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  1. Article: Groundwater mixing in an alkaline paleolake: Eocene Green River Formation, Wyoming

    Baddouh, M'bark / Carroll, Alan R / Jagniecki, Elliot A / Beard, Brian L / Lowenstein, Tim K / Johnson, Clark M

    Palaeogeography, palaeoclimatology, palaeoecology. 2021 Jan. 01, v. 561

    2021  

    Abstract: Tufa in the Little Mesa area of the northern Bridger Basin has been interpreted to record carbonate deposition via subaqueous and subaerial springs emanating near the shoreline of Eocene Lake Gosiute. Sedimentary facies record an overall transgression, ... ...

    Abstract Tufa in the Little Mesa area of the northern Bridger Basin has been interpreted to record carbonate deposition via subaqueous and subaerial springs emanating near the shoreline of Eocene Lake Gosiute. Sedimentary facies record an overall transgression, culminating with mound structures that reach up to 9 m in height and 40 m in diameter. Mounds exhibit a strong positive, linear covariance between δ¹³C and δ¹⁸O, defining a slope of ~1. Similar trends occur in many other paleolake deposits, where they are interpreted to reflect changes in evaporation, atmospheric CO₂ exchange, and organic matter burial. However, δ¹³C and δ¹⁸O in this study also covary strongly with ⁸⁷Sr/⁸⁶Sr, a new finding that is inconsistent with previously proposed mechanisms. We conclude that Little Mesa isotopic trends reflect mixing of groundwater with low ⁸⁷Sr/⁸⁶Sr, δ¹⁸O and δ¹³C and lake water with opposite characteristics. Low ⁸⁷Sr/⁸⁶Sr in groundwater likely resulted from interaction with marine carbonate strata within the Sevier fold and thrust belt to the west, whereas drainage from Precambrian-cored uplifts that bounded Lake Gosiute to the north, east, and south was responsible for higher lake water ratios.Little Mesa carbonate facies are all less radiogenic than any time-equivalent facies near the center of the basin, implying horizontal and vertical gradients in Lake Gosiute ⁸⁷Sr/⁸⁶Sr. Previous studies have shown that the lowest ⁸⁷Sr/⁸⁶Sr in basin center deposits correspond to lake highstands. Results of this study support the hypothesis that climatic modulation of surface runoff and spring emanations from the Sevier belt were principally responsible for precessional-scale expansions and contractions of Lake Gosiute. More broadly, groundwater discharge may represent an important but underappreciated contributor to covariance between ⁸⁷Sr/⁸⁶Sr ratios, δ¹³C and δ¹⁸O in closed paleolake systems.
    Keywords Eocene epoch ; basins ; carbon dioxide ; carbonates ; covariance ; drainage ; evaporation ; groundwater ; lakes ; organic matter ; palaeogeography ; paleoclimatology ; paleoecology ; runoff ; shorelines ; spring ; Green River ; Wyoming
    Language English
    Dates of publication 2021-0101
    Publishing place Elsevier B.V.
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 417718-6
    ISSN 0031-0182
    ISSN 0031-0182
    DOI 10.1016/j.palaeo.2020.110038
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

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  2. Article: Defining distinct RNA-protein interactomes of SARS-CoV-2 genomic and subgenomic RNAs.

    Whitworth, Isabella T / Knoener, Rachel A / Puray-Chavez, Maritza / Halfmann, Peter / Romero, Sofia / Baddouh, M'bark / Scalf, Mark / Kawaoka, Yoshihiro / Kutluay, Sebla B / Smith, Lloyd M / Sherer, Nathan M

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Host RNA binding proteins recognize viral RNA and play key roles in virus replication and antiviral defense mechanisms. SARS-CoV-2 generates a series of tiered subgenomic RNAs (sgRNAs), each encoding distinct viral protein(s) that regulate different ... ...

    Abstract Host RNA binding proteins recognize viral RNA and play key roles in virus replication and antiviral defense mechanisms. SARS-CoV-2 generates a series of tiered subgenomic RNAs (sgRNAs), each encoding distinct viral protein(s) that regulate different aspects of viral replication. Here, for the first time, we demonstrate the successful isolation of SARS-CoV-2 genomic RNA and three distinct sgRNAs (N, S, and ORF8) from a single population of infected cells and characterize their protein interactomes. Over 500 protein interactors (including 260 previously unknown) were identified as associated with one or more target RNA at either of two time points. These included protein interactors unique to a single RNA pool and others present in multiple pools, highlighting our ability to discriminate between distinct viral RNA interactomes despite high sequence similarity. The interactomes indicated viral associations with cell response pathways including regulation of cytoplasmic ribonucleoprotein granules and posttranscriptional gene silencing. We validated the significance of five protein interactors predicted to exhibit antiviral activity (APOBEC3F, TRIM71, PPP1CC, LIN28B, and MSI2) using siRNA knockdowns, with each knockdown yielding increases in viral production. This study describes new technology for studying SARS-CoV-2 and reveals a wealth of new viral RNA-associated host factors of potential functional significance to infection.
    Language English
    Publishing date 2023-05-16
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.05.15.540806
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Defining Distinct RNA-Protein Interactomes of SARS-CoV-2 Genomic and Subgenomic RNAs.

    Whitworth, Isabella T / Knoener, Rachel A / Puray-Chavez, Maritza / Halfmann, Peter / Romero, Sofia / Baddouh, M'bark / Scalf, Mark / Kawaoka, Yoshihiro / Kutluay, Sebla B / Smith, Lloyd M / Sherer, Nathan M

    Journal of proteome research

    2023  Volume 23, Issue 1, Page(s) 149–160

    Abstract: Host RNA binding proteins recognize viral RNA and play key roles in virus replication and antiviral mechanisms. SARS-CoV-2 generates a series of tiered subgenomic RNAs (sgRNAs), each encoding distinct viral protein(s) that regulate different aspects of ... ...

    Abstract Host RNA binding proteins recognize viral RNA and play key roles in virus replication and antiviral mechanisms. SARS-CoV-2 generates a series of tiered subgenomic RNAs (sgRNAs), each encoding distinct viral protein(s) that regulate different aspects of viral replication. Here, for the first time, we demonstrate the successful isolation of SARS-CoV-2 genomic RNA and three distinct sgRNAs (N, S, and ORF8) from a single population of infected cells and characterize their protein interactomes. Over 500 protein interactors (including 260 previously unknown) were identified as associated with one or more target RNA. These included protein interactors unique to a single RNA pool and others present in multiple pools, highlighting our ability to discriminate between distinct viral RNA interactomes despite high sequence similarity. Individual interactomes indicated viral associations with cell response pathways, including regulation of cytoplasmic ribonucleoprotein granules and posttranscriptional gene silencing. We tested the significance of three protein interactors in these pathways (APOBEC3F, PPP1CC, and MSI2) using siRNA knockdowns, with several knockdowns affecting viral gene expression, most consistently PPP1CC. This study describes a new technology for high-resolution studies of SARS-CoV-2 RNA regulation and reveals a wealth of new viral RNA-associated host factors of potential functional significance to infection.
    MeSH term(s) Humans ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; Subgenomic RNA ; RNA, Viral/genetics ; RNA, Viral/metabolism ; COVID-19/genetics ; Virus Replication/genetics ; Genomics ; RNA-Binding Proteins/genetics
    Chemical Substances Subgenomic RNA ; RNA, Viral ; MSI2 protein, human ; RNA-Binding Proteins
    Language English
    Publishing date 2023-12-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.3c00506
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  4. Article: An 11 million-year-long record of astronomically forced fluvial-alluvial deposition and paleoclimate change in the Early Cretaceous Songliao synrift basin, China

    Liu, Wei / Baddouh, M'bark / Gao, Youfeng / Hinnov, Linda A / Li, Haiyan / Wang, Chengshan / Wang, Pujun / Wu, Huaichun / Yang, Tianshui / Zhang, Shihong

    Palaeogeography, palaeoclimatology, palaeoecology. 2020 Mar. 01, v. 541

    2020  

    Abstract: In the Cretaceous Songliao Basin, northeastern China, boreholes have recovered detailed geologic data from sub-basins that developed during the early rifting of the basin. Among these, the Lower Cretaceous Shahezi Formation (K1s) in the Songshen 4 (SS4) ... ...

    Abstract In the Cretaceous Songliao Basin, northeastern China, boreholes have recovered detailed geologic data from sub-basins that developed during the early rifting of the basin. Among these, the Lower Cretaceous Shahezi Formation (K1s) in the Songshen 4 (SS4) Well is represented by an 836-m-thick succession of fluvial-alluvial deposits, with coals distributed throughout the upper part of the formation. Gamma-ray (GR) logging data are quantitatively related to grain size-defined litho-facies that recur throughout the succession, with high GR values in mudstones and low GR values in sandstones. Cyclostratigraphic analysis of the GR log reveals depositional cycling at frequencies that are consistent with those of the Earth's astronomical parameters. The results also indicate that occurrence of coal beds occur every ~100 kyr, when development of vegetation at the depositional site was promoted by humid climate. We propose a model of astronomically forced hydroclimate change to explain the cycling of depositional environments between fluvial and alluvial conditions. The model describes a principally fluvial environment that episodically experienced, at one extreme, advancing alluvial conditions involving a drop in base level, lake recession and increased aridity (conglomerates and coarse sands), and at the other extreme, an advancing lakeshore with a rise in base level and increased humidity (fine sands, silts, muds and coal). A floating astronomical time scale was established by calibrating long orbital eccentricity (405-kyr) cycles interpreted along the GR series. The results indicate that the duration of the K1s is 11.14 Myr (27.5405-kyr long orbital eccentricity cycles), corresponding to an average sedimentation rate of 6.55 cm/kyr. The recognition of astronomical forcing in this early Cretaceous fluvial-alluvial-dominated depositional setting offers a new framework for interpreting the sedimentary cyclicity and dynamics of early rift basins and for developing time scales.
    Keywords basins ; coal ; data collection ; dry environmental conditions ; Early Cretaceous epoch ; gamma radiation ; humid zones ; humidity ; lakes ; models ; paleoclimatology ; periodicity ; sandstone ; sedimentation rate ; vegetation ; China
    Language English
    Dates of publication 2020-0301
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 417718-6
    ISSN 0031-0182
    ISSN 0031-0182
    DOI 10.1016/j.palaeo.2019.109555
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 67/162: Show issues

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  5. Article ; Online: Defining distinct RNA-protein interactomes of SARS-CoV-2 genomic and subgenomic RNAs

    Whitworth, Isabella T. / Knoener, Rachel A. / Puray-Chavez, Maritza / Halfmann, Peter / Romero, Sofia / Baddouh, M’bark / Scalf, Mark / Kawaoka, Yoshihiro / Kutluay, Sebla B. / Smith, Lloyd M. / Sherer, Nathan M.

    bioRxiv

    Abstract: Host RNA binding proteins recognize viral RNA and play key roles in virus replication and antiviral defense mechanisms. SARS-CoV-2 generates a series of tiered subgenomic RNAs (sgRNAs), each encoding distinct viral protein(s) that regulate different ... ...

    Abstract Host RNA binding proteins recognize viral RNA and play key roles in virus replication and antiviral defense mechanisms. SARS-CoV-2 generates a series of tiered subgenomic RNAs (sgRNAs), each encoding distinct viral protein(s) that regulate different aspects of viral replication. Here, for the first time, we demonstrate the successful isolation of SARS-CoV-2 genomic RNA and three distinct sgRNAs (N, S, and ORF8) from a single population of infected cells and characterize their protein interactomes. Over 500 protein interactors (including 260 previously unknown) were identified as associated with one or more target RNA at either of two time points. These included protein interactors unique to a single RNA pool and others present in multiple pools, highlighting our ability to discriminate between distinct viral RNA interactomes despite high sequence similarity. The interactomes indicated viral associations with cell response pathways including regulation of cytoplasmic ribonucleoprotein granules and posttranscriptional gene silencing. We validated the significance of five protein interactors predicted to exhibit antiviral activity (APOBEC3F, TRIM71, PPP1CC, LIN28B, and MSI2) using siRNA knockdowns, with each knockdown yielding increases in viral production. This study describes new technology for studying SARS-CoV-2 and reveals a wealth of new viral RNA-associated host factors of potential functional significance to infection.
    Keywords covid19
    Language English
    Publishing date 2023-05-16
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2023.05.15.540806
    Database COVID19

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  6. Article ; Online: Defining distinct RNA-protein interactomes of SARS-CoV-2 genomic and subgenomic RNAs

    Whitworth, Isabella T / Knoener, Rachel / Puray Chavez, Maritza / Halfmann, Peter / Romero, Sofia / Baddouh, M'bark / Scalf, Mark / Kawaoka, Yoshihiro / Kutluay, Sebla B / Smith, Lloyd M / Sherer, Nathan M

    bioRxiv

    Abstract: Host RNA binding proteins recognize viral RNA and play key roles in virus replication and antiviral defense mechanisms. SARS-CoV-2 generates a series of tiered subgenomic RNAs (sgRNAs), each encoding distinct viral protein(s) that regulate different ... ...

    Abstract Host RNA binding proteins recognize viral RNA and play key roles in virus replication and antiviral defense mechanisms. SARS-CoV-2 generates a series of tiered subgenomic RNAs (sgRNAs), each encoding distinct viral protein(s) that regulate different aspects of viral replication. Here, for the first time, we demonstrate the successful isolation of SARS-CoV-2 genomic RNA and three distinct sgRNAs (N, S, and ORF8) from a single population of infected cells and characterize their protein interactomes. Over 500 protein interactors (including 260 previously unknown) were identified as associated with one or more target RNA at either of two time points. These included protein interactors unique to a single RNA pool and others present in multiple pools, highlighting our ability to discriminate between distinct viral RNA interactomes despite high sequence similarity. The interactomes indicated viral associations with cell response pathways including regulation of cytoplasmic ribonucleoprotein granules and posttranscriptional gene silencing. We validated the significance of five protein interactors predicted to exhibit antiviral activity (APOBEC3F, TRIM71, PPP1CC, LIN28B, and MSI2) using siRNA knockdowns, with each knockdown yielding increases in viral production. This study describes new technology for studying SARS-CoV-2 and reveals a wealth of new viral RNA-associated host factors of potential functional significance to infection.
    Keywords covid19
    Language English
    Publishing date 2023-05-16
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2023.05.15.540806
    Database COVID19

    Full text online

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

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