scholarly journals Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens

2015 ◽  
Author(s):  
Clemens L Weiß ◽  
Verena J Schuenemann ◽  
Jane Devos ◽  
Gautam Shirsekar ◽  
Ella Reiter ◽  
...  
Keyword(s):  
Dna Fragmentation ◽  
Dna Degradation ◽  
Herbarium Specimens ◽  
Decay Kinetics ◽  
Strand Breaks ◽  
Last 300 Years ◽  
Computational Procedures ◽  
Breaking Points ◽  
Kinetics Of ◽  
Historical Nature

Herbaria archive a record of changes of worldwide plant biodiversity harboring millions of specimens that contain DNA suitable for genome sequencing. To profit from this resource, it is fundamental to understand in detail the process of DNA degradation in herbarium specimens. We investigated patterns of DNA fragmentation -length and base composition at breaking points-, and nucleotide misincorporation by analyzing 86 herbarium samples spanning the last 300 years using Illumina shot-gun sequencing. We found an exponential decay relationship between DNA fragmentation and time, and estimated a per nucleotide fragmentation rate of 1.66 x 10-4 per year, which is ten times faster than the rate estimated for fossilized bones. Additionally, we found that strand breaks occur specially before purines, and that depurination-driven DNA breakage occurs constantly through time and can to a great extent explain decreasing fragment length over time. Similar of what has been found analyzing ancient DNA from bones, we found a strong correlation between the deamination-driven accumulation of cytosine (C) to thymine (T) substitutions and time, which reinforces the importance of substitution patterns to authenticate the ancient/historical nature of DNA fragments. Accurate estimations of DNA degradation through time will allow informed decisions about laboratory and computational procedures to take advantage of the vast collection of worldwide herbarium specimens.

scholarly journals Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens

2016 ◽  
Vol 3 (6) ◽  
pp. 160239 ◽  
Author(s):  
Clemens L. Weiß ◽  
Verena J. Schuenemann ◽  
Jane Devos ◽  
Gautam Shirsekar ◽  
Ella Reiter ◽  
...  
Keyword(s):  
Dna Fragmentation ◽  
Dna Degradation ◽  
Herbarium Specimens ◽  
Decay Kinetics ◽  
Strand Breaks ◽  
Dna Breakage ◽  
Last 300 Years ◽  
Computational Procedures ◽  
Kinetics Of ◽  
Historical Nature

Herbaria archive a record of changes of worldwide plant biodiversity harbouring millions of specimens that contain DNA suitable for genome sequencing. To profit from this resource, it is fundamental to understand in detail the process of DNA degradation in herbarium specimens. We investigated patterns of DNA fragmentation and nucleotide misincorporation by analysing 86 herbarium samples spanning the last 300 years using Illumina shotgun sequencing. We found an exponential decay relationship between DNA fragmentation and time, and estimated a per nucleotide fragmentation rate of 1.66 × 10 −4 per year, which is six times faster than the rate estimated for ancient bones. Additionally, we found that strand breaks occur specially before purines, and that depurination-driven DNA breakage occurs constantly through time and can to a great extent explain decreasing fragment length over time. Similar to what has been found analysing ancient DNA from bones, we found a strong correlation between the deamination-driven accumulation of cytosine to thymine substitutions and time, which reinforces the importance of substitution patterns to authenticate the ancient/historical nature of DNA fragments. Accurate estimations of DNA degradation through time will allow informed decisions about laboratory and computational procedures to take advantage of the vast collection of worldwide herbarium specimens.

scholarly journals PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Deepti Sharma ◽  
Louis De Falco ◽  
Sivaraman Padavattan ◽  
Chang Rao ◽  
Susana Geifman-Shochat ◽  
...  
Keyword(s):  
Dna Damage ◽  
Mutational Analysis ◽  
Catalytic Efficiency ◽  
Double Strand Breaks ◽  
Genomic Integrity ◽  
Dna Double Strand Breaks ◽  
Strand Breaks ◽  
Nucleosome Core ◽  
Epigenetic Marker ◽  
Kinetics Of

AbstractThe poly(ADP-ribose) polymerase, PARP1, plays a key role in maintaining genomic integrity by detecting DNA damage and mediating repair. γH2A.X is the primary histone marker for DNA double-strand breaks and PARP1 localizes to H2A.X-enriched chromatin damage sites, but the basis for this association is not clear. We characterize the kinetics of PARP1 binding to a variety of nucleosomes harbouring DNA double-strand breaks, which reveal that PARP1 associates faster with (γ)H2A.X- versus H2A-nucleosomes, resulting in a higher affinity for the former, which is maximal for γH2A.X-nucleosome that is also the activator eliciting the greatest poly-ADP-ribosylation catalytic efficiency. The enhanced activities with γH2A.X-nucleosome coincide with increased accessibility of the DNA termini resulting from the H2A.X-Ser139 phosphorylation. Indeed, H2A- and (γ)H2A.X-nucleosomes have distinct stability characteristics, which are rationalized by mutational analysis and (γ)H2A.X-nucleosome core crystal structures. This suggests that the γH2A.X epigenetic marker directly facilitates DNA repair by stabilizing PARP1 association and promoting catalysis.

Spectra and decay kinetics of trimethyldioxetane chemiluminescence

1975 ◽  
Vol 34 (2) ◽  
pp. 326-331 ◽  
Author(s):  
Irene Simo ◽  
Joachim Stauff
Keyword(s):  
Decay Kinetics ◽  
Kinetics Of

Picosecond decay kinetics of CdS luminescence studied by a streak camera

1979 ◽  
Vol 31 (4) ◽  
pp. 253-256 ◽  
Author(s):  
T. Kobayashi ◽  
Y. Segawa ◽  
S. Namba
Keyword(s):  
Streak Camera ◽  
Decay Kinetics ◽  
Kinetics Of

Decay Kinetics of Electron Emission from MgO Films in AC Plasma Display Panels

2008 ◽  
Vol 1 ◽  
pp. 091203 ◽  
Author(s):  
Takeru Okada ◽  
Takashi Furutani ◽  
Toshihiro Yoshioka
Keyword(s):  
Electron Emission ◽  
Decay Kinetics ◽  
Plasma Display Panels ◽  
Plasma Display ◽  
Kinetics Of

RecF, UvrD, RecX and RecN proteins suppress DNA degradation at DNA double-strand breaks in Escherichia coli

Biochimie ◽  
2018 ◽  
Vol 148 ◽  
pp. 116-126 ◽  
Author(s):  
Isidoro Feliciello ◽  
Davor Zahradka ◽  
Ksenija Zahradka ◽  
Siniša Ivanković ◽  
Nikolina Puc ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Dna Degradation ◽  
Double Strand Breaks ◽  
Dna Double Strand Breaks ◽  
Strand Breaks ◽  
Recn Proteins

scholarly journals Repair Kinetics of Genomic Interstrand DNA Cross-Links: Evidence for DNA Double-Strand Break-Dependent Activation of the Fanconi Anemia/BRCA Pathway

2004 ◽  
Vol 24 (1) ◽  
pp. 123-134 ◽  
Author(s):  
Andreas Rothfuss ◽  
Markus Grompe
Keyword(s):  
Fanconi Anemia ◽  
Strand Break ◽  
S Phase ◽  
Dna Double Strand Breaks ◽  
Subsequent Formation ◽  
Strand Breaks ◽  
Dna Double Strand Break ◽  
Cross Links ◽  
Kinetics Of

ABSTRACT The detailed mechanisms of DNA interstrand cross-link (ICL) repair and the involvement of the Fanconi anemia (FA)/BRCA pathway in this process are not known. Present models suggest that recognition and repair of ICL in human cells occur primarily during the S phase. Here we provide evidence for a refined model in which ICLs are recognized and are rapidly incised by ERCC1/XPF independent of DNA replication. However, the incised ICLs are then processed further and DNA double-strand breaks (DSB) form exclusively in the S phase. FA cells are fully proficient in the sensing and incision of ICL as well as in the subsequent formation of DSB, suggesting a role of the FA/BRCA pathway downstream in ICL repair. In fact, activation of FANCD2 occurs slowly after ICL treatment and correlates with the appearance of DSB in the S phase. In contrast, activation is rapid after ionizing radiation, indicating that the FA/BRCA pathway is specifically activated upon DSB formation. Furthermore, the formation of FANCD2 foci is restricted to a subpopulation of cells, which can be labeled by bromodeoxyuridine incorporation. We therefore conclude that the FA/BRCA pathway, while being dispensable for the early events in ICL repair, is activated in S-phase cells after DSB have formed.

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