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Investigation of a Biological Repair Scheme [chapter]

Vincent Danos, Jérôme Féret, Walter Fontana, Russell Harmer, Jean Krivine
2009 Lecture Notes in Computer Science  
We also a use a series of refinements, starting from a very simple interaction set, which we feel gives an interesting and intuitive rationale for the working of the final repair scheme.  ...  This note details an interaction pattern for the allocation of a scarce biological resource where and when it is needed. It is entirely based on a mass action stochastic dynamics.  ...  As we understand it in this paper, a scheme or a pattern is a set of interactions between biological agents (we use the neutral term agent throughout this paper, but one can think of them as idealised  ... 
doi:10.1007/978-3-540-95885-7_1 fatcat:zode5a5rsvfe7e7q5dzpscztku

Pulsed brachytherapy: a modelled consideration of repair parameter uncertainties and their influence on treatment duration extension and daytime-only "block-schemes"

T S A Underwood, R G Dale, A M Bidmead, C A Nalder, P R Blake
2011 British Journal of Radiology  
The potential use of "block-schemes" (blocks of PB pulses separated by night-time gaps) is also investigated.  ...  Calculations are performed using the biologically effective dose (BED) as a tissue-specific comparison metric.  ...  The possible use of daytime-only block-schemes for cervical cancer is investigated here.  ... 
doi:10.1259/bjr/58276427 pmid:21266397 pmcid:PMC3473649 fatcat:6bax3jittjek7k3nzfdi64la5a

Recent Advances in Cyclonucleosides: C-Cyclonucleosides and Spore Photoproducts in Damaged DNA

Yuichi Yoshimura, Hiroki Takahata
2012 Molecules  
Because they are structural analogs, cyclonucleosides and oligodeoxynucleotides containing them would be useful tools for investigating the biological functions and conformations of DNA, RNA as well as  ...  C-Cyclonucleosides bridged by a carbon chain between the base and sugar moieties are the most attractive from the synthetic points of view as well as for use as biological tools.  ...  Due to the structural bias existing in a molecule, cyclonucleosides and oligodeoxynucleotides containing them would be useful biological tools for investigating the functions and conformations of DNA,  ... 
doi:10.3390/molecules171011630 pmid:23023688 pmcid:PMC6268316 fatcat:lpy4smlzrnelxbsxxc3uarngdm

Chemical investigation of light induced DNA bipyrimidine damage and repair

Korbinian Heil, David Pearson, Thomas Carell
2011 Chemical Society Reviews  
Moreover, a brief summary on their usage in analysing repair and tolerance processes as well as their biological effects is provided.  ...  In order to be able to investigate how nature's repair and tolerance mechanisms protect the integrity of genetic information, oligonucleotides containing sequence and site-specific UV lesions are essential  ...  a oxetane such as azetidine. 35 Furthermore, a synthetic route to the phosphoramidite of this thio analogue is available. 36 Although the toolset for investigation of (6-4) and Dewar repair with synthesized  ... 
doi:10.1039/c000407n pmid:21076781 fatcat:cvxecnv53javfapocj5mh7kd5q

Pulse Frequency in Pulsed Brachytherapy Based on Tissue Repair Kinetics

P SMINIA, C SCHNEIDER, K KOEDOODER, G VANTIENHOVEN, L BLANK, D GONZALEZGONZALEZ
1998 International Journal of Radiation Oncology, Biology, Physics  
Purpose: Investigation of normal tissue sparing in pulsed brachytherapy (PB) relative to continuous low-dose rate irradiation (CLDR) by adjusting pulse frequency based on tissue repair characteristics.  ...  Hence, a therapeutic gain might be obtained when changing from CLDR to PB by adjusting the physical dose in such a way that the biological dose on the tumor is maintained.  ...  The great influence of tissue-repair kinetics on the biological effect in four different pulse schemes was also discussed in their paper.  ... 
doi:10.1016/s0360-3016(98)00023-6 pmid:9588929 fatcat:2yq6bz5iuvbkpeo4j5le6rb5vq

Epimeric 2-Deoxyribose Lesions: Products from the Improper Chemical Repair of 2-Deoxyribose Radicals

Nicholas J. Amato, Yinsheng Wang
2014 Chemical Research in Toxicology  
Here, we review one family of DNA lesions, the epimeric 2-deoxyribose lesions, which arise from the improper chemical repair of the 2-deoxyribose radicals.  ...  We placed our emphasis of discussion on the formation of these lesions, their impact on the structure and stability of duplex DNA, their biological consequences, their potential therapeutic relevance,  ...  Toxicol. 2014, 27, 470−479 3. 3 . 3 Biological Consequences. Investigations about the impact of the C3′-epimeric lesions on biological processes are limited.  ... 
doi:10.1021/tx400430g pmid:24517165 pmcid:PMC4002128 fatcat:dshjfmekove6hikqqwz7mefpqq

Poly(ADP-Ribose)—A Unique Natural Polymer Structural Features, Biological Role and Approaches to the Chemical Synthesis

Mikhail S. Drenichev, Sergey N. Mikhailov
2015 Nucleosides, Nucleotides & Nucleic Acids  
One of them, poly(ADP-ribose)polymerase-1 (PARP-1) is considered to be a perspective target for the design of new drugs, affecting PAR metabolism.  ...  Federation 2 Poly(ADP-ribose) (PAR) is a natural polymer, taking part in numerous important cellular processes. Several enzymes are involved in biosynthesis and degradation of PAR.  ...  SCHEME 2 2 Formation of repair complex on nicked DNA. SCHEME 4 4 Synthesis of protected 2 -O-α-D-ribofuranosyladenosine.  ... 
doi:10.1080/15257770.2014.984073 pmid:25774719 fatcat:cpeubpgnkjfbdobozeja6wyn5e

Hormetins as Novel Components of Cosmeceuticals and Aging Interventions

Suresh Rattan
2015 Cosmetics  
The basis of hormesis lies in the molecular pathways of stress response, which are essential for the survival of a biological system by activation of maintenance and repair mechanisms in response to stress  ...  Moderate physical exercise is the best example of a hormetin that brings about a wide range of health beneficial hormesis by first challenging the system.  ...  It is known that the survival of a biological system is a constant struggle between the occurrence of molecular damage and the mechanisms of maintenance and repair.  ... 
doi:10.3390/cosmetics2010011 fatcat:vg52fphkafabnojfj3tudycm7y

Monte Carlo study of a high resolution monolithic silicon diode array for MRI-linac applications

M. Gargett, B.M. Oborn, S. Alnaghy, M. Petasecca, A. Rosenfeld, P. Metcalfe
2016 Radiotherapy and Oncology  
The elongation of repair half-time (long) increased the NTCP twice or much higher in case of hypo-fraction scheme.  ...  By use of stochastic biological model applying for Gaussian distribution, the effects of the NTCP variation of repair parameters of the immune system as well as the intercellular uncertainty of normal  ... 
doi:10.1016/s0167-8140(16)30161-x fatcat:vplzojiwwra7xhs4rugwv4267y

Proteins are Not Recruited: A Plea for Better Diction

Elizabeth N Grotemeyer, Koan Briggs, Christopher J Fischer
2019 Emerging Trends in Kinetics and Thermodynamics  
Indeed, we should never say that proteins are recruited to binding partners or binding sites since this implies both a nonexistent level of communication within biological systems and a non-existent process  ...  Nearly all biological processes proceed or are controlled by protein-protein or protein-ligand binding reactions.  ...  repair enzymes to a site of DNA damage.  ... 
doi:10.36959/672/587 fatcat:vycsykfpdja5jjcvqfcaymfy6m

Biology Contributions Biological equivalence between LDR and PDR in cervical cancer: multifactor analysis usingthe linear-quadratic model

José Guilherme Couto, Rui Pirraco, Isabel Bravo
2011 Journal of Contemporary Brachytherapy  
The purpose of this work was the biological comparison between Low Dose Rate (LDR) and Pulsed Dose Rate (PDR) in cervical cancer regarding the discontinuation of the afterloading system used for the LDR  ...  In the analyses of the influence of PDR parameters in the biological equivalence between LDR and PDR treatments (Phase 1), it was calculated that if the pulse dose in PDR was kept equal to the LDR dose  ...  Lurdes Trigo, director of the Brachytherapy Service of the Oporto Oncology Institute, for the support given to this study. No funds were received for the execution of this work.  ... 
doi:10.5114/jcb.2011.24820 pmid:23346123 pmcid:PMC3551353 fatcat:3umo7m5mmnfvphmh7wrgurg6au

Abasic and Oxidized Abasic Site Reactivity in DNA: Enzyme Inhibition, Cross-Linking, and Nucleosome Catalyzed Reactions

Marc M. Greenberg
2013 Accounts of Chemical Research  
Chemically synthesized oligonucleotides containing abasic lesions provide substrates that have allowed researchers to discover a range of interesting chemical properties of potential biological importance  ...  In addition, bacterial repair enzymes can convert an interstrand crosslink derived from C4-AP into a double-strand break, the most deleterious form of DNA damage.  ...  In mammalian cells the primary repair pathway begins with 5'-incision of the AP lesion by apurinic endonuclease 1 (Ape1). 24 The remnants of the AP site (dRP, Scheme 6) are removed in a βelimination  ... 
doi:10.1021/ar400229d pmid:24369694 pmcid:PMC3944396 fatcat:swvt35wwxrhwhoog4t2y4fusqy

Single Molecule Localization Microscopy Analyses of DNA-Repair Foci and Clusters Detected Along Particle Damage Tracks

Michael Hausmann, Charlotte Neitzel, Elizaveta Bobkova, David Nagel, Andreas Hofmann, Tatyana Chramko, Elena Smirnova, Olga Kopečná, Eva Pagáčová, Alla Boreyko, Evgeny Krasavin, Iva Falkova (+5 others)
2020 Frontiers in Physics  
Nevertheless, there are a lot of open questions concerning the understanding of damaging mechanisms and repair processes within the light of radiosensitivity and thus, individualized medical applications  ...  The data reveal a cell type specific nano-architecture of DNA damage foci along particle tracks and their dynamic molecular re-arrangements during repair.  ...  Up to now research has delivered a huge amount of knowledge and findings of biological, epigenetic response to low-LET (Linear Energy Transfer) photon and high-LET particle irradiation; thereby a lot of  ... 
doi:10.3389/fphy.2020.578662 fatcat:vgfqykdpcff4dao2gjpsjpirma

Radiobiological investigations at tumor cell lines by exploiting chrono-biological aspects of chronological dose distributions [article]

W. Ulmer
2011 arXiv   pre-print
The goal of this study is to elaborate an optimal fractionation scheme with regard to the irradiation of tumors.  ...  The determination of the survival fractions provides an optimum exploitation of radiation damages, when the ATP-concentration assumes a maximum value.  ...  It appears that the delivery of high single doses in a therapy scheme makes only sense, if chrono-biological principles are accounted for.  ... 
arXiv:1111.6811v3 fatcat:s5jzzphhlvfshocsbfxqaablyu

Radical–radical reactions of superoxide: a potential route to toxicity

Christine C. Winterbourn, Anthony J. Kettle
2003 Biochemical and Biophysical Research Communications - BBRC  
These reactions are usually considered to be repair processes and have received little biological attention.  ...  The relative contributions of addition and repair vary depending on the properties of the phenol.  ...  Acknowledgment This work was supported by the Health Research Council of New Zealand.  ... 
doi:10.1016/s0006-291x(03)00810-6 pmid:12763053 fatcat:ewyvv2szcbglnk5uyte5jqlmay
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