LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 18

Search options

  1. Article: Serial Capture Affinity Purification and Integrated Structural Modeling of the H3K4me3 Binding and DNA Damage Related WDR76:SPIN1 Complex.

    Liu, Xingyu / Zhang, Ying / Wen, Zhihui / Hao, Yan / Banks, Charles A S / Lange, Jeffrey J / Cesare, Joseph / Bhattacharya, Saikat / Slaughter, Brian D / Unruh, Jay R / Florens, Laurence / Workman, Jerry L / Washburn, Michael P

    bioRxiv : the preprint server for biology

    2023  

    Abstract: WDR76 is a multifunctional protein involved in many cellular functions. With a diverse and complicated protein interaction network, dissecting the structure and function of specific WDR76 complexes is needed. We previously demonstrated the ability of the ...

    Abstract WDR76 is a multifunctional protein involved in many cellular functions. With a diverse and complicated protein interaction network, dissecting the structure and function of specific WDR76 complexes is needed. We previously demonstrated the ability of the Serial Capture Affinity Purification (SCAP) method to isolate specific complexes by introducing two proteins of interest as baits at the same time. Here, we applied SCAP to dissect a subpopulation of WDR76 in complex with SPIN1, a histone marker reader that specifically recognizes trimethylated histone H3 lysine4 (H3K4me3). In contrast to the SCAP analysis of the SPIN1:SPINDOC complex, H3K4me3 was copurified with the WDR76:SPIN1 complex. In combination with crosslinking mass spectrometry, we built an integrated structural model of the complex which revealed that SPIN1 recognized the H3K4me3 epigenetic mark while interacting with WDR76. Lastly, interaction network analysis of copurifying proteins revealed the potential role of the WDR76:SPIN1 complex in the DNA damage response.
    Teaser: In contrast to the SPINDOC/SPIN1 complex, analyses reveal that the WDR76/SPIN1 complex interacts with core histones and is involved in DNA damage.
    Language English
    Publishing date 2023-02-03
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.01.31.526478
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  2. Article ; Online: Assessing the differences in operative and patient-reported outcomes between lateral approaches for lumbar fusion: a systematic review and indirect meta-analysis.

    Bhatti, Atiq Ur Rehman / Cesare, Joseph / Wahood, Waseem / Alvi, Mohammed Ali / Onyedimma, Chiduziem E / Ghaith, Abdul Karim / Akinnusotu, Oluwatoyin / El Sammak, Sally / Freedman, Brett A / Sebastian, Arjun S / Bydon, Mohamad

    Journal of neurosurgery. Spine

    2022  , Page(s) 1–17

    Abstract: Objective: Anterior-to-psoas lumbar interbody fusion (ATP-LIF), more commonly referred to as oblique lateral interbody fusion, and lateral transpsoas lumbar interbody fusion (LTP-LIF), also known as extreme lateral interbody fusion, are the two commonly ...

    Abstract Objective: Anterior-to-psoas lumbar interbody fusion (ATP-LIF), more commonly referred to as oblique lateral interbody fusion, and lateral transpsoas lumbar interbody fusion (LTP-LIF), also known as extreme lateral interbody fusion, are the two commonly used lateral approaches for performing a lumbar fusion procedure. These approaches help overcome some of the technical challenges associated with traditional approaches for lumbar fusion. In this systematic review and indirect meta-analysis, the authors compared operative and patient-reported outcomes between these two select approaches using available studies.
    Methods: Using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) approach, the authors conducted an electronic search using the PubMed, EMBASE, and Scopus databases for studies published before May 1, 2019. Indirect meta-analysis was conducted on fusion rate, cage movement (subsidence plus migration), permanent deficits, and transient deficits; results were depicted as forest plots of proportions (effect size [ES]).
    Results: A total of 63 studies were included in this review after applying the exclusion criteria, of which 26 studies investigated the outcomes of ATP-LIF, while 37 studied the outcomes of LTP-LIF. The average fusion rate was found to be similar between the two groups (ES 0.97, 95% CI 0.84-1.00 vs ES 0.94, 95% CI 0.91-0.97; p = 0.561). The mean incidence of cage movement was significantly higher in the ATP-LIF group compared with the LTP-LIF group (stand-alone: ES 0.15, 95% CI 0.06-0.27 vs ES 0.09, 95% CI 0.04-0.16 [p = 0.317]; combined: ES 0.18, 95% CI 0.07-0.32 vs ES 0.02, 95% CI 0.00-0.05 [p = 0.002]). The mean incidence of reoperations was significantly higher in patients undergoing ATP-LIF than in those undergoing LTP-LIF (ES 0.02, 95% CI 0.01-0.03 vs ES 0.04, 95% CI 0.02-0.07; p = 0.012). The mean incidence of permanent deficits was similar between the two groups (stand-alone: ES 0.03, 95% CI 0.01-0.06 vs ES 0.05, 95% CI 0.01-0.12 [p = 0.204]; combined: ES 0.03, 95% CI 0.01-0.06 vs ES 0.03, 95% CI 0.00-0.08 [p = 0.595]). The postoperative changes in visual analog scale (VAS) and Oswestry Disability Index (ODI) scores were both found to be higher for ATP-LIF relative to LTP-LIF (VAS: weighted average 4.11 [SD 2.03] vs weighted average 3.75 [SD 1.94] [p = 0.004]; ODI: weighted average 28.3 [SD 5.33] vs weighted average 24.3 [SD 4.94] [p < 0.001]).
    Conclusions: These analyses indicate that while both approaches are associated with similar fusion rates, ATP-LIF may be related to higher odds of cage movement and reoperations as compared with LTP-LIF. Furthermore, there is no difference in rates of permanent deficits between the two procedures.
    Language English
    Publishing date 2022-04-22
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2158643-3
    ISSN 1547-5646 ; 1547-5654
    ISSN (online) 1547-5646
    ISSN 1547-5654
    DOI 10.3171/2022.2.SPINE211164
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  3. Article: Longitudinal Large-Scale Semiquantitative Proteomic Data Stability Across Multiple Instrument Platforms

    Lu, Congcong / Glisovic-Aplenc, Tina / Bernt, Kathrin M. / Nestler, Kevin / Cesare, Joseph / Cao, Lusha / Lee, Hyoungjoo / Fazelinia, Hossein / Chinwalla, Asif / Xu, Yang / Shestova, Olga / Xing, Yi / Gill, Saar / Li, Mingyao / Garcia, Benjamin / Aplenc, Richard

    Journal of proteome research. 2021 Oct. 20, v. 20, no. 11

    2021  

    Abstract: With the rapid developments in mass spectrometry (MS)-based proteomics methods, label-free semiquantitative proteomics has become an increasingly popular tool for profiling global protein abundances in an unbiased manner. However, the reproducibility of ... ...

    Abstract With the rapid developments in mass spectrometry (MS)-based proteomics methods, label-free semiquantitative proteomics has become an increasingly popular tool for profiling global protein abundances in an unbiased manner. However, the reproducibility of these data across time and LC–MS platforms is not well characterized. Here, we evaluate the performance of three LC–MS platforms (Orbitrap Elite, Q Exactive HF, and Orbitrap Fusion) in label-free semiquantitative analysis of cell surface proteins over a six-year period. Sucrose gradient ultracentrifugation was used for surfaceome enrichment, following gel separation for in-depth protein identification. With our established workflow, we consistently detected and reproducibly quantified >2300 putative cell surface proteins in a human acute myeloid leukemia (AML) cell line on all three platforms. To our knowledge this is the first study reporting highly reproducible semiquantitative proteomic data collection of biological replicates across multiple years and LC–MS platforms. These data provide experimental justification for semiquantitative proteomic study designs that are executed over multiyear time intervals and on different platforms. Multiyear and multiplatform experimental designs will likely enable larger scale proteomic studies and facilitate longitudinal proteomic studies by investigators lacking access to high throughput MS facilities. Data are available via ProteomeXchange with identifier PXD022721.
    Keywords cell lines ; data collection ; gels ; humans ; mass spectrometry ; myeloid leukemia ; proteome ; proteomics ; research ; sucrose ; ultracentrifugation
    Language English
    Dates of publication 2021-1020
    Size p. 5203-5211.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.1c00624
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

  4. Article ; Online: Publisher Correction: SARS-CoV-2 disrupts host epigenetic regulation via histone mimicry.

    Kee, John / Thudium, Samuel / Renner, David M / Glastad, Karl / Palozola, Katherine / Zhang, Zhen / Li, Yize / Lan, Yemin / Cesare, Joseph / Poleshko, Andrey / Kiseleva, Anna A / Truitt, Rachel / Cardenas-Diaz, Fabian L / Zhang, Xianwen / Xie, Xuping / Kotton, Darrell N / Alysandratos, Konstantinos D / Epstein, Jonathan A / Shi, Pei-Yong /
    Yang, Wenli / Morrisey, Edward / Garcia, Benjamin A / Berger, Shelley L / Weiss, Susan R / Korb, Erica

    Nature

    2023  Volume 613, Issue 7945, Page(s) E5

    Language English
    Publishing date 2023-01-10
    Publishing country England
    Document type Published Erratum
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-022-05631-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  5. Article ; Online: Author Correction: SARS-CoV-2 disrupts host epigenetic regulation via histone mimicry.

    Kee, John / Thudium, Samuel / Renner, David M / Glastad, Karl / Palozola, Katherine / Zhang, Zhen / Li, Yize / Lan, Yemin / Cesare, Joseph / Poleshko, Andrey / Kiseleva, Anna A / Truitt, Rachel / Cardenas-Diaz, Fabian L / Zhang, Xianwen / Xie, Xuping / Kotton, Darrell N / Alysandratos, Konstantinos D / Epstein, Jonathan A / Shi, Pei-Yong /
    Yang, Wenli / Morrisey, Edward / Garcia, Benjamin A / Berger, Shelley L / Weiss, Susan R / Korb, Erica

    Nature

    2023  Volume 614, Issue 7949, Page(s) E44

    Language English
    Publishing date 2023-02-06
    Publishing country England
    Document type Published Erratum
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-023-05764-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  6. Article ; Online: Outcomes following surgical versus endovascular treatment of spinal dural arteriovenous fistula: a systematic review and meta-analysis.

    Goyal, Anshit / Cesare, Joseph / Lu, Victor M / Alvi, Mohammed Ali / Kerezoudis, Panagiotis / Brinjikji, Waleed / Nasr, Deena / Lanzino, Guiseppe / Bydon, Mohamad

    Journal of neurology, neurosurgery, and psychiatry

    2019  Volume 90, Issue 10, Page(s) 1139–1146

    Abstract: Although surgical resection is associated with a complete cure in most cases of spinal dural arteriovenous fistulas (SDAVF), there has been an increasing trend towards embolisation. We performed a systematic review and meta-analysis comparing surgical ... ...

    Abstract Although surgical resection is associated with a complete cure in most cases of spinal dural arteriovenous fistulas (SDAVF), there has been an increasing trend towards embolisation. We performed a systematic review and meta-analysis comparing surgical resection with endovascular treatment in terms of success of treatment, rate of recurrence and complications. A literature search was conducted using Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Strength of evidence was assessed using the Grading of Recommendations Assessment, Development and Evaluation Working Group system. Surgical outcomes such as initial treatment failure, late recurrence, neurological improvement and complications were compared between the two approaches. We included 57 studies with 2029 patients, of which 32 studies with 1341 patients directly compared surgery (n=590) and embolisation (n=751). Surgery was found to be associated with significantly lower odds of initial treatment failure (OR: 0.15, 95% CI 0.09 to 0.24, I
    MeSH term(s) Central Nervous System Vascular Malformations/therapy ; Dura Mater ; Embolization, Therapeutic/methods ; Enbucrilate/therapeutic use ; Endovascular Procedures/methods ; Humans ; Ligation ; Neurosurgical Procedures/methods ; Spinal Cord/blood supply ; Tissue Adhesives/therapeutic use ; Treatment Outcome
    Chemical Substances Tissue Adhesives ; Enbucrilate (F8CEP82QNP)
    Keywords covid19
    Language English
    Publishing date 2019-05-29
    Publishing country England
    Document type Comparative Study ; Journal Article ; Meta-Analysis ; Systematic Review
    ZDB-ID 3087-9
    ISSN 1468-330X ; 0022-3050
    ISSN (online) 1468-330X
    ISSN 0022-3050
    DOI 10.1136/jnnp-2019-320648
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  7. Article ; Online: Comparing outcomes of fusion versus repeat discectomy for recurrent lumbar disc herniation: A systematic review and meta-analysis.

    Kerezoudis, Panagiotis / Goncalves, Sandy / Cesare, Joseph D / Alvi, Mohammed Ali / Kurian, Dennis P / Sebastian, Arjun S / Nassr, Ahmad / Bydon, Mohamad

    Clinical neurology and neurosurgery

    2018  Volume 171, Page(s) 70–78

    Abstract: Objectives: Current surgical treatment options for one-time recurrent lumbar disc herniation (RLDH) include repeat discectomy or discectomy supplemented with fusion. Significant contention exists within the surgical spine community with regard to the ... ...

    Abstract Objectives: Current surgical treatment options for one-time recurrent lumbar disc herniation (RLDH) include repeat discectomy or discectomy supplemented with fusion. Significant contention exists within the surgical spine community with regard to the most effective treatment modality. The objective of this study is to compare reoperation rates and patient reported outcomes following fusion versus repeat discectomy for RLDH.
    Patients and methods: The electronic literature search was performed in Ovid Medline/Pubmed, EMBASE and Cochrane, Scopus and China National Knowledge Infrastructure for human studies directly comparing repeat discectomy with fusion for ipsilateral or contralateral RLDH. Random effects meta-analysis was conducted to pool the estimates of effect, using mean differences (MD) and odds ratios (OR) for continuous and categorical outcomes, respectively.
    Results: A total of 1405 patients with RLDH (746 fusions and 659 repeat discectomies) from 15 studies (13 observational and 2 randomized controlled trials) were analyzed. Mean time to reherniation was 54.4 ± 30.4 months, while average follow-up time was 40 ± 11.7 months (range: 12-92.6). No difference was found between fusions and repeat discectomies with regards to related reoperations (OR: 0.68; 95% C.I: 0.14-3.2). Changes in PRO scores from baseline to last follow-up were also similar between the two groups, including VAS-back pain (MD, -0.3; 95% CI, -1.4 to 0.7), VAS-leg pain (MD, -0.3; 95% CI, -1.4 to 0.7), ODI (MD, 0.6; 95% CI, -0.2 to 1.4), JOA (MD: 1.0; 95% CI: 0.02 to 2.0) and MacNab satisfaction (OR: 1.5; 95% CI, 0.9 to 2.3).
    Conclusion: Available evidence shows that in treating one-time recurrent disc herniations, repeat discectomy and fusion are associated with comparable reoperation rates, incidence of dural tears, functional outcomes as well as satisfaction with surgical treatment at last follow-up. Future longitudinal, randomized controlled trials should be completed to validate any associations found in this study.
    MeSH term(s) Diskectomy/adverse effects ; Diskectomy, Percutaneous/methods ; Humans ; Intervertebral Disc Degeneration/surgery ; Intervertebral Disc Displacement/surgery ; Lumbar Vertebrae/surgery ; Spinal Fusion/adverse effects ; Treatment Outcome
    Language English
    Publishing date 2018-05-29
    Publishing country Netherlands
    Document type Comparative Study ; Journal Article ; Meta-Analysis ; Systematic Review
    ZDB-ID 193107-6
    ISSN 1872-6968 ; 0303-8467
    ISSN (online) 1872-6968
    ISSN 0303-8467
    DOI 10.1016/j.clineuro.2018.05.023
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  8. Article ; Online: Truncated titin proteins in dilated cardiomyopathy.

    McAfee, Quentin / Chen, Christina Yingxian / Yang, Yifan / Caporizzo, Matthew A / Morley, Michael / Babu, Apoorva / Jeong, Sunhye / Brandimarto, Jeffrey / Bedi, Kenneth C / Flam, Emily / Cesare, Joseph / Cappola, Thomas P / Margulies, Kenneth / Prosser, Benjamin / Arany, Zolt

    Science translational medicine

    2021  Volume 13, Issue 618, Page(s) eabd7287

    Abstract: Truncating variants ... ...

    Abstract Truncating variants in
    MeSH term(s) Adult ; Alleles ; Cardiomyopathy, Dilated/genetics ; Connectin/genetics ; Connectin/metabolism ; Humans ; Myocytes, Cardiac/metabolism
    Chemical Substances Connectin ; TTN protein, human
    Language English
    Publishing date 2021-11-03
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2518854-9
    ISSN 1946-6242 ; 1946-6234
    ISSN (online) 1946-6242
    ISSN 1946-6234
    DOI 10.1126/scitranslmed.abd7287
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  9. Article ; Online: Longitudinal Large-Scale Semiquantitative Proteomic Data Stability Across Multiple Instrument Platforms.

    Lu, Congcong / Glisovic-Aplenc, Tina / Bernt, Kathrin M / Nestler, Kevin / Cesare, Joseph / Cao, Lusha / Lee, Hyoungjoo / Fazelinia, Hossein / Chinwalla, Asif / Xu, Yang / Shestova, Olga / Xing, Yi / Gill, Saar / Li, Mingyao / Garcia, Benjamin / Aplenc, Richard

    Journal of proteome research

    2021  Volume 20, Issue 11, Page(s) 5203–5211

    Abstract: With the rapid developments in mass spectrometry (MS)-based proteomics methods, label-free semiquantitative proteomics has become an increasingly popular tool for profiling global protein abundances in an unbiased manner. However, the reproducibility of ... ...

    Abstract With the rapid developments in mass spectrometry (MS)-based proteomics methods, label-free semiquantitative proteomics has become an increasingly popular tool for profiling global protein abundances in an unbiased manner. However, the reproducibility of these data across time and LC-MS platforms is not well characterized. Here, we evaluate the performance of three LC-MS platforms (Orbitrap Elite, Q Exactive HF, and Orbitrap Fusion) in label-free semiquantitative analysis of cell surface proteins over a six-year period. Sucrose gradient ultracentrifugation was used for surfaceome enrichment, following gel separation for in-depth protein identification. With our established workflow, we consistently detected and reproducibly quantified >2300 putative cell surface proteins in a human acute myeloid leukemia (AML) cell line on all three platforms. To our knowledge this is the first study reporting highly reproducible semiquantitative proteomic data collection of biological replicates across multiple years and LC-MS platforms. These data provide experimental justification for semiquantitative proteomic study designs that are executed over multiyear time intervals and on different platforms. Multiyear and multiplatform experimental designs will likely enable larger scale proteomic studies and facilitate longitudinal proteomic studies by investigators lacking access to high throughput MS facilities. Data are available via ProteomeXchange with identifier PXD022721.
    MeSH term(s) Humans ; Mass Spectrometry/methods ; Proteome/analysis ; Proteomics/methods ; Reproducibility of Results ; Workflow
    Chemical Substances Proteome
    Language English
    Publishing date 2021-10-20
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.1c00624
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  10. Article ; Online: SARS-CoV-2 disrupts host epigenetic regulation via histone mimicry.

    Kee, John / Thudium, Samuel / Renner, David M / Glastad, Karl / Palozola, Katherine / Zhang, Zhen / Li, Yize / Lan, Yemin / Cesare, Joseph / Poleshko, Andrey / Kiseleva, Anna A / Truitt, Rachel / Cardenas-Diaz, Fabian L / Zhang, Xianwen / Xie, Xuping / Kotton, Darrell N / Alysandratos, Konstantinos D / Epstein, Jonathan A / Shi, Pei-Yong /
    Yang, Wenli / Morrisey, Edward / Garcia, Benjamin A / Berger, Shelley L / Weiss, Susan R / Korb, Erica

    Nature

    2022  Volume 610, Issue 7931, Page(s) 381–388

    Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged at the end of 2019 and caused the devastating global pandemic of coronavirus disease 2019 (COVID-19), in part because of its ability to effectively suppress host cell ... ...

    Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged at the end of 2019 and caused the devastating global pandemic of coronavirus disease 2019 (COVID-19), in part because of its ability to effectively suppress host cell responses
    MeSH term(s) COVID-19/genetics ; COVID-19/metabolism ; COVID-19/virology ; Chromatin/genetics ; Chromatin/metabolism ; Chromatin Assembly and Disassembly ; Epigenesis, Genetic ; Epigenome/genetics ; Histones/chemistry ; Histones/metabolism ; Host Microbial Interactions ; Humans ; Molecular Mimicry ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; SARS-CoV-2/pathogenicity ; Viral Proteins/chemistry ; Viral Proteins/genetics ; Viral Proteins/metabolism
    Chemical Substances Chromatin ; Histones ; ORF8 protein, SARS-CoV-2 ; Viral Proteins
    Language English
    Publishing date 2022-10-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-022-05282-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

To top