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  1. Article ; Online: Mechanical stress affects dynamics and rheology of the human genome.

    Caragine, Christina M / Kanellakopoulos, Nikitas / Zidovska, Alexandra

    Soft matter

    2021  Volume 18, Issue 1, Page(s) 107–116

    Abstract: Material properties of the genome are critical for proper cellular function - they directly affect timescales and length scales of DNA transactions such as transcription, replication and DNA repair, which in turn impact all cellular ... ...

    Abstract Material properties of the genome are critical for proper cellular function - they directly affect timescales and length scales of DNA transactions such as transcription, replication and DNA repair, which in turn impact all cellular processes
    MeSH term(s) Cell Nucleus ; DNA/genetics ; Genome, Human ; Humans ; Rheology ; Stress, Mechanical
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2021-12-22
    Publishing country England
    Document type Journal Article
    ZDB-ID 2191476-X
    ISSN 1744-6848 ; 1744-683X
    ISSN (online) 1744-6848
    ISSN 1744-683X
    DOI 10.1039/d1sm00983d
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Anomalous coarsening of coalescing nucleoli in human cells.

    Arsenadze, Giorgi / Caragine, Christina M / Coakley, Taylor / Eshghi, Iraj / Yang, Yuwei / Wofford, Alex / Zidovska, Alexandra

    Biophysical journal

    2024  

    Abstract: Coarsening is a ubiquitous phenomenon in droplet systems near thermodynamic equilibrium-as an increase in droplet size lowers the system's free energy-however, coarsening of droplets in nonequilibrium systems, such as the cell nucleus, is far from ... ...

    Abstract Coarsening is a ubiquitous phenomenon in droplet systems near thermodynamic equilibrium-as an increase in droplet size lowers the system's free energy-however, coarsening of droplets in nonequilibrium systems, such as the cell nucleus, is far from understood. Liquid condensates in the cell nucleus, like nucleoli, form by liquid-liquid phase separation and play a key role in the nuclear organization. In human cells, nucleolar droplets are nucleated at the beginning of the cell cycle and coarsen with time by coalescing with each other. Upon coarsening, human nucleoli exhibit an anomalous volume distribution P(V)∼V
    Language English
    Publishing date 2024-01-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2024.01.005
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 235: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MO 2: Show issues

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  3. Article ; Online: CRISPR in cancer biology and therapy.

    Katti, Alyna / Diaz, Bianca J / Caragine, Christina M / Sanjana, Neville E / Dow, Lukas E

    Nature reviews. Cancer

    2022  Volume 22, Issue 5, Page(s) 259–279

    Abstract: Over the past decade, CRISPR has become as much a verb as it is an acronym, transforming biomedical research and providing entirely new approaches for dissecting all facets of cell biology. In cancer research, CRISPR and related tools have offered a ... ...

    Abstract Over the past decade, CRISPR has become as much a verb as it is an acronym, transforming biomedical research and providing entirely new approaches for dissecting all facets of cell biology. In cancer research, CRISPR and related tools have offered a window into previously intractable problems in our understanding of cancer genetics, the noncoding genome and tumour heterogeneity, and provided new insights into therapeutic vulnerabilities. Here, we review the progress made in the development of CRISPR systems as a tool to study cancer, and the emerging adaptation of these technologies to improve diagnosis and treatment.
    MeSH term(s) Biology ; CRISPR-Cas Systems ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Gene Editing ; Genome ; Humans ; Neoplasms/genetics ; Neoplasms/therapy
    Language English
    Publishing date 2022-02-22
    Publishing country England
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural
    ZDB-ID 2062767-1
    ISSN 1474-1768 ; 1474-175X
    ISSN (online) 1474-1768
    ISSN 1474-175X
    DOI 10.1038/s41568-022-00441-w
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5563: 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.MG 24: Show issues

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  4. Article ; Online: Nucleolar dynamics and interactions with nucleoplasm in living cells.

    Caragine, Christina M / Haley, Shannon C / Zidovska, Alexandra

    eLife

    2019  Volume 8

    Abstract: Liquid-liquid phase separation (LLPS) has been recognized as one of the key cellular organizing principles and was shown to be responsible for formation of membrane-less organelles such as nucleoli. Although nucleoli were found to behave like liquid ... ...

    Abstract Liquid-liquid phase separation (LLPS) has been recognized as one of the key cellular organizing principles and was shown to be responsible for formation of membrane-less organelles such as nucleoli. Although nucleoli were found to behave like liquid droplets, many ramifications of LLPS including nucleolar dynamics and interactions with the surrounding liquid remain to be revealed. Here, we study the motion of human nucleoli
    MeSH term(s) Adenosine Triphosphate/chemistry ; Cell Nucleolus/chemistry ; Cell Nucleolus/genetics ; Cell Nucleus/chemistry ; Cell Nucleus/genetics ; Chromatin/chemistry ; Chromatin/genetics ; Humans ; Kinetics ; Nuclear Proteins/chemistry ; Nuclear Proteins/genetics
    Chemical Substances Chromatin ; Nuclear Proteins ; Adenosine Triphosphate (8L70Q75FXE)
    Language English
    Publishing date 2019-11-26
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.47533
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  5. Article ; Online: Surface Fluctuations and Coalescence of Nucleolar Droplets in the Human Cell Nucleus.

    Caragine, Christina M / Haley, Shannon C / Zidovska, Alexandra

    Physical review letters

    2018  Volume 121, Issue 14, Page(s) 148101

    Abstract: The nucleolus is a membraneless organelle embedded in chromatin solution inside the cell nucleus. By analyzing surface dynamics and fusion kinetics of human nucleoli in vivo, we find that the nucleolar surface exhibits subtle, but measurable, shape ... ...

    Abstract The nucleolus is a membraneless organelle embedded in chromatin solution inside the cell nucleus. By analyzing surface dynamics and fusion kinetics of human nucleoli in vivo, we find that the nucleolar surface exhibits subtle, but measurable, shape fluctuations and that the radius of the neck connecting two fusing nucleoli grows in time as r(t)∼t^{1/2}. This is consistent with liquid droplets with low surface tension ∼10^{-6}  N m^{-1} coalescing within an outside fluid of high viscosity ∼10^{3}  Pa s. Our study presents a noninvasive approach of using natural probes and their dynamics to investigate material properties of the cell and its constituents.
    MeSH term(s) Cell Nucleolus/chemistry ; Cell Nucleolus/physiology ; Cell Nucleus/chemistry ; Cell Nucleus/physiology ; Chromatin/chemistry ; Chromatin/physiology ; HeLa Cells ; Humans ; Models, Biological ; Rheology
    Chemical Substances Chromatin
    Language English
    Publishing date 2018-10-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 208853-8
    ISSN 1079-7114 ; 0031-9007
    ISSN (online) 1079-7114
    ISSN 0031-9007
    DOI 10.1103/PhysRevLett.121.148101
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    In stock of ZB MED Bonn / Germany

    Z 4' 58/153: Show issues

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  6. Article ; Online: Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens.

    Morris, John A / Caragine, Christina / Daniloski, Zharko / Domingo, Júlia / Barry, Timothy / Lu, Lu / Davis, Kyrie / Ziosi, Marcello / Glinos, Dafni A / Hao, Stephanie / Mimitou, Eleni P / Smibert, Peter / Roeder, Kathryn / Katsevich, Eugene / Lappalainen, Tuuli / Sanjana, Neville E

    Science (New York, N.Y.)

    2023  Volume 380, Issue 6646, Page(s) eadh7699

    Abstract: Most variants associated with complex traits and diseases identified by genome-wide association studies (GWAS) map to noncoding regions of the genome with unknown effects. Using ancestrally diverse, biobank-scale GWAS data, massively parallel CRISPR ... ...

    Abstract Most variants associated with complex traits and diseases identified by genome-wide association studies (GWAS) map to noncoding regions of the genome with unknown effects. Using ancestrally diverse, biobank-scale GWAS data, massively parallel CRISPR screens, and single-cell transcriptomic and proteomic sequencing, we discovered 124
    MeSH term(s) Humans ; Clustered Regularly Interspaced Short Palindromic Repeats ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; Proteomics ; Quantitative Trait Loci ; Single-Cell Analysis ; Multifactorial Inheritance ; Blood Cells ; RNA-Seq ; Disease/genetics
    Language English
    Publishing date 2023-05-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.adh7699
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 27: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 77: Show issues

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  7. Article ; Online: Restoration ecology: two-sex dynamics and cost minimization.

    Molnár, Ferenc / Caragine, Christina / Caraco, Thomas / Korniss, Gyorgy

    PloS one

    2013  Volume 8, Issue 10, Page(s) e77332

    Abstract: We model a spatially detailed, two-sex population dynamics, to study the cost of ecological restoration. We assume that cost is proportional to the number of individuals introduced into a large habitat. We treat dispersal as homogeneous diffusion in a ... ...

    Abstract We model a spatially detailed, two-sex population dynamics, to study the cost of ecological restoration. We assume that cost is proportional to the number of individuals introduced into a large habitat. We treat dispersal as homogeneous diffusion in a one-dimensional reaction-diffusion system. The local population dynamics depends on sex ratio at birth, and allows mortality rates to differ between sexes. Furthermore, local density dependence induces a strong Allee effect, implying that the initial population must be sufficiently large to avert rapid extinction. We address three different initial spatial distributions for the introduced individuals; for each we minimize the associated cost, constrained by the requirement that the species must be restored throughout the habitat. First, we consider spatially inhomogeneous, unstable stationary solutions of the model's equations as plausible candidates for small restoration cost. Second, we use numerical simulations to find the smallest rectangular cluster, enclosing a spatially homogeneous population density, that minimizes the cost of assured restoration. Finally, by employing simulated annealing, we minimize restoration cost among all possible initial spatial distributions of females and males. For biased sex ratios, or for a significant between-sex difference in mortality, we find that sex-specific spatial distributions minimize the cost. But as long as the sex ratio maximizes the local equilibrium density for given mortality rates, a common homogeneous distribution for both sexes that spans a critical distance yields a similarly low cost.
    MeSH term(s) Animal Distribution/physiology ; Animals ; Computer Simulation ; Conservation of Natural Resources ; Ecosystem ; Female ; Male ; Models, Statistical ; Monte Carlo Method ; Population Density ; Population Dynamics ; Reproduction/physiology ; Sex Factors ; Sex Ratio
    Language English
    Publishing date 2013-10-28
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0077332
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