scholarly journals Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

2019 ◽  
Vol 116 (51) ◽  
pp. 25900-25908 ◽  
Author(s):  
Evan P. Starr ◽  
Erin E. Nuccio ◽  
Jennifer Pett-Ridge ◽  
Jillian F. Banfield ◽  
Mary K. Firestone
Keyword(s):  
Carbon Cycling ◽  
Temporal Dynamics ◽  
Rna Viruses ◽  
Marker Genes ◽  
Experimental Conditions ◽  
Time Resolved ◽  
Host Cell Death ◽  
Root Litter ◽  
Viral Communities ◽  
Microbial Systems

Viruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health, and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in soil, 1 of the most complex microbial systems. Here, we assembled 48 individual metatranscriptomes from 4 habitats within a planted soil sampled over a 22-d time series: Rhizosphere alone, detritosphere alone, rhizosphere with added root detritus, and unamended soil (4 time points and 3 biological replicates). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker genes. Based on viral phylogeny, much of the diversity wasNarnaviridaethat may parasitize fungi orLeviviridae, which may infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral and host communities were structured based on the presence of root litter. Clear temporal dynamics byLeviviridaeand their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant, and active in soil. When viral infection causes host cell death, it may mobilize cell carbon in a process that may represent an overlooked component of soil carbon cycling.

scholarly journals Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

2019 ◽  
Author(s):  
Evan P. Starr ◽  
Erin E. Nuccio ◽  
Jennifer Pett-Ridge ◽  
Jillian F. Banfield ◽  
Mary K. Firestone
Keyword(s):  
Carbon Cycling ◽  
Rna Viruses ◽  
Marker Gene ◽  
Experimental Conditions ◽  
Time Resolved ◽  
Host Cell Death ◽  
Microbial System ◽  
Viral Communities ◽  
Time Signature ◽  
Viral Sequences

AbstractViruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in the most complex microbial system, soil. Here, we assembled 48 individual metatranscriptomes from four habitats within a soil sampled over a 22-day time series: rhizosphere alone, detritosphere alone, a combination of the two, and unamended soil (four time points and three biological replicates per time point). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker gene content. Based on viral phylogeny, much of the diversity wasNarnaviridaethat parasitize fungi orLeviviridaethat infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral communities were structured based on the presence of litter, while putative hosts appeared to be impacted by both the presence of litter and roots. A clear time signature fromLeviviridaeand their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant and active in soil. Their replication causes host cell death, mobilizing carbon in a process that represents a largely overlooked component of carbon cycling in soil.

scholarly journals Dynamics in coastal RNA viruses and bacteriophages are driven by shifts in the community phylogenetic structure

2019 ◽  
Author(s):  
Julia A. Gustavsen ◽  
Curtis A. Suttle
Keyword(s):  
High Throughput Sequencing ◽  
Temporal Dynamics ◽  
Rna Viruses ◽  
Phylogenetic Signal ◽  
Marine Ecosystem ◽  
Marker Genes ◽  
Phylogenetic Groups ◽  
Eukaryotic Phytoplankton ◽  
Viral Marker ◽  
Viral Communities

AbstractMarine microbes including viruses are an essential part of the marine ecosystem that forms the base of the foodweb, and drives biogeochemical cycles. Marine viral communities display repeatable changes in abundance and community composition throughout time; however, whether these changes reflect shifts in dominance within evolutionarily related groups of viruses and their hosts is unexplored. To examine these dynamics, changes in the composition and phylogenetic makeup of two ecologically important groups of viruses, and their potential hosts, were sampled every two weeks for 13 months at a coastal site in British Columbia, Canada. Changes in the taxonomic composition within DNA bacteriophages related to T4-like viruses and marnavirus-like RNA viruses infecting eukaryotic phytoplankton, as well as bacteria and eukaryotes, were examined using amplicon sequencing of gene fragments encoding the major capsid protein (gp23), the RNA-dependent RNA polymerase (RdRp) and the 16S and 18S ribosomes, respectively. The results showed that for both viral marker genes, the dominant groups of phylogenetically-related viruses shifted over time and contained many transient taxa and few persistent taxa; yet, different community structures were observed in these different viral communities. Additionally, with strong lagged correlations between viral richness and community similarity of putative hosts, the results imply that viruses influence the composition of the host communities.ImportanceUsing high-throughput sequencing of coastal seawater collected every two weeks for one year, the dynamics of two groups of ecologically important groups of viruses were described in the context of their putative hosts and the environment. There was a large diversity of viruses and putative hosts in this study, and groups of phylogenetically-related viruses showed temporal dynamics in dominance. Examining the richness of viruses by phylogenetic groups showed different dynamics of either boom-bust or continued persistence. At the OTU-level, some members of these related groups persisted throughout time, while others were more ephemeral. These findings were put in context of potential quasispecies behaviour, and the dynamics of putative hosts. These results showed that temporal dynamics of viral communities have a phylogenetic signal which is important for understanding the ecology of these viruses since it elucidated one of the drivers of the community structure.

scholarly journals Massively parallel, time-resolved single-cell RNA sequencing with scNT-Seq

2019 ◽  
Author(s):  
Qi Qiu ◽  
Peng Hu ◽  
Kiya W. Govek ◽  
Pablo G. Camara ◽  
Hao Wu
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Temporal Dynamics ◽  
Embryonic Stem ◽  
Droplet Microfluidics ◽  
Massively Parallel ◽  
Specific Gene ◽  
Time Resolved ◽  
Single Cell Rna Sequencing ◽  
Rna Biogenesis

ABSTRACTSingle-cell RNA sequencing offers snapshots of whole transcriptomes but obscures the temporal dynamics of RNA biogenesis and decay. Here we present single-cell new transcript tagging sequencing (scNT-Seq), a method for massively parallel analysis of newly-transcribed and pre-existing RNAs from the same cell. This droplet microfluidics-based method enables high-throughput chemical conversion on barcoded beads, efficiently marking metabolically labeled newly-transcribed RNAs with T-to-C substitutions. By simultaneously measuring new and old transcriptomes, scNT-Seq reveals neuronal subtype-specific gene regulatory networks and time-resolved RNA trajectories in response to brief (minutes) versus sustained (hours) neuronal activation. Integrating scNT-Seq with genetic perturbation reveals that DNA methylcytosine dioxygenases may inhibit stepwise transition from pluripotent embryonic stem cell state to intermediate and totipotent two-cell-embryo-like (2C-like) states by promoting global RNA biogenesis. Furthermore, pulse-chase scNT-Seq enables transcriptome-wide measurements of RNA stability in rare 2C-like cells. Time-resolved single-cell transcriptomic analysis thus opens new lines of inquiry regarding cell-type-specific RNA regulatory mechanisms.

scholarly journals Metabolic and immune markers for precise monitoring of COVID-19 severity and treatment

2021 ◽  
Author(s):  
André F. Rendeiro ◽  
Charles Kyriakos Vorkas ◽  
Jan Krumsiek ◽  
Harjot Singh ◽  
Shashi Kapatia ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
Severe Disease ◽  
Deep Understanding ◽  
Response To Therapy ◽  
High Dimensional ◽  
Time Resolved ◽  
Novel Approach ◽  
Metabolomic Data ◽  
Clinical Action ◽  
Rich Information

AbstractDeep understanding of the SARS-CoV-2 effects on host molecular pathways is paramount for the discovery of early biomarkers of outcome of coronavirus disease 2019 (COVID-19) and the identification of novel therapeutic targets. In that light, we generated metabolomic data from COVID-19 patient blood using high-throughput targeted nuclear magnetic resonance (NMR) spectroscopy and high-dimensional flow cytometry. We find considerable changes in serum metabolome composition of COVID-19 patients associated with disease severity, and response to tocilizumab treatment. We built a clinically annotated, biologically-interpretable space for precise time-resolved disease monitoring and characterize the temporal dynamics of metabolomic change along the clinical course of COVID-19 patients and in response to therapy. Finally, we leverage joint immuno-metabolic measurements to provide a novel approach for patient stratification and early prediction of severe disease. Our results show that high-dimensional metabolomic and joint immune-metabolic readouts provide rich information content for elucidation of the host’s response to infection and empower discovery of novel metabolic-driven therapies, as well as precise and efficient clinical action.

scholarly journals Viruses in the Built Environment (VIBE) meeting report

Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Aaron J. Prussin ◽  
Jessica A. Belser ◽  
Werner Bischoff ◽  
Scott T. Kelley ◽  
Kaisen Lin ◽  
...  
Keyword(s):  
Built Environment ◽  
Temporal Dynamics ◽  
Virus Detection ◽  
Future Research ◽  
Meeting Report ◽  
Knowledge Gaps ◽  
Research Areas ◽  
Viral Communities ◽  
Bacteria And Fungi ◽  
Definition Of

Abstract Background During a period of rapid growth in our understanding of the microbiology of the built environment in recent years, the majority of research has focused on bacteria and fungi. Viruses, while probably as numerous, have received less attention. In response, the Alfred P. Sloan Foundation supported a workshop entitled “Viruses in the Built Environment (VIBE),” at which experts in environmental engineering, environmental microbiology, epidemiology, infection prevention, fluid dynamics, occupational health, metagenomics, and virology convened to synthesize recent advances and identify key research questions and knowledge gaps regarding viruses in the built environment. Results Four primary research areas and funding priorities were identified. First, a better understanding of viral communities in the built environment is needed, specifically which viruses are present and their sources, spatial and temporal dynamics, and interactions with bacteria. Second, more information is needed about viruses and health, including viral transmission in the built environment, the relationship between virus detection and exposure, and the definition of a healthy virome. The third research priority is to identify and evaluate interventions for controlling viruses and the virome in the built environment. This encompasses interactions among viruses, buildings, and occupants. Finally, to overcome the challenge of working with viruses, workshop participants emphasized that improved sampling methods, laboratory techniques, and bioinformatics approaches are needed to advance understanding of viruses in the built environment. Conclusions We hope that identifying these key questions and knowledge gaps will engage other investigators and funding agencies to spur future research on the highly interdisciplinary topic of viruses in the built environment. There are numerous opportunities to advance knowledge, as many topics remain underexplored compared to our understanding of bacteria and fungi.

Round Turbulent Thermals, Puffs, Starting Plumes and Starting Jets in Uniform Crossflow

2003 ◽  
Author(s):  
F. J. Diez ◽  
L. P. Bernal ◽  
G. M. Faeth
Keyword(s):  
Fresh Water ◽  
Salt Water ◽  
Water Channel ◽  
Reynolds Numbers ◽  
Ccd Cameras ◽  
Experimental Conditions ◽  
Time Resolved ◽  
Buoyant Flows ◽  
Video Images ◽  
Density Ratios

The self-preserving properties of round turbulent thermals, puffs, starting plumes and starting jets, in unstratified and uniform crossflow, were investigated experimentally. The experiments involved dye-containing fresh water (for nonbuoyant flows) and salt water (for buoyant flows) sources injected vertically downward into crossflowing fresh water within a water channel. Time-resolved video images of the flows were obtained using CCD cameras. Experimental conditions were as follows: source exit diameters of 3.2 and 6.4 mm, source Reynolds numbers of 2,500–16,000, source/ambient velocity ratios of 4–35, source/ambient density ratios (for buoyant flows) of 1.073 and 1.150, volumes of injected source fluid (for thermals and puffs) comprising 16–318 source diameters, streamwise (vertical) penetration distances of 0–200 source diameters and 0–13 Morton length scales (for buoyant flows) and crosstream (horizontal) penetration distances of 0–620 source diameters. Near-source behavior varied significantly with source properties but the flows generally became turbulent for streamwise distances within 5 source diameters from the source and became self-preserving for streamwise distances from the source greater than 40–50 source diameters. Crosstream motion satisfied the no-slip convection approximation. Streamwise motion for self-preserving conditions satisfied the behavior of corresponding self-preserving flows in still fluids: round thermals and puffs in still fluids for round thermals and puffs in crossflow and two-dimensional line thermals and puffs in still fluids for round starting plumes and jets in crossflow. The no-slip convection approximation for crossflow motion combined with self-preserving approximations for streamwise motion was also effective for predicting flow trajectories at self-preserving conditions for steady round turbulent plumes and jets in crossflow.

A Novel Near-Infrared Fluorescence Sensor for H2O2 Based on N-Acetyl-L-Cysteine-Capped Gold Nanoparticles

2017 ◽  
Vol 46 ◽  
pp. 234-240
Author(s):  
Wen Juan Dong ◽  
Ji Yan Han ◽  
Xin Wu ◽  
Li Fan ◽  
Wen Ting Liang
Keyword(s):  
Hydrogen Peroxide ◽  
Gold Nanoparticles ◽  
Fluorescence Quenching ◽  
Near Infrared ◽  
Fluorescence Probe ◽  
Fluorescence Emission ◽  
Excitation Wavelength ◽  
Experimental Conditions ◽  
Time Resolved ◽  
Near Infrared Fluorescence

A novel near-infrared fluorescence quenching method has been developed for the determination of hydrogen peroxide based on N-acetyl-L-cysteine-capped gold nanoparticles (NAC-AuNPs) as a fluorescence probe. The prepared gold nanoparticles with the size of about 1.91 nm exhibited strong near-infrared fluorescence emission at 693 nm with excitation wavelength at 450 nm in aqueous solution. The fluorescence intensity of NAC-AuNPs was quenched dramatically by adding hydrogen peroxide. Therefore, it could be used to detect hydrogen peroxide based on the fluorescence quenching intensity was linear with the concentration of hydrogen peroxide. Under the optimal experimental conditions, the linear range and detection limit were 1.0×10-6 –3.0×10-2 mol/L and 1.0×10-7 mol/L, respectively. The possible quenching mechanism was investigated by time-resolved fluorescence spectroscopy. The proposed method was simple, sensitive and showed good repeatability and stability.

scholarly journals Quantitative sampling and analysis of trace elements in atmospheric aerosols: impactor characterization and Synchrotron-XRF mass calibration

2010 ◽  
Vol 3 (5) ◽  
pp. 1473-1485 ◽  
Author(s):  
A. Richard ◽  
N. Bukowiecki ◽  
P. Lienemann ◽  
M. Furger ◽  
M. Fierz ◽  
...  
Keyword(s):  
Trace Elements ◽  
Atmospheric Aerosols ◽  
Collection Efficiency ◽  
Ambient Air ◽  
Pollution Source ◽  
Data Sets ◽  
Size Segregation ◽  
Ambient Aerosols ◽  
Experimental Conditions ◽  
Time Resolved

Abstract. Identification of trace elements in ambient air can add substantial information to pollution source apportionment studies, although they do not contribute significantly to emissions in terms of mass. A method for quantitative size and time-resolved trace element evaluation in ambient aerosols with a rotating drum impactor and synchrotron radiation based X-ray fluorescence is presented. The impactor collection efficiency curves and size segregation characteristics were investigated in an experiment with oil and salt particles. Cutoff diameters were determined through the ratio of size distributions measured with two particle sizers. Furthermore, an external calibration technique to empirically link fluorescence intensities to ambient concentrations was developed. Solutions of elemental standards were applied with an ink-jet printer on thin films and area concentrations were subsequently evaluated with external wet chemical methods. These customized and reusable reference standards enable quantification of different data sets analyzed under varying experimental conditions.

scholarly journals Quantitative phosphoproteomics unveils temporal dynamics of thrombin signaling in human endothelial cells

Blood ◽  
2014 ◽  
Vol 123 (12) ◽  
pp. e22-e36 ◽  
Author(s):  
Maartje van den Biggelaar ◽  
Juan Ramon Hernández-Fernaud ◽  
Bart L. van den Eshof ◽  
Lisa J. Neilson ◽  
Alexander B. Meijer ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Temporal Dynamics ◽  
Human Endothelial Cells ◽  
Time Resolved ◽  
Future Studies ◽  
Key Points ◽  
First Time ◽  
Quantitative Phosphoproteomics

Key Points This is the first time-resolved quantitative phosphoproteomic analysis of thrombin signaling in human endothelial cells. We provide 2224 phosphosites regulated by thrombin as a unique resource for future studies on thrombin and PAR signaling.

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