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https://www.readbyqxmd.com/read/28525990/transversions-have-larger-regulatory-effects-than-transitions
#1
Cong Guo, Ian C McDowell, Michael Nodzenski, Denise M Scholtens, Andrew S Allen, William L Lowe, Timothy E Reddy
BACKGROUND: Transversions (Tv's) are more likely to alter the amino acid sequence of proteins than transitions (Ts's), and local deviations in the Ts:Tv ratio are indicative of evolutionary selection on genes. Whether the two different types of mutations have different effects in non-protein-coding sequences remains unknown. Genetic variants primarily impact gene expression by disrupting the binding of transcription factors (TFs) and other DNA-binding proteins. Because Tv's cause larger changes in the shape of a DNA backbone, we hypothesized that Tv's would have larger impacts on TF binding and gene expression...
May 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28525760/snapshot-nucleo-cytoskeletal-interactions
#2
Cátia S Janota, Francisco J Calero-Cuenca, Judite Costa, Edgar R Gomes
The nucleus is connected to the cytoskeleton, and these connections are involved in multiple functions such as nuclear positioning, shape and stiffness, cytoskeleton organization, mechanotransduction, gene expression, chromosome positioning, DNA repair, and cell migration.
May 18, 2017: Cell
https://www.readbyqxmd.com/read/28523562/bioinformatics-tools-for-genome-wide-epigenetic-research
#3
Vladimir Espinosa Angarica, Antonio Del Sol
Epigenetics play a central role in the regulation of many important cellular processes, and dysregulations at the epigenetic level could be the source of serious pathologies, such as neurological disorders affecting brain development, neurodegeneration, and intellectual disability. Despite significant technological advances for epigenetic profiling, there is still a need for a systematic understanding of how epigenetics shapes cellular circuitry, and disease pathogenesis. The development of accurate computational approaches for analyzing complex epigenetic profiles is essential for disentangling the mechanisms underlying cellular development, and the intricate interaction networks determining and sensing chromatin modifications and DNA methylation to control gene expression...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28523547/dna-methylation-in-major-depressive-disorder
#4
Ehsan Pishva, Bart P F Rutten, Daniel van den Hove
Epigenetic mechanisms regulate gene expression, influencing protein levels and ultimately shaping phenotypes during life. However, both stochastic epigenetic variations and environmental reprogramming of the epigenome might influence neurodevelopment and ageing, and this may contribute to the origins of mental ill-health. Studying the role of epigenetic mechanisms is challenging, as genotype-, tissue- and cell type-dependent epigenetic changes have to be taken into account, while the nature of mental disorders also poses significant challenges for linking them with biological profiles...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28523542/eating-disorders-and-epigenetics
#5
Lea Thaler, Howard Steiger
Eating disorders (EDs) are characterized by intense preoccupation with shape and weight and maladaptive eating practices. The complex of symptoms that characterize EDs often arise through the activation of latent genetic potentials by environmental exposures, and epigenetic mechanisms are believed to link environmental exposures to gene expression. This chapter provides an overview of genetic factors acting in the etiology of EDs. It then provides a background to the hypothesis that epigenetic mechanisms link stresses such as obstetric complications and childhood abuse as well as effects of malnutrition to eating disorders (EDs)...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28523272/structural-elements-regulating-aaa-protein-quality-control-machines
#6
REVIEW
Chiung-Wen Chang, Sukyeong Lee, Francis T F Tsai
Members of the ATPases Associated with various cellular Activities (AAA+) superfamily participate in essential and diverse cellular pathways in all kingdoms of life by harnessing the energy of ATP binding and hydrolysis to drive their biological functions. Although most AAA+ proteins share a ring-shaped architecture, AAA+ proteins have evolved distinct structural elements that are fine-tuned to their specific functions. A central question in the field is how ATP binding and hydrolysis are coupled to substrate translocation through the central channel of ring-forming AAA+ proteins...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28523015/transcription-factors-in-fungi-tfome-dynamics-three-major-families-and-dual-specificity-tfs
#7
Ekaterina Shelest
Transcription factors (TFs) are essential regulators of gene expression in a cell; the entire repertoire of TFs (TFome) of a species reflects its regulatory potential and the evolutionary history of the regulatory mechanisms. In this work, I give an overview of fungal TFs, analyze TFome dynamics, and discuss TF families and types of particular interest. Whole-genome annotation of TFs in more than 200 fungal species revealed ~80 families of TFs that are typically found in fungi. Almost half of the considered genomes belonged to basidiomycetes and zygomycetes, which have been underrepresented in earlier annotations due to dearth of sequenced genomes...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28521766/the-histone-h3-variant-h3-3-regulates-gene-body-dna-methylation-in-arabidopsis-thaliana
#8
Heike Wollmann, Hume Stroud, Ramesh Yelagandula, Yoshiaki Tarutani, Danhua Jiang, Li Jing, Bhagyshree Jamge, Hidenori Takeuchi, Sarah Holec, Xin Nie, Tetsuji Kakutani, Steven E Jacobsen, Frédéric Berger
BACKGROUND: Gene bodies of vertebrates and flowering plants are occupied by the histone variant H3.3 and DNA methylation. The origin and significance of these profiles remain largely unknown. DNA methylation and H3.3 enrichment profiles over gene bodies are correlated and both have a similar dependence on gene transcription levels. This suggests a mechanistic link between H3.3 and gene body methylation. RESULTS: We engineered an H3.3 knockdown in Arabidopsis thaliana and observed transcription reduction that predominantly affects genes responsive to environmental cues...
May 18, 2017: Genome Biology
https://www.readbyqxmd.com/read/28521053/compaction-and-condensation-of-dna-mediated-by-the-c-terminal-domain-of-hfq
#9
Antoine Malabirade, Kai Jiang, Krzysztof Kubiak, Alvaro Diaz-Mendoza, Fan Liu, Jeroen A van Kan, Jean-François Berret, Véronique Arluison, Johan R C van der Maarel
Hfq is a bacterial protein that is involved in several aspects of nucleic acids metabolism. It has been described as one of the nucleoid associated proteins shaping the bacterial chromosome, although it is better known to influence translation and turnover of cellular RNAs. Here, we explore the role of Escherichia coli Hfq's C-terminal domain in the compaction of double stranded DNA. Various experimental methodologies, including fluorescence microscopy imaging of single DNA molecules confined inside nanofluidic channels, atomic force microscopy, isothermal titration microcalorimetry and electrophoretic mobility assays have been used to follow the assembly of the C-terminal and N-terminal regions of Hfq on DNA...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28514924/rapid-and-annealing-free-self-assembly-of-dna-building-blocks-for-3d-hydrogel-chaperoned-by-cationic-comb-type-copolymers
#10
Zheng Zhang, Yuyang Wu, Feng Yu, Chaoqun Niu, Zhi Du, Yong Chen, Jie Du
The construction and self-assembly of DNA building blocks are the foundation of bottom-up development of three-dimensional DNA nanostructures or hydrogels. However, most self-assembly from DNA components is impeded by the mishybridized intermediates or the thermodynamic instability. To enable rapid production of complicated DNA objects with high yields no need for annealing process, herein different DNA building blocks (Y-shaped, L- and L'-shaped units) were assembled in presence of a cationic comb-type copolymer, poly (L-lysine)-graft-dextran (PLL-g-Dex), under physiological conditions...
May 18, 2017: Journal of Biomaterials Science. Polymer Edition
https://www.readbyqxmd.com/read/28514427/illuminating-developmental-biology-through-photochemistry
#11
Lukasz Kowalik, James K Chen
Developmental biology has been continually shaped by technological advances, evolving from a descriptive science into one immersed in molecular and cellular mechanisms. Most recently, genome sequencing and 'omics' profiling have provided developmental biologists with a wealth of genetic and biochemical information; however, fully translating this knowledge into functional understanding will require new experimental capabilities. Photoactivatable probes have emerged as particularly valuable tools for investigating developmental mechanisms, as they can enable rapid, specific manipulations of DNA, RNA, proteins, and cells with spatiotemporal precision...
May 17, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28507345/genetic-variation-and-phylogeographic-structure-of-the-cotton-aphid-aphis-gossypii-based-on-mitochondrial-dna-and-microsatellite-markers
#12
Xing-Ya Wang, Xian-Ming Yang, Bin Lu, Li-Hong Zhou, Kong-Ming Wu
Aphis gossypii, one of the most important agricultural pests in the world, can cause serious economic losses in the main crop-producing areas. To clarify issues such as the genetic differentiation, genetic structure, and demographic history of A. gossypii populations, we used 10 nuclear microsatellite loci (SSR) and two mitochondrial gene sequences (COI and Cytb) to investigate genetic diversity and population structure of A. gossypii populations that were collected from 33 sampling sites in China from different climatic zones...
May 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28505481/altered-development-oxidative-stress-and-dna-damage-in-leptodactylus-chaquensis-anura-leptodactylidae-larvae-exposed-to-poultry-litter
#13
L M Curi, P M Peltzer, C Martinuzzi, M A Attademo, S Seib, M F Simoniello, R C Lajmanovich
Poultry litter (PL), which is usually used as organic fertilizer, is a source of nutrients, metals, veterinary pharmaceuticals and bacterial pathogens, which, through runoff, may end up in the nearest aquatic ecosystems. In this study, Leptodactylus chaquensis at different development stages (eggs, larval stages 28 and 31 here referred to as stages I, II and III respectively) were exposed to PL test sediments as follows: 6.25% (T1), 12.5% (T2); 25% (T3); 50% (T4); 75% (T5); 100% PL (T6) and to dechlorinated water as control...
May 11, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28503201/dna-methylation-and-dna-methyltransferases
#14
REVIEW
John R Edwards, Olya Yarychkivska, Mathieu Boulard, Timothy H Bestor
The prevailing views as to the form, function, and regulation of genomic methylation patterns have their origin many years in the past, at a time when the structure of the mammalian genome was only dimly perceived, when the number of protein-encoding mammalian genes was believed to be at least five times greater than the actual number, and when it was not understood that only ~10% of the genome is under selective pressure and likely to have biological function. We use more recent findings from genome biology and whole-genome methylation profiling to provide a reappraisal of the shape of genomic methylation patterns and the nature of the changes that they undergo during gametogenesis and early development...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28501914/skermanella-mucosa-sp-nov-isolated-from-crude-oil-contaminated-soil
#15
Y Subhash, Da-Eun Yoon, Sang-Seob Lee
A novel Gram-stain negative, small rod-shaped bacterium (strain 8-14-6(T)) was isolated from hydrocarbon contaminated desert soil collected from Kuwait. Strain 8-14-6(T) grew at 5-37 °C, pH 6.0-8.8 and 0-2% (w/v) of NaCl concentration. Casein, starch, Tween 20 and Tween 80 were hydrolyzed while urea, chitin, DNA and carboxymethyl-cellulose were not hydrolyzed by strain 8-14-6(T). The major cellular fatty acids were identified as C18:1ω6c/C18:1ω7c, C16:0 and iso-C16:1I/C14:03-OH. Strain 8-14-6(T) produced diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified phospholipids, two unidentified lipids and five unidentified amino lipids as polar lipids...
May 13, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28500524/cytoskeletal-proteins-in-caulobacter-crescentus-spatial-orchestrators-of-cell-cycle-progression-development-and-cell-shape
#16
Kousik Sundararajan, Erin D Goley
Caulobacter crescentus, an aquatic Gram-negative α-proteobacterium, is dimorphic, as a result of asymmetric cell divisions that give rise to a free-swimming swarmer daughter cell and a stationary stalked daughter. Cell polarity of vibrioid C. crescentus cells is marked by the presence of a stalk at one end in the stationary form and a polar flagellum in the motile form. Progression through the cell cycle and execution of the associated morphogenetic events are tightly controlled through regulation of the abundance and activity of key proteins...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28500521/overview-of-the-diverse-roles-of-bacterial-and-archaeal-cytoskeletons
#17
Linda A Amos, Jan Löwe
As discovered over the past 25 years, the cytoskeletons of bacteria and archaea are complex systems of proteins whose central components are dynamic cytomotive filaments. They perform roles in cell division, DNA partitioning, cell shape determination and the organisation of intracellular components. The protofilament structures and polymerisation activities of various actin-like, tubulin-like and ESCRT-like proteins of prokaryotes closely resemble their eukaryotic counterparts but show greater diversity. Their activities are modulated by a wide range of accessory proteins but these do not include homologues of the motor proteins that supplement filament dynamics to aid eukaryotic cell motility...
2017: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/28499405/a-comparative-molecular-and-3-dimensional-structural-investigation-into-cross-continental-and-novel-avian-trypanosoma-spp-in-australia
#18
Crystal Cooper, R C Andrew Thompson, Adriana Botero, Amanda Kristancic, Christopher Peacock, Yaowanuj Kirilak, Peta L Clode
BACKGROUND: Molecular and structural information on avian Trypanosoma spp. throughout Australia is limited despite their intrinsic value in understanding trypanosomatid evolution, diversity, and structural biology. In Western Australia tissue samples (n = 429) extracted from 93 birds in 25 bird species were screened using generic PCR primers to investigate the diversity of Trypanosoma spp. To investigate avian trypanosome structural biology the first 3-dimensional ultrastructural models of a Trypanosoma spp...
May 12, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28499037/ball-with-hair-modular-functionalization-of-highly-stable-g-quadruplex-dna-nano-scaffolds-through-n2-guanine-modification
#19
Christopher Jacques Lech, Anh Tuân Phan
Functionalized nanoparticles have seen valuable applications, particularly in the delivery of therapeutic and diagnostic agents in biological systems. However, the manufacturing of such nano-scale systems with the consistency required for biological application can be challenging, as variation in size and shape have large influences in nanoparticle behavior in vivo. We report on the development of a versatile nano-scaffold based on the modular functionalization of a DNA G-quadruplex. DNA sequences are functionalized in a modular fashion using well-established phosphoramidite chemical synthesis with nucleotides containing modification of the amino (N2) position of the guanine base...
May 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28496157/rna-seq-based-genome-wide-analysis-reveals-loss-of-inter-chromosomal-regulation-in-breast-cancer
#20
Jesús Espinal-Enríquez, Cristóbal Fresno, Guillermo Anda-Jáuregui, Enrique Hernández-Lemus
Breast cancer is a complex heterogeneous disease. Common hallmark features of cancer can be found. Their origin may be traced back to their intricate relationships governing regulatory programs during the development of this disease. To unveil distinctive features of the transcriptional regulation program in breast cancer, a pipeline for RNA-seq analysis in 780 breast cancer and 101 healthy breast samples, at gene expression and network level, was implemented. Inter-chromosomal relationships between genes resulted strikingly scarce in a cancer network, in comparison to its healthy counterpart...
May 11, 2017: Scientific Reports
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