المؤلفون: Said Nadeem, Ömür Baysal, Ragıp Soner Silme, Burak Şener

المساهمون: MÜ, Fen Fakültesi, Moleküler Biyoloji ve Genetik Bölümü, Şener, Burak, Baysal, Ömür, Silme, Ragıp Soner

المصدر: Acta Chimica Slovenica, Vol 68, Iss 4, Pp 781-790 (2021)

مصطلحات موضوعية: DNA, Bacterial, Alkylation, viruses, genetic processes, detection, DNA, Single-Stranded, kit designing, Biosensing Techniques, Bacillus subtilis, environment and public health, chemistry.chemical_compound, bacterial pathogens, dna probe, QD1-999, Fluorescent Dyes, General Environmental Science, biology, nanotechnology, Adenine, Hybridization probe, biology.organism_classification, Fluorescence, Thymine, enzymes and coenzymes (carbohydrates), Chemistry, DNA probe, chemistry, Biochemistry, naked-eye chemosensor, health occupations, General Earth and Planetary Sciences, Colorimetry, Bacterial pathogens, Naked eye, DNA Probes, Clavibacter michiganensis, Nitrocellulose, DNA

الوصف: A rapid and confident tool to identify and diagnose bacterial pathogens with more accuracy using DNA as fingerprints is necessary. Herein, we report a smart chemosensor having a terminal adenine sticking to the thymine of single-stranded DNA (ssDNA) through supramolecular interactions and, which leaves ssDNA when the same ssDNA matches with the targeting desired DNA. We have synthesized a naked-eye coloured chemosensor with carbazole. As a model genetic material, DNA of Clavibacter michiganensis subsp. michiganensis was hybridized to ssDNA and immobilized over nitrocellulose membrane. The prepared adenine-chemosensor, by passing through the nitrocellulose-ssDNA membrane caused the formation of ssDNA nitrocellulose-ssDNA-adenine-chemosensor. FTIR results of the immobilized ssDNAs showed that the matching of same ssDNA releases the adenine-chemosensor from the surface of nitrocellulose-ssDNA that results in formation of the double stranded DNA. The selectivity of chemosensor was also confirmed with different bacterial DNA (Bacillus subtilis) as control. These data highlights accurate and reliable results of a new diagnostic kit prototype promising for further studies, which is able to diagnose DNA quickly and precisely.

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4b82f00ce1b9ee8d5520684baf344d24Test
https://journals.matheo.si/index.php/ACSi/article/view/6749Test

المؤلفون: Chunpeng Craig Wan, Muhammad Farrukh Nisar, Chunhua Zhang, Zhiguo Shan, Mingxi Li

المصدر: Oxidative Medicine and Cellular Longevity
Oxidative Medicine and Cellular Longevity, Vol 2021 (2021)

مصطلحات موضوعية: Aging, genetic processes, Review Article, Computational biology, Health benefits, Gut flora, Biochemistry, Antioxidants, Catechin, Human health, chemistry.chemical_compound, Animals, Biflavonoids, Humans, natural sciences, Theaflavin, Black tea, Inflammation, QH573-671, biology, fungi, Neurodegenerative Diseases, Cell Biology, General Medicine, Biological potential, biology.organism_classification, Gastrointestinal Microbiome, chemistry, Osteoporosis, Cytology

الوصف: Huge epidemiological and clinical studies have confirmed that black tea is a rich source of health-promoting ingredients, such as catechins and theaflavins (TFs). Furthermore, TF derivatives mainly include theaflavin (TF1), theaflavin-3-gallate (TF2A), theaflavin-3′-gallate (TF2B), and theaflavin-3,3′-digallate (TF3). All of these TFs exhibit extensive usages in pharmaceutics, foods, and traditional medication systems. Various indepth studies reported that how TFs modulates health effects in cellular and molecular mechanisms. The available literature regarding the pharmacological activities of TFs has revealed that TF3 has remarkable anti-inflammatory, antioxidant, anticancer, antiobesity, antiosteoporotic, and antimicrobial properties, thus posing significant effects on human health. The current manuscript summarizes both the chemistry and various pharmacological effects of TFs on human health, lifestyle or aging associated diseases, and populations of gut microbiota. Furthermore, the biological potential of TFs has also been focused to provide a deeper understanding of its mechanism of action.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c20b365d01fc35c642ec7e6c6cacb28aTest
https://doi.org/10.1155/2021/6256618Test

المؤلفون: Peter Chi, Kai-Hang Lei, Tzu-Yu Lee, Hao-Yen Chang, Han-Lin Yang, Xinxing Lyu, Hsin-Yi Yeh, Megan Chastain, Hung-Wen Li, Dinh Duc Nguyen, Weihang Chai

المصدر: Nature Communications, Vol 12, Iss 1, Pp 1-15 (2021)
Nature Communications

مصطلحات موضوعية: DNA Replication, Saccharomyces cerevisiae Proteins, Science, genetic processes, RAD51, General Physics and Astronomy, Electrophoretic Mobility Shift Assay, Saccharomyces cerevisiae, DNA-binding protein, complex mixtures, General Biochemistry, Genetics and Molecular Biology, Article, Protein filament, Recombinases, chemistry.chemical_compound, Replication Protein A, DNA-binding proteins, Recombinase, Humans, Immunoprecipitation, Replication protein A, Multidisciplinary, General Chemistry, Crosstalk (biology), enzymes and coenzymes (carbohydrates), HEK293 Cells, chemistry, Ionic strength, Biophysics, health occupations, Rad51 Recombinase, biological phenomena, cell phenomena, and immunity, human activities, DNA, HeLa Cells, Protein Binding

الوصف: Replication stress causes replication fork stalling, resulting in an accumulation of single-stranded DNA (ssDNA). Replication protein A (RPA) and CTC1-STN1-TEN1 (CST) complex bind ssDNA and are found at stalled forks, where they regulate RAD51 recruitment and foci formation in vivo. Here, we investigate crosstalk between RPA, CST, and RAD51. We show that CST and RPA localize in close proximity in cells. Although CST stably binds to ssDNA with a high affinity at low ionic strength, the interaction becomes more dynamic and enables facilitated dissociation at high ionic strength. CST can coexist with RPA on the same ssDNA and target RAD51 to RPA-coated ssDNA. Notably, whereas RPA-coated ssDNA inhibits RAD51 activity, RAD51 can assemble a functional filament and exhibit strand-exchange activity on CST-coated ssDNA at high ionic strength. Our findings provide mechanistic insights into how CST targets and tethers RAD51 to RPA-coated ssDNA in response to replication stress.
During replication stress, the RPA protein complex coats single-stranded DNA to preclude RAD51 loading. Here, the authors show how RPA and CST crosstalk to regulate RAD51 activity.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f5432e726fecfb2f9718f809af98f616Test
https://doaj.org/article/ecb6eb4b3da245efbbff43e501310a5dTest

المؤلفون: Hongzhi Li, Chen Wang, André Nussenzweig, Raphael Souza Pavani, Nicholas Zolnerowich, Jacob Paiano, Li Zheng, Wei Wu, Barry P. Sleckman, Binghui Shen, Bo-Ruei Chen

المصدر: Genes & Development. 35:1356-1367

مصطلحات موضوعية: DNA Replication, Exonuclease, Nuclease, DNA Repair, biology, DNA synthesis, DNA polymerase, genetic processes, DNA, Single-Stranded, Cell biology, chemistry.chemical_compound, chemistry, Dna breaks, Genetics, biology.protein, DNA Breaks, Double-Stranded, Homologous Recombination, Tumor Suppressor p53-Binding Protein 1, Homologous recombination, DNA, Polymerase, Developmental Biology

الوصف: Double-strand break (DSB) repair choice is greatly influenced by the initial processing of DNA ends. 53BP1 limits the formation of recombinogenic single-strand DNA (ssDNA) in BRCA1-deficient cells, leading to defects in homologous recombination (HR). However, the exact mechanisms by which 53BP1 inhibits DSB resection remain unclear. Previous studies have identified two potential pathways: protection against DNA2/EXO1 exonucleases presumably through the Shieldin (SHLD) complex binding to ssDNA, and localized DNA synthesis through the CTC1-STN1-TEN1 (CST) and DNA polymerase α (Polα) to counteract resection. Using a combinatorial approach of END-seq, SAR-seq, and RPA ChIP-seq, we directly assessed the extent of resection, DNA synthesis, and ssDNA, respectively, at restriction enzyme-induced DSBs. We show that, in the presence of 53BP1, Polα-dependent DNA synthesis reduces the fraction of resected DSBs and the resection lengths in G0/G1, supporting a previous model that fill-in synthesis can limit the extent of resection. However, in the absence of 53BP1, Polα activity is sustained on ssDNA yet does not substantially counter resection. In contrast, EXO1 nuclease activity is essential for hyperresection in the absence of 53BP1. Thus, Polα-mediated fill-in partially limits resection in the presence of 53BP1 but cannot counter extensive hyperresection due to the loss of 53BP1 exonuclease blockade. These data provide the first nucleotide mapping of DNA synthesis at resected DSBs and provide insight into the relationship between fill-in polymerases and resection exonucleases.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6813987cbee383022ac615a0ce2cc09dTest
https://doi.org/10.1101/gad.348667.121Test

المؤلفون: Rosalinda Xiong, Antoine Simoneau, Lee Zou

المصدر: Genes & Development. 35:1271-1289

مصطلحات موضوعية: 0303 health sciences, DNA synthesis, DNA damage, Poly ADP ribose polymerase, genetic processes, RAD51, DNA replication, Cell cycle, Biology, 3. Good health, Cell biology, enzymes and coenzymes (carbohydrates), 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, chemistry, 030220 oncology & carcinogenesis, PARP inhibitor, Genetics, DNA, 030304 developmental biology, Developmental Biology

الوصف: PARP inhibitor (PARPi) is widely used to treat BRCA1/2-deficient tumors, but why PARPi is more effective than other DNA-damaging drugs is unclear. Here, we show that PARPi generates DNA double-strand breaks (DSBs) predominantly in a trans cell cycle manner. During the first S phase after PARPi exposure, PARPi induces single-stranded DNA (ssDNA) gaps behind DNA replication forks. By trapping PARP on DNA, PARPi prevents the completion of gap repair until the next S phase, leading to collisions of replication forks with ssDNA gaps and a surge of DSBs. In the second S phase, BRCA1/2-deficient cells are unable to suppress origin firing through ATR, resulting in continuous DNA synthesis and more DSBs. Furthermore, BRCA1/2-deficient cells cannot recruit RAD51 to repair collapsed forks. Thus, PARPi induces DSBs progressively through trans cell cycle ssDNA gaps, and BRCA1/2-deficient cells fail to slow down and repair DSBs over multiple cell cycles, explaining the unique efficacy of PARPi in BRCA1/2-deficient cells.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_________::c13b1480c149d8ba8056206d8c2ea6dcTest
https://doi.org/10.1101/gad.348479.121Test

المؤلفون: Jianling Zhong, Trung Q. Tran, Alexander J. Hartemink, David M. MacAlpine, Sneha Mitra

المصدر: Nucleic Acids Research

مصطلحات موضوعية: AcademicSubjects/SCI00010, genetic processes, Saccharomyces cerevisiae, Computational biology, Biology, Genome, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Gene Expression Regulation, Fungal, Genetics, Transcriptional regulation, Nucleosome, natural sciences, RNA-Seq, Transcription factor, Narese/7, 030304 developmental biology, Epigenomics, Regulation of gene expression, 0303 health sciences, Computational Biology, High-Throughput Nucleotide Sequencing, Chromatin, Nucleosomes, Narese/24, chemistry, Mutation, Chromatin Immunoprecipitation Sequencing, Genome, Fungal, Algorithms, 030217 neurology & neurosurgery, DNA, Transcription Factors

الوصف: Chromatin is a tightly packaged structure of DNA and protein within the nucleus of a cell. The arrangement of different protein complexes along the DNA modulates and is modulated by gene expression. Measuring the binding locations and occupancy levels of different transcription factors (TFs) and nucleosomes is therefore crucial to understanding gene regulation. Antibody-based methods for assaying chromatin occupancy are capable of identifying the binding sites of specific DNA binding factors, but only one factor at a time. In contrast, epigenomic accessibility data like MNase-seq, DNase-seq, and ATAC-seq provide insight into the chromatin landscape of all factors bound along the genome, but with little insight into the identities of those factors. Here, we present RoboCOP, a multivariate state space model that integrates chromatin accessibility data with nucleotide sequence to jointly compute genome-wide probabilistic scores of nucleosome and TF occupancy, for hundreds of different factors. We apply RoboCOP to MNase-seq and ATAC-seq data to elucidate the protein-binding landscape of nucleosomes and 150 TFs across the yeast genome, and show that our model makes better predictions than existing methods. We also compute a chromatin occupancy profile of the yeast genome under cadmium stress, revealing chromatin dynamics associated with transcriptional regulation.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4d5d19380d7ca75d3a09df97d5744766Test
https://doi.org/10.1093/nar/gkab553Test

المؤلفون: Dongqing Xu, Baoling Yang, Tingting Ran, Fenglian Chu, Haixia Li, Weiwu Wang

المصدر: Indian J Microbiol

مصطلحات موضوعية: 0106 biological sciences, genetic processes, 01 natural sciences, Microbiology, Prodigiosin, 03 medical and health sciences, chemistry.chemical_compound, Transcription (biology), Sigma factor, 010608 biotechnology, RNA polymerase, Gene cluster, Original Research Article, 0303 health sciences, biology, 030306 microbiology, Chemistry, Promoter, biochemical phenomena, metabolism, and nutrition, equipment and supplies, biology.organism_classification, Cell biology, carbohydrates (lipids), Serratia marcescens, bacteria, rpoS

الوصف: RpoS, an alternative sigma factor of RNA polymerase, regulates the expression of a great deal of genes involved in stationary-phase survival and stress response. To identify the function of RpoS homologue in Serratia marcescens FS14, in-frame deletion mutant of rpoS was constructed. It was found that RpoS activates the biosynthesis of prodigiosin in FS14 which is just opposite to what was observed in Serratia sp. ATCC 39006. We also demonstrated that RpoS positively regulates the prodigiosin production by activating the transcription of pig cluster in FS14, and the transcription of pig cluster is RpoS-dependent. Further study showed that the differences in the promoters of pig clusters in FS14 and 39006 lead to the different selection of the sigma factors and result in the different regulation mechanisms. The -10 element and the spacer region between -10 and -35 elements of the pig cluster in FS14 are vital for the RpoS recognition in FS14. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-021-00952-4.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3218099f3feb15f740abd2294a6758dcTest
https://doi.org/10.1007/s12088-021-00952-4Test

المؤلفون: Liang Wang, Alex C. Soupir, Jinyong Huang

المصدر: Epigenetics

مصطلحات موضوعية: 0301 basic medicine, Cancer Research, genetic processes, Bisulfite sequencing, Computational biology, Biology, DNA-binding protein, DNA sequencing, Epigenome, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, natural sciences, Molecular Biology, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Methylation, DNA Methylation, 030104 developmental biology, CpG site, chemistry, Cell-free fetal DNA, 030220 oncology & carcinogenesis, DNA methylation, CpG Islands, Cell-Free Nucleic Acids, DNA, Research Paper

الوصف: Methylation signatures in cell-free DNA (cfDNA) have shown great sensitivity and specificity in the characterization of tumour status and classification of tumour types, as well as the response to therapy and recurrence. Currently, most cfDNA methylation studies are based on bisulphite conversion, especially targeted bisulphite sequencing, while enrichment-based methods such as cfMeDIP-seq are beginning to show potential. Here, we report an enrichment-based ultra-low input cfDNA methylation profiling method using methyl-CpG binding proteins capture, termed cfMBD-seq. We optimized the conditions for cfMBD capture by adjusting the amount of MethylCap protein along with using methylated filler DNA. Our data show high correlation between low input cfMBD-seq and standard MBD-seq (>1000 ng input). When compared to cfMEDIP-seq, cfMBD-seq demonstrates higher sequencing data quality with more sequenced reads passed filter and less duplicate rate. cfMBD-seq also outperforms cfMeDIP-seq in the enrichment of CpG islands. This new bisulphite-free ultra-low input methylation profiling technology has great potential in non-invasive and cost-effective cancer detection and classification.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::882661df7c6972068b89c41c5998fb15Test
https://doi.org/10.1080/15592294.2021.1896984Test

المؤلفون: Marcel Turcotte, Aseel Awdeh, Theodore J. Perkins

المصدر: BMC Bioinformatics, Vol 22, Iss 1, Pp 1-21 (2021)
BMC Bioinformatics

مصطلحات موضوعية: Chromatin Immunoprecipitation, Computer science, Reliability (computer networking), genetic processes, lcsh:Computer applications to medicine. Medical informatics, Biochemistry, Genome, Signal, DNA sequencing, chemistry.chemical_compound, 03 medical and health sciences, 0302 clinical medicine, Bias, Structural Biology, natural sciences, Molecular Biology, lcsh:QH301-705.5, 030304 developmental biology, Controls, 0303 health sciences, Reproducibility, biology, Noise (signal processing), business.industry, Applied Mathematics, High-Throughput Nucleotide Sequencing, Reproducibility of Results, Contrast (statistics), Pattern recognition, Sequence Analysis, DNA, Chip, Computer Science Applications, Weighting, ChIP-seq, Histone, chemistry, lcsh:Biology (General), biology.protein, Chromatin Immunoprecipitation Sequencing, lcsh:R858-859.7, Artificial intelligence, business, Chromatin immunoprecipitation, Peak calling, Algorithms, DNA, 030217 neurology & neurosurgery, Research Article

الوصف: Background Chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq), initially introduced more than a decade ago, is widely used by the scientific community to detect protein/DNA binding and histone modifications across the genome. Every experiment is prone to noise and bias, and ChIP-seq experiments are no exception. To alleviate bias, the incorporation of control datasets in ChIP-seq analysis is an essential step. The controls are used to account for the background signal, while the remainder of the ChIP-seq signal captures true binding or histone modification. However, a recurrent issue is different types of bias in different ChIP-seq experiments. Depending on which controls are used, different aspects of ChIP-seq bias are better or worse accounted for, and peak calling can produce different results for the same ChIP-seq experiment. Consequently, generating “smart” controls, which model the non-signal effect for a specific ChIP-seq experiment, could enhance contrast and increase the reliability and reproducibility of the results. Result We propose a peak calling algorithm, Weighted Analysis of ChIP-seq (WACS), which is an extension of the well-known peak caller MACS2. There are two main steps in WACS: First, weights are estimated for each control using non-negative least squares regression. The goal is to customize controls to model the noise distribution for each ChIP-seq experiment. This is then followed by peak calling. We demonstrate that WACS significantly outperforms MACS2 and AIControl, another recent algorithm for generating smart controls, in the detection of enriched regions along the genome, in terms of motif enrichment and reproducibility analyses. Conclusions This ultimately improves our understanding of ChIP-seq controls and their biases, and shows that WACS results in a better approximation of the noise distribution in controls.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2708fcb3af349f5ded151af2aa0bd2a0Test
https://doaj.org/article/3d0f3ca77ba84cfa914356385e9ad0e2Test

المؤلفون: Wanlong Tan, Wendong Liu, Lina Hou, Kunfeng Xie, Fei Li, Weiwei Xie, Yunze Fang

المصدر: Journal of Cancer

مصطلحات موضوعية: 0301 basic medicine, viruses, Proliferation, genetic processes, Heterogeneous nuclear ribonucleoprotein F, FOXO1, environment and public health, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Phosphoinositide 3‑kinase/protein kinase B signalling pathway, LY294002, Protein kinase B, PI3K/AKT/mTOR pathway, Gene knockdown, Forkhead box O1, Chemistry, Bladder cancer, Cell biology, 030104 developmental biology, Oncology, 030220 oncology & carcinogenesis, health occupations, Phosphorylation, Chromatin immunoprecipitation, Research Paper

الوصف: Our previous study showed that heterogeneous nuclear ribonucleoprotein F (hnRNP-F) could induce epithelial-mesenchymal transition and metastasis in bladder cancer (BC), however, the role and mechanism of hnRNP-F in mediating the proliferative ability of BC cells remain unclear. HnRNP-F promoted the proliferation of BC cells by using BC cell lines and cell counting kit-8 (CCK8), colony formation and flow cytometry assays in vitro. Furthermore, the association of hnRNP-F with the phosphoinositide 3‑kinase (PI3K)/protein kinase B (AKT) signalling pathway was confirmed by western blotting after bioinformatic analysis. HnRNP-F expression was significantly decreased by treatment with the PI3K/AKT signalling pathway inhibitor LY294002, whereas hnRNP-F knockdown did not significantly affect PI3K or AKT expression, suggesting that hnRNP-F is likely a downstream target of the PI3K/AKT pathway. Forkhead box O1 (FOXO1) is a molecule downstream of PI3K/AKT and can be inhibited by phosphorylation. In addition, chromatin immunoprecipitation (ChIP) and luciferase reporter assays indicated that FOXO1 expression was negatively correlated with hnRNP-F expression as FOXO1 was found to bind to the promoter region of hnRNP-F mRNA and inhibit its transcription. To sum up, our findings suggest that hnRNP-F expression is regulated by the PI3K/AKT-mediated phosphorylation of FOXO1, with phosphorylation inhibiting FOXO1, which subsequently allows hnRNP-F to promote proliferation. This finding is a novel discovery in BC and could help reveal the mechanism of BC progression.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::370e6c36efae530e1e91447774aa73f3Test
https://doi.org/10.7150/jca.50490Test