1
|
Oshidari R, Mekhail K, Seeber A. Mobility and Repair of Damaged DNA: Random or Directed? Trends Cell Biol 2020; 30:144-156. [DOI: 10.1016/j.tcb.2019.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 12/24/2022]
|
2
|
Witberg G, Lev E, Ber Y, Tabachnik T, Sela S, Belo I, Leshem-Lev D, Margel D. Vascular endothelium function among male carriers of BRCA 1&2 germline mutation. Oncotarget 2019; 10:5041-5051. [PMID: 31489114 PMCID: PMC6707947 DOI: 10.18632/oncotarget.27118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/29/2019] [Indexed: 12/14/2022] Open
Abstract
Background: Breast cancer susceptibility genes 1&2 (BRCA1&2) mutations hinder DNA-repair. Germline mutations in these genes are known to cause cancer; however, they may have other consequences. In this study we evaluated for the first time, the effect of the BRCA mutations on the vascular endothelium of young healthy males. Results: The study included 82 participants (53 BRCA mutation positive-carriers and 29 negative-carriers). Subjects mean age was 40. There were no significant differences in the baseline characteristics of the two groups. BRCA-carriers had significantly higher levels of EPCs (fraction of CD34+/VEGF or CD133+/VEGF positive-cells) compared to non-carriers of the mutation (median 6.78[1.96,14.48]% vs. 1.46[0.65,6.18]%, p < 0.001, and median 7.17[1.70,16.69]% vs. 1.54[0.85,5.10]%, p < 0.001, respectively). This difference remained consistent after multivariate adjustment. We did not identify differences in endothelial function, endothelial damage markers and EPCs activity between the two groups. Methods: This was a prospective cohort study to test the association between BRCA status and possible endothelial alterations. The Study population included males, 18-50 years, with no cardiovascular morbidity, who were referred for BRCA screening. We tested the endothelial system by: Endothelial progenitor cells (EPC) production, endothelial function (EndoPAT2000), endothelial damage and related hormonal levels. We stratified the cohort by germline BRCA status and compared measurements between BRCA mutation positive- and negative-carriers. Conclusions: Male BRCA1&2 mutation positive-carriers had increased level of EPCs which may reflect a subclinical accumulative endothelial damage. These novel findings suggest that the effect of mutations in BRCA is not limited to increased cancer risk, but may affect the cardiovascular system.
Collapse
Affiliation(s)
- Guy Witberg
- Department of Cardiology, Rabin Medical Center, Petach Tikva, Israel.,The Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eli Lev
- Department of Cardiology, Rabin Medical Center, Petach Tikva, Israel.,Department of Cardiology, Assuta Ashdod University Hospital, Ashdod, Israel.,Faculty of Medicine, Ben Gurion University, Be'er Sheva, Israel
| | - Yaara Ber
- Department of Urology, Rabin Medical Center, Petach Tikva, Israel
| | - Tzlil Tabachnik
- Department of Urology, Rabin Medical Center, Petach Tikva, Israel
| | - Sivan Sela
- Department of Urology, Rabin Medical Center, Petach Tikva, Israel
| | - Ira Belo
- Department of Urology, Rabin Medical Center, Petach Tikva, Israel
| | - Dorit Leshem-Lev
- Department of Cardiology, Rabin Medical Center, Petach Tikva, Israel.,The Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - David Margel
- The Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Urology, Rabin Medical Center, Petach Tikva, Israel
| |
Collapse
|
3
|
Acharya N, Manohar K, Peroumal D, Khandagale P, Patel SK, Sahu SR, Kumari P. Multifaceted activities of DNA polymerase η: beyond translesion DNA synthesis. Curr Genet 2018; 65:649-656. [PMID: 30535880 DOI: 10.1007/s00294-018-0918-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 10/27/2022]
Abstract
DNA polymerases are evolved to extend the 3'-OH of a growing primer annealed to a template DNA substrate. Since replicative DNA polymerases have a limited role while replicating structurally distorted template, translesion DNA polymerases mostly from Y-family come to the rescue of stalled replication fork and maintain genome stability. DNA polymerase eta is one such specialized enzyme whose function is directly associated with casual development of certain skin cancers and chemo-resistance. More than 20 years of extensive studies are available to support TLS activities of Polη in bypassing various DNA lesions, in addition, limited but crucial growing evidence also exist to suggest Polη possessing TLS-independent cellular functions. In this review, we have mostly focused on non-TLS activities of Polη from different organisms including our recent findings from pathogenic yeast Candida albicans.
Collapse
Affiliation(s)
- Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India.
| | - Kodavati Manohar
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Doureradjou Peroumal
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Prashant Khandagale
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Shraddheya Kumar Patel
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Satya Ranjan Sahu
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Premlata Kumari
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| |
Collapse
|
4
|
Rueden CT, Schindelin J, Hiner MC, DeZonia BE, Walter AE, Arena ET, Eliceiri KW. ImageJ2: ImageJ for the next generation of scientific image data. BMC Bioinformatics 2017; 18:529. [PMID: 29187165 PMCID: PMC5708080 DOI: 10.1186/s12859-017-1934-z] [Citation(s) in RCA: 3009] [Impact Index Per Article: 429.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 11/14/2017] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software's ability to handle the requirements of modern science. RESULTS We rewrote the entire ImageJ codebase, engineering a redesigned plugin mechanism intended to facilitate extensibility at every level, with the goal of creating a more powerful tool that continues to serve the existing community while addressing a wider range of scientific requirements. This next-generation ImageJ, called "ImageJ2" in places where the distinction matters, provides a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. CONCLUSIONS Scientific imaging benefits from open-source programs that advance new method development and deployment to a diverse audience. ImageJ has continuously evolved with this idea in mind; however, new and emerging scientific requirements have posed corresponding challenges for ImageJ's development. The described improvements provide a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs. Future efforts will focus on implementing new algorithms in this framework and expanding collaborations with other popular scientific software suites.
Collapse
Affiliation(s)
- Curtis T Rueden
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA
| | - Johannes Schindelin
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Mark C Hiner
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA
| | - Barry E DeZonia
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA
| | - Alison E Walter
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Ellen T Arena
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Kevin W Eliceiri
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA.
- Morgridge Institute for Research, Madison, Wisconsin, USA.
| |
Collapse
|
5
|
Rueden CT, Schindelin J, Hiner MC, DeZonia BE, Walter AE, Arena ET, Eliceiri KW. ImageJ2: ImageJ for the next generation of scientific image data. BMC Bioinformatics 2017. [PMID: 29187165 DOI: 10.1186/s12859-017-1934-z.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software's ability to handle the requirements of modern science. RESULTS We rewrote the entire ImageJ codebase, engineering a redesigned plugin mechanism intended to facilitate extensibility at every level, with the goal of creating a more powerful tool that continues to serve the existing community while addressing a wider range of scientific requirements. This next-generation ImageJ, called "ImageJ2" in places where the distinction matters, provides a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. CONCLUSIONS Scientific imaging benefits from open-source programs that advance new method development and deployment to a diverse audience. ImageJ has continuously evolved with this idea in mind; however, new and emerging scientific requirements have posed corresponding challenges for ImageJ's development. The described improvements provide a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs. Future efforts will focus on implementing new algorithms in this framework and expanding collaborations with other popular scientific software suites.
Collapse
Affiliation(s)
- Curtis T Rueden
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA
| | - Johannes Schindelin
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA.,Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Mark C Hiner
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA
| | - Barry E DeZonia
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA
| | - Alison E Walter
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA.,Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Ellen T Arena
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA.,Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Kevin W Eliceiri
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA. .,Morgridge Institute for Research, Madison, Wisconsin, USA.
| |
Collapse
|
6
|
Telomeres and telomerase. Methods 2017; 114:1-3. [PMID: 28107827 DOI: 10.1016/j.ymeth.2017.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
|