Academic literature on the topic 'In vitro DNA Repair Mechanisms'
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Journal articles on the topic "In vitro DNA Repair Mechanisms"
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Dikomey, E. "Bestimmung der DNA-Schädigung in vitro." Nuklearmedizin 49, S 01 (2010): S64—S68. http://dx.doi.org/10.1055/s-0038-1626526.
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SummaryIonising irradiation acts primarily via induction of DNA damage, among which doublestrand breaks are the most important lesions. These lesions may lead to lethal chromosome aberrations, which are the main reason for cell inactivation. Double-strand breaks can be repaired by several different mechanisms. The regulation of these mechanisms appears be fairly different for normal and tumour cells. Among different cell lines capacity of doublestrand break repair varies by only few percents and is known to be determined mostly by genetic factors. Knowledge about doublestrand break repair mechanisms and their regulation is important for the optimal application of ionising irradiation in medicine.
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Guo, Hongrui, Huan Liu, Hongbin Wu, Hengmin Cui, Jing Fang, Zhicai Zuo, Junliang Deng, Yinglun Li, Xun Wang, and Ling Zhao. "Nickel Carcinogenesis Mechanism: DNA Damage." International Journal of Molecular Sciences 20, no. 19 (September 21, 2019): 4690. http://dx.doi.org/10.3390/ijms20194690.
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Nickel (Ni) is known to be a major carcinogenic heavy metal. Occupational and environmental exposure to Ni has been implicated in human lung and nasal cancers. Currently, the molecular mechanisms of Ni carcinogenicity remain unclear, but studies have shown that Ni-caused DNA damage is an important carcinogenic mechanism. Therefore, we conducted a literature search of DNA damage associated with Ni exposure and summarized known Ni-caused DNA damage effects. In vitro and vivo studies demonstrated that Ni can induce DNA damage through direct DNA binding and reactive oxygen species (ROS) stimulation. Ni can also repress the DNA damage repair systems, including direct reversal, nucleotide repair (NER), base excision repair (BER), mismatch repair (MMR), homologous-recombination repair (HR), and nonhomologous end-joining (NHEJ) repair pathways. The repression of DNA repair is through direct enzyme inhibition and the downregulation of DNA repair molecule expression. Up to now, the exact mechanisms of DNA damage caused by Ni and Ni compounds remain unclear. Revealing the mechanisms of DNA damage from Ni exposure may contribute to the development of preventive strategies in Ni carcinogenicity.
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Lai, Ying-Ta, and Warren Masker. "In Vitro Repair of Gaps in Bacteriophage T7 DNA." Journal of Bacteriology 180, no. 23 (December 1, 1998): 6193–202. http://dx.doi.org/10.1128/jb.180.23.6193-6202.1998.
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ABSTRACT An in vitro system based upon extracts of Escherichia coli infected with bacteriophage T7 was used to study the mechanism of double-strand break repair. Double-strand breaks were placed in T7 genomes by cutting with a restriction endonuclease which recognizes a unique site in the T7 genome. These molecules were allowed to repair under conditions where the double-strand break could be healed by (i) direct joining of the two partial genomes resulting from the break, (ii) annealing of complementary versions of 17-bp sequences repeated on either side of the break, or (iii) recombination with intact T7 DNA molecules. The data show that while direct joining and single-strand annealing contributed to repair of double-strand breaks, these mechanisms made only minor contributions. The efficiency of repair was greatly enhanced when DNA molecules that bridge the region of the double-strand break (referred to as donor DNA) were provided in the reaction mixtures. Moreover, in the presence of the donor DNA most of the repaired molecules acquired genetic markers from the donor DNA, implying that recombination between the DNA molecules was instrumental in repairing the break. Double-strand break repair in this system is highly efficient, with more than 50% of the broken molecules being repaired within 30 min under some experimental conditions. Gaps of 1,600 nucleotides were repaired nearly as well as simple double-strand breaks. Perfect homology between the DNA sequence near the break site and the donor DNA resulted in minor (twofold) improvement in the efficiency of repair. However, double-strand break repair was still highly efficient when there were inhomogeneities between the ends created by the double-strand break and the T7 genome or between the ends of the donor DNA molecules and the genome. The distance between the double-strand break and the ends of the donor DNA molecule was critical to the repair efficiency. The data argue that ends of DNA molecules formed by double-strand breaks are typically digested by between 150 and 500 nucleotides to form a gap that is subsequently repaired by recombination with other DNA molecules present in the same reaction mixture or infected cell.
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Freyer, G. A., S. Davey, J. V. Ferrer, A. M. Martin, D. Beach, and P. W. Doetsch. "An alternative eukaryotic DNA excision repair pathway." Molecular and Cellular Biology 15, no. 8 (August 1995): 4572–77. http://dx.doi.org/10.1128/mcb.15.8.4572.
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DNA lesions induced by UV light, cyclobutane pyrimidine dimers, and (6-4)pyrimidine pyrimidones are known to be repaired by the process of nucleotide excision repair (NER). However, in the fission yeast Schizosaccharomyces pombe, studies have demonstrated that at least two mechanisms for excising UV photo-products exist; NER and a second, previously unidentified process. Recently we reported that S. pombe contains a DNA endonuclease, SPDE, which recognizes and cleaves at a position immediately adjacent to cyclobutane pyrimidine dimers and (6-4)pyrimidine pyrimidones. Here we report that the UV-sensitive S. pombe rad12-502 mutant lacks SPDE activity. In addition, extracts prepared from the rad12-502 mutant are deficient in DNA excision repair, as demonstrated in an in vitro excision repair assay. DNA repair activity was restored to wild-type levels in extracts prepared from rad12-502 cells by the addition of partially purified SPDE to in vitro repair reaction mixtures. When the rad12-502 mutant was crossed with the NER rad13-A mutant, the resulting double mutant was much more sensitive to UV radiation than either single mutant, demonstrating that the rad12 gene product functions in a DNA repair pathway distinct from NER. These data directly link SPDE to this alternative excision repair process. We propose that the SPDE-dependent DNA repair pathway is the second DNA excision repair process present in S. pombe.
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Kunkel, Thomas A., Katarzyna Bebenek, John D. Roberts, Mary P. Fitzgerald, and David C. Thomas. "Analysis of fidelity mechanisms with eukaryotic DNA replication and repair proteins." Genome 31, no. 1 (January 1, 1989): 100–103. http://dx.doi.org/10.1139/g89-019.
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We are investigating the mechanisms for producing or avoiding errors during DNA synthesis catalyzed by DNA replication and repair proteins purified from eukaryotic sources. Using assays that monitor the fidelity of a single round of DNA synthesis in vitro, we have defined the error frequency and mutational specificity of the four classes of animal cell DNA polymerases (α, β, δ, γ), and the fidelity of an SV40 origin-dependent DNA replication complex in extracts of HeLa cells.Key words: error frequency, repair proteins, polymerases, mutational specificity, fidelity mechanisms.
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George, Vazhappilly Cijo, and H. P. Vasantha Rupasinghe. "Apple Flavonoids Suppress Carcinogen-Induced DNA Damage in Normal Human Bronchial Epithelial Cells." Oxidative Medicine and Cellular Longevity 2017 (2017): 1–12. http://dx.doi.org/10.1155/2017/1767198.
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Scope. Human neoplastic transformation due to DNA damage poses an increasing global healthcare concern. Maintaining genomic integrity is crucial for avoiding tumor initiation and progression. The present study aimed to investigate the efficacy of an apple flavonoid fraction (AF4) against various carcinogen-induced toxicity in normal human bronchial epithelial cells and its mechanism of DNA damage response and repair processes. Methods and Results. AF4-pretreated cells were exposed to nicotine-derived nitrosamine ketones (NNK), NNK acetate (NNK-Ae), methotrexate (MTX), and cisplatin to validate cytotoxicity, total reactive oxygen species, intracellular antioxidants, DNA fragmentation, and DNA tail damage. Furthermore, phosphorylated histone (γ-H2AX) and proteins involved in DNA damage (ATM/ATR, Chk1, Chk2, and p53) and repair (DNA-PKcs and Ku80) mechanisms were evaluated by immunofluorescence and western blotting, respectively. The results revealed that AF4-pretreated cells showed lower cytotoxicity, total ROS generation, and DNA fragmentation along with consequent inhibition of DNA tail moment. An increased level of γ-H2AX and DNA damage proteins was observed in carcinogen-treated cells and that was significantly (p≤0.05) inhibited in AF4-pretreated cells, in an ATR-dependent manner. AF4 pretreatment also facilitated the phosphorylation of DNA-PKcs and thus initiation of repair mechanisms. Conclusion. Apple flavonoids can protect in vitro oxidative DNA damage and facilitate repair mechanisms.
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Tadi, Satish Kumar, Robin Sebastian, Sumedha Dahal, Ravi K. Babu, Bibha Choudhary, and Sathees C. Raghavan. "Microhomology-mediated end joining is the principal mediator of double-strand break repair during mitochondrial DNA lesions." Molecular Biology of the Cell 27, no. 2 (January 15, 2016): 223–35. http://dx.doi.org/10.1091/mbc.e15-05-0260.
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Mitochondrial DNA (mtDNA) deletions are associated with various mitochondrial disorders. The deletions identified in humans are flanked by short, directly repeated mitochondrial DNA sequences; however, the mechanism of such DNA rearrangements has yet to be elucidated. In contrast to nuclear DNA (nDNA), mtDNA is more exposed to oxidative damage, which may result in double-strand breaks (DSBs). Although DSB repair in nDNA is well studied, repair mechanisms in mitochondria are not characterized. In the present study, we investigate the mechanisms of DSB repair in mitochondria using in vitro and ex vivo assays. Whereas classical NHEJ (C-NHEJ) is undetectable, microhomology-mediated alternative NHEJ efficiently repairs DSBs in mitochondria. Of interest, robust microhomology-mediated end joining (MMEJ) was observed with DNA substrates bearing 5-, 8-, 10-, 13-, 16-, 19-, and 22-nt microhomology. Furthermore, MMEJ efficiency was enhanced with an increase in the length of homology. Western blotting, immunoprecipitation, and protein inhibition assays suggest the involvement of CtIP, FEN1, MRE11, and PARP1 in mitochondrial MMEJ. Knockdown studies, in conjunction with other experiments, demonstrated that DNA ligase III, but not ligase IV or ligase I, is primarily responsible for the final sealing of DSBs during mitochondrial MMEJ. These observations highlight the central role of MMEJ in maintenance of mammalian mitochondrial genome integrity and is likely relevant for deletions observed in many human mitochondrial disorders.
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Kuzminov, Andrei. "Recombinational Repair of DNA Damage inEscherichia coli and Bacteriophage λ." Microbiology and Molecular Biology Reviews 63, no. 4 (December 1, 1999): 751–813. http://dx.doi.org/10.1128/mmbr.63.4.751-813.1999.
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SUMMARY Although homologous recombination and DNA repair phenomena in bacteria were initially extensively studied without regard to any relationship between the two, it is now appreciated that DNA repair and homologous recombination are related through DNA replication. In Escherichia coli, two-strand DNA damage, generated mostly during replication on a template DNA containing one-strand damage, is repaired by recombination with a homologous intact duplex, usually the sister chromosome. The two major types of two-strand DNA lesions are channeled into two distinct pathways of recombinational repair: daughter-strand gaps are closed by the RecF pathway, while disintegrated replication forks are reestablished by the RecBCD pathway. The phage λ recombination system is simpler in that its major reaction is to link two double-stranded DNA ends by using overlapping homologous sequences. The remarkable progress in understanding the mechanisms of recombinational repair in E. coli over the last decade is due to the in vitro characterization of the activities of individual recombination proteins. Putting our knowledge about recombinational repair in the broader context of DNA replication will guide future experimentation.
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Kozhina, R. A., V. N. Chausov, E. A. Kuzmina, and A. V. Boreyko. "Induction and repair of DNA double-strand breaks in hippocampal neurons of miсe of different age after exposure to 60Со γ-rays in vivo and in vitro." EPJ Web of Conferences 177 (2018): 06001. http://dx.doi.org/10.1051/epjconf/201817706001.
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One of the central problems of modern radiobiology is the study of DNA damage induction and repair mechanisms in central nervous system cells, in particular, in hippocampal cells. The study of the regularities of molecular damage formation and repair in the hippocampus cells is of special interest, because these cells, unlike most cells of the central nervous system (CNS), keep proliferative activity, i.e. ability to neurogenesis. Age-related changes in hippocampus play an important role, which could lead to radiosensitivity changes in neurons to the ionizing radiation exposure. Regularities in DNA double-strand breaks (DSB) induction and repair in different aged mice hippocampal cells in vivo and in vitro under the action of γ-rays 60Со were studied with DNA comet-assay. The obtained dose dependences of DNA DSB induction are linear both in vivo and in vitro. It is established that in young animals' cells, the degree of DNA damage is higher than in older animals. It is shown that repair kinetics is basically different for exposure in vivo and in vitro.
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Lans, Hannes, and Wim Vermeulen. "Nucleotide Excision Repair in Caenorhabditis elegans." Molecular Biology International 2011 (August 17, 2011): 1–12. http://dx.doi.org/10.4061/2011/542795.
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Nucleotide excision repair (NER) plays an essential role in many organisms across life domains to preserve and faithfully transmit DNA to the next generation. In humans, NER is essential to prevent DNA damage-induced mutation accumulation and cell death leading to cancer and aging. NER is a versatile DNA repair pathway that repairs many types of DNA damage which distort the DNA helix, such as those induced by solar UV light. A detailed molecular model of the NER pathway has emerged from in vitro and live cell experiments, particularly using model systems such as bacteria, yeast, and mammalian cell cultures. In recent years, the versatility of the nematode C. elegans to study DNA damage response (DDR) mechanisms including NER has become increasingly clear. In particular, C. elegans seems to be a convenient tool to study NER during the UV response in vivo, to analyze this process in the context of a developing and multicellular organism, and to perform genetic screening. Here, we will discuss current knowledge gained from the use of C. elegans to study NER and the response to UV-induced DNA damage.
Dissertations / Theses on the topic "In vitro DNA Repair Mechanisms"
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GUARDAMAGNA, ISABELLA. "A new functional in vitro cell-free assay to evaluate DNA repair mechanisms." Doctoral thesis, Università degli studi di Pavia, 2020. http://hdl.handle.net/11571/1301947.
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DNA is exposed to endogenous and exogenous agents that are
potential causes of several pathological processes; for this reason,
eukaryotic cells developed many mechanisms able to control and repair
lesions. One of them, Nucleotide Excision Repair (NER) is a highly versatile
and complex system by which UV-photolesions, such as cyclobutane
pyrimidine dimers (CPDs) or pyrimidine (6-4) pyrimidone photoproducts (6-
4PPs), are recognized and removed.
A key factor, involved in the recognition of chromatin photolesions, is
DDB2 (DNA Damaged binding protein 2) thanks to its ability of creating a
complex together with DDB1 (UV-DDB complex). Recently, it was
demonstrated that DDB2 binds directly PCNA (Proliferating Cell Nuclear
Antigen) through a conserved sequence called PIP-box; the disruption of
this binding in the mutated form (DDB2PCNA-) induces a delayed DNA
damage recognition but also an inefficient DNA repair activation.
To better clarify this delay, it was developed a new functional in vitro
cell-free system in which repair activity, in isolated nuclei, was evaluated.
Its responsiveness was also evaluated with different type of DNA lesions,
activating different DNA repair processes, increasing further its
applicability.
Moreover, the involvement of DDB1 was studied as possible actor
when DDB2 loses its function. In the presence of DDB2PCNA- protein, the
DNA repair process is inefficient, nevertheless, not completely blocked. For
this reason, it was hypothesized a possible ability of DDB1 to bind directly
PCNA, when DDB2 is altered or ineffective.
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Liton, Kumar Saha. "Differential Micronucleus Frequency in Isogenic Human Cells Deficient in DNA Repair Pathways Is a Valuable Indicator for Evaluating Genotoxic Agents and Their Genotoxic Mechanisms." Kyoto University, 2019. http://hdl.handle.net/2433/242428.
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付記する学位プログラム名: 充実した健康長寿社会を築く総合医療開発リーダー育成プログラムKyoto University (京都大学)
0048
新制・課程博士
博士(医科学)
甲第21696号
医科博第100号
新制||医科||7(附属図書館)
京都大学大学院医学研究科医科学専攻
(主査)教授 齊藤 博英, 教授 清水 章, 教授 Shohab YOUSSEFIAN
学位規則第4条第1項該当
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Ruiz, Alarcón Rafael. "Targeting DNA repair mechanisms in aggresive neuroblastoma." Thesis, Högskolan i Skövde, Institutionen för hälsovetenskaper, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-19821.
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Neuroblastoma is a tumour derived from cells of the nervous system and is the most common solid tumour in childhood. MYCN amplified and 11q-deleted neuroblastoma, two high-risk neuroblastoma were investigated in this study. RAD51 gene family includes six central genes for the dsDNA breaks repair by homologous recombination, which has been reported as important in varying types of cancer. The study aims to investigate if the dysregulation of this gene family could be involved in the unstable genome of 11q-deleted neuroblastoma, and to better understand the link between both high-risk tumours. The RAD51 family genes’ expression level was measured by RT-qPCR in samples of 11q-deleted and MYCN-amplified neuroblastoma that were treated with a UVC treatment and were recovered during varying hours. R2 database and DAVID were used to study the RAD51 family’s expression levels, associated event-free survivability, and altered pathways. RAD51 family is highly dysregulated in these tumours, four genes of six were found to be altered in high-risk neuroblastoma. Four of six genes presented altered expression levels in 11q-loss, and three of six in the MYCN-amplified case after the UVC treatment. The event-free survival probability analysis shown that the levels of expressions associated with high-risk neuroblastoma coincide with those that represent a poor life expectancy. Altered pathways were different in each type of tumour. 11q-deletion neuroblastoma’s pathways were associated with the nervous system development, and MYCN-amplified was related to the immune system. This study suggests that 11q-loss neuroblastoma presents a greater RAD51 family dysregulation compared with MYCN-amplified one, which could explain why its genome is unstable.
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Gessner, Sophia Johanna. "Molecular mechanisms of DNA repair in Mycobacterium tuberculosis." Doctoral thesis, University of Cape Town, 2017. http://hdl.handle.net/11427/26861.
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The mycobacterial DNA damage and repair pathways involved in the emergence of drug-resistance during host infection remain poorly understood, yet are critical to any efforts to develop novel "anti-evolution" drugs aimed at reducing the capacity of Mycobacterium tuberculosis to adapt genetically during tuberculosis (TB) treatment. The thesis presented here aimed to investigate the contribution of the DNA damage (SOS) response in adaptive mutagenesis, and focused on two specific components: the role of the specialist translesion synthesis DNA polymerase, DnaE2, in mutagenesis under stress and, secondly, the function of the mycobacterial homologue of a putative SOS response associated peptidase (SRAP) protein which has been identified in comparative genomics analyses of organisms possessing a DnaE2-type C family DNA polymerase. This work focused on the putative SRAP protein which was predicted to form part of the mycobacterial DNA damage response as a functional switch by binding DNA in an autoproteolytic dependent manner. To this end, SRAP deletion mutants were generated for both M. smegmatis (MSMEG_1891) and M. tuberculosis (Rv3226c). Despite the fact that SRAP was upregulated in both M. smegmatis and M. tuberculosis following genotoxic stress, no DNA damage phenotype was detected in any SRAP deletion mutant using a variety of DNA damaging agents. In parallel, an eGFP-tagged M. smegmatis SRAP allele was constructed to enable visualisation of SRAP upregulation and sub-cellular recruitment using fluorescent microscopy; however no eGFP expression could be visualised after MMC treatment. It was not clear whether this was due to faulty eGFP expression in the fusion protein, or to low-level induction of SRAP. In a biochemical approach to elucidate SRAP function, soluble M. smegmatis SRAP protein was expressed and purified using a N-terminal hexa-histidine tag. No proteolytic activity was detected in gelatine or casein zymography, perhaps indicating that SRAP has a very specific substrate. Moreover, while it was predicted that autocatalytic cleavage of the C-terminus was required for activation of SRAP, no such cleavage was detected using hexa-histidine tag staining, possibly pointing to a set of very specific conditions for activation. In combination, therefore, neither microbiological nor biochemical assays could elucidate a definitive role for SRAP in the mycobacterial DNA damage response. DnaE2 has been directly implicated in induced mutagenesis to rifampicin (Rif) resistance in Mycobacterium tuberculosis following exposure of bacilli to genotoxic stress. In previous work in our group, a vitamin B₁₂-sensitive ΔmetH strain was found to form "B₁₂-resistant" suppressor mutants at a frequency higher than could be explained by spontaneous mutagenesis alone. The first part of this thesis investigated the potential role of DnaE2 in the high-frequency emergence of B₁₂-resistance by mutating DnaE2 in the ΔmetH background. Whereas elimination of polymerase function in a DnaE2ᴬᴵᴬ mutant abrogated DNA damage-induced mutagenesis to Rif resistance, no change in B₁₂ sensitivity was detected in a ΔmetH dnaE2ᴬᴵᴬ double mutant. PCR sequencing of spontaneous B₁₂-resistant mutants revealed mutations in genes previously associated with the suppressor phenotype; moreover, there was no apparent difference in the nature of mutations observed in both parental and dnaE2ᴬᴵᴬ mutant strains. Instead, these results suggest that an alternative mechanism must exist to enable adaptive mutagenesis in methionine-starved mycobacteria.
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Malik, Shivani. "REGULATORY MECHANISMS OF TRANSCRIPTION AND ASSOCIATED DNA REPAIR." OpenSIUC, 2012. https://opensiuc.lib.siu.edu/dissertations/626.
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Transcription is a crucial regulatory step in gene regulation modulated by several proteins. Any misregulation during transcription can lead to many diseases including cancer, neurodegenerative disorders and aging making it imperative to have a detailed mechanistic view of the process. Over the recent years, 26S proteasome has been implicated in transcriptional regulation through its proteolytic and non-proteolytic activities. While, the proteolytic role of proteasome in transcription has been extensively studied, its non-proteolytic function is poorly understood. Thus, one of my thesis aims had been to analyze the non-proteolytic role of proteasome in transcription. My results have revealed the non-proteolytic role of 26S proteasome in establishing a specific protein interaction network at the promoter for stimulated transcriptional initiation in vivo . In addition to its roles in transcription, 26S proteasome also plays an important role in the degradation of RNA polymerase II stalled at DNA lesion facilitating the rapid repair of transcriptionally active genes through a process of transcription coupled repair (TCR). My studies have addressed the key question of the fate of RNA polymerase II stalled at a lesion. My findings show that RNA polymerase II interacts with an elongation and TCR-specific factor, Rad26p. Upon encountering a lesion, RNA polymerase II stalls and unloads Rad26p on the site of DNA damage. Subsequently, the elongating RNA polymerase II is disassembled through the degradation of its largest subunit, Rpb1p. Further; our studies have also uncovered a novel role of Rad26p in chromatin disassembly, which facilitates transcriptional elongation and hence TCR. This work provides valuable insights into interplay of chromatin structure, transcriptional elongation and TCR. Finally, extending the regulatory knowledge of sense transcriptional initiation to antisense, my work has revealed the extensive participation of GTFs in the process. Collectively, results of above studies provide a comprehensive view of transcription and associated process of active genome repair.
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Shell, Scarlet Sara. "Mechanisms of initiation of DNA mismatch repair in Saccharomyces cerevisiae." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2008. http://wwwlib.umi.com/cr/ucsd/fullcit?p3307558.
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Thesis (Ph. D.)--University of California, San Diego, 2008.Title from first page of PDF file (viewed July 23, 2008). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references.
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De, Silva Inusha Udanie. "Mechanisms of repair of DNA damage produced by antitumour drugs." Thesis, University College London (University of London), 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.404490.
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Cannan, Wendy J. "Mechanisms and Dynamics of Oxidative DNA Damage Repair in Nucleosomes." ScholarWorks @ UVM, 2016. http://scholarworks.uvm.edu/graddis/628.
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DNA provides the blueprint for cell function and growth, as well as ensuring continuity from one cell generation to the next. In order to compact, protect, and regulate this vital information, DNA is packaged by histone proteins into nucleosomes, which are the fundamental subunits of chromatin. Reactive oxygen species, generated by both endogenous and exogenous agents, can react with DNA, altering base chemistry and generating DNA strand breaks. Left unrepaired, these oxidation products can result in mutations and/or cell death. The Base Excision Repair (BER) pathway exists to deal with damaged bases and single-stranded DNA breaks. However, the packaging of DNA into chromatin provides roadblocks to repair. Damaged DNA bases may be buried within nucleosomes, where they are inaccessible to repair enzymes and other DNA binding proteins. Previous in vitro studies by our lab have demonstrated that BER enzymes can function within this challenging environment, albeit in a reduced capacity.
Exposure to ionizing radiation often results in multiple, clustered oxidative lesions. Near-simultaneous BER of two lesions located on opposing strands within a single helical turn of DNA of one another creates multiple DNA single-strand break intermediates. This, in turn, may create a potentially lethal double-strand break (DSB) that can no longer be repaired by BER. To determine if chromatin offers protection from this phenomenon, we incubated DNA glycosylases with nucleosomes containing clustered damages in an attempt to generate DSBs. We discovered that nucleosomes offer substantial protection from inadvertent DSB formation. Steric hindrance by the histone core in the nucleosome was a major factor in restricting DSB formation. As well, lesions positioned very close to one another were refractory to processing, with one lesion blocking or disrupting access to the second site. The nucleosome itself appears to remain intact during DSB formation, and in some cases, no DNA is released from the histones. Taken together, these results suggest that in vivo, DSBs generated by BER occur primarily in regions of the genome associated with elevated rates of nucleosome turnover or remodeling, and in the short linker DNA segments that lie between adjacent nucleosomes.
DNA ligase IIIα (LigIIIα) catalyzes the final step in BER. In order to facilitate repair, DNA ligase must completely encircle the DNA helix. Thus, DNA ligase must at least transiently disrupt histone-DNA contacts. To determine how LigIIIα functions in nucleosomes, given this restraint, we incubated the enzyme with nick-containing nucleosomes. We found that a nick located further within the nucleosome was ligated at a lower rate than one located closer to the edge. This indicated that LigIIIα must wait for DNA to spontaneously, transiently unwrap from the histone octamer to expose the nick for recognition. Remarkably, the disruption that must occur for ligation is both limited and transient: the nucleosome remains resistant to enzymatic digest before and during ligation, and reforms completely once LigIIIα dissociates.
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Shivji, Mahmud K. K. "Nucleotide excision repair of DNA : dissection and reconstitution in vitro." Thesis, Open University, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.309860.
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Shen, Ying. "Studies on the mechanisms of RNA-driven DNA repair and modification." Diss., Georgia Institute of Technology, 2011. http://hdl.handle.net/1853/45969.
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Our previous studies have demonstrated that RNA can serve as a template for double-strand break (DSB) repair in the yeast Saccharomyces cerevisiae using synthetic RNA-containing oligonucleotides (oligos). Following this initial work, we show that the RNA tract of RNA-containing oligos can be copied into DNA to transfer a genetic change at the chromosomal level also in the bacterium Escherichia coli and in human cells. Exploiting the use of oligos containing ribonucleoside monophosphates (rNMPs), we developed a molecular approach to generate RNA/DNA hybrids of chosen sequence and structure at the chromosomal level in both yeast and E. coli cells. Such technique allows us to study how rNMPs present in the DNA genome of cells are tolerated by cells, what factors recognize and target rNMPs in DNA and to what extent the embedded rNMPs may alter genome integrity. Here we proved that mispaired rNMPs embedded into genomic DNA, if not removed, serve as templates for DNA synthesis during chromosomal replication and produce a genetic change. We discovered that mispaired rNMPs that are embedded in genomic DNA are not only targeted by ribonucleases H (RNases H) but also by the mismatch repair (MMR) system both in yeast and in E. coli. Our data reveal novel substrates for the MMR system, and also uncover an unpredicted competition between RNase H and MMR for the RNA/DNA mispairs.
Books on the topic "In vitro DNA Repair Mechanisms"
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Thomas, Allison E. DNA repair: Damage, repair mechanisms, and aging. Hauppauge, N.Y: Nova Science Publisher's, 2010.
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Simic, Michael G., Lawrence Grossman, Arthur C. Upton, and David S. Bergtold, eds. Mechanisms of DNA Damage and Repair. Boston, MA: Springer US, 1986. http://dx.doi.org/10.1007/978-1-4615-9462-8.
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H, Vos Jean-Michel, ed. DNA repair mechanisms: Impact on human diseases and cancer. New York: Springer-Verlag, 1995.
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G, Simic Michael, Grossman Lawrence 1924-, Upton Arthur C. 1923-, and United States. National Bureau of Standards., eds. Mechanisms of DNA damage and repair: Implications for carcinogenesis and risk assessment. New York: Plenum Press, 1986.
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Lambert, Muriel W., and Jacques Laval, eds. DNA Repair Mechanisms and Their Biological Implications in Mammalian Cells. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4684-1327-4.
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NATO Advanced Research Workshop on DNA Repair Mechanisms and Their Biological Implications in Mammalian Cells (1988 Fontevrault-l'Abbaye, France). DNA repair mechanisms and their biological implications in mammalian cells. New York: Plenum Press, 1989.
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I, Ahmad Shamim, and Hanaoka Fumio 1946-, eds. Molecular mechanisms of xeroderma pigmentosum. New York, N.Y: Springer Science+Business Media, 2008.
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Naegeli, Hanspeter. Mechanisms of DNA damage recognition in mammalian cells. Heidelberg: Springer-Verlag, 1997.
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Mechanisms of DNA damage recognition in mammalian cells. New York: Chapman & Hall, 1997.
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Correcting the blueprint of life: An historical account of the discovery of DNA repair mechanisms. Plainview, N.Y: Cold Spring Harbor Laboratory Press, 1997.
Find full textBook chapters on the topic "In vitro DNA Repair Mechanisms"
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Meyn, Raymond E., W. Timothy Jenkins, and David Murray. "Radiation Damage to DNA in Various Animal Tissues: A Comparison of Yields and Repair In Vivo and In Vitro." In Mechanisms of DNA Damage and Repair, 151–58. Boston, MA: Springer US, 1986. http://dx.doi.org/10.1007/978-1-4615-9462-8_16.
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Summers, William C., and Peter M. Glazer. "Mismatch Repair in Mammalian Cells: Approaches to the in Vitro Study of DNA Mismatch Correction Reactions." In DNA Repair Mechanisms and Their Biological Implications in Mammalian Cells, 255–61. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4684-1327-4_24.
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Lindahl, Tomas. "DNA Glycosylases in DNA Repair." In Mechanisms of DNA Damage and Repair, 335–40. Boston, MA: Springer US, 1986. http://dx.doi.org/10.1007/978-1-4615-9462-8_36.
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Hirsch-Kauffmann, M., H. Schwaiger, B. Auer, R. Schneider, H. Herzog, H. Klocker, and Manfred Schweiger. "Aging and DNA Repair." In Molecular Mechanisms of Aging, 51–59. Berlin, Heidelberg: Springer Berlin Heidelberg, 1990. http://dx.doi.org/10.1007/978-3-642-84224-5_4.
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Curigliano, Giuseppe. "Targeting DNA Repair." In Mechanisms of Drug Resistance in Cancer Therapy, 161–80. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/164_2017_31.
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Salles, Bernard, and Patrick Calsou. "In Vitro Excision Repair Assay in Schizosaccharomyces pombe." In DNA Repair Protocols, 327–35. Totowa, NJ: Humana Press, 1999. http://dx.doi.org/10.1007/978-1-4612-1608-7_26.
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Frosina, Guido, Enrico Cappelli, Paola Fortini, and Eugenia Dogliotti. "In Vitro Base Excision Repair Assay Using Mammalian Cell Extracts." In DNA Repair Protocols, 301–15. Totowa, NJ: Humana Press, 1999. http://dx.doi.org/10.1007/978-1-4612-1608-7_24.
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IIiakis, George, and Nge Cheong. "In Vitro Rejoining of Double-Strand Breaks in Genomic DNA." In DNA Repair Protocols, 473–85. Totowa, NJ: Humana Press, 1999. http://dx.doi.org/10.1007/978-1-4612-1608-7_39.
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Salles, Bernard, and Christian Provot. "In Vitro Chemiluminescence Assay to Measure Excision Repair in Cell Extracts." In DNA Repair Protocols, 393–401. Totowa, NJ: Humana Press, 1999. http://dx.doi.org/10.1007/978-1-4612-1608-7_31.
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Dresler, Steven L. "DNA Repair Mechanisms and Carcinogenesis." In The Pathobiology of Neoplasia, 173–97. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4684-5523-6_9.
Full textConference papers on the topic "In vitro DNA Repair Mechanisms"
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Ma, Yan, Bin Chen, Scott J. Weir, Atul Butte, and Andrew K. Godwin. "Abstract B20: In silico and in vitro drug screening identifies new therapeutic approaches targeting DNA double-strand breaks repair in Ewing sarcoma." In Abstracts: AACR Special Conference: Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; November 9-12, 2015; Fort Lauderdale, Florida. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.pedca15-b20.
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Bartz, Raquel, Ping Fu, Hagir Suliman, Karen Welty-Wolf, and Claude Piantadosi. "Staph Aureus Sepsis Induces Lung And Renal Mitochondrial DNA Repair Mechanisms." In American Thoracic Society 2011 International Conference, May 13-18, 2011 • Denver Colorado. American Thoracic Society, 2011. http://dx.doi.org/10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a3865.
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Tutt, Andrew. "Abstract PL04-02: Synthetic lethality: Targeting DNA repair mechanisms in clinical trials." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-pl04-02.
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Do Eun Kim, Eun Jung Lee, Timothy P. Martens, Rina Kara, Hina W. Chaudhry, Silviu Itescu, and Kevin D. Costa. "Engineered Cardiac Tissues for in vitro Assessment of Contractile Function and Repair Mechanisms." In Conference Proceedings. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2006. http://dx.doi.org/10.1109/iembs.2006.259753.
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Do Eun Kim, Eun Jung Lee, Timothy P. Martens, Rina Kara, Hina W. Chaudhry, Silviu Itescu, and Kevin D. Costa. "Engineered Cardiac Tissues for in vitro Assessment of Contractile Function and Repair Mechanisms." In Conference Proceedings. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2006. http://dx.doi.org/10.1109/iembs.2006.4397534.
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Sharma, Vivek, Simran Khurana, Nard Kubben, Kotb Abdelmohsen, Philipp Oberdoerffer, Myriam Gorospe, and Tom Misteli. "Abstract PR03: A lncRNA regulates DNA repair by homologous recombination." In Abstracts: AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines; December 4-7, 2015; Boston, MA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.nonrna15-pr03.
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Altenberg, B., and K. O. Greulich. "Laser microbeam - kinetic studies combined with molecule - structures reveal mechanisms of DNA repair." In SPIE NanoScience + Engineering. SPIE, 2011. http://dx.doi.org/10.1117/12.893652.
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Qi, Jinpeng, Wu Yizhi, and Ding Yongsheng. "Kinetic theory approach to modeling of DNA damage repair mechanisms under external perturbations." In 8th International Vacuum Electron Sources Conference and Nanocarbon (2010 IVESC). IEEE, 2010. http://dx.doi.org/10.1109/ivesc.2010.5644249.
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Carpenter, Brittany L., and Kathleen L. O'Connor. "Abstract 2204: Integrin α6β4 regulates expression of Areg and Ereg through DNA repair-dependent mechanisms." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-2204.
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Cuella-Martin, Raquel, Catarina Oliveira, Helen E. Lockstone, Suzanne Snellenberg, Natalia Grolmusova, and J. Ross Chapman. "Abstract PR20: A 53BP1 integrates DNA repair and p53-dependent cell fate decisions via distinct mechanisms." In Abstracts: AACR Special Conference on DNA Repair: Tumor Development and Therapeutic Response; November 2-5, 2016; Montreal, QC, Canada. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1557-3125.dnarepair16-pr20.
Full textReports on the topic "In vitro DNA Repair Mechanisms"
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Wilson, Thomas E., Avraham A. Levy, and Tzvi Tzfira. Controlling Early Stages of DNA Repair for Gene-targeting Enhancement in Plants. United States Department of Agriculture, March 2012. http://dx.doi.org/10.32747/2012.7697124.bard.
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Gene targeting (GT) is a much needed technology as a tool for plant research and for the precise engineering of crop species. Recent advances in this field have shown that the presence of a DNA double-strand break (DSB) in a genomic locus is critical for the integration of an exogenous DNA molecule introduced into this locus. This integration can occur via either non-homologous end joining (NHEJ) into the break or homologous recombination (HR) between the broken genomic DNA and the introduced vector. A bottleneck for DNA integration via HR is the machinery responsible for homology search and strand invasion. Important proteins in this pathway are Rad51, Rad52 and Rad54. We proposed to combine our respective expertise: on the US side, in the design of zincfinger nucleases (ZFNs) for the induction of DNA DSBs at any desired genomic locus and in the integration of DNA molecules via NHEJ; and on the Israeli side in the HR events, downstream of the DSB, that lead to homology search and strand invasion. We sought to test three major pathways of targeted DNA integration: (i) integration by NHEJ into DSBs induced at desired sites by specially designed ZFNs; (ii) integration into DSBs induced at desired sites combined with the use of Rad51, Rad52 and Rad54 proteins to maximize the chances for efficient and precise HR-mediated vector insertion; (iii) stimulation of HR by Rad51, Rad52 and Rad54 in the absence of DSB induction. We also proposed to study the formation of dsT-DNA molecules during the transformation of plant cells. dsT-DNA molecules are an important substrate for HR and NHEJ-mediatedGT, yet the mode of their formation from single stranded T-DNA molecules is still obscure. In addition we sought to develop a system for assembly of multi-transgene binary vectors by using ZFNs. The latter may facilitate the production of binary vectors that may be ready for genome editing in transgenic plants. ZFNs were proposed for the induction of DSBs in genomic targets, namely, the FtsH2 gene whose loss of function can easily be identified in somatic tissues as white sectors, and the Cruciferin locus whose targeting by a GFP or RFP reporter vectors can give rise to fluorescent seeds. ZFNs were also proposed for the induction of DSBs in artificial targets and for assembly of multi-gene vectors. We finally sought to address two important cell types in terms of relevance to plant transformation, namely GT of germinal (egg) cells by floral dipping, and GT in somatic cells by root and leave transformation. To be successful, we made use of novel optimized expression cassettes that enable coexpression of all of the genes of interest (ZFNs and Rad genes) in the right tissues (egg or root cells) at the right time, namely when the GT vector is delivered into the cells. Methods were proposed for investigating the complementation of T-strands to dsDNA molecules in living plant cells. During the course of this research, we (i) designed, assembled and tested, in vitro, a pair of new ZFNs capable of targeting the Cruciferin gene, (ii) produced transgenic plants which expresses for ZFN monomers for targeting of the FtsH2 gene. Expression of these enzymes is controlled by constitutive or heat shock induced promoters, (iii) produced a large population of transgenic Arabidopsis lines in which mutated mGUS gene was incorporated into different genomic locations, (iv) designed a system for egg-cell-specific expression of ZFNs and RAD genes and initiate GT experiments, (v) demonstrated that we can achieve NHEJ-mediated gene replacement in plant cells (vi) developed a system for ZFN and homing endonuclease-mediated assembly of multigene plant transformation vectors and (vii) explored the mechanism of dsTDNA formation in plant cells. This work has substantially advanced our understanding of the mechanisms of DNA integration into plants and furthered the development of important new tools for GT in plants.
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Tzfira, Tzvi, Michael Elbaum, and Sharon Wolf. DNA transfer by Agrobacterium: a cooperative interaction of ssDNA, virulence proteins, and plant host factors. United States Department of Agriculture, December 2005. http://dx.doi.org/10.32747/2005.7695881.bard.
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Agrobacteriumtumefaciensmediates genetic transformation of plants. The possibility of exchanging the natural genes for other DNA has led to Agrobacterium’s emergence as the primary vector for genetic modification of plants. The similarity among eukaryotic mechanisms of nuclear import also suggests use of its active elements as media for non-viral genetic therapy in animals. These considerations motivate the present study of the process that carries DNA of bacterial origin into the host nucleus. The infective pathway of Agrobacterium involves excision of a single-stranded DNA molecule (T-strand) from the bacterial tumor-inducing plasmid. This transferred DNA (T-DNA) travels to the host cell cytoplasm along with two virulence proteins, VirD2 and VirE2, through a specific bacteriumplant channel(s). Little is known about the precise structure and composition of the resulting complex within the host cell and even less is known about the mechanism of its nuclear import and integration into the host cell genome. In the present proposal we combined the expertise of the US and Israeli labs and revealed many of the biophysical and biological properties of the genetic transformation process, thus enhancing our understanding of the processes leading to nuclear import and integration of the Agrobacterium T-DNA. Specifically, we sought to: I. Elucidate the interaction of the T-strand with its chaperones. II. Analyzing the three-dimensional structure of the T-complex and its chaperones in vitro. III. Analyze kinetics of T-complex formation and T-complex nuclear import. During the past three years we accomplished our goals and made the following major discoveries: (1) Resolved the VirE2-ssDNA three-dimensional structure. (2) Characterized VirE2-ssDNA assembly and aggregation, along with regulation by VirE1. (3) Studied VirE2-ssDNA nuclear import by electron tomography. (4) Showed that T-DNA integrates via double-stranded (ds) intermediates. (5) Identified that Arabidopsis Ku80 interacts with dsT-DNA intermediates and is essential for T-DNA integration. (6) Found a role of targeted proteolysis in T-DNA uncoating. Our research provide significant physical, molecular, and structural insights into the Tcomplex structure and composition, the effect of host receptors on its nuclear import, the mechanism of T-DNA nuclear import, proteolysis and integration in host cells. Understanding the mechanical and molecular basis for T-DNA nuclear import and integration is an essential key for the development of new strategies for genetic transformation of recalcitrant plant species. Thus, the knowledge gained in this study can potentially be applied to enhance the transformation process by interfering with key steps of the transformation process (i.e. nuclear import, proteolysis and integration). Finally, in addition to the study of Agrobacterium-host interaction, our research also revealed some fundamental insights into basic cellular mechanisms of nuclear import, targeted proteolysis, protein-DNA interactions and DNA repair.
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Weil, Clifford F., Anne B. Britt, and Avraham Levy. Nonhomologous DNA End-Joining in Plants: Genes and Mechanisms. United States Department of Agriculture, July 2001. http://dx.doi.org/10.32747/2001.7585194.bard.
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Repair of DNA breaks is an essential function in plant cells as well as a crucial step in addition of modified DNA to plant cells. In addition, our inability to introduce modified DNA to its appropriate locus in the plant genome remains an important hurdle in genetically engineering crop species.We have taken a combined forward and reverse genetics approach to examining DNA double strand break repair in plants, focusing primarily on nonhomologous DNA end-joining. The forward approach utilizes a gamma-plantlet assay (miniature plants that are metabolically active but do not undergo cell division, due to cell cycle arrest) and has resulted in identification of five Arabidopsis mutants, including a new one defective in the homolog of the yeast RAD10 gene. The reverse genetics approach has identified knockouts of the Arabidopsis homologs for Ku80, DNA ligase 4 and Rad54 (one gene in what proves to be a gene family involved in DNA repair as well as chromatin remodeling and gene silencing)). All these mutants have phenotypic defects in DNA repair but are otherwise healthy and fertile. Additional PCR based screens are in progress to find knockouts of Ku70, Rad50, and Mre11, among others. Two DNA end-joining assays have been developed to further our screens and our ability to test candidate genes. One of these involves recovering linearized plasmids that have been added to and then rejoined in plant cells; plasmids are either recovered directly or transformed into E. coli and recovered. The products recovered from various mutant lines are then compared. The other assay involves using plant transposon excision to create DNA breaks in yeast cells and then uses the yeast cell as a system to examine those genes involved in the repair and to screen plant genes that might be involved as well. This award supported three graduate students, one in Israel and two in the U.S., as well as a technician in the U.S., and is ultimately expected to result directly in five publications and one Masters thesis.
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Mawassi, Munir, and Valerian V. Dolja. Role of the viral AlkB homologs in RNA repair. United States Department of Agriculture, June 2014. http://dx.doi.org/10.32747/2014.7594396.bard.
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AlkB proteins that repair DNA via reversing methylation damage are conserved in a broad range of prokaryotes and eukaryotes including plants. Surprisingly, AlkB-domains were discovered in the genomes of numerous plant positive-strand RNA viruses, majority of which belong to the family Flexiviridae. The major goal of this research was to reveal the AlkB functions in the viral infection cycle using a range of complementary genetic and biochemical approaches. Our hypotheses was that AlkB is required for efficient replication and genetic stability of viral RNA genomes The major objectives of the research were to identify the functions of GVA AlkB domain throughout the virus infection cycle in N. benthamiana and grapevine, to investigate possible RNA silencing suppression activity of the viral AlkBs, and to characterize the RNA demethylation activity of the mutated GVA AlkBs in vitro and in vivo to determine methylation status of the viral RNA. Over the duration of project, we have made a very substantial progress with the first two objectives. Because of the extreme low titer of the virus particles in plants infected with the AlkB mutant viruses, we were unable to analyze RNA demethylation activity and therefore had to abandon third objective. The major achievements with our objectives were demonstration of the AlkB function in virus spread and accumulation in both experimental and natural hosts of GVA, discovery of the functional cooperation and physical interaction between AlkB and p10 AlkB in suppression of plant RNA silencing response, developing a powerful virus vector technology for grapevine using GLRaV-2-derived vectors for functional genomics and pathogen control in grapevine, and in addition we used massive parallel sequencing of siRNAs to conduct comparative analysis of the siRNA populations in grape plants infected with AlkB-containing GLRaV-3 versus GLRaV-2 that does not encode AlkB. This analysis revealed dramatically reduced levels of virus-specific siRNAs in plants infected with GLRaV-3 compared to that in GLRaV-2 infection implicating AlkB in suppression of siRNA formation. We are pleased to report that BARD funding resulted in 5 publications directly supported by BARD, one US patent, and 9 more publications also relevant to project. Moreover, two joint manuscripts that summarize work on GVA AlkB (led by Israeli PI) and on viral siRNAs in grapevine (led by US PI in collaboration with University of Basel) are in preparation.
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Christopher, David A., and Avihai Danon. Plant Adaptation to Light Stress: Genetic Regulatory Mechanisms. United States Department of Agriculture, May 2004. http://dx.doi.org/10.32747/2004.7586534.bard.
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Original Objectives: 1. Purify and biochemically characterize RB60 orthologs in higher plant chloroplasts; 2. Clone the gene(s) encoding plant RB60 orthologs and determine their structure and expression; 3. Manipulate the expression of RB60; 4. Assay the effects of altered RB60 expression on thylakoid biogenesis and photosynthetic function in plants exposed to different light conditions. In addition, we also examined the gene structure and expression of RB60 orthologs in the non-vascular plant, Physcomitrella patens and cloned the poly(A)-binding protein orthologue (43 kDa RB47-like protein). This protein is believed to a partner that interacts with RB60 to bind to the psbA5' UTR. Thus, to obtain a comprehensive view of RB60 function requires analysis of its biochemical partners such as RB43. Background & Achievements: High levels of sunlight reduce photosynthesis in plants by damaging the photo system II reaction center (PSII) subunits, such as D1 (encoded by the chloroplast tpsbAgene). When the rate of D1 synthesis is less than the rate of photo damage, photo inhibition occurs and plant growth is decreased. Plants use light-activated translation and enhanced psbAmRNA stability to maintain D1 synthesis and replace the photo damaged 01. Despite the importance to photosynthetic capacity, these mechanisms are poorly understood in plants. One intriguing model derived from the algal chloroplast system, Chlamydomonas, implicates the role of three proteins (RB60, RB47, RB38) that bind to the psbAmRNA 5' untranslated leader (5' UTR) in the light to activate translation or enhance mRNA stability. RB60 is the key enzyme, protein D1sulfide isomerase (Pill), that regulates the psbA-RN :Binding proteins (RB's) by way of light-mediated redox potentials generated by the photosystems. However, proteins with these functions have not been described from higher plants. We provided compelling evidence for the existence of RB60, RB47 and RB38 orthologs in the vascular plant, Arabidopsis. Using gel mobility shift, Rnase protection and UV-crosslinking assays, we have shown that a dithiol redox mechanism which resembles a Pill (RB60) activity regulates the interaction of 43- and 30-kDa proteins with a thermolabile stem-loop in the 5' UTR of the psbAmRNA from Arabidopsis. We discovered, in Arabidopsis, the PD1 gene family consists of II members that differ in polypeptide length from 361 to 566 amino acids, presence of signal peptides, KDEL motifs, and the number and positions of thioredoxin domains. PD1's catalyze the reversible formation an disomerization of disulfide bonds necessary for the proper folding, assembly, activity, and secretion of numerous enzymes and structural proteins. PD1's have also evolved novel cellular redox functions, as single enzymes and as subunits of protein complexes in organelles. We provide evidence that at least one Pill is localized to the chloroplast. We have used PDI-specific polyclonal and monoclonal antisera to characterize the PD1 (55 kDa) in the chloroplast that is unevenly distributed between the stroma and pellet (containing membranes, DNA, polysomes, starch), being three-fold more abundant in the pellet phase. PD1-55 levels increase with light intensity and it assembles into a high molecular weight complex of ~230 kDa as determined on native blue gels. In vitro translation of all 11 different Pill's followed by microsomal membrane processing reactions were used to differentiate among PD1's localized in the endoplasmic reticulum or other organelles. These results will provide.1e insights into redox regulatory mechanisms involved in adaptation of the photosynthetic apparatus to light stress. Elucidating the genetic mechanisms and factors regulating chloroplast photosynthetic genes is important for developing strategies to improve photosynthetic efficiency, crop productivity and adaptation to high light environments.
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Epel, Bernard, and Roger Beachy. Mechanisms of intra- and intercellular targeting and movement of tobacco mosaic virus. United States Department of Agriculture, November 2005. http://dx.doi.org/10.32747/2005.7695874.bard.
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To cause disease, plant viruses must replicate and spread locally and systemically within the host. Cell-to-cell virus spread is mediated by virus-encoded movement proteins (MPs), which modify the structure and function of plasmodesmata (Pd), trans-wall co-axial membranous tunnels that interconnect the cytoplasm of neighboring cells. Tobacco mosaic virus (TMV) employ a single MP for cell- cell spread and for which CP is not required. The PIs, Beachy (USA) and Epel (Israel) and co-workers, developed new tools and approaches for study of the mechanism of spread of TMV that lead to a partial identification and molecular characterization of the cellular machinery involved in the trafficking process. Original research objectives: Based on our data and those of others, we proposed a working model of plant viral spread. Our model stated that MPᵀᴹⱽ, an integral ER membrane protein with its C-terminus exposed to the cytoplasm (Reichel and Beachy, 1998), alters the Pd SEL, causes the Pd cytoplasmic annulus to dilate (Wolf et al., 1989), allowing ER to glide through Pd and that this gliding is cytoskeleton mediated. The model claimed that in absence of MP, the ER in Pd (the desmotubule) is stationary, i.e. does not move through the Pd. Based on this model we designed a series of experiments to test the following questions: -Does MP potentiate ER movement through the Pd? - In the presence of MP, is there communication between adjacent cells via ER lumen? -Does MP potentiate the movement of cytoskeletal elements cell to cell? -Is MP required for cell-to-cell movement of ER membranes between cells in sink tissue? -Is the binding in situ of MP to RNA specific to vRNA sequences or is it nonspecific as measured in vitro? And if specific: -What sequences of RNA are involved in binding to MP? And finally, what host proteins are associated with MP during intracellular targeting to various subcellular targets and what if any post-translational modifications occur to MP, other than phosphorylation (Kawakami et al., 1999)? Major conclusions, solutions and achievements. A new quantitative tool was developed to measure the "coefficient of conductivity" of Pd to cytoplasmic soluble proteins. Employing this tool, we measured changes in Pd conductivity in epidermal cells of sink and source leaves of wild-type and transgenic Nicotiana benthamiana (N. benthamiana) plants expressing MPᵀᴹⱽ incubated both in dark and light and at 16 and 25 ᵒC (Liarzi and Epel, 2005 (appendix 1). To test our model we measured the effect of the presence of MP on cell-to-cell spread of a cytoplasmic fluorescent probe, of two ER intrinsic membrane protein-probes and two ER lumen protein-probes fused to GFP. The effect of a mutant virus that is incapable of cell-to-cell spread on the spread of these probes was also determined. Our data shows that MP reduces SEL for cytoplasmic molecules, dilates the desmotubule allowing cell-cell diffusion of proteins via the desmotubule lumen and reduces the rate of spread of the ER membrane probes. Replicase was shown to enhance cell-cell spread. The data are not in support of the proposed model and have led us to propose a new model for virus cell-cell spread: this model proposes that MP, an integral ER membrane protein, forms a MP:vRNAER complex and that this ER-membrane complex diffuses in the lipid milieu of the ER into the desmotubule (the ER within the Pd), and spreads cell to cell by simple diffusion in the ER/desmotubule membrane; the driving force for spread is the chemical potential gradient between an infected cell and contingent non-infected neighbors. Our data also suggests that the virus replicase has a function in altering the Pd conductivity. Transgenic plant lines that express the MP gene of the Cg tobamovirus fused to YFP under the control the ecdysone receptor and methoxyfenocide ligand were generated by the Beachy group and the expression pattern and the timing and targeting patterns were determined. A vector expressing this MPs was also developed for use by the Epel lab . The transgenic lines are being used to identify and isolate host genes that are required for cell-to-cell movement of TMV/tobamoviruses. This line is now being grown and to be employed in proteomic studies which will commence November 2005. T-DNA insertion mutagenesis is being developed to identify and isolate host genes required for cell-to-cell movement of TMV.
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Eldar, Avigdor, and Donald L. Evans. Streptococcus iniae Infections in Trout and Tilapia: Host-Pathogen Interactions, the Immune Response Toward the Pathogen and Vaccine Formulation. United States Department of Agriculture, December 2000. http://dx.doi.org/10.32747/2000.7575286.bard.
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In Israel and in the U.S., Streptococcus iniae is responsible for considerable losses in various fish species. Poor understanding of its virulence factors and limited know-how-to of vaccine formulation and administration are the main reasons for the limited efficacy of vaccines. Our strategy was that in order to Improve control measures, both aspects should be equally addressed. Our proposal included the following objectives: (i) construction of host-pathogen interaction models; (ii) characterization of virulence factors and immunodominant antigens, with assessment of their relative importance in terms of protection and (iii) genetic identification of virulence factors and genes, with evaluation of the protective effect of recombinant proteins. We have shown that two different serotypes are involved. Their capsular polysaccharides (CPS) were characterized, and proved to play an important role in immune evasion and in other consequences of the infection. This is an innovative finding in fish bacteriology and resembles what, in other fields, has become apparent in the recent years: S. iniae alters surface antigens. By so doing, the pathogen escapes immune destruction. Immunological assays (agar-gel immunodiffusion and antibody titers) confirmed that only limited cross recognition between the two types occurs and that capsular polysaccharides are immunodominant. Vaccination with purified CPS (as an acellular vaccine) results in protection. In vitro and ex-vivo models have allowed us to unravel additional insights of the host-pathogen interactions. S. iniae 173 (type II) produced DNA fragmentation of TMB-8 cells characteristic of cellular necrosis; the same isolate also prevented the development of apoptosis in NCC. This was determined by finding reduced expression of phosphotidylserine (PS) on the outer membrane leaflet of NCC. NCC treated with this isolate had very high levels of cellular necrosis compared to all other isolates. This cellular pathology was confirmed by observing reduced DNA laddering in these same treated cells. Transmission EM also showed characteristic necrotic cellular changes in treated cells. To determine if the (in vitro) PCD/apoptosis protective effects of #173 correlated with any in vivo activity, tilapia were injected IV with #173 and #164 (an Israeli type I strain). Following injection, purified NCC were tested (in vitro) for cytotoxicity against HL-60 target cells. Four significant observations were made : (i) fish injected with #173 had 100-400% increased cytotoxicity compared to #164 (ii) in vivo activation occurred within 5 minutes of injection; (iii) activation occurred only within the peripheral blood compartment; and (iv) the isolate that protected NCC from apoptosis in vitro caused in vivo activation of cytotoxicity. The levels of in vivo cytotoxicity responses are associated with certain pathogens (pathogen associated molecular patterns/PAMP) and with the tissue of origin of NCC. NCC from different tissue (i.e. PBL, anterior kidney, spleen) exist in different states of differentiation. Random amplified polymorphic DNA (RAPD) analysis revealed the "adaptation" of the bacterium to the vaccinated environment, suggesting a "Darwinian-like" evolution of any bacterium. Due to the selective pressure which has occurred in the vaccinated environment, type II strains, able to evade the protective response elicited by the vaccine, have evolved from type I strains. The increased virulence through the appropriation of a novel antigenic composition conforms with pathogenic mechanisms described for other streptococci. Vaccine efficacy was improved: water-in-oil formulations were found effective in inducing protection that lasted for a period of (at least) 6 months. Protection was evaluated by functional tests - the protective effect, and immunological parameters - elicitation of T- and B-cells proliferation. Vaccinated fish were found to be resistant to the disease for (at least) six months; protection was accompanied by activation of the cellular and the humoral branches.
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Galili, Gad, and Alan Bennett. Role of Molecular Chaperone in Wheat Storage Protein Assembly. United States Department of Agriculture, April 1995. http://dx.doi.org/10.32747/1995.7604926.bard.
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Following sequestration into the ER, wheat gliadins assemble into complexes that initiate the formation of protein bodies. In the present work we have characterized the DNA sequence and regulation of expression of a plant BiP and also studied its interaction with wheat storage proteins as well as its role in the maturation of these storage proteins. In the Israeli lab, immunoprecipitation studies were made using anti BiP and anti storage proteins sera, both in wheat and in transgenic tobacco plants expressing a wheat gliadin storage proteins. In both cases, we could show that BiP interacts with the gliadin storage proteins. In addition, we could show that BiP also played an important role in the initial assembly of the gliadins. In the American lab, the complexity, structure and properties of tomato BiP was characterized at the molecular and biochemical levels. In addition, tomato BiP was also overexpressed in bacteria and the overexpressed protein was found to be active. The cooperative findings of the Israeli and American labs clearly improves our understanding of the structure and expression of a plant BiP as well as its role in the maturation of storage proteins in plants seeds. In addition, it will serve as a foundation for future studies of the mechanisms of BiP function in in vitro studies using purified storage proteins and purified recombinant active BiP.
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Evans, Donald L., Avigdor Eldar, Liliana Jaso-Friedmann, and Herve Bercovier. Streptococcus Iniae Infection in Trout and Tilapia: Host-Pathogen Interactions, the Immune Response Towards the Pathogen and Vaccine Formulation. United States Department of Agriculture, February 2005. http://dx.doi.org/10.32747/2005.7586538.bard.
Full textAbstract:
The objectives of the BARD proposal were to determine the mechanisms of nonspecific cytotoxic cells (NCC) that are necessary to provide heightened innate resistance to infection and to identify the antigenic determinants in Streptococcus iniae that are best suited for vaccine development. Our central hypothesis was that anti-bacterial immunity in trout and tilapia can only be acquired by combining "innate" NCC responses with antibody responses to polysaccharide antigens. These Objectives were accomplished by experiments delineated by the following Specific Aims: Specific aim (SA) #1 (USA) "Clone and Identify the Apoptosis Regulatory Genes in NCC"; Specific aim #2 (USA)"Identify Regulatory Factors that Control NCC Responses to S. iniae"; Specific aim #3 (Israel) "Characterize the Biological Properties of the S. iniae Capsular Polysaccharide"; and Specific aim #4 (Israel) "Development of an Acellular Vaccine". Our model of S. iniae pathogenesis encompassed two approaches, identify apoptosis regulatory genes and proteins in tilapia that affected NCC activities (USA group) and determine the participation of S.iniae capsular polysaccharides as potential immunogens for the development of an acellular vaccine (Israel group). We previously established that it was possible to immunize tilapia and trout against experimental S. difficile/iniaeinfections. However these studies indicated that antibody responses in protected fish were short lived (3-4 months). Thus available vaccines were useful for short-term protection only. To address the issues of regulation of pathogenesis and immunogens of S. iniae, we have emphasized the role of the innate immune response regarding activation of NCC and mechanisms of invasiveness. Considerable progress was made toward accomplishing SA #1. We have cloned the cDNA of the following tilapia genes: cellular apoptosis susceptibility (CAS/AF547173»; tumor necrosis factor alpha (TNF / A Y 428948); and nascent polypeptide-associated complex alpha polypeptide (NACA/ A Y168640). Similar attempts were made to sequence the tilapia FasLgene/cDNA, however these experiments were not successful. Aim #2 was to "Identify Regulatory Factors that Control NCC Responses to S. iniae." To accomplish this, a new membrane receptor has been identified that may control innate responses (including apoptosis) of NCC to S. iniae. The receptor is a membrane protein on teleost NCC. This protein (NCC cationic antimicrobial protein-1/ncamp-1/AAQ99138) has been sequenced and the cDNA cloned (A Y324398). In recombinant form, ncamp-l kills S. iniae in vitro. Specific aim 3 ("Characterize the Biological Properties of the S.iniae Capsular Polysaccharide") utilized an in- vitro model using rainbow trout primary skin epithelial cell mono layers. These experiments demonstrated colonization into epithelial cells followed by a rapid decline of viable intracellular bacteria and translocation out of the cell. This pathogenesis model suggested that the bacterium escapes the endosome and translocates through the rainbow trout skin barrier to further invade and infect the host. Specific aim #4 ("Development of an Acellular Vaccine") was not specifically addressed. These studies demonstrated that several different apoptotic regulatory genes/proteins are expressed by tilapia NCC. These are the first studies demonstrating that such factors exist in tilapia. Because tilapia NCC bind to and are activated by S. iniae bacterial DNA, we predict that the apoptotic regulatory activity of S. iniae previously demonstrated by our group may be associated with innate antibacterial responses in tilapia.
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Cohen, Yuval, Christopher A. Cullis, and Uri Lavi. Molecular Analyses of Soma-clonal Variation in Date Palm and Banana for Early Identification and Control of Off-types Generation. United States Department of Agriculture, October 2010. http://dx.doi.org/10.32747/2010.7592124.bard.
Full textAbstract:
Date palm (Phoenix dactylifera L.) is the major fruit tree grown in arid areas in the Middle East and North Africa. In the last century, dates were introduced to new regions including the USA. Date palms are traditionally propagated through offshoots. Expansion of modern date palm groves led to the development of Tissue Culture propagation methods that generate a large number of homogenous plants, have no seasonal effect on plant source and provide tools to fight the expansion of date pests and diseases. The disadvantage of this procedure is the occurrence of off-type trees which differ from the original cultivar. In the present project we focused on two of the most common date palm off-types: (1) trees with reduced fruit setting, in which most of the flowers turn into three-carpel parthenocarpic fruits. In a severe form, multi-carpel flowers and fruitlets (with up to six or eight carpels instead of the normal three-carpel flowers) are also formed. (2) dwarf trees, having fewer and shorter leaves, very short trunk and are not bearing fruits at their expected age, compared to the normal trees. Similar off-types occur in other crop species propagated by tissue culture, like banana (mainly dwarf plants) or oil palm (with a common 'Mantled' phenotype with reduced fruit setting and occurrence of supernumerary carpels). Some off-types can only be detected several years after planting in the fields. Therefore, efficient methods for prevention of the generation of off-types, as well as methods for their detection and early removal, are required for date palms, as well as for other tissue culture propagated crops. This research is aimed at the understanding of the mechanisms by which off-types are generated, and developing markers for their early identification. Several molecular and genomic approaches were applied. Using Methylation Sensitive AFLP and bisulfite sequencing, we detected changes in DNA methylation patterns occurring in off-types. We isolated and compared the sequence and expression of candidate genes, genes related to vegetative growth and dwarfism and genes related to flower development. While no sequence variation were detected, changes in gene expression, associated with the severity of the "fruit set" phenotype were detected in two genes - PdDEF (Ortholog of rice SPW1, and AP3 B type MADS box gene), and PdDIF (a defensin gene, highly homologous to the oil palm gene EGAD). We applied transcriptomic analyses, using high throughput sequencing, to identify genes differentially expressed in the "palm heart" (the apical meristem and the region of embryonic leaves) of dwarf vs. normal trees. Among the differentially expressed genes we identified genes related to hormonal biosynthesis, perception and regulation, genes related to cell expansion, and genes related to DNA methylation. Using Representation Difference Analyses, we detected changes in the genomes of off-type trees, mainly chloroplast-derived sequences that were incorporated in the nuclear genome and sequences of transposable elements. Sequences previously identified as differing between normal and off-type trees of oil palms or banana, successfully identified variation among date palm off-types, suggesting that these represent highly labile regions of monocot genomes. The data indicate that the date palm genome, similarly to genomes of other monocot crops as oil palm and banana, is quite unstable when cells pass through a cycle of tissue culture and regeneration. Changes in DNA sequences, translocation of DNA fragments and alteration of methylation patterns occur. Consequently, patterns of gene expression are changed, resulting in abnormal phenotypes. The data can be useful for future development of tools for early identification of off-type as well as for better understanding the phenomenon of somaclonal variation during propagation in vitro.