Genomics -- Swine -- Cameroon -- Domestic animals -- Genome sequencing -- Protein sequencing -- Single nucleotide polymorphisms -- Viral genomics
Language	English
Publishing date	2024-03-21
Publisher	Public Library of Science (PLoS)
Publishing country	de
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Humoral and circulating follicular helper T cell responses in recovered patients with COVID-19.

Nature medicine

2020 Volume 26, Issue 9, Page(s) 1428–1434

Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has dramatically expedited global vaccine development ... ...

Abstract	The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has dramatically expedited global vaccine development efforts
MeSH term(s)	Angiotensin-Converting Enzyme 2 ; Animals ; Antibodies, Neutralizing/immunology ; Antibodies, Neutralizing/pharmacology ; Antibodies, Viral/immunology ; Antibodies, Viral/pharmacology ; Antigens, Viral/immunology ; COVID-19 ; Chlorocebus aethiops ; Coronavirus Infections/immunology ; Coronavirus Infections/pathology ; Coronavirus Infections/virology ; Epitopes/immunology ; Humans ; Immunity, Cellular/immunology ; Pandemics ; Peptidyl-Dipeptidase A/genetics ; Peptidyl-Dipeptidase A/immunology ; Pneumonia, Viral/immunology ; Pneumonia, Viral/pathology ; Pneumonia, Viral/virology ; Spike Glycoprotein, Coronavirus/antagonists & inhibitors ; Spike Glycoprotein, Coronavirus/immunology ; T-Lymphocytes, Helper-Inducer/immunology ; Vero Cells/immunology
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Antigens, Viral ; Epitopes ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Keywords	covid19
Language	English
Publishing date	2020-07-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1220066-9
ISSN	1546-170X ; 1078-8956
ISSN (online)	1546-170X
ISSN	1078-8956
DOI	10.1038/s41591-020-0995-0
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Article ; Online: Humoral and circulating follicular helper T cell responses in recovered patients with COVID-19

Nature Medicine

2020 Volume 26, Issue 9, Page(s) 1428–1434

Keywords	General Biochemistry, Genetics and Molecular Biology ; General Medicine ; covid19
Language	English
Publisher	Springer Science and Business Media LLC
Publishing country	us
Document type	Article ; Online
ZDB-ID	1220066-9
ISSN	1546-170X ; 1078-8956
ISSN (online)	1546-170X
ISSN	1078-8956
DOI	10.1038/s41591-020-0995-0
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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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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Book ; Online: Full genome sequence analysis of African swine fever virus isolates from Cameroon

Goatley, Lynnette C / Freimanis, Graham / Tennakoon, Chandana / Foster, Thomas J / Quershi, Mehnaz / Dixon, Linda K / Batten, Carrie / Forth, Jan Hendrik / Wade, Abel / Netherton, Chris

[Preprint]

2023

Abstract: African swine fever is a devastating disease of domestic pigs that has spread across the globe since its introduction into Georgia in 2007. The etiological agent is a large double-stranded DNA virus with a genome of 170 to 180 kb in length depending on ... ...

Abstract	African swine fever is a devastating disease of domestic pigs that has spread across the globe since its introduction into Georgia in 2007. The etiological agent is a large double-stranded DNA virus with a genome of 170 to 180 kb in length depending on the isolate. Much of the differences in genome length between isolates are due to variations in the copy number of five different multigene families that are encoded in repetitive regions that are towards the termini of the covalently closed ends of the genome. Molecular epidemiology of ASFV is primarily based on Sanger sequencing of a few conserved and variable regions, but due to the stability of the dsDNA genome changes in the variable regions occur relatively slowly. Observations in Europe and Asia have shown that changes in other genetic loci can occur and that this could be useful in molecular tracking. ASFV has been circulating in Western Africa for at least forty years. It is therefore reasonable to assume that changes may have accumulated in regions of the genome other than the standard targets over the years. At present only one full genome sequence is available for an isolate from Western Africa, that of a highly virulent isolate collected from Benin during an outbreak in 1997. In Cameroon, ASFV was first reported in 1981 and outbreaks have been reported to the present day and is considered endemic. Here we report three full genome sequences from Cameroon isolates of 1982, 1994 and 2018 outbreaks and identify novel single nucleotide polymorphisms and insertion-deletions that may prove useful for molecular epidemiology studies in Western Africa and beyond.
Keywords	Text ; ddc:630
Subject code	580
Language	English
Publishing date	2023-10-12
Publisher	Cold Spring Harbor Laboratory
Publishing country	de
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Vaccination and timing influence SIV immune escape viral dynamics in vivo.

Loh, Liyen / Petravic, Janka / Batten, C Jane / Davenport, Miles P / Kent, Stephen J

PLoS pathogens

2008 Volume 4, Issue 1, Page(s) e12

Abstract: CD8+ cytotoxic T lymphocytes (CTL) can be effective at controlling HIV-1 in humans and SIV in macaques, but their utility is partly offset by mutational escape. The kinetics of CTL escape and reversion of escape mutant viruses upon transmission to MHC- ... ...

Abstract	CD8+ cytotoxic T lymphocytes (CTL) can be effective at controlling HIV-1 in humans and SIV in macaques, but their utility is partly offset by mutational escape. The kinetics of CTL escape and reversion of escape mutant viruses upon transmission to MHC-mismatched hosts can help us understand CTL-mediated viral control and the fitness cost extracted by immune escape mutation. Traditional methods for following CTL escape and reversion are, however, insensitive to minor viral quasispecies. We developed sensitive quantitative real-time PCR assays to track the viral load of SIV Gag164-172 KP9 wild-type (WT) and escape mutant (EM) variants in pigtail macaques. Rapid outgrowth of EM virus occurs during the first few weeks of infection. However, the rate of escape plateaued soon after, revealing a prolonged persistence of WT viremia not detectable by standard cloning and sequencing methods. The rate of escape of KP9 correlated with levels of vaccine-primed KP9-specific CD8+ T cells present at that time. Similarly, when non-KP9 responder (lacking the restricting Mane-A*10 allele) macaques were infected with SHIVmn229 stock containing a mixture of EM and WT virus, rapid reversion to WT was observed over the first 2 weeks following infection. However, the rate of reversion to WT slowed dramatically over the first month of infection. The serial quantitation of escape mutant viruses evolving during SIV infection shows that rapid dynamics of immune escape and reversion can be observed in early infection, particularly when CD8 T cells are primed by vaccination. However, these early rapid rates of escape and reversion are transient and followed by a significant slowing in these rates later during infection, highlighting that the rate of escape is significantly influenced by the timing of its occurrence.
MeSH term(s)	Acute Disease ; Animals ; Base Sequence ; Chronic Disease ; Epitopes, T-Lymphocyte/immunology ; Immunity, Cellular/immunology ; Macaca nemestrina ; Molecular Sequence Data ; Mutation ; RNA, Viral/analysis ; Reverse Transcriptase Polymerase Chain Reaction ; Simian Acquired Immunodeficiency Syndrome/blood ; Simian Acquired Immunodeficiency Syndrome/immunology ; Simian Acquired Immunodeficiency Syndrome/virology ; Simian Immunodeficiency Virus/genetics ; Simian Immunodeficiency Virus/immunology ; T-Lymphocytes, Cytotoxic/immunology ; Time Factors ; Vaccination
Chemical Substances	Epitopes, T-Lymphocyte ; RNA, Viral
Language	English
Publishing date	2008-01-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7366
ISSN (online)	1553-7374
ISSN	1553-7366
DOI	10.1371/journal.ppat.0040012
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Article: Humoral and circulating follicular helper T cell responses in recovered patients with COVID-19

Nat Med

Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has dramatically expedited global vaccine development efforts1-3, most targeting the viral 'spike' glycoprotein (S). S localizes on the virion surface and mediates recognition of ... ...

Abstract	The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has dramatically expedited global vaccine development efforts1-3, most targeting the viral 'spike' glycoprotein (S). S localizes on the virion surface and mediates recognition of cellular receptor angiotensin-converting enzyme 2 (ACE2)4-6. Eliciting neutralizing antibodies that block S-ACE2 interaction7-9, or indirectly prevent membrane fusion10, constitute an attractive modality for vaccine-elicited protection11. However, although prototypic S-based vaccines show promise in animal models12-14, the immunogenic properties of S in humans are poorly resolved. In this study, we characterized humoral and circulating follicular helper T cell (cTFH) immunity against spike in recovered patients with coronavirus disease 2019 (COVID-19). We found that S-specific antibodies, memory B cells and cTFH are consistently elicited after SARS-CoV-2 infection, demarking robust humoral immunity and positively associated with plasma neutralizing activity. Comparatively low frequencies of B cells or cTFH specific for the receptor binding domain of S were elicited. Notably, the phenotype of S-specific cTFH differentiated subjects with potent neutralizing responses, providing a potential biomarker of potency for S-based vaccines entering the clinic. Overall, although patients who recovered from COVID-19 displayed multiple hallmarks of effective immune recognition of S, the wide spectrum of neutralizing activity observed suggests that vaccines might require strategies to selectively target the most potent neutralizing epitopes.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #641392
Database	COVID19

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Article ; Online: Immunogenic profile of SARS-CoV-2 spike in individuals recovered from COVID-19

medRxiv

Abstract: The rapid global spread of SARS-CoV-2 and resultant mortality and social disruption have highlighted the need to better understand coronavirus immunity to expedite vaccine development efforts. Multiple candidate vaccines, designed to elicit protective ... ...

Abstract	The rapid global spread of SARS-CoV-2 and resultant mortality and social disruption have highlighted the need to better understand coronavirus immunity to expedite vaccine development efforts. Multiple candidate vaccines, designed to elicit protective neutralising antibodies targeting the viral spike glycoprotein, are rapidly advancing to clinical trial. However, the immunogenic properties of the spike protein in humans are unresolved. To address this, we undertook an in-depth characterisation of humoral and cellular immunity against SARS-CoV-2 spike in humans following mild to moderate SARS-CoV-2 infection. We find serological antibody responses against spike are routinely elicited by infection and correlate with plasma neutralising activity and capacity to block ACE2/RBD interaction. Expanded populations of spike-specific memory B cells and circulating T follicular helper cells (cTFH) were detected within convalescent donors, while responses to the receptor binding domain (RBD) constitute a minor fraction. Using regression analysis, we find high plasma neutralisation activity was associated with increased spike-specific antibody, but notably also with the relative distribution of spike-specific cTFH subsets. Thus both qualitative and quantitative features of B and T cell immunity to spike constitute informative biomarkers of the protective potential of novel SARS-CoV-2 vaccines.
Keywords	covid19
Language	English
Publishing date	2020-05-21
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.05.17.20104869
Database	COVID19

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Article: Characterization of the kynurenine pathway and quinolinic Acid production in macaque macrophages.

Lim, Chai K / Yap, Margaret M C / Kent, Stephen J / Gras, Gabriel / Samah, Boubekeur / Batten, Jane C / De Rose, Robert / Heng, Benjamin / Brew, Bruce J / Guillemin, Gilles J

International journal of tryptophan research : IJTR

2013 Volume 6, Page(s) 7–19

Abstract: The kynurenine pathway (KP) and one of its end-products, the excitotoxin quinolinic acid (QUIN), are involved in the pathogenesis of several major neuroinflammatory brain diseases. A relevant animal model to study KP metabolism is now needed to assess ... ...

Abstract	The kynurenine pathway (KP) and one of its end-products, the excitotoxin quinolinic acid (QUIN), are involved in the pathogenesis of several major neuroinflammatory brain diseases. A relevant animal model to study KP metabolism is now needed to assess whether intervention in this pathway may improve the outcome of such diseases. Humans and macaques share a very similar genetic makeup. In this study, we characterized the KP metabolism in macaque primary macrophages of three different species in comparison to human cells. We found that the KP profiles in simian macrophages were very similar to those in humans when challenged with inflammatory cytokines. Further, we found that macaque macrophages are capable of producing a pathophysiological concentration of QUIN. Our data validate the simian model as a relevant model to study the human cellular KP metabolism in the context of inflammation.
Language	English
Publishing date	2013-05-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	2517435-6
ISSN	1178-6469
ISSN	1178-6469
DOI	10.4137/IJTR.S11789
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