Academic literature on the topic 'DNA Replication Stre'
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Journal articles on the topic "DNA Replication Stre"
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Sutormin, Dmitry A., Alina Kh Galivondzhyan, Alexander V. Polkhovskiy, Sofia O. Kamalyan, Konstantin V. Severinov, and Svetlana A. Dubiley. "Diversity and Functions of Type II Topoisomerases." Acta Naturae 13, no. 1 (March 15, 2021): 59–75. http://dx.doi.org/10.32607/actanaturae.11058.
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The DNA double helix provides a simple and elegant way to store and copy genetic information. However, the processes requiring the DNA helix strands separation, such as transcription and replication, induce a topological side-effect supercoiling of the molecule. Topoisomerases comprise a specific group of enzymes that disentangle the topological challenges associated with DNA supercoiling. They relax DNA supercoils and resolve catenanes and knots. Here, we review the catalytic cycles, evolution, diversity, and functional roles of type II topoisomerases in organisms from all domains of life, as well as viruses and other mobile genetic elements.
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Mishra, Garima, Lavi S. Bigman, and Yaakov Levy. "ssDNA diffuses along replication protein A via a reptation mechanism." Nucleic Acids Research 48, no. 4 (January 10, 2020): 1701–14. http://dx.doi.org/10.1093/nar/gkz1202.
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Abstract Replication protein A (RPA) plays a critical role in all eukaryotic DNA processing involving single-stranded DNA (ssDNA). Contrary to the notion that RPA provides solely inert protection to transiently formed ssDNA, the RPA–ssDNA complex acts as a dynamic DNA processing unit. Here, we studied the diffusion of RPA along 60 nt ssDNA using a coarse-grained model in which the ssDNA–RPA interface was modeled by both aromatic and electrostatic interactions. Our study provides direct evidence of bulge formation during the diffusion of ssDNA along RPA. Bulges can form at a few sites along the interface and store 1–7 nt of ssDNA whose release, upon bulge dissolution, leads to propagation of ssDNA diffusion. These findings thus support the reptation mechanism, which involves bulge formation linked to the aromatic interactions, whose short range nature reduces cooperativity in ssDNA diffusion. Greater cooperativity and a larger diffusion coefficient for ssDNA diffusion along RPA are observed for RPA variants with weaker aromatic interactions and for interfaces homogenously stabilized by electrostatic interactions. ssDNA propagation in the latter instance is characterized by lower probabilities of bulge formation; thus, it may fit the sliding-without-bulge model better than the reptation model. Thus, the reptation mechanism allows ssDNA mobility despite the extensive and high affinity interface of RPA with ssDNA. The short-range aromatic interactions support bulge formation while the long-range electrostatic interactions support the release of the stored excess ssDNA in the bulge and thus the overall diffusion.
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Nurwanti, Ratri, Dian Putri Permatasari, Ika Fitria, Zakki Munawar Ahmad, and Yohana Dwivi Anggraini. "Efek Stres terhadap False Memory Recall dan Recognition." Suksma: Jurnal Psikologi Universitas Sanata Dharma 3, no. 2 (October 30, 2022): 60–73. http://dx.doi.org/10.24071/suksma.v3i2.5188.
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Memory is often thought of as a video recorder that can record and store events precisely as they occur. Whereas in addition to being constructive, memory is also reconstructive, which means that memory can change due to certain conditions, resulting in false memories. The effect of stress on false memory was tested in this between-subject design experiment. Participants in this study (N = 38) were divided into two conditions through a random assignment process, control conditions (N = 27) and stress or experiment conditions (N = 11). We used a modified Trier Social Stress Test-Group to induce stress and Deese-Roediger-McDermott Paradigm to measure false memory. The independent sample t-test showed that there was no significant difference on false memory recall and false memory recognition between participants in the experiment condition and participants in the control condition. This indicated that stress did not affect false memory. The implications of this finding are the importance of replicating similar studies investigating stress induction in various stages of memory processing and forms of stress induction to produce a more precise understanding of the stress and false memory mechanism.
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Taghfir, Dimas Bima, Syaiful Anwar, and Budi Adi Kristanto. "Kualitas benih dan pertumbuhan bibit cabai (Capsicum frutescens l.) pada perlakuan suhu dan wadah penyimpanan yang berbeda." Journal of Agro Complex 2, no. 2 (June 10, 2018): 137. http://dx.doi.org/10.14710/joac.2.2.137-147.
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Setting the temperature of the storage space of seeds and storage containers will greatly affect the quality of the seed. The aim of this research was to study the effect of temperature treatment, storage container and their interaction on seed quality and seedling growth of chilli. The study was conducted in Jetis Village and Laboratory of Plant Physiology and Breeding, Faculty of Animal and Agricultural Sciences, Diponegoro University from January to June 2017. The study was conducted using nesting experiments on the basis of Completely Randomized Design (RAL). The first factor was Storage Temperature (R1 = Room Temperature 24-29 oC, R2 = Refrigerator Temperature 5oC) and second factor was storage container nested at storage temperature that was (P1 = Alumunium foil, P2 = Paper and P3 = Plastic). Each treatment had 5 replications and each replication consisted of 100 seeds, so there were 30 experimental units. The data were analyzed by using analysis of variance (ANOVA) and continued with test of HSD (Honesty Significant Difference) 5% significance level. The results showed that the storage temperature (5oC) temperature increased the temperature and the seed vigor index was larger than the room temperature (28oC), the aluminum foil packaging produced the maximum growth potential and germination rate was higher than the plastic and paper packaging but there was no different growth rate and index vigor. Low storage space temperatures (5oC) can not maintain maximum seed quality where the 4 parameters were still below the standard quality of the seed. Seeds stored in low temperature (5oC) rooms producedfresh weight and dry weight of seedlings larger than high temperature (28oC), but the number of leaves, seed height and hypothetical vigor index were not significantly different. The aluminum foil packaging producedfresh weight and dry weight of seeds higher than plastic and paper packaging. However, the number of leaves, the height of seed and the hypothetical vigor index were notsignificantly different. Keywords : Temperature, container store, seeds quality, seedling growth, chilli.
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Harami, Gábor M., Zoltán J. Kovács, Rita Pancsa, János Pálinkás, Veronika Baráth, Krisztián Tárnok, András Málnási-Csizmadia, and Mihály Kovács. "Phase separation by ssDNA binding protein controlled via protein−protein and protein−DNA interactions." Proceedings of the National Academy of Sciences 117, no. 42 (October 5, 2020): 26206–17. http://dx.doi.org/10.1073/pnas.2000761117.
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Bacterial single-stranded (ss)DNA-binding proteins (SSB) are essential for the replication and maintenance of the genome. SSBs share a conserved ssDNA-binding domain, a less conserved intrinsically disordered linker (IDL), and a highly conserved C-terminal peptide (CTP) motif that mediates a wide array of protein−protein interactions with DNA-metabolizing proteins. Here we show that theEscherichia coliSSB protein forms liquid−liquid phase-separated condensates in cellular-like conditions through multifaceted interactions involving all structural regions of the protein. SSB, ssDNA, and SSB-interacting molecules are highly concentrated within the condensates, whereas phase separation is overall regulated by the stoichiometry of SSB and ssDNA. Together with recent results on subcellular SSB localization patterns, our results point to a conserved mechanism by which bacterial cells store a pool of SSB and SSB-interacting proteins. Dynamic phase separation enables rapid mobilization of this protein pool to protect exposed ssDNA and repair genomic loci affected by DNA damage.
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Brazda, Vaclav, Miroslav Fojta, and Richard P. Bowater. "Structures and stability of simple DNA repeats from bacteria." Biochemical Journal 477, no. 2 (January 22, 2020): 325–39. http://dx.doi.org/10.1042/bcj20190703.
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DNA is a fundamentally important molecule for all cellular organisms due to its biological role as the store of hereditary, genetic information. On the one hand, genomic DNA is very stable, both in chemical and biological contexts, and this assists its genetic functions. On the other hand, it is also a dynamic molecule, and constant changes in its structure and sequence drive many biological processes, including adaptation and evolution of organisms. DNA genomes contain significant amounts of repetitive sequences, which have divergent functions in the complex processes that involve DNA, including replication, recombination, repair, and transcription. Through their involvement in these processes, repetitive DNA sequences influence the genetic instability and evolution of DNA molecules and they are located non-randomly in all genomes. Mechanisms that influence such genetic instability have been studied in many organisms, including within human genomes where they are linked to various human diseases. Here, we review our understanding of short, simple DNA repeats across a diverse range of bacteria, comparing the prevalence of repetitive DNA sequences in different genomes. We describe the range of DNA structures that have been observed in such repeats, focusing on their propensity to form local, non-B-DNA structures. Finally, we discuss the biological significance of such unusual DNA structures and relate this to studies where the impacts of DNA metabolism on genetic stability are linked to human diseases. Overall, we show that simple DNA repeats in bacteria serve as excellent and tractable experimental models for biochemical studies of their cellular functions and influences.
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Kobayashi, Masaki, Yusuke Deguchi, Yuka Nozaki, and Yoshikazu Higami. "Contribution of PGC-1α to Obesity- and Caloric Restriction-Related Physiological Changes in White Adipose Tissue." International Journal of Molecular Sciences 22, no. 11 (June 2, 2021): 6025. http://dx.doi.org/10.3390/ijms22116025.
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Peroxisome proliferator-activated receptor γ coactivator-1 α (PGC-1α) regulates mitochondrial DNA replication and mitochondrial gene expression by interacting with several transcription factors. White adipose tissue (WAT) mainly comprises adipocytes that store triglycerides as an energy resource and secrete adipokines. The characteristics of WAT vary in response to systemic and chronic metabolic alterations, including obesity or caloric restriction. Despite a small amount of mitochondria in white adipocytes, accumulated evidence suggests that mitochondria are strongly related to adipocyte-specific functions, such as adipogenesis and lipogenesis, as well as oxidative metabolism for energy supply. Therefore, PGC-1α is expected to play an important role in WAT. In this review, we provide an overview of the involvement of mitochondria and PGC-1α with obesity- and caloric restriction-related physiological changes in adipocytes and WAT.
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Yurliasni, Yurliasni, and Herawati Latif. "Pengaruh Warna Kerabang Dan Lama Penyimpanan Pada Suhu Beebeda Terhadap Kualitas Suhu Konsumsi." Jurnal Agripet 7, no. 1 (March 29, 2016): 35–38. http://dx.doi.org/10.17969/agripet.v7i1.3310.
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ABSTRACT. The objective of this research is to learn the effect of shell color and storage length on egg quality. The research was held at the Animal Nutrion Laboratory Departement of Agriculture, Syiah Kuala University. The treatments were shell color 30 SC (dark brown): 30-40 SC (white) with 10 replication and store in 27 0C and 10 0C for 35 days. The observation was taken every 7 days. Parameters measured were foam ability and Haugh Unit by group random sampling design with factorial pattern. The result shows that temperature and storage length significantly effect foam ability but not in haugh unit. Storage temperature and storage temperature at 10 0C show that foam ability is better with the average of 422.31 cm3. Compared to 27 0C with the average of 394.04 cm3. On the other hand shell color has no effect both on foam ability and Haugh Unit. In general, shell color, storage length and storage temperature have no effect on egg quality.
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Andriyani Lestariningsih, Wiwid, Muhamad Gilang Arindra Putra, Aulia Rahmania Putri, Budi Prabowo, Fadel Muhammad, Prakas Santoso, Cakra Adiwijaya, et al. "Struktur Komposisi dan Estimasi Cadangan Karbon Tegakan Ekosistem Mangrove di Pulau Sangiang, Banten." Jurnal Ilmu Kelautan Lesser Sunda 2, no. 2 (July 29, 2022): 13–20. http://dx.doi.org/10.29303/jikls.v2i2.59.
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The mangrove ecosystem is a coastal ecosystem that is important for humans. Mangroves absorb carbon in the atmosphere and store it in biomass or sediment. So, in other words, mangroves play a significant role in mitigating global climate change. This study aimed to examine the structure of the mangrove ecosystem composition and estimate standing carbon stocks on Sangiang Island, Banten. The data taken was for the categories of trees, saplings, and seedlings (consisting of mangrove species, DBH, and height). The study was conducted at three stations with three replications for each station. The allometric formula obtained the estimated carbon stock from the stand biomass value. The results showed that 11 species of mangrove species were found with an average density of 1266 ind/ha (trees), 3733 ind/ha (saplings), and <70% (seedlings). Then the estimated average carbon stock in Sangiang Island, Banten is 271.29 tons/ha.
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Sinansari, Shofihar, Vitas Atmadi Prakoso, Erma Primanita Hayuningtyas, Bambang Priadi, Sri Sundari, and Eni Kusrini. "Pengaruh Padat Tebar terhadap Konsumsi Oksigen dan Respons Stres Ikan Cupang Alam (Betta imbellis)." OLDI (Oseanologi dan Limnologi di Indonesia) 6, no. 1 (April 28, 2021): 11. http://dx.doi.org/10.14203/oldi.2021.v6i1.314.
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<strong>Effect of Stocking Density on Oxygen Consumption and Stress Response in Crescent Betta (<em>Betta imbellis</em>)</strong>. Stocking density is one of the determinant parameters for fish growth optimization in aquaculture systems due to its relationship with fish metabolism. Information about the impact of different stocking densities on crescent betta (<em>Betta imbellis</em>) metabolism was not available yet. This study was aimed to analyze the effect of stocking density on oxygen consumption, critical oxygen level, and stress responses in crescent betta.The study was carried out under three different stocking density treatments: 5, 10, and 15 fish/L with three replications using 2.74 ± 0.23 cm total length and 0.22 ± 0.05 g body weight tested fishes.The parameters observed were oxygen consumption, ventilation rate, blood glucose level, cortisol, and critical oxygen level. The result showed that the highest oxygen consumption was found at 5 fish/L stocking density treatment (3.01 ± 0.28 mg O<sub>2</sub>/g/h), which was significantly different from 10 fish/L (1.01 ± 0.21 mg O<sub>2</sub>/g/h) and 15 fish/L (0.92 ± 0.08 mg O<sub>2</sub>/g/h) stocking density treatments. Oxygen consumptions under hypoxic condition was not significantly different compared to normoxic condition.The ventilation rate tends to increase significantly along with the increasing of stocking densities. Critical oxygen levels were not significantly different among the treatments,with the value of 3.31 ± 0.65 mg/L, 3.14 ± 0.29 mg/L, and 2.83 ± 0.19 mg/L for stocking density of 5, 10, and 15 fish/L, respectively. The blood glucose level at 15 fish/L stocking density was significantly higher than others, whereas the cortisol levels was not significantly different among the treatments. The results of this study provided information that the increasing stocking density of cressent betta will decrease their metabolism activity and increase ventilation rate. However, the increase of ventilation rate was negatively correlated with oxygen consumption per breath at higher stocking densities due to decrease in fish activity; and higher stocking densities will decrease oxygen consumption. Based on the results, it can be concluded that the ideal stocking density for crescent betta is 5 fish/L. The increasing of stocking density will decrease oxygen consumption rates and increase the stress level of crescent betta.
Dissertations / Theses on the topic "DNA Replication Stre"
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ROSSI, SILVIA EMMA. "INTERPLAY BETWEEN THE DNA HELICASES PIF1 AND RRM3, THE NUCLEASE DNA2 AND THE CHECKPOINT PATHWAYS IN THE MAINTENANCE OF THE DNA REPLICATION FORK INTEGRITY." Doctoral thesis, Università degli Studi di Milano, 2017. http://hdl.handle.net/2434/471797.
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Eukaryotic cells have evolved the ATR/hCHK1, MEC1/RAD53 kinase-mediated signal transduction pathway, known as replication checkpoint, to protect and stabilize stalled replication forks in human cells and budding yeasts, respectively.
rad53 mutants, exposed to high doses of the DNA replication inhibitor hydroxyurea (HU), accumulate hemireplicated, gapped and reversed forks, while treatments with low HU doses induce massive chromosome fragmentation.
The aim of my work was to better understand the molecular mechanisms through which Rad53 prevents unusual alterations of the architecture of the stalled replication forks and chromosome fragility, under replication stress.
We revealed that Rrm3 and Pif1, DNA helicases assisting fork progression across pausing sites in unperturbed conditions, are detrimental in rad53 mutants experiencing HU-induced replication stress. Rrm3 and Pif1 ablation synergistically rescues cell lethality, chromosome fragmentation, replisome dissociation, fork reversal and ssDNA gaps formation at the forks of rad53 cells exposed to replication stress. We provide evidence that Pif1 and Rrm3 associate with stalled DNA replication forks and are regulated through Rad53-mediated phosphorylation.
Our findings uncover a new replication-stress-induced regulative loop in which Rad53 down regulates the Pif1 DNA helicases at the stalled replication forks.
In the second part of this thesis we examined the crosstalk between Rrm3, Pif1, the mediator of the DNA damage checkpoint Rad9 and the nuclease Dna2, during unperturbed DNA replication. The experimental evidence collected in this second part of the project, together with pioneering work previously reported from other laboratories, strongly suggests that Dna2, Pif1 and Rrm3 cooperate to finalize late stages of DNA replication.
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GNOCCHI, ANDREA. "UNDERSTANDING THE IMPACT OF REPLICATION STRESS ON THE EXPRESSION OF EARLY GENES IN MOUSE EMBRYONIC STEM CELLS." Doctoral thesis, Università degli Studi di Milano, 2021. http://hdl.handle.net/2434/814703.
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Embryonic stem cells (ESCs) are characterized by a rapid cell cycle, which leads to high replication stress (RS) in otherwise unperturbed conditions. The mechanisms that ESCs adopt to cope with their endogenous RS, however, remain to this day elusive. In our recent work we demonstrated that the activation of the checkpoint kinase ATR in response to RS leads to a broad activation of 2-cells stage specific genes in mouse ESCs. This response relies on the up-regulation of Dux, a transcription factor encoded in a macrosatellite sequence repeated in tandem. Dux is repressed by variant Polycomb repressive complex 1 (vPRC1) in unperturbed ESCs, independently from PRC2 presence.
Here we demonstrate that RS causes a major rearrangement of both PRC1 and PRC2 in ESCs nuclei, resulting in a major loss of both repressive marks in correspondence to target promoters. Surprisingly, Dux undergoes an increase in vPRC1 occupancy upon RS in an ATR-dependent manner, possibly due to PRC1 involvement in the replication of highly repeated DNA sequences. More interestingly, Dux activation upon RS requires the presence of PRC2. This result is possibly due to PRC2 proved role in the processing of stalled replication forks, which are the main structure signaling RS. In agreement to this data, also the fork remodeling translocases HLTF and ZRANB3 displayed an effect in Dux activation following RS.
Taken together, our results show that the up-regulation of 2-cells genes following RS not only requires ATR activation, but also downstream remodeling processes.
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Rodier, Denise N. "Degenerate Oligonucleotide Primed-PCR: Thermalcycling Modifications and Comparison Studies." VCU Scholars Compass, 2006. http://scholarscompass.vcu.edu/etd/1496.
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Degenerate Oligonucleotide Primed-PCR (DOP-PCR) can potentially enhance analysis of low copy number DNA samples. Theoretically, this procedure replicates fragments of the genome that can then be used for downstream multiplex STR analysis. The objective of this study is to optimize DOP-PCR by examining ramplelongation times and cycle numbers in the non-specific amplification portion of DOP-PCR, and by modifying the degenerate primer. Additionally, other methods such as Multiple Displacement Amplification (MDA) and Low Copy Number PCR (LCN PCR) were examined for their ability to create accurate DNA profiles from low DNA input amounts. Increasing the ramplelongation times showed no effect on downstream STR amplification success. An increase of cycle number increased DNA yield, but STR amplification success was undetermined. Although modifying the degenerate primer to one with a higher degeneracy decreased DNA yield, it ultimately improved STR amplification success. In comparison studies, LCN PCR produced higher STR amplification success than MDA.
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Fryzelková, Jana. "Úloha helikázy RECQ5 při stabilizaci a opravě replikačních vidlic po jejich kolizi s transkripčním komplexem." Master's thesis, 2017. http://www.nusl.cz/ntk/nusl-355971.
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The progression of replication forks can be slowed down or paused by various external and internal factors during DNA replication. This phenomenon is referred to as replication stress and substantially contributes to genomic instability that is a hallmark of cancer. Transcription complex belongs to the internal replication-interfering factors and represents a barrier for progression of the replication complex. The replication forks are slowed down or paused while passing through the transcriptionally active regions of the genome that can lead to subsequent collapse of stalled forks and formation of DNA double-strand breaks, especially under conditions of increased replication stress. DNA helicase RECQ5 is significantly involved in maintenance of genomic stability during replication stress, but the mechanisms of its action are not clear. In this diploma theses, we have shown that RECQ5 helicase, in collaboration with BRCA1 protein, participates in the resolution of collisions between replication and transcription complexes. BRCA1 protein is a key factor in the homologous recombination process, which is essential for the restart of stalled replication forks. Furthermore, we have shown that RECQ5 helicase is involved in ubiquitination of PCNA protein at stalled replication forks. Key words DNA...