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Article ; Online: The kinetics of SARS-CoV-2 viremia in COVID-19 patients receiving remdesivir.

Krifors, Anders / Karlsson, Linda / Ekman, Martin / Lorant, Camilla / Skorup, Paul

European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology

2023 Volume 42, Issue 8, Page(s) 951–958

Abstract: Detection of SARS-CoV-2 RNA in serum, viremia, has been linked to disease severity and outcome. The kinetics of viremia in patients receiving remdesivir has not been thoroughly studied and could help predict treatment response and outcome. We ... ...

Abstract	Detection of SARS-CoV-2 RNA in serum, viremia, has been linked to disease severity and outcome. The kinetics of viremia in patients receiving remdesivir has not been thoroughly studied and could help predict treatment response and outcome. We investigated the kinetics of SARS-CoV-2 viremia and factors associated with baseline viremia, viral clearance and 30-day mortality in patients receiving remdesivir. An observational study including 378 hospitalised patients (median age 67 years, 67% male) sampled with serum SARS-CoV-2 RT-PCR within ± 24 h of initiation of remdesivir treatment. Baseline viremia was present in 206 (54%) patients with a median Ct value of 35.3 (IQR = 33.3-37.1). In patients with baseline viremia, the estimated probability of viral clearance was 72% by day 5. Ct values decreased significantly during remdesivir treatment for viremic patients, indicating an increase in viral load. In total, 44 patients (12%) died within 30 days, and mortality was significantly associated with viremia at baseline (OR = 2.45, p = 0.01) and lack of viral clearance by day 5 (OR = 4.8, p = < 0.01). Viral clearance was not associated with any individual risk factor. Viremia appears to be a prognostic marker before and during remedesivir treatment. The resolution of viremia was similar to patients not receiving remdesivir in other studies, and the decrease in Ct values during treatment questions the antiviral capacity of remdesivir in vivo. Prospective studies are warranted to confirm our findings.
MeSH term(s)	Humans ; Male ; Aged ; Female ; COVID-19 ; SARS-CoV-2 ; Kinetics ; Viremia/drug therapy ; RNA, Viral ; COVID-19 Drug Treatment ; Antiviral Agents/therapeutic use
Chemical Substances	remdesivir (3QKI37EEHE) ; RNA, Viral ; Antiviral Agents
Language	English
Publishing date	2023-05-27
Publishing country	Germany
Document type	Observational Study ; Journal Article
ZDB-ID	603155-9
ISSN	1435-4373 ; 0934-9723 ; 0722-2211
ISSN (online)	1435-4373
ISSN	0934-9723 ; 0722-2211
DOI	10.1007/s10096-023-04627-4
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Article ; Online: Bed and rise times during the Age of Enlightenment: A case report.

van Egmond, Lieve / Ekman, Martin / Benedict, Christian

Journal of sleep research

2019 Volume 28, Issue 6, Page(s) e12862

Abstract: Studies have shown that our modern electrical lighting environment reduces naturally occurring seasonal variations in sleep-wake rhythms, such as longer sleep during the winter versus summer. However, less is known about how timing and duration of sleep ... ...

Abstract	Studies have shown that our modern electrical lighting environment reduces naturally occurring seasonal variations in sleep-wake rhythms, such as longer sleep during the winter versus summer. However, less is known about how timing and duration of sleep were affected by the seasons in the premodern era, before the invention of electrical lighting. The Swedish researcher Olof Hiorter collected and documented geophysical data every hour during wakefulness in Uppsala, Sweden, between December 1746 and November 1747. In this way, his bed and rise times could be approximated. The data revealed that Hiorter's rise times occurred around 1 hr before sunrise in winter versus 1 hr after sunrise in summer. No such association was observed between the time of sunset and Hiorter's bedtimes. Finally, the time in bed was about 3.5-4 hr shorter in summer compared to winter. This 273-year-old case report suggests that time in bed and rise times of people from the premodern era exhibited seasonal variations.
MeSH term(s)	Humans ; Male ; Middle Aged ; Circadian Rhythm/physiology ; History, 18th Century ; Lighting/trends ; Seasons ; Sleep/physiology ; Sweden ; Wakefulness/physiology
Language	English
Publishing date	2019-04-22
Publishing country	England
Document type	Historical Article ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1122722-9
ISSN	1365-2869 ; 0962-1105
ISSN (online)	1365-2869
ISSN	0962-1105
DOI	10.1111/jsr.12862
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Zs.A 3464: 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)
Zs.MO 343: Show issues

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Book: The changing level of the Baltic Sea during 300 years

Ekman, Martin

a clue to understanding the earth

2009

Author's details	Martin Ekman
Language	English
Size	155 S, Ill., graph. Darst.
Publisher	Summer Institute for Historical Geophysics
Publishing place	Godby
Document type	Book
ISBN	9789529252411 ; 9529252412
Database	Former special subject collection: coastal and deep sea fishing

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Article ; Online: High abundance and expression of transposases in bacteria from the Baltic Sea.

Vigil-Stenman, Theoden / Ininbergs, Karolina / Bergman, Birgitta / Ekman, Martin

The ISME journal

2017 Volume 11, Issue 11, Page(s) 2611–2623

Abstract: Transposases are mobile genetic elements suggested to have an important role in bacterial genome plasticity and host adaptation but their transcriptional activity in natural bacterial communities is largely unexplored. Here we analyzed metagenomes and - ... ...

Abstract	Transposases are mobile genetic elements suggested to have an important role in bacterial genome plasticity and host adaptation but their transcriptional activity in natural bacterial communities is largely unexplored. Here we analyzed metagenomes and -transcriptomes of size fractionated (0.1-0.8, 0.8-3.0 and 3.0-200 μm) bacterial communities from the brackish Baltic Sea, and adjacent marine waters. The Baltic Sea transposase levels, up to 1.7% of bacterial genes and 2% of bacterial transcripts, were considerably higher than in marine waters and similar to levels reported for extreme environments. Large variations in expression were found between transposase families and groups of bacteria, with a two-fold higher transcription in Cyanobacteria than in any other phylum. The community-level results were corroborated at the genus level by Synechococcus transposases reaching up to 5.2% of genes and 6.9% of transcripts, which is in contrast to marine Synechococcus that largely lack these genes. Levels peaked in Synechococcus from the largest size fraction, suggesting high frequencies of lateral gene transfer and high genome plasticity in colony-forming picocyanobacteria. Together, the results support an elevated rate of transposition-based genome change and adaptation in bacterial populations of the Baltic Sea, and possibly also of other highly dynamic estuarine waters.
MeSH term(s)	Bacteria/classification ; Bacteria/enzymology ; Bacteria/genetics ; Bacteria/isolation & purification ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Baltic States ; Gene Transfer, Horizontal ; Genome, Bacterial ; Metagenome ; Phylogeny ; Seawater/microbiology ; Transposases/genetics ; Transposases/metabolism
Chemical Substances	Bacterial Proteins ; Transposases (EC 2.7.7.-)
Language	English
Publishing date	2017-07-21
Publishing country	England
Document type	Journal Article
ZDB-ID	2406536-5
ISSN	1751-7370 ; 1751-7362
ISSN (online)	1751-7370
ISSN	1751-7362
DOI	10.1038/ismej.2017.114
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Article ; Online: Microbial metagenomics in the Baltic Sea: Recent advancements and prospects for environmental monitoring.

Ininbergs, Karolina / Bergman, Birgitta / Larsson, John / Ekman, Martin

Ambio

2015 Volume 44 Suppl 3, Page(s) 439–450

Abstract: Metagenomics refers to the analysis of DNA from a whole community. Metagenomic sequencing of environmental DNA has greatly improved our knowledge of the identity and function of microorganisms in aquatic, terrestrial, and human biomes. Although open ... ...

Abstract	Metagenomics refers to the analysis of DNA from a whole community. Metagenomic sequencing of environmental DNA has greatly improved our knowledge of the identity and function of microorganisms in aquatic, terrestrial, and human biomes. Although open oceans have been the primary focus of studies on aquatic microbes, coastal and brackish ecosystems are now being surveyed. Here, we review so far published studies on microbes in the Baltic Sea, one of the world's largest brackish water bodies, using high throughput sequencing of environmental DNA and RNA. Collectively the data illustrate that Baltic Sea microbes are unique and highly diverse, and well adapted to this brackish-water ecosystem, findings that represent a novel base-line knowledge necessary for monitoring purposes and a sustainable management. More specifically, the data relate to environmental drivers for microbial community composition and function, assessments of the microbial biodiversity, adaptations and role of microbes in the nitrogen cycle, and microbial genome assembly from metagenomic sequences. With these discoveries as background, prospects of using metagenomics for Baltic Sea environmental monitoring are discussed.
MeSH term(s)	Biodiversity ; Ecosystem ; Environmental Monitoring/methods ; Metagenomics/methods ; Oceans and Seas ; Seawater/microbiology
Language	English
Publishing date	2015-05-29
Publishing country	Sweden
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120759-3
ISSN	1654-7209 ; 0044-7447
ISSN (online)	1654-7209
ISSN	0044-7447
DOI	10.1007/s13280-015-0663-7
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Zs Bio Ambio: Show issues
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Article ; Online: Diverse roles of the GlcP glucose permease in free-living and symbiotic cyanobacteria.

Picossi, Silvia / Flores, Enrique / Ekman, Martin

Plant signaling & behavior

2013 Volume 8, Issue 12, Page(s) e27416

Abstract: Certain cyanobacteria can form symbiotic associations with plants, where the symbiont supplies the plant partner with nitrogen and in return obtains sugars. We recently showed that in the symbiotic cyanobacterium Nostoc punctiforme, a glucose specific ... ...

Abstract	Certain cyanobacteria can form symbiotic associations with plants, where the symbiont supplies the plant partner with nitrogen and in return obtains sugars. We recently showed that in the symbiotic cyanobacterium Nostoc punctiforme, a glucose specific permease, GlcP, is necessary for the symbiosis to be formed. Results presented here from growth yield measurements of mutant strains with inactivated or overexpressing sugar transporters suggest that GlcP could be induced by a symbiosis specific substance. We also discuss that the transporter may have a role other than nutritional once the symbiosis is established, i.e., during infection, and more specifically in the chemotaxis of the symbiont. Phylogenetic analysis shows that the distribution of GlcP among cyanobacteria is likely influenced by horizontal gene transfer, but also that it is not correlated with symbiotic competence. Instead, regulatory patterns of the transporter in Nostoc punctiforme likely constitute symbiosis specific adaptations.
MeSH term(s)	Chemotaxis/drug effects ; Evolution, Molecular ; Glucose/pharmacology ; Nostoc/cytology ; Nostoc/drug effects ; Nostoc/enzymology ; Nostoc/growth & development ; Phosphoenolpyruvate Sugar Phosphotransferase System/metabolism ; Phylogeny ; Symbiosis/drug effects
Chemical Substances	Phosphoenolpyruvate Sugar Phosphotransferase System (EC 2.7.1.-) ; phosphoenolpyruvate-glucose phosphotransferase (EC 2.7.1.-) ; Glucose (IY9XDZ35W2)
Language	English
Publishing date	2013-12-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1559-2324
ISSN (online)	1559-2324
DOI	10.4161/psb.27416
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Cellular and functional specificity among ferritin-like proteins in the multicellular cyanobacterium Nostoc punctiforme.

Ekman, Martin / Sandh, Gustaf / Nenninger, Anja / Oliveira, Paulo / Stensjö, Karin

Environmental microbiology

2014 Volume 16, Issue 3, Page(s) 829–844

Abstract: Ferritin-like proteins constitute a remarkably heterogeneous protein family, including ferritins, bacterioferritins and Dps proteins. The genome of the filamentous heterocyst-forming cyanobacterium Nostoc punctiforme encodes five ferritin-like proteins. ... ...

Abstract	Ferritin-like proteins constitute a remarkably heterogeneous protein family, including ferritins, bacterioferritins and Dps proteins. The genome of the filamentous heterocyst-forming cyanobacterium Nostoc punctiforme encodes five ferritin-like proteins. In the present paper, we report a multidimensional characterization of these proteins. Our phylogenetic and bioinformatics analyses suggest both structural and physiological differences among the ferritin-like proteins. The expression of these five genes responded differently to hydrogen peroxide treatment, with a significantly higher rise in transcript level for Npun_F3730 as compared with the other four genes. A specific role for Npun_F3730 in the cells tolerance against hydrogen peroxide was also supported by the inactivation of Npun_F3730, Npun_R5701 and Npun_R6212; among these, only the ΔNpun_F3730 strain showed an increased sensitivity to hydrogen peroxide compared with wild type. Analysis of promoter-GFP reporter fusions of the ferritin-like genes indicated that Npun_F3730 and Npun_R5701 were expressed in all cell types of a diazotrophic culture, while Npun_F6212 was expressed specifically in heterocysts. Our study provides the first comprehensive analysis combining functional differentiation and cellular specificity within this important group of proteins in a multicellular cyanobacterium.
MeSH term(s)	Amino Acid Sequence ; Computational Biology ; Ferritins/genetics ; Ferritins/metabolism ; Gene Expression Regulation, Bacterial/drug effects ; Green Fluorescent Proteins/genetics ; Green Fluorescent Proteins/metabolism ; Hydrogen Peroxide/pharmacology ; Iron/metabolism ; Nostoc/classification ; Nostoc/drug effects ; Nostoc/genetics ; Nostoc/metabolism ; Oxidants/pharmacology ; Phylogeny ; Sequence Alignment
Chemical Substances	Oxidants ; Green Fluorescent Proteins (147336-22-9) ; Ferritins (9007-73-2) ; Hydrogen Peroxide (BBX060AN9V) ; Iron (E1UOL152H7)
Language	English
Publishing date	2014-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.12233
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Article ; Online: Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-qPCR

Smyrlaki, Ioanna / Ekman, Martin / Vondracek, Martin / Papanicoloau, Natali / Lentini, Antonio / Aarum, Johan / Muradrasoli, Shaman / Albert, Jan / Högberg, Björn / Reinius, Björn

Abstract: Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The most widely used method of COVID-19 diagnostics is a reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay, ... ...

Abstract	Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The most widely used method of COVID-19 diagnostics is a reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay, detecting the presence of SARS-CoV-2 RNA in patient samples, typically from nasopharyngeal swabs. The RNA extraction is a major bottleneck in current COVID-19 testing, in terms of turn-around, logistics, component availability and cost, which delays or completely precludes COVID-19 diagnostics in many settings. Efforts to simplify the current methods are important, as increased diagnostic availability and efficiency is expected to benefit patient care and infection control. Here, we describe methods to circumvent RNA extraction in COVID-19 testing by performing RT-qPCR directly on heat-inactivated subject samples as well as samples lysed with readily available detergents. Our data, including cross-comparisons with clinically diagnosed patient samples, suggest that direct RT-qPCR is a viable option to extraction-based COVID-19 diagnostics. We argue that significant savings in terms of time and cost can be achieved by embracing RNA-extraction-free protocols, that feeds directly into the established PCR-based testing pipeline. This could aid the expansion of COVID-19 testing.
Keywords	covid19
Publisher	MedRxiv; WHO
Document type	Article ; Online
DOI	10.1101/2020.04.17.20067348
Database	COVID19

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Article ; Online: Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-qPCR

Smyrlaki, Ioanna / Ekman, Martin / Vondracek, Martin / Papanicoloau, Natali / Lentini, Antonio / Aarum, Johan / Muradrasoli, Shaman / Albert, Jan / Högberg, Björn / Reinius, Björn

medRxiv

Abstract	Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The most widely used method of COVID-19 diagnostics is a reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay, detecting the presence of SARS-CoV-2 RNA in patient samples, typically from nasopharyngeal swabs. The RNA extraction is a major bottleneck in current COVID-19 testing, in terms of turn-around, logistics, component availability and cost, which delays or completely precludes COVID-19 diagnostics in many settings. Efforts to simplify the current methods are important, as increased diagnostic availability and efficiency is expected to benefit patient care and infection control. Here, we describe methods to circumvent RNA extraction in COVID-19 testing by performing RT-qPCR directly on heat-inactivated subject samples as well as samples lysed with readily available detergents. Our data, including cross-comparisons with clinically diagnosed patient samples, suggest that direct RT-qPCR is a viable option to extraction-based COVID-19 diagnostics. We argue that significant savings in terms of time and cost can be achieved by embracing RNA-extraction-free protocols, that feeds directly into the established PCR-based testing pipeline. This could aid the expansion of COVID-19 testing.
Keywords	covid19
Language	English
Publishing date	2020-04-18
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.04.17.20067348
Database	COVID19

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Article ; Online: Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes.

Alneberg, Johannes / Bennke, Christin / Beier, Sara / Bunse, Carina / Quince, Christopher / Ininbergs, Karolina / Riemann, Lasse / Ekman, Martin / Jürgens, Klaus / Labrenz, Matthias / Pinhassi, Jarone / Andersson, Anders F

Communications biology

2020 Volume 3, Issue 1, Page(s) 119

Abstract: The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 ... ...

Abstract	The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes' placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data.
MeSH term(s)	Aquatic Organisms/genetics ; Archaea/genetics ; Bacteria/genetics ; Base Sequence ; Ecology ; Ecosystem ; Genome, Archaeal ; Genome, Bacterial ; Machine Learning ; Metagenome ; Metagenomics/methods ; Phylogeny ; Plankton/microbiology ; Sequence Analysis, DNA/methods
Language	English
Publishing date	2020-03-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-020-0856-x
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