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Book ; Online: (Table 1) Hydrogen- and carbon-isotope compositions of methane and pore water hydrogen-isotope compositions in DSDP Hole 96-618, supplementary data to: Burke, Roger A; Sackett, William M; Brooks, James M (1986): Hydrogen- and carbon-isotope compositions of methane from Deep Sea Drilling Project Site 618, Orca Basin. In: Bouma, AH; Coleman, JM; Meyer, AW; et al. (eds.), Initial Reports of the Deep Sea Drilling Project (U.S. Govt. Printing Office), 96, 777-780

Burke, Roger A / Brooks, James M / Sackett, William M

1986

Abstract: ... isotope compositions (dD-H2O) in several samples from the uppermost 100 m of Orca Basin sediments show ... of the methane production within the Orca Basin system occurs in sediments deeper than about 5 m sub-bottom ...

Abstract	Hydrogen- and carbon-isotope compositions of methane (dD-CH4 and d13C-CH4) and pore water hydrogen-isotope compositions (dD-H2O) in several samples from the uppermost 100 m of Orca Basin sediments show little variation with depth and have mean values of - 184, -73.5, and 7 per mil, respectively. The dD-CH4 is typical of that generally found in deep-sea sediments and suggests that the methane was produced biologically almost entirely via the CO2 reduction pathway. Production of small amounts of methane (-15% of the total) from acetate dissimilation cannot be completely ruled out, however. The pore water is more enriched in deuterium than present day Gulf of Mexico deep water, suggesting that the brine found at the bottom of Orca Basin was formed at a time when appreciably more isotopically light water was tied up in continental ice sheets than is at present. The d13C-CH4 values reported here are similar to previously determined brine d13C-CH4, but substantially more enriched in 13C than previously determined pore water d13C-CH4. Isotopic evidence and the decrease in interstitial salinity with depth suggest that most of the methane production within the Orca Basin system occurs in sediments deeper than about 5 m sub-bottom. Small deposits of isotopically anomalous methane occurring in near-surface sediments may be the result of spatially variable inputs of slumped material to the sediments underlying the anoxic, hypersaline brine.
Language	English
Dates of publication	1986-9999
Size	Online-Ressource
Publisher	PANGAEA - Data Publisher for Earth & Environmental Science
Publishing place	Bremen/Bremerhaven
Document type	Book ; Online
Note	This dataset is supplement to doi:10.2973/dsdp.proc.96.148.1986
DOI	10.1594/PANGAEA.788215
Database	Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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Article: RNase L-induced bodies sequester subgenomic flavivirus RNAs and re-establish host RNA decay.

Watkins, J Monty / Burke, James M

bioRxiv : the preprint server for biology

2024

Abstract: Subgenomic flavivirus RNAs (sfRNAs) are structured RNA elements encoded in the 3'-UTR of flaviviruses that promote viral infection by inhibiting cellular RNA decay machinery. Herein, we analyze the production of sfRNAs using single-molecule RNA ... ...

Abstract	Subgenomic flavivirus RNAs (sfRNAs) are structured RNA elements encoded in the 3'-UTR of flaviviruses that promote viral infection by inhibiting cellular RNA decay machinery. Herein, we analyze the production of sfRNAs using single-molecule RNA fluorescence
Language	English
Publishing date	2024-03-27
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.03.25.586660
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Article ; Online: Regulation of ribonucleoprotein condensates by RNase L during viral infection.

Burke, James M

Wiley interdisciplinary reviews. RNA

2022 Volume 14, Issue 4, Page(s) e1770

Abstract: In response to viral infection, mammalian cells activate several innate immune pathways to antagonize viral gene expression. Upon recognition of viral double-stranded RNA, protein kinase R (PKR) phosphorylates the alpha subunit of eukaryotic initiation ... ...

Abstract	In response to viral infection, mammalian cells activate several innate immune pathways to antagonize viral gene expression. Upon recognition of viral double-stranded RNA, protein kinase R (PKR) phosphorylates the alpha subunit of eukaryotic initiation factor 2 (eIF2α) on serine 51. This inhibits canonical translation initiation, which broadly antagonizes viral protein synthesis. It also promotes the assembly of cytoplasmic ribonucleoprotein complexes termed stress granules (SGs). SGs are widely thought to promote cell survival and antiviral signaling. However, co-activation of the OAS/RNase L antiviral pathway inhibits the assembly of SGs and promotes the assembly of an alternative ribonucleoprotein complex termed an RNase L-dependent body (RLB). The formation of RLBs has been observed in response to double-stranded RNA, dengue virus infection, or SARS-CoV-2 infection. Herein, we review the distinct biogenesis pathways and properties of SGs and RLBs, and we provide perspective on their potential functions during the antiviral response. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Turnover and Surveillance > Regulation of RNA Stability RNA Export and Localization > RNA Localization.
MeSH term(s)	Animals ; Humans ; Ribonucleoproteins/genetics ; Ribonucleoproteins/metabolism ; RNA, Double-Stranded ; COVID-19 ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; Antiviral Agents ; Mammals/genetics ; Mammals/metabolism
Chemical Substances	2-5A-dependent ribonuclease (EC 3.1.26.-) ; Ribonucleoproteins ; RNA, Double-Stranded ; Antiviral Agents
Language	English
Publishing date	2022-12-07
Publishing country	United States
Document type	Review ; Journal Article
ZDB-ID	2634714-3
ISSN	1757-7012 ; 1757-7004
ISSN (online)	1757-7012
ISSN	1757-7004
DOI	10.1002/wrna.1770
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Article ; Online: Heart Failure after Transcatheter Aortic Valve Implantation: Application of the Most Impactful Strain Imaging Techniques.

Burke, Gordon M / Popma, Jeffrey J / Chang, James D

CASE (Philadelphia, Pa.)

2023 Volume 8, Issue 1, Page(s) 4–10

Language	English
Publishing date	2023-11-29
Publishing country	United States
Document type	Case Reports
ISSN	2468-6441
ISSN (online)	2468-6441
DOI	10.1016/j.case.2023.10.003
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Article ; Online: Mechanisms and consequences of mRNA destabilization during viral infections.

Shehata, Soraya I / Watkins, J Monty / Burke, James M / Parker, Roy

Virology journal

2024 Volume 21, Issue 1, Page(s) 38

Abstract: During viral infection there is dynamic interplay between the virus and the host to regulate gene expression. In many cases, the host induces the expression of antiviral genes to combat infection, while the virus uses "host shut-off" systems to better ... ...

Abstract	During viral infection there is dynamic interplay between the virus and the host to regulate gene expression. In many cases, the host induces the expression of antiviral genes to combat infection, while the virus uses "host shut-off" systems to better compete for cellular resources and to limit the induction of the host antiviral response. Viral mechanisms for host shut-off involve targeting translation, altering host RNA processing, and/or inducing the degradation of host mRNAs. In this review, we discuss the diverse mechanisms viruses use to degrade host mRNAs. In addition, the widespread degradation of host mRNAs can have common consequences including the accumulation of RNA binding proteins in the nucleus, which leads to altered RNA processing, mRNA export, and changes to transcription.
MeSH term(s)	Humans ; Gene Expression Regulation ; RNA, Messenger/genetics ; Viruses/genetics ; Virus Diseases ; Antiviral Agents ; Virus Replication
Chemical Substances	RNA, Messenger ; Antiviral Agents
Language	English
Publishing date	2024-02-06
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2160640-7
ISSN	1743-422X ; 1743-422X
ISSN (online)	1743-422X
ISSN	1743-422X
DOI	10.1186/s12985-024-02305-1
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Article ; Online: Single-cell analysis of RNase L-mediated mRNA decay.

Cusic, Renee / Watkins, J Monty / Burke, James M

Methods in enzymology

2023 Volume 692, Page(s) 157–175

Abstract: Ribonuclease L (RNase L) is a mammalian endoribonuclease that initiates the mass degradation of cellular mRNAs in response to double-stranded RNA or viral infection. The kinetic rate of mRNA decay upon RNase L activation has been elusive because RNase L ... ...

Abstract	Ribonuclease L (RNase L) is a mammalian endoribonuclease that initiates the mass degradation of cellular mRNAs in response to double-stranded RNA or viral infection. The kinetic rate of mRNA decay upon RNase L activation has been elusive because RNase L is heterogeneously activated with respect to time in individual cells. Herein, we describe a method using immunofluorescence combined with single-molecule fluorescence in situ hybridization (smFISH) to determine single-cell mRNA decay rates upon RNase L activation. Using these approaches, we deduce that the rate of mRNA decay upon RNase L activation is extremely rapid, whereby the half-life of stable mRNAs such as GAPDH mRNA is reduced to ∼15 minutes in individual cells. This allows for RNase L to degrade nearly every mRNA in a cell in less than 1 hour, which is much faster than the decay rate that would be derived using bulk measurement techniques for mRNA levels, such as qRT-PCR. These single-cell approaches can generally be employed to resolve mRNA decay kinetics in additional contexts.
MeSH term(s)	Animals ; In Situ Hybridization, Fluorescence ; Endoribonucleases/genetics ; Endoribonucleases/metabolism ; RNA Stability ; Single-Cell Analysis ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Mammals/genetics
Chemical Substances	2-5A-dependent ribonuclease (EC 3.1.26.-) ; Endoribonucleases (EC 3.1.-) ; RNA, Messenger
Language	English
Publishing date	2023-05-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1557-7988
ISSN (online)	1557-7988
DOI	10.1016/bs.mie.2023.04.016
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Article ; Online: Sometimes mechanical, never routine: aortic valve replacement in young adults.

Krieger, Eric V / Burke, Christopher R / McCabe, James M

Heart (British Cardiac Society)

2023 Volume 109, Issue 11, Page(s) 814–816

MeSH term(s)	Humans ; Young Adult ; Aortic Valve/diagnostic imaging ; Aortic Valve/surgery ; Heart Valve Prosthesis ; Transcatheter Aortic Valve Replacement ; Aortic Valve Stenosis/surgery ; Treatment Outcome
Language	English
Publishing date	2023-05-15
Publishing country	England
Document type	Editorial ; Comment
ZDB-ID	1303417-0
ISSN	1468-201X ; 1355-6037
ISSN (online)	1468-201X
ISSN	1355-6037
DOI	10.1136/heartjnl-2022-322150
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Article ; Online: G3BP1-dependent condensation of translationally inactive viral RNAs antagonizes infection.

Burke, James M / Ratnayake, Oshani C / Watkins, J Monty / Perera, Rushika / Parker, Roy

Science advances

2024 Volume 10, Issue 5, Page(s) eadk8152

Abstract: G3BP1 is an RNA binding protein that condenses untranslating messenger RNAs into stress granules (SGs). G3BP1 is inactivated by multiple viruses and is thought to antagonize viral replication by SG-enhanced antiviral signaling. Here, we show that neither ...

Abstract	G3BP1 is an RNA binding protein that condenses untranslating messenger RNAs into stress granules (SGs). G3BP1 is inactivated by multiple viruses and is thought to antagonize viral replication by SG-enhanced antiviral signaling. Here, we show that neither G3BP1 nor SGs generally alter the activation of innate immune pathways. Instead, we show that the RNAs encoded by West Nile virus, Zika virus, and severe acute respiratory syndrome coronavirus 2 are prone to G3BP1-dependent RNA condensation, which is enhanced by limiting translation initiation and correlates with the disruption of viral replication organelles and viral RNA replication. We show that these viruses counteract condensation of their RNA genomes by inhibiting the RNA condensing function of G3BP proteins, hijacking the RNA decondensing activity of eIF4A, and/or maintaining efficient translation. These findings argue that RNA condensation can function as an intrinsic antiviral mechanism, which explains why many viruses inactivate G3BP proteins and suggests that SGs may have arisen as a vestige of this antiviral mechanism.
MeSH term(s)	Humans ; DNA Helicases ; RNA Helicases ; Poly-ADP-Ribose Binding Proteins ; RNA, Viral ; RNA Recognition Motif Proteins ; Antiviral Agents ; Zika Virus ; Zika Virus Infection
Chemical Substances	DNA Helicases (EC 3.6.4.-) ; RNA Helicases (EC 3.6.4.13) ; Poly-ADP-Ribose Binding Proteins ; RNA, Viral ; RNA Recognition Motif Proteins ; Antiviral Agents ; G3BP1 protein, human (EC 3.6.4.12)
Language	English
Publishing date	2024-01-31
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.adk8152
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Article ; Online: Nucleic acid-protein condensates in innate immune signaling.

Corbet, Giulia A / Burke, James M / Parker, Roy

The EMBO journal

2022 Volume 42, Issue 7, Page(s) e111870

Abstract: The presence of foreign nucleic acids in the cytosol is a marker of infection. Cells have sensors, also known as pattern recognition receptors (PRRs), in the cytosol that detect foreign nucleic acid and initiate an innate immune response. Recent studies ... ...

Abstract	The presence of foreign nucleic acids in the cytosol is a marker of infection. Cells have sensors, also known as pattern recognition receptors (PRRs), in the cytosol that detect foreign nucleic acid and initiate an innate immune response. Recent studies have reported the condensation of multiple PRRs including PKR, NLRP6, and cGAS, with their nucleic acid activators into discrete nucleoprotein assemblies. Nucleic acid-protein condensates form due to multivalent interactions and can create high local concentrations of components. The formation of PRR-containing condensates may alter the magnitude or timing of PRR activation. In addition, unique condensates form following RNase L activation or during paracrine signaling from virally infected cells that may play roles in antiviral defense. These observations suggest that condensate formation may be a conserved mechanism that cells use to regulate activation of the innate immune response and open an avenue for further investigation into the composition and function of these condensates. Here we review the nucleic acid-protein granules that are implicated in the innate immune response, discuss general consequences of condensate formation and signal transduction, as well as what outstanding questions remain.
MeSH term(s)	Nucleic Acids ; Immunity, Innate ; Receptors, Pattern Recognition ; Signal Transduction ; Cytosol
Chemical Substances	Nucleic Acids ; Receptors, Pattern Recognition
Language	English
Publishing date	2022-09-30
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	586044-1
ISSN	1460-2075 ; 0261-4189
ISSN (online)	1460-2075
ISSN	0261-4189
DOI	10.15252/embj.2022111870
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Article ; Online: Pedigree diversity and implications for genetic selection of Katahdin sheep.

Nilson, Sara M / Burke, Joan M / Murdoch, Brenda M / Morgan, James L M / Lewis, Ronald M

Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie

2023 Volume 141, Issue 3, Page(s) 304–316

Abstract: The Katahdin hair breed gained popularity in the United States as low input and prolific, with a propensity to exhibit parasite resistance. With the introduction of genomically enhanced estimated breeding values (GEBV) to the Katahdin genetic evaluation, ...

Abstract	The Katahdin hair breed gained popularity in the United States as low input and prolific, with a propensity to exhibit parasite resistance. With the introduction of genomically enhanced estimated breeding values (GEBV) to the Katahdin genetic evaluation, defining the diversity present in the breed is pertinent. Utilizing pedigree records (n = 92,030) from 1984 to 2019 from the National Sheep Improvement Program, our objectives were to (i) estimate the completeness and quality of the pedigree, (ii) calculate diversity statistics for the whole pedigree and relevant reference subpopulations and (iii) assess the impact of current diversity on genomic selection. Reference 1 was Katahdins born from 2017 to 2019 (n = 23,494), while reference 2 was a subset with at least three generations of Katahdin ancestry (n = 9327). The completeness of the whole pedigree, and the pedigrees of reference 1 and reference 2, were above 50% through the fourth, fifth and seventh generation of ancestors, respectively. Effective population size (N
MeSH term(s)	Sheep/genetics ; Animals ; Genetic Variation ; Pedigree ; Inbreeding ; Population Density ; Selection, Genetic
Language	English
Publishing date	2023-12-18
Publishing country	Germany
Document type	Journal Article
ZDB-ID	631363-2
ISSN	1439-0388 ; 0044-3581 ; 0931-2668 ; 1742-4488
ISSN (online)	1439-0388
ISSN	0044-3581 ; 0931-2668 ; 1742-4488
DOI	10.1111/jbg.12842
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