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  1. Article ; Online: Ten simple rules for being a faculty advocate of first-year graduate students.

    Janes, Kevin A

    PLoS computational biology

    2021  Volume 17, Issue 9, Page(s) e1009379

    MeSH term(s) Biomedical Engineering/education ; Computational Biology ; Education, Graduate ; Empathy ; Faculty/psychology ; Humans ; Mentoring ; Mentors ; Students/psychology ; Universities ; Virginia
    Language English
    Publishing date 2021-09-30
    Publishing country United States
    Document type Editorial
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1009379
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A unique treatment of "candy cane" Roux syndrome following Roux-en-Y gastric bypass: a multidisciplinary approach.

    Janes, Lindsay / Varban, Oliver A / Platt, Kevin / Schulman, Allison R

    VideoGIE : an official video journal of the American Society for Gastrointestinal Endoscopy

    2023  Volume 8, Issue 5, Page(s) 206–207

    Abstract: Video 1Closure of blind limb after gastric bypass as a treatment for candy cane limb syndrome. ...

    Abstract Video 1Closure of blind limb after gastric bypass as a treatment for candy cane limb syndrome.
    Language English
    Publishing date 2023-04-11
    Publishing country United States
    Document type Journal Article
    ISSN 2468-4481
    ISSN (online) 2468-4481
    DOI 10.1016/j.vgie.2022.12.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Three Modes of Viral Adaption by the Heart.

    Griffiths, Cameron D / Shah, Millie / Shao, William / Borgman, Cheryl A / Janes, Kevin A

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Viruses elicit long-term adaptive responses in the tissues they infect. Understanding viral adaptions in humans is difficult in organs such as the heart, where primary infected material is not routinely collected. In search of asymptomatic infections ... ...

    Abstract Viruses elicit long-term adaptive responses in the tissues they infect. Understanding viral adaptions in humans is difficult in organs such as the heart, where primary infected material is not routinely collected. In search of asymptomatic infections with accompanying host adaptions, we mined for cardio-pathogenic viruses in the unaligned reads of nearly one thousand human hearts profiled by RNA sequencing. Among virus-positive cases (~20%), we identified three robust adaptions in the host transcriptome related to inflammatory NFκB signaling and post-transcriptional regulation by the p38-MK2 pathway. The adaptions are not determined by the infecting virus, and they recur in infections of human or animal hearts and cultured cardiomyocytes. Adaptions switch states when NFκB or p38-MK2 are perturbed in cells engineered for chronic infection by the cardio-pathogenic virus, coxsackievirus B3. Stratifying viral responses into reversible adaptions adds a targetable systems-level simplification for infections of the heart and perhaps other organs.
    Language English
    Publishing date 2024-03-29
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.03.28.587274
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Fragile epitopes-Antibody's guess is as good as yours.

    Janes, Kevin A

    Science signaling

    2020  Volume 13, Issue 616

    Abstract: Monoclonal antibodies recognize epitopes so specifically that altering a single residue can disrupt binding. In this issue ... ...

    Abstract Monoclonal antibodies recognize epitopes so specifically that altering a single residue can disrupt binding. In this issue of
    MeSH term(s) Animals ; Antibodies, Monoclonal/chemistry ; Antibodies, Monoclonal/genetics ; Antibodies, Monoclonal/immunology ; Antibody Affinity/genetics ; Antibody Specificity/genetics ; Epitopes/chemistry ; Epitopes/genetics ; Epitopes/immunology ; Humans
    Chemical Substances Antibodies, Monoclonal ; Epitopes
    Language English
    Publishing date 2020-01-28
    Publishing country United States
    Document type Journal Article ; Review ; Comment
    ZDB-ID 2417226-1
    ISSN 1937-9145 ; 1945-0877
    ISSN (online) 1937-9145
    ISSN 1945-0877
    DOI 10.1126/scisignal.aaz8130
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Patient-derived response estimates from zero-passage organoids of luminal breast cancer.

    Przanowska, Róża K / Labban, Najwa / Przanowski, Piotr / Hawes, Russell B / Atkins, Kristen A / Showalter, Shayna L / Janes, Kevin A

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Background: Primary luminal breast cancer cells lose their identity rapidly in standard tissue culture, which is problematic for testing hormone interventions and molecular pathways specific to the luminal subtype. Breast cancer organoids are thought to ...

    Abstract Background: Primary luminal breast cancer cells lose their identity rapidly in standard tissue culture, which is problematic for testing hormone interventions and molecular pathways specific to the luminal subtype. Breast cancer organoids are thought to retain tumor characteristics better, but long-term viability of luminal-subtype cases is a persistent challenge. Our goal was to adapt short-term organoids of luminal breast cancer for parallel testing of genetic and pharmacologic perturbations.
    Methods: We freshly isolated patient-derived cells from luminal tumor scrapes, miniaturized the organoid format into 5 μl replicates for increased throughput, and set an endpoint of 14 days to minimize drift. Therapeutic hormone targeting was mimicked in these "zero-passage" organoids by withdrawing β-estradiol and adding 4-hydroxytamoxifen. We also examined sulforaphane as an electrophilic stress and commercial neutraceutical with reported anti-cancer properties. Downstream mechanisms were tested genetically by lentiviral transduction of two complementary sgRNAs and Cas9 stabilization for the first week of organoid culture. Transcriptional changes were measured by RT-qPCR or RNA sequencing, and organoid phenotypes were quantified by serial brightfield imaging, digital image segmentation, and regression modeling of cellular doubling times.
    Results: We achieved >50% success in initiating luminal breast cancer organoids from tumor scrapes and maintaining them to the 14-day zero-passage endpoint. Success was mostly independent of clinical parameters, supporting general applicability of the approach. Abundance of
    Conclusions: Zero-passage organoids are a rapid and scalable way to interrogate properties of luminal breast cancer cells from patient-derived material. This includes testing drug mechanisms of action in different clinical cohorts. A future goal is to relate inter-patient variability of zero-passage organoids to long-term outcomes.
    Language English
    Publishing date 2024-03-27
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.03.24.586432
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Three Modes of Viral Adaption by the Heart

    Griffiths, Cameron D. / Shah, Millie / Shao, William / Borgman, Cheryl A. / Janes, Kevin A.

    bioRxiv

    Abstract: Viruses elicit long-term adaptive responses in the tissues they infect. Understanding viral adaptions in humans is difficult in organs such as the heart, where primary infected material is not routinely collected. In search of asymptomatic infections ... ...

    Abstract Viruses elicit long-term adaptive responses in the tissues they infect. Understanding viral adaptions in humans is difficult in organs such as the heart, where primary infected material is not routinely collected. In search of asymptomatic infections with accompanying host adaptions, we mined for cardio-pathogenic viruses in the unaligned reads of nearly one thousand human hearts profiled by RNA sequencing. Among virus-positive cases (~20%), we identified three robust adaptions in the host transcriptome related to inflammatory NFkappaB signaling and post-transcriptional regulation by the p38-MK2 pathway. The adaptions are not determined by the infecting virus, and they recur in infections of human or animal hearts and cultured cardiomyocytes. Adaptions switch states when NFkappaB or p38-MK2 are perturbed in cells engineered for chronic infection by the cardio-pathogenic virus, coxsackievirus B3. Stratifying viral responses into reversible adaptions adds a targetable systems-level simplification for infections of the heart and perhaps other organs.
    Keywords covid19
    Language English
    Publishing date 2024-03-29
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2024.03.28.587274
    Database COVID19

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  7. Article: A genetic mosaic mouse model illuminates the pre-malignant progression of basal-like breast cancer.

    Zeng, Jianhao / Singh, Shambhavi / Jiang, Ying / Casarez, Eli / Atkins, Kristen A / Janes, Kevin A / Zong, Hui

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Basal-like breast cancer is an aggressive breast cancer subtype, often characterized by a deficiency in : Summary statement: A mouse model recapitulates the process of human basal-like breast tumorigenesis initiated from ... ...

    Abstract Basal-like breast cancer is an aggressive breast cancer subtype, often characterized by a deficiency in
    Summary statement: A mouse model recapitulates the process of human basal-like breast tumorigenesis initiated from sporadic
    Language English
    Publishing date 2023-04-28
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.04.25.538333
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Ten simple rules for being a faculty advocate of first-year graduate students.

    Kevin A Janes

    PLoS Computational Biology, Vol 17, Iss 9, p e

    2021  Volume 1009379

    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2021-09-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: A genetic mosaic mouse model illuminates the pre-malignant progression of basal-like breast cancer.

    Zeng, Jianhao / Singh, Shambhavi / Zhou, Xian / Jiang, Ying / Casarez, Eli / Atkins, Kristen A / Janes, Kevin A / Zong, Hui

    Disease models & mechanisms

    2023  Volume 16, Issue 11

    Abstract: Basal-like breast cancer (BLBC) is highly aggressive, and often characterized by BRCA1 and p53 deficiency. Although conventional mouse models enabled the investigation of BLBC at malignant stages, its initiation and pre-malignant progression remain ... ...

    Abstract Basal-like breast cancer (BLBC) is highly aggressive, and often characterized by BRCA1 and p53 deficiency. Although conventional mouse models enabled the investigation of BLBC at malignant stages, its initiation and pre-malignant progression remain understudied. Here, we leveraged a mouse genetic system known as mosaic analysis with double markers (MADM) to study BLBC initiation by generating rare GFP+Brca1, p53-deficient mammary cells alongside RFP+ wild-type sibling cells. After confirming the close resemblance of mammary tumors arising in this model to human BLBC at both transcriptomic and genomic levels, we focused our studies on the pre-malignant progression of BLBC. Initiated GFP+ mutant cells showed a stepwise pre-malignant progression trajectory from focal expansion to hyper-alveolarization and then to micro-invasion. Furthermore, despite morphological similarities to alveoli, hyper-alveolarized structures actually originate from ductal cells based on twin-spot analysis of GFP-RFP sibling cells. Finally, luminal-to-basal transition occurred exclusively in cells that have progressed to micro-invasive lesions. Our MADM model provides excellent spatiotemporal resolution to illuminate the pre-malignant progression of BLBC, and should enable future studies on early detection and prevention for this cancer.
    MeSH term(s) Mice ; Animals ; Humans ; Female ; Breast Neoplasms/genetics ; Breast Neoplasms/pathology ; Tumor Suppressor Protein p53/genetics ; Mammary Neoplasms, Animal/genetics ; Breast/pathology
    Chemical Substances Tumor Suppressor Protein p53
    Language English
    Publishing date 2023-11-13
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2451104-3
    ISSN 1754-8411 ; 1754-8403
    ISSN (online) 1754-8411
    ISSN 1754-8403
    DOI 10.1242/dmm.050219
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: A genetic mosaic mouse model illuminates the pre-malignant progression of basal-like breast cancer

    Jianhao Zeng / Shambhavi Singh / Xian Zhou / Ying Jiang / Eli Casarez / Kristen A. Atkins / Kevin A. Janes / Hui Zong

    Disease Models & Mechanisms, Vol 16, Iss

    2023  Volume 11

    Keywords mouse genetic mosaic model ; basal-like breast cancer ; brca1 ; pre-malignancy ; spatiotemporal analysis of tumor initiation ; Medicine ; R ; Pathology ; RB1-214
    Language English
    Publishing date 2023-11-01T00:00:00Z
    Publisher The Company of Biologists
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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