• BMB Reports
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• v.56 no.2
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• pp.108-113
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• 2023

Cohesin is a ring-shaped protein complex that comprises the SMC1, SMC3, and α-kleisin proteins, STAG1/2/3 subunits, and auxiliary factors. Cohesin participates in chromatin remodeling, chromosome segregation, DNA replication, and gene expression regulation during the cell cycle. Mitosis-specific α-kleisin factor RAD21 and meiosis-specific α-kleisin factor REC8 are expressed in embryonic stem cells (ESCs) to maintain pluripotency. Here, we demonstrated that RAD21 and REC8 were involved in maintaining genomic stability and modulating chromatin modification in murine ESCs. When the kleisin subunits were depleted, DNA repair genes were downregulated, thereby reducing cell viability and causing replication protein A (RPA) accumulation. This finding suggested that the repair of exposed single-stranded DNA was inefficient. Furthermore, the depletion of kleisin subunits induced DNA hypermethylation by upregulating DNA methylation proteins. Thus, we proposed that the cohesin complex plays two distinct roles in chromatin remodeling and genomic integrity to ensure the maintenance of pluripotency in ESCs.

• International journal of advanced smart convergence
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• v.13 no.3
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• pp.150-155
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• 2024

Genomic data plays a transformative role in medicine, biology, and forensic science, offering insights that drive advancements in clinical diagnosis, personalized medicine, and crime scene investigation. Despite its potential, the integration and analysis of diverse genomic datasets remain challenging due to compatibility issues and the specialized nature of existing tools. This paper presents the GenomeSync system, designed to overcome these limitations by utilizing the Hadoop framework for large-scale data handling and integration. GenomeSync enhances data accessibility and analysis through SQL-based search capabilities and machine learning techniques, facilitating the identification of genetic traits and the resolution of forensic cases. By pre-processing DNA profiles from crime scenes, the system calculates similarity scores to identify and aggregate related genomic data, enabling accurate prediction models and personalized treatment recommendations. GenomeSync offers greater flexibility and scalability, supporting complex analytical needs across industries. Its robust cloud-based infrastructure ensures data integrity and high performance, positioning GenomeSync as a crucial tool for reliable, data-driven decision-making in the genomic era.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.11
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• pp.1561-1565
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• 2006

The objective of this study was to investigate the anti-oxidative effects of taurine on sperm characteristics for in vitro storage of boar semen. Semen was randomly divided into 10 groups in conical tubes and treated with different concentrations of taurine (25-100 mM) with or without $250{\mu}M$ $H_2O_2$. The percentage of motile spermatozoa in taurine groups after 6 and 9 h were significantly higher at >94% and 87%, respectively, compared to the control group ($85.1{\pm}0.5$ and $72.4{\pm}0.3$, p<0.05). The sperm motility in taurine with $H_2O_2$ after 6 h incubation was slightly decreased compared to the taurine alone treatment, but after 9 and 12 h incubation % sperm motility dropped sharply in taurine with $H_2O_2$ ($75.3{\pm}0.3$ and $69.6{\pm}2.9$, p<0.05). For 3, 9 and 12 h incubation, sperm viability in the control was lower than in taurine groups, irrespective of taurine concentration. In eosin Y and nigrosin staining (ENS), the sperm survival rates (%) for 6 h incubation were significantly higher in 25 mM ($76.0{\pm}0.6$) and 50 mM taurine groups ($78.0{\pm}0.7$), respectively. Sperm survival rates for 9 and 12 h incubation were higher in taurine groups (${\geq}48%$ in 9 h and ${\geq}42%$ in 12 h) compared to controls ($43.0{\pm}2.1$ and $31.0{\pm}0.6$, respectively). In the hyoosmotic swelling test (HOST), sperm membrane integrity was similar to the results of sperm survival. These experiments indicate that supplementation of taurine to the semen extender can increase the sperm characteristics(motility, viability, survival and membrane integrity).

• Molecules and Cells
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• v.19 no.3
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• pp.303-309
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• 2005

The end of eukaryotic genomic DNA is capped by a specialized structure called as "telomere" which consists of the repetitive array of nucleotide sequence, TTAGGG, in humans and mice, and a variety of binding proteins. Telomerase is a ribonucleoprotein (RNP) complex responsible for the elongation of telomeres to maintain the genomic integrity, and is composed of telomerase reverse transcriptase (TERT), telomerase RNA component (TERC), and their associated factors regulating the catalytic activity of telomerase. Although it is now apparent that telomerase protects cells from apoptosis via the maintenance of genomic integrity by stabilizing telomeres, our understanding for the physiological role of telomerase is yet far from completion, and emerging evidence suggests that telomerase has additional extratelomeric roles in mediating cell survival and anti-apoptotic functions against various cytotoxic stresses. Here we summarize and discuss how telomerase and telomeres are involved in mediating cellular protection against apoptosis.

• Journal of Genetic Medicine
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• v.13 no.1
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• pp.1-13
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• 2016

Although some mutations are beneficial and are the driving force behind evolution, it is important to maintain DNA integrity and stability because it contains genetic information. However, in the oxygen-rich environment we live in, the DNA molecule is under constant threat from endogenous or exogenous insults. DNA damage could trigger the DNA damage response (DDR), which involves DNA repair, the regulation of cell cycle checkpoints, and the induction of programmed cell death or senescence. Dysregulation of these physiological responses to DNA damage causes developmental defects, neurological defects, premature aging, infertility, immune system defects, and tumors in humans. Some human syndromes are characterized by unique neurological phenotypes including microcephaly, mental retardation, ataxia, neurodegeneration, and neuropathy, suggesting a direct link between genomic instability resulting from defective DDR and neuropathology. In this review, rare human genetic disorders related to abnormal DDR and damage repair with neural defects will be discussed.

• International Journal of Oral Biology
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• v.47 no.2
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• pp.17-24
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• 2022

Preserving intact genetic material and delivering it to the next generation are the most significant tasks of living organisms. The integrity of DNA sequences is under constant threat from endogenous and exogenous factors. The accumulation of damaged or incompletely-repaired DNA can cause serious problems in cells, including cell death or cancer development. Various DNA damage detection systems and repair mechanisms have evolved at the cellular level. Although the mechanisms of these responses have been extensively studied, the global RNA expression profiles associated with genomic instability are not well-known. To detect global gene expression changes under different DNA damage and hypoxic conditions, we performed RNA-seq after treating human cervical cancer cells with ionizing radiation (IR), hydroxyurea, mitomycin C (MMC), or 1% O₂ (hypoxia). Results showed that the expression of 184-1037 genes was altered by each stimulus. We found that the expression of 51 genes changed under IR, MMC, and hypoxia. These findings revealed damage-specific genes that varied differently according to each stimulus and common genes that are universally altered in genetic instability.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.3
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• pp.340-345
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• 2008

Oxidative stress is one of the major causes of failure of in vitro storage of boar semen. Reactive oxygen species (ROS) are one of the important mediators of oxidative stress during in vitro storage of boar semen. Our study examined the effects of taurine on sperm characteristic and on in vitro developmental embryos during in vitro storage of boar semen for 7 days. Semen was randomly aliquoted into 3 centrifuge tubes and treated with different concentrations of taurine (25-100 mM). The characteristics of boar sperm were analyzed for motility by light microscopy, viability by using a Makler counting chamber and membrane integrity by a hypoosmotic swelling test (HOST). The percentages of motile spermatozoa in taurine groups after 5 days were significantly higher compared to the control. Sperm viability in the control was lower than in taurine groups after 7 days irrespective of different taurine concentration. In the hyoosmotic swelling test (HOST), significantly higher results were obtained in taurine groups after 3 days. Also, the developmental rates of IVM/IVF porcine embryos from semen treated with pyruvate and taurine were significantly increased when compared with the control (p<0.05). These results indicate that supplementation of taurine as an antioxidant in boar semen extender can improve the semen quality.

• Journal of Oral Medicine and Pain
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• v.31 no.1
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• pp.1-16
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• 2006

The most important progress in diagnostic sciences is the increased sensitivity and specificity in diagnostic procedures due to the development of micromethodologies and increasing availability of immunological and molecular biological reagents. The technological advances led to consider the diagnostic use of saliva for an array of analytes and DNA source. The purpose of the present study was to compare DNA from saliva with those from blood and buccal swab, to evaluate diagnostic and forensic application of saliva, to investigate the changes of genomic DNA in saliva according to the storage temperature and period of saliva samples, and to evaluate the integrity of the DNA from saliva stored under various storage conditions by PCR analysis. Peripheral venous blood, unstimulated whole saliva, stimulated whole saliva, and buccal swab were obtained from healthy 10 subjects (mean age: $29.9{\pm}9.8$ years) and genomic DNA was extracted using commercial kit. For the study of effects of various storage conditions on genomic DNA from saliva, stimulated whole saliva were obtained from healthy 20 subjects (mean age: $32.3{\pm}6.6$ years). After making aliquots from fresh saliva, they were stored at room temperature, $4^{\circ}C$, $-20^{\circ}C$, and $-70^{\circ}C$. Saliva samples after lyophilization and dry-out procedure were stored at room temperature. After 1, 3, and 5 months, the same experiment was performed to investigate the changes in genomic DNA in saliva samples. In case of saliva aliquots stored at room temperature and dry-out samples, the results in 2 weeks were also included. Integrity of DNA from saliva stored under various storage conditions was also evaluated by PCR amplification analysis of $\beta$-globin gene fragments (989-bp). The results were as follows: 1. Concentration of genomic DNA extracted from saliva was lower than that from blood (p<0.05), but there were no significant differences among various types of saliva samples. Purities of genomic DNA extracted from stimulated whole saliva and lyophilized one were significantly higher than that from blood (p<0.05). Purity of genomic DNA extracted from buccal swab was lower than those from various types of saliva samples (p<0.05). 2. Concentration of genomic DNA from saliva stored at room temperature showed gradual reduction after 1 month, and decreased significantly in 3 and 5 months (p<0.05, p<0.01, respectively). Purities of DNA from saliva stored for 3 and 5 months showed significant differences with those of fresh saliva and stored saliva for 1 month (p<0.05). 3. In the case of saliva stored at $4^{\circ}C$ and $-20^{\circ}C$, there were no significant changes of concentration of genomic DNA in 3 months. Concentration of DNA decreased significantly in 5 months (p<0.05). 4. There were no significant differences of concentration of genomic DNA from saliva stored at $-70^{\circ}C$ and from lyophilized one according to storage period. Concentration of DNA showed decreasing tendency in 5 months. 5. Concentration of genomic DNA immediately extracted from saliva dried on Petri dish were 60% compared with that of fresh saliva. Concentration of DNA from saliva stored at room temperature after dry-out showed rapid reduction within 2 weeks (p<0.05). 6. Amplification of $\beta$-globin gene using PCR was successful in all lyophilized saliva stored for 5 months. At the time of 1 month, $\beta$-globin gene was successfully amplified in all saliva samples stored at $-20^{\circ}C$ and $-70^{\circ}C$, and in some saliva samples stored at $4^{\circ}C$. $\beta$-globin gene was failed to amplify in saliva stored at room temperature and dry-out saliva.

• Molecules and Cells
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• v.37 no.8
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• pp.569-574
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• 2014

As a scaffold, SLX4/FANCP interacts with multiple proteins involved in genome integrity. Although not having recognizable catalytic domains, SLX4 participates in diverse genome maintenance pathways by delivering nucleases where they are needed, and promoting their cooperative execution to prevent genomic instabilities. Physiological importance of SLX4 is emphasized by the identification of causative mutations of SLX4 genes in patients diagnosed with Fanconi anemia (FA), a rare recessive genetic disorder characterized by genomic instability and predisposition to cancers. Recent progress in understanding functional roles of SLX4 has greatly expanded our knowledge in the repair of DNA interstrand crosslinks (ICLs), Holliday junction (HJ) resolution, telomere homeostasis and regulation of DNA damage response induced by replication stress. Here, these diverse functions of SLX4 are reviewed in detail.

• Animal cells and systems
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• v.15 no.3
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• pp.251-258
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• 2011

Ciliates are considered one of the most diverse protozoa and play significant roles in ecology. For successful taxonomic study of these microscopic eukaryotes, a staining procedure is necessary, due mainly to intrinsic difficulties in recognizing characteristics from living cells. Although molecular taxonomy has been used to resolve the ambiguities associated with traditional morphology-based taxonomy, extraction of genomic DNA from stained ciliate cells is not available yet. In the present study, we describe a method to extract genomic DNA from a single protargol-impregnated euplotid cell. By using $HgCl_2$ as a fixative and modulating the exposure time of bleach solution in the protargol impregnation, high-quality genomic DNA can successfully be extracted from a stained single cell with minimal loss of morphological integrity. This technique will contribute to the effectiveness of combined approaches of molecular and morphological taxonomy from single ciliate cells.