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https://www.readbyqxmd.com/read/29332303/mitochondrial-dna-nuclear-context-and-the-risk-for-carcinogenesis
#1
REVIEW
Brett A Kaufman, Martin Picard, Neal Sondheimer
The inheritance of mitochondrial DNA (mtDNA) from mother to child is complicated by differences in the stability of the mitochondrial genome. Although the germ line mtDNA is protected through the minimization of replication between generations, sequence variation can occur either through mutation or due to changes in the ratio between distinct genomes that are present in the mother (known as heteroplasmy). Thus, the unpredictability in transgenerational inheritance of mtDNA may cause the emergence of pathogenic mitochondrial and cellular phenotypes in offspring...
January 14, 2018: Environmental and Molecular Mutagenesis
https://www.readbyqxmd.com/read/29332159/transposable-elements-genome-innovation-chromosome-diversity-and-centromere-conflict
#2
REVIEW
Savannah J Klein, Rachel J O'Neill
Although it was nearly 70 years ago when transposable elements (TEs) were first discovered "jumping" from one genomic location to another, TEs are now recognized as contributors to genomic innovations as well as genome instability across a wide variety of species. In this review, we illustrate the ways in which active TEs, specifically retroelements, can create novel chromosome rearrangements and impact gene expression, leading to disease in some cases and species-specific diversity in others. We explore the ways in which eukaryotic genomes have evolved defense mechanisms to temper TE activity and the ways in which TEs continue to influence genome structure despite being rendered transpositionally inactive...
January 13, 2018: Chromosome Research
https://www.readbyqxmd.com/read/29331527/construction-of-sake-yeast-with-low-production-of-dimethyl-trisulfide-precursor-by-a-self-cloning-method
#3
Yuriko Ikeda, Atsuko Isogai, Yuta Moriyoshi, Ryoko Kanda, Kazuhiro Iwashita, Tsutomu Fujii
Dimethyl trisulfide (DMTS) is the primary component responsible for "hineka", the stale aroma of Japanese sake. Deletion of the MRI1 or MDE1 gene of sake yeast, encoding 5'-methylthioribose-1-phosphate isomerase and 5'-methylthioribulose-1-phosphate dehydratase, respectively, has been reported to greatly reduce the amount of DMTS precursor (DMTS-P1) in sake and to suppress the formation of DMTS during storage. In this study, we constructed sake yeast strains lacking MRI1 gene function by a self-cloning method...
January 10, 2018: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/29330295/epigenetic-reprogramming-of-pericentromeric-satellite-dna-in-premalignant-and-malignant-lesions
#4
Nadine H Brueckmann, Christina B Pedersen, Henrik J Ditzel, Morten F Gjerstorff
Repression of repetitive DNA is important for maintaining genomic stability, but is often perturbed in cancer. For instance, the megabase satellite domain at chromosome 1q12 is a common site of genetic rearrangements, such as translocations and deletions. Polycomb-group (PcG) proteins can be observed as large subnuclear domains called polycomb bodies, the composition and cellular function of which has remained elusive. This study, demonstrates that polycomb bodies are canonical subunits of the multiprotein polycomb repressive complex 1 (PRC1) deposited on 1q12 pericentromeric satellite DNA, which are normally maintained as constitutive heterochromatin by other mechanisms...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29330052/esco2-knockdown-inhibits-cell-proliferation-and-induces-apoptosis-in-human-gastric-cancer-cells
#5
Hongmei Chen, Lei Zhang, Wenting He, Liu Tao, Yang Zhao, Hao Chen, Yumin Li
Establishment of cohesion 1 homolog 2 (ESCO2), an essential gene for cohesion regulation and genomic stability, has not been studied in human gastric cancer (GC). We found that ESCO2 knockdown in human GC cell lines dramatically inhibited cell proliferation and induced cell apoptosis in vitro and suppressed tumor xenograft development in vivo. Furthermore, adenosine monophosphate-activated protein kinase (AMPK) was activated following the suppression of its downstream targets, including mammalian target of rapamycin (mTOR) and p70 ribosomal S6 kinase 1 (p70S6K1), and this result was consistent with p53 activation...
January 9, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29329424/brassinosteroids-regulate-pavement-cell-growth-by-mediating-bin2-induced-microtubule-stabilization
#6
Xiaolei Liu, Qin Yang, Yuan Wang, Linhai Wang, Ying Fu, Xuelu Wang
Brassinosteroids (BRs), a group of plant steroid hormones, play important roles in regulating plant development. The cytoskeleton also affects key developmental processes and a deficiency in BR biosynthesis or signaling leads to abnormal phenotypes similar to those of microtubule-defective mutants. However, how BRs regulate microtubule and cell morphology remains unknown. Here, using liquid chromatography-tandem mass spectrometry, we identified tubulin proteins that interact with Arabidopsis BRASSINOSTEROID INSENSITIVE2 (BIN2), a negative regulator of BR responses in plants...
January 10, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29329249/scaffolding-for-repair-understanding-molecular-functions-of-the-smc5-6-complex
#7
REVIEW
Mariana Diaz, Ales Pecinka
Chromosome organization, dynamics and stability are required for successful passage through cellular generations and transmission of genetic information to offspring. The key components involved are Structural maintenance of chromosomes (SMC) complexes. Cohesin complex ensures proper chromatid alignment, condensin complex chromosome condensation and the SMC5/6 complex is specialized in the maintenance of genome stability. Here we summarize recent knowledge on the composition and molecular functions of SMC5/6 complex...
January 12, 2018: Genes
https://www.readbyqxmd.com/read/29328552/changes-in-chromosome-counts-and-patterns-in-cho-cell-lines-upon-generation-of-recombinant-cell-lines-and-subcloning
#8
Sabine Vcelar, Michael Melcher, Norbert Auer, Astrid Hrdina, Anja Puklowski, Friedrich Leisch, Vaibhav Jadhav, Till Wenger, Martina Baumann, Nicole Borth
Chinese hamster ovary cells are the number one production system for therapeutic proteins. A pre-requirement for their use in industrial production of biopharmaceuticals is to be clonal, thus originating from a single cell in order to be phenotypically and genomically identical. In the present study it was evaluated whether standard procedures, such as the generation of a recombinant cell line in combination with selection for a specific and stable phenotype (expression of the recombinant product) or subcloning have any impact on karyotype stability or homogeneity in CHO cells...
January 12, 2018: Biotechnology Journal
https://www.readbyqxmd.com/read/29328538/conflict-between-heterozygote-advantage-and-hybrid-incompatibility-in-haplodiploids-and-sex-chromosomes
#9
Ana-Hermina Ghenu, Alexandre Blanckaert, Roger K Butlin, Jonna Kulmuni, Claudia Bank
In many diploid species the sex chromosomes play a special role in mediating reproductive isolation. In haplodiploids, where females are diploid and males haploid, the whole genome behaves similarly to the X/Z chromosomes of diploids. Therefore, haplodiploid systems can serve as a model for the role of sex chromosomes in speciation and hybridization. A previously described population of Finnish Formica wood ants displays genome-wide signs of ploidally and sexually antagonistic selection resulting from hybridization...
January 12, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29327403/biogenesis-and-regulatory-hierarchy-of-phased-small-interfering-rnas-in-plants
#10
REVIEW
Pingchuan Deng, Sajid Muhammad, Min Cao, Liang Wu
Several varieties of small RNAs including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are generated in plants to regulate development, genome stability, and response to adverse environments. Phased siRNA (phasiRNA) is a type of secondary siRNA that is processed from a miRNA-mediated cleavage of RNA transcripts, increasing silencing efficiency or simultaneously suppressing multiple target genes. Trans-acting siRNAs (ta-siRNAs) are a particular class of phasiRNA produced from non-coding transcripts that silence targets in trans...
January 11, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29327330/microbiome-analysis-and-omics-studies-of-microbial-denitrification-processes-in-wastewater-treatment-recent-advances
#11
REVIEW
Lili Miao, Zhipei Liu
Nitrogen pollution is an increasingly severe worldwide problem because of drainage of nitrogen-containing wastewater and intensive application of nitrogen-containing fertilizers. Denitrification, a key process in nitrogen cycles, is commonly employed for nitrogen removal in engineered wastewater treatment systems. Biological denitrification is performed by denitrifying microbes (bacteria) that use nitrate as terminal electron acceptor. Better understanding the functions of diverse microbial populations in denitrification-based wastewater treatment systems, and the interactions of these populations with operating environments, is essential for improving both treatment performance and system stability...
January 9, 2018: Science China. Life Sciences
https://www.readbyqxmd.com/read/29327083/r-loops-targets-for-nuclease-cleavage-and-repeat-instability
#12
REVIEW
Catherine H Freudenreich
R-loops form when transcribed RNA remains bound to its DNA template to form a stable RNA:DNA hybrid. Stable R-loops form when the RNA is purine-rich, and are further stabilized by DNA secondary structures on the non-template strand. Interestingly, many expandable and disease-causing repeat sequences form stable R-loops, and R-loops can contribute to repeat instability. Repeat expansions are responsible for multiple neurodegenerative diseases, including Huntington's disease, myotonic dystrophy, and several types of ataxias...
January 11, 2018: Current Genetics
https://www.readbyqxmd.com/read/29327010/dna-methylation-assay-using-droplet-based-dna-melting-curve-analysis
#13
F-W Liu, H-F Liao, S-P Lin, Y-W Lu
DNA methylation is an epigenetic regulation of gene expression, which has drawn great attention in biomedical research due to its association with various diseases. A robust, inexpensive platform to detect and quantify the methylation status in a specific genomic region is necessary. In this study, an on-chip analytical technique of cytosine methylation with droplets in a microchannel is proposed. Genomic DNA samples are encapsulated into a series of droplets and transported through a detection region, where a stable temperature gradient is created...
January 12, 2018: Lab on a Chip
https://www.readbyqxmd.com/read/29325627/epigenetic-mechanisms-underlying-nervous-system-diseases
#14
Irfan A Qureshi, Mark F Mehler
Epigenetic mechanisms act as control systems for modulating genomic structure and activity in response to evolving profiles of cell-extrinsic, cell-cell, and cell-intrinsic signals. These dynamic processes are responsible for mediating cell- and tissue-specific gene expression and function and gene-gene and gene-environmental interactions. The major epigenetic mechanisms include DNA methylation and hydroxymethylation; histone protein posttranslational modifications, nucleosome remodeling/repositioning, and higher-order chromatin reorganization; noncoding RNA regulation; and RNA editing...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29323273/histone-octamer-rearranges-to-adapt-to-dna-unwrapping
#15
Silvija Bilokapic, Mike Strauss, Mario Halic
Nucleosomes, the basic units of chromatin, package and regulate expression of eukaryotic genomes. Although the structure of the intact nucleosome is well characterized, little is known about structures of partially unwrapped, transient intermediates. In this study, we present nine cryo-EM structures of distinct conformations of nucleosome and subnucleosome particles. These structures show that initial DNA breathing induces conformational changes in the histone octamer, particularly in histone H3, that propagate through the nucleosome and prevent symmetrical DNA opening...
January 2018: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29321878/asymmetric-reproductive-interference-the-consequences-of-cross-pollination-on-reproductive-success-in-sexual-apomictic-populations-of-potentilla-puberula-rosaceae
#16
Christoph Dobeš, Susanne Scheffknecht, Yulia Fenko, Dagmar Prohaska, Christina Sykora, Karl Hülber
Apomixis evolves from a sexual background and usually is linked to polyploidization. Pseudogamous gametophytic apomicts, which require a fertilization to initiate seed development, of various ploidy levels frequently co-occur with their lower-ploid sexual ancestors, but the stability of such mixed populations is affected by reproductive interferences mediated by cross-pollination. Thereby, reproductive success of crosses depends on the difference in ploidy levels of mating partners, that is, on tolerance of deviation from the balanced ratio of maternal versus paternal genomes...
January 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29321819/the-induction-of-endoreduplication-and-polyploidy-by-elevated-expression-of-14-3-3%C3%AE
#17
Cecil J Gomes, Sara M Centuori, Michael W Harman, Charles W Putnam, Charles W Wolgemuth, Jesse D Martinez
Several studies have demonstrated that specific 14-3-3 isoforms are frequently elevated in cancer and that these proteins play a role in human tumorigenesis. 14-3-3γ, an isoform recently demonstrated to function as an oncoprotein, is overexpressed in a variety of human cancers; however, its role in promoting tumorigenesis remains unclear. We previously reported that overexpression of 14-3-3γ caused the appearance of polyploid cells, a phenotype demonstrated to have profound tumor promoting properties. Here we examined the mechanism driving 14-3-3γ-induced polyploidization and the effect this has on genomic stability...
November 2017: Genes & Cancer
https://www.readbyqxmd.com/read/29321269/adding-levels-of-complexity-enhances-robustness-and-evolvability-in-a-multilevel-genotype-phenotype-map
#18
Pablo Catalán, Andreas Wagner, Susanna Manrubia, José A Cuesta
Robustness and evolvability are the main properties that account for the stability and accessibility of phenotypes. They have been studied in a number of computational genotype-phenotype maps. In this paper, we study a metabolic genotype-phenotype map defined in toyLIFE, a multilevel computational model that represents a simplified cellular biology. toyLIFE includes several levels of phenotypic expression, from proteins to regulatory networks to metabolism. Our results show that toyLIFE shares many similarities with other seemingly unrelated computational genotype-phenotype maps...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29318605/leukocyte-telomere-length-in-relation-to-risk-of-lung-adenocarcinoma-incidence-findings-from-the-singapore-chinese-health-study
#19
Jian-Min Yuan, Kenneth B Beckman, Renwei Wang, Caroline Bull, Jennifer Adams-Haduch, Joyce Y Huang, Aizhen Jin, Patricia Opresko, Anne B Newman, Yun-Ling Zheng, Michael Fenech, Woon-Puay Koh
Telomeres are crucial in the maintenance of chromosome integrity and genomic stability. Critically short telomeres can trigger programmed cell death while cells with longer telomeres may have increased likelihood of replicative errors, resulting in genetic mutations and chromosomal alterations, and ultimately promoting oncogenesis. Data on telomere length and lung cancer risk from large prospective cohort studies are spare. Relative telomere length in peripheral blood leukocytes was quantified using a validated monochrome multiplex quantitative polymerase chain reaction (qPCR) method in 26,540 participants of the Singapore Chinese Health Study...
January 10, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29317756/non-coding-rnas-predict-recurrence-free-survival-of-patients-with-hypoxic-tumours
#20
Victor D Martinez, Natalie S Firmino, Erin A Marshall, Kevin W Ng, Brennan J Wadsworth, Christine Anderson, Wan L Lam, Kevin L Bennewith
Hypoxia promotes tumour aggressiveness and reduces patient survival. A spectrum of poor outcome among patients with hypoxic tumours suggests that additional factors modulate how tumours respond to hypoxia. PIWI-interacting RNAs (piRNAs) are small non-coding RNAs with a pivotal role in genomic stability and epigenetic regulation of gene expression. We reported that cancer type-specific piRNA signatures vary among patients. However, remarkably homogenous piRNA profiles are detected across patients with renal cell carcinoma, a cancer characterized by constitutive upregulation of hypoxia-related signaling induced by common mutation or loss of von Hippel-Lindau factor (VHL)...
January 9, 2018: Scientific Reports
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