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  1. Article ; Online: Innovations in biophysics: A sampling of ideas celebrating Ned Seeman's legacy.

    Schlick, Tamar

    Biophysical journal

    2022  Volume 121, Issue 24, Page(s) E1–E2

    MeSH term(s) Biophysics
    Language English
    Publishing date 2022-12-09
    Publishing country United States
    Document type Editorial
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2022.11.030
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 235: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (1.OG)
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    Zs.MO 2: Show issues

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  2. Article ; Online: Riboswitch Distribution in the Human Gut Microbiome Reveals Common Metabolite Pathways.

    Quarta, Giulio / Schlick, Tamar

    The journal of physical chemistry. B

    2024  

    Abstract: Riboswitches are widely distributed, conserved RNAs which regulate metabolite levels in bacterial cells through direct, noncovalent binding of their cognate metabolite. Various riboswitch families are highly enriched in gut bacteria, suggestive of a ... ...

    Abstract Riboswitches are widely distributed, conserved RNAs which regulate metabolite levels in bacterial cells through direct, noncovalent binding of their cognate metabolite. Various riboswitch families are highly enriched in gut bacteria, suggestive of a symbiotic relationship between the host and bacteria. Previous studies of the distribution of riboswitches have examined bacterial taxa broadly. Thus, the distribution of riboswitches associated with bacteria inhabiting the intestines of healthy individuals is not well understood. To address these questions, we survey the gut microbiome for riboswitches by including an international database of prokaryotic genomes from the gut samples. Using Infernal, a program that uses RNA-specific sequence and structural features, we survey this data set using existing riboswitch models. We identify 22 classes of riboswitches with vitamin cofactors making up the majority of riboswitch-associated pathways. Our finding is reproducible in other representative databases from the oral as well as the marine microbiomes, underscoring the importance of thiamine pyrophosphate, cobalamin, and flavin mononucleotide in gene regulation. Interestingly, riboswitches do not vary significantly across microbiome representatives from around the world despite major taxonomic differences; this suggests an underlying conservation. Further studies elucidating the role of bacterial riboswitches in the host metabolome are needed to illuminate the consequences of our finding.
    Language English
    Publishing date 2024-04-24
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.4c00267
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Isabella L. Karle: A Crystallography Pioneer.

    Schlick, Tamar

    DNA and cell biology

    2021  Volume 40, Issue 7, Page(s) 843–847

    Abstract: The life and work of crystallography pioneer Isabella L. Karle is recounted (1921-2017), as researched from the literature and personal stories of colleagues and family. Her story includes her family background, education at the University of Michigan, ... ...

    Abstract The life and work of crystallography pioneer Isabella L. Karle is recounted (1921-2017), as researched from the literature and personal stories of colleagues and family. Her story includes her family background, education at the University of Michigan, research on the Manhattan Project, and 63 productive years at the Naval Research Laboratory. Her life-long partnership and scientific collaboration with husband Jerome Karle, 1985 Nobel Prize winner in Chemistry with Herbert Hauptman, is a big part of her story; however, Isabella has also established herself as a crystallographer
    MeSH term(s) Crystallography ; Crystallography, X-Ray/history ; Crystallography, X-Ray/methods ; Female ; History, 20th Century ; History, 21st Century ; Humans ; Nobel Prize
    Language English
    Publishing date 2021-06-14
    Publishing country United States
    Document type Biography ; Historical Article ; Journal Article
    ZDB-ID 1024454-2
    ISSN 1557-7430 ; 0198-0238 ; 1044-5498
    ISSN (online) 1557-7430
    ISSN 0198-0238 ; 1044-5498
    DOI 10.1089/dna.2021.0372
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    Zs.A 2061: Show issues Location:
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  4. Article ; Online: Eight Suggestions for Future Leaders of Science and Technology.

    Schlick, Tamar

    Biophysicist (Rockville, Md.)

    2020  Volume 1, Issue 1, Page(s) 1–5

    Language English
    Publishing date 2020-01-01
    Publishing country United States
    Document type Journal Article
    ISSN 2578-6970
    ISSN (online) 2578-6970
    DOI 10.35459/tbp.2019.000123
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  5. Article ; Online: Multiscale Genome Organization: Dazzling Subject and Inventive Methods.

    Schlick, Tamar

    Biophysical journal

    2020  Volume 118, Issue 9, Page(s) E1–E3

    Keywords covid19
    Language English
    Publishing date 2020-04-16
    Publishing country United States
    Document type Editorial ; Research Support, N.I.H., Extramural
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2020.04.007
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    Zs.A 235: Show issues Location:
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  6. Article ; Online: From butterflies to bits

    Tamar Schlick

    Biophysical Reports, Vol 1, Iss 1, Pp 100010- (2021)

    A sweeping vision for the code of life

    2021  

    Keywords Physics ; QC1-999 ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2021-09-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics.

    Li, Zilong / Schlick, Tamar

    Nucleic acids research

    2023  Volume 52, Issue 2, Page(s) 583–599

    Abstract: The structure and dynamics of the eukaryotic genome are intimately linked to gene regulation and transcriptional activity. Many chromosome conformation capture experiments like Hi-C have been developed to detect genome-wide contact frequencies and ... ...

    Abstract The structure and dynamics of the eukaryotic genome are intimately linked to gene regulation and transcriptional activity. Many chromosome conformation capture experiments like Hi-C have been developed to detect genome-wide contact frequencies and quantify loop/compartment structures for different cellular contexts and time-dependent processes. However, a full understanding of these events requires explicit descriptions of representative chromatin and chromosome configurations. With the exponentially growing amount of data from Hi-C experiments, many methods for deriving 3D structures from contact frequency data have been developed. Yet, most reconstruction methods use polymer models with low resolution to predict overall genome structure. Here we present a Brownian Dynamics (BD) approach termed Hi-BDiSCO for producing 3D genome structures from Hi-C and Micro-C data using our mesoscale-resolution chromatin model based on the Discrete Surface Charge Optimization (DiSCO) model. Our approach integrates reconstruction with chromatin simulations at nucleosome resolution with appropriate biophysical parameters. Following a description of our protocol, we present applications to the NXN, HOXC, HOXA and Fbn2 mouse genes ranging in size from 50 to 100 kb. Such nucleosome-resolution genome structures pave the way for pursuing many biomedical applications related to the epigenomic regulation of chromatin and control of human disease.
    MeSH term(s) Animals ; Humans ; Mice ; Chromatin/genetics ; Chromosomes/genetics ; Genome ; Molecular Conformation ; Nucleosomes
    Chemical Substances Chromatin ; Nucleosomes
    Language English
    Publishing date 2023-12-12
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkad1121
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    Zs.A 1067: Show issues Location:
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  8. Article: Abolished frameshifting for predicted structure-stabilizing SARS-CoV-2 mutants: Implications to alternative conformations and their statistical structural analyses.

    Dey, Abhishek / Yan, Shuting / Schlick, Tamar / Laederach, Alain

    bioRxiv : the preprint server for biology

    2024  

    Abstract: The SARS-CoV-2 frameshifting element (FSE) has been intensely studied and explored as a therapeutic target for coronavirus diseases including COVID-19. Besides the intriguing virology, this small RNA is known to adopt many length-dependent conformations, ...

    Abstract The SARS-CoV-2 frameshifting element (FSE) has been intensely studied and explored as a therapeutic target for coronavirus diseases including COVID-19. Besides the intriguing virology, this small RNA is known to adopt many length-dependent conformations, as verified by multiple experimental and computational approaches. However, the role these alternative conformations play in the frameshifting mechanism and how to quantify this structural abundance has been an ongoing challenge. Here, we show by DMS and dual-luciferase functional assays that previously predicted FSE mutants (using the RAG graph theory approach) suppress structural transitions and abolish frameshifting. Furthermore, correlated mutation analysis of DMS data by three programs (DREEM, DRACO, and DANCE-MaP) reveals important differences in their estimation of specific RNA conformations, suggesting caution in the interpretation of such complex conformational landscapes. Overall, the abolished frameshifting in three different mutants confirms that all alternative conformations play a role in the pathways of ribosomal transition.
    Language English
    Publishing date 2024-03-29
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.03.28.586935
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Publisher Correction: Biomolecular modeling thrives in the age of technology.

    Schlick, Tamar / Portillo-Ledesma, Stephanie

    Nature computational science

    2021  Volume 1, Issue 11, Page(s) 767

    Language English
    Publishing date 2021-01-14
    Publishing country United States
    Document type Published Erratum
    ISSN 2662-8457
    ISSN (online) 2662-8457
    DOI 10.1038/s43588-021-00170-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: MGO on the go: Multiscale genome symposium - annual biophysical society meeting 2021.

    Schlick, Tamar / Bishop, Thomas C

    Biophysical reviews

    2021  Volume 13, Issue 3, Page(s) 309–310

    Language English
    Publishing date 2021-05-14
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2486483-3
    ISSN 1867-2469 ; 1867-2450
    ISSN (online) 1867-2469
    ISSN 1867-2450
    DOI 10.1007/s12551-021-00799-5
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