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https://www.readbyqxmd.com/read/28214612/dynamic-organization-of-mitotic-chromosomes
#1
REVIEW
Kazuhisa Kinoshita, Tatsuya Hirano
The assembly of rod-shaped chromosomes during mitosis is an essential prerequisite for faithful segregation of genetic information into daughter cells. Despite the long history of chromosome research, it is only recently that we have acquired powerful approaches and crucial tools that help to unlock the secret of this seemingly complex process. In particular, in vitro assays, mammalian genetics, Hi-C analyses and computer simulations have provided valuable information during the past two years. These studies are now beginning to elucidate how the core components of mitotic chromosomes, namely, histones, topoisomerase IIα and condensins, cooperate with each other to convert very long stretches of DNA into rod-shaped chromosomes...
February 16, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28213379/slowed-decay-of-mrnas-enhances-platelet-specific-translation
#2
Eric W Mills, Rachel Green, Nicholas T Ingolia
Platelets are anucleate cytoplasmic fragments that lack genomic DNA, but continue to synthesize protein using a pool of mRNAs, ribosomes, and regulatory small RNAs inherited from the precursor megakaryocyte (MK). The regulatory processes that shape the platelet transcriptome and the full scope of platelet translation have remained elusive. Using RNA-Seq and ribosome profiling of primary human platelets, we show the platelet transcriptome encompasses a subset of transcripts detected by RNA-Seq analysis of in vitro derived MK cells and these platelet-enriched transcripts are broadly occupied by ribosomes...
February 17, 2017: Blood
https://www.readbyqxmd.com/read/28213279/tethering-rna-to-chromatin-for-fluorescence-microscopy-based-analysis-of-nuclear-organization
#3
Teresa Pankert, Thibaud Jegou, Maïwen Caudron-Herger, Karsten Rippe
Nuclear RNAs emerge as important factors to orchestrate the dynamic organization of the nucleus into functional subcompartments. By tethering RNAs to distinct genomic loci, the RNA-dependent chromatin changes can be dissected by fluorescence microscopic analysis. Here we describe how this approach is implemented in mammalian cells. It involves two high-affinity protein-nucleic acid interactions that can established with number of different protein domains and DNA and RNA sequences. A prototypic system is described here in detail: It consists of the binding of MS2 bacteriophage coat protein to its RNA recognition sequence and the interaction between the bacterial LacI repressor protein to its target lacO operator DNA sequences...
February 14, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28212554/afb1-hepatocarcinogenesis-is-via-lipid-peroxidation-that-inhibits-dna-repair-sensitizes-mutation-susceptibility-and-induces-aldehyde-dna-adducts-at-p53-mutational-hotspot-codon-249
#4
Mao-Wen Weng, Hyun-Wook Lee, Bongkun Choi, Hsiang-Tsui Wang, Yu Hu, Manju Mehta, Dhimant Desai, Shantu Amin, Yi Zheng, Moon-Shong Tang
Aflatoxin B1 (AFB1) contamination in the food chain is a major cause of hepatocellular carcinoma (HCC). More than 60% of AFB1 related HCC carry p53 codon 249 mutations but the causal mechanism remains unclear. We found that 1) AFB1 induces two types of DNA adducts in human hepatocytes, AFB1-8,9-epoxide-deoxyguanosine (AFB1-E-dG) induced by AFB1-E and cyclic α-methyl-γ-hydroxy-1,N2-propano-dG (meth-OH-PdG) induced by lipid peroxidation generated acetaldehyde (Acet) and crotonaldehyde (Cro); 2) the level of meth-OH-PdG is >30 fold higher than the level of AFB1-E-dG; 3) AFB1, Acet, and Cro, but not AFB1-E, preferentially induce DNA damage at codon 249; 4) methylation at -CpG- sites enhances meth-OH-PdG formation at codon 249; and 5) repair of meth-OH-PdG at codon 249 is poor...
February 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28211519/palindromic-amplification-of-the-erbb2-oncogene-in-primary-her2-positive-breast-tumors
#5
Michael Marotta, Taku Onodera, Jeffrey Johnson, G Thomas Budd, Takaaki Watanabe, Xiaojiang Cui, Armando E Giuliano, Atsushi Niida, Hisashi Tanaka
Oncogene amplification confers a growth advantage to tumor cells for clonal expansion. There are several, recurrently amplified oncogenes throughout the human genome. However, it remains unclear whether this recurrent amplification is solely a manifestation of increased fitness resulting from random amplification mechanisms, or if a genomic locus-specific amplification mechanism plays a role. Here we show that the ERBB2 oncogene at 17q12 is susceptible to palindromic gene amplification, a mechanism characterized by the inverted (palindromic) duplication of genomic segments, in HER2-positive breast tumors...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211311/oleiagrimonas-citrea-sp-nov-a-marine-bacterium-isolated-from-tidal-flat-sediment-and-emended-description-of-the-genus-oleiagrimonas-fang-et-al-2015-and-oleiagrimonas-soli
#6
Sung-Hyun Yang, Hyun-Seok Seo, Chi Nam Seong, Kae Kyoung Kwon
A Gram-negative, aerobic, rod-shaped (1.8-2.3 μm  0.4-0.6 μm), and motile marine bacterium, designated as MEBiC09124T was isolated from tidal flat sediment of the Suncheon Bay, South Korea. The 16S rRNA gene sequence analysis revealed that strain MEBiC09124T showed high similarity with the Oleiagrimonas soli 3.5XT (96.7%). Growth was observed at 18-38 OC (optimum 30 OC), at pH 4.0-8.5 (optimum pH 7.5) and with 0-6 % (optimum 2.5%) NaCl. The predominant cellular fatty acids were iso-C15 : 0 (22.6%), iso-C16 : 0 (16...
February 3, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28211309/chryseobacterium-reticulitermitis-sp-nov-isolated-from-the-gut-of-reticulitermes-aculabialis
#7
Yun Zhao, Yu Wang, Dan Hong Li, Yu Deng, Hong Yang
A Gram-staining-negative, non-motile, aerobic and rod-shaped bacterium, strain Ra1T, was isolated from the gut of a wood-feeding lower termite, Reticulitermes aculabialis. Phylogenetic analysis of 16S rRNA gene sequences showed that the strain was closely related to Chryseobacterium rigui JCM 18078T (96.7%). Growth was observed at 15-45℃ (optimum 30℃), at pH 6.0-9.0 (optimum pH 8.0) and in the presence of 0-2% NaCl (optimum 0%). The DNA G+C content of strain Ra1T was 39.9 mol%. The cells contained MK-6 as the sole respiratory quinone and the major fatty acids were iso-C15:0, iso-C17:0, summed feature 3 (comprising C16:1ω6c and/or C16:1ω7c) and summed feature 9 (comprising C16:0 10-methyl and/or iso-C17:1ω9c)...
February 2, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28209641/mechanisms-for-initiating-cellular-dna-replication
#8
REVIEW
Franziska Bleichert, Michael R Botchan, James M Berger
Cellular DNA replication factories depend on ring-shaped hexameric helicases to aid DNA synthesis by processively unzipping the parental DNA helix. Replicative helicases are loaded onto DNA by dedicated initiator, loader, and accessory proteins during the initiation of DNA replication in a tightly regulated, multistep process. We discuss here the molecular choreography of DNA replication initiation across the three domains of life, highlighting similarities and differences in the strategies used to deposit replicative helicases onto DNA and to melt the DNA helix in preparation for replisome assembly...
February 16, 2017: Science
https://www.readbyqxmd.com/read/28202537/in-search-of-the-mechanism-that-shapes-the-neutrophil-s-nucleus
#9
REVIEW
Katia Georgopoulos
The organization of the genome within the confines of the nuclear compartment is considered a key contributor to transcription and DNA replication, repair, and recombination. A typical higher eukaryotic cell has a spherical nucleus that is ∼10 µm in diameter. This is not the case for a neutrophil, a short-lived innate immune cell with an unusual multilobular nuclear structure that may serve purposes outside nuclear functions. In this issue of Genes & Development, Zhu and colleagues (pp. 141-153) investigate the neutrophil's genome organization and the mechanisms that contribute to its unique nuclear shape...
January 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/28199775/a-photoregulated-dna-based-rotary-system-and-direct-observation-of-its-rotational-movement
#10
Yangyang Yang, Ryu Tashiro, Yuki Suzuki, Tomoko Emura, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo
Various DNA-based nanodevices have been developed on the nanometer scale using light as regulation input. However, the programmed controllability is still a major challenge for these artificial nanodevices. Herein, we demonstrate a rotary DNA nanostructure in which the rotations are controlled by light. A bar-shaped DNA rotor, fabricated as a stiff double-crossover molecule, was placed on the top of a rectangular DNA tile. The photoresponsive oligonucleotides modified with azobenzenes were employed as switching motifs to release/trap the rotor at specific angular position on DNA tile by switching photoirradiations between ultraviolet and visible light...
February 15, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28198425/organic-nitrogen-rearranges-both-structure-and-activity-of-the-soil-borne-microbial-seedbank
#11
Márcio F A Leite, Yao Pan, Jaap Bloem, Hein Ten Berge, Eiko E Kuramae
Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28194461/a-3d-microblade-structure-for-precise-and-parallel-droplet-splitting-on-digital-microfluidic-chips
#12
Cheng Dong, Yanwei Jia, Jie Gao, Tianlan Chen, Pui-In Mak, Mang-I Vai, Rui P Martins
Existing digital microfluidic (DMF) chips exploit the electrowetting on dielectric (EWOD) force to perform droplet splitting. However, the current splitting methods are not flexible and the volume of the droplets suffers from a large variation. Herein, we propose a DMF chip featuring a 3D microblade structure to enhance the droplet-splitting performance. By exploiting the EWOD force for shaping and manipulating the mother droplet, we obtain an average dividing error of <2% in the volume of the daughter droplets for a number of fluids such as deionized water, DNA solutions and DNA-protein mixtures...
February 14, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28191927/foldectures-3d-molecular-architectures-from-self-assembly-of-peptide-foldamers
#13
Sung Hyun Yoo, Hee-Seung Lee
The wide range of fascinating supramolecular architectures found in nature, from DNA double helices to giant protein shells, inspires researchers to mimic the diverse shapes and functions of natural systems. Thus, a variety of artificial molecular platforms have been developed by assembling DNA-, peptide-, and protein-based building blocks for medicinal and biological applications. There has also been a significant interest in the research of non-natural oligomers (i.e., foldamers) that fold into well-defined secondary structures analogous to those found in proteins, because the assemblies of foldamers are expected not only to form biomimetic supramolecular architectures that resemble those of nature but also to display unique functions and unprecedented topologies at the same time due to their different folding propensities from those of natural building blocks...
February 13, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28191892/mechanism-and-timing-of-mcm2-7-ring-closure-during-dna-replication-origin-licensing
#14
Simina Ticau, Larry J Friedman, Kanokwan Champasa, Ivan R Corrêa, Jeff Gelles, Stephen P Bell
The opening and closing of two ring-shaped Mcm2-7 DNA helicases is necessary to license eukaryotic origins of replication, although the mechanisms controlling these events are unclear. The origin-recognition complex (ORC), Cdc6 and Cdt1 facilitate this process by establishing a topological link between each Mcm2-7 hexamer and origin DNA. Using colocalization single-molecule spectroscopy and single-molecule Förster resonance energy transfer (FRET), we monitored ring opening and closing of Saccharomyces cerevisiae Mcm2-7 during origin licensing...
February 13, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28191853/hyperplectonemes-a-higher-order-compact-and-dynamic-dna-self-organization
#15
Aleksandre Japaridze, Georgi Muskhelishvili, Fabrizio Benedetti, Agni Gavriilidou, Renato Zenobi, Paolo De Los Rios, Giovanni Longo, Giovanni Dietler
Bacterial chromosome has a compact structure that dynamically changes its shape in response to bacterial growth rate and growth phase. Determining how chromatin remains accessible to DNA binding proteins and transcription machinery is crucial to understand the link between genetic regulation, DNA structure and topology. Here, we study very large supercoiled dsDNA using high-resolution characterization, theoretical modelling and molecular dynamics calculations. We unveil a new type of highly ordered DNA organization forming in the presence of attractive DNA-DNA interactions, which we call hyperplectonemes...
February 13, 2017: Nano Letters
https://www.readbyqxmd.com/read/28190841/hairpin-shaped-dna-templated-copper-nanoparticles-for-fluorescence-detection-of-adenosine-triphosphate-based-on-ligation-mediated-exonuclease-cleavage
#16
Wenping Zhu, Liyan Dai, Zengchen Liu, Weijie Yang, Chunxiang Zhao, Yanxia Li, Yahong Chen
DNA-templated copper nanoparticles (CuNPs) have recently received considerable interest as functional fluorescent probes for biochemical analysis. In this work, a novel ATP-dependent ligation reactions (ATP-DLR) based ATP assay strategy was proposed by using hairpin-shaped (HS) DNA templated CuNPs as a fluorescent probe. Nick sealing by T4 DNA ligase leads to the formation of intact HS DNA, which can resist the exonuclease cleavage and be taken as the template for CuNPs formation, resulting in strong fluorescence...
2017: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
https://www.readbyqxmd.com/read/28188144/elevated-rate-of-genome-rearrangements-in-radiation-resistant-bacteria
#17
Jelena Repar, Fran Supek, Tin Klanjscek, Tobias Warnecke, Ksenija Zahradka, Davor Zahradka
A number of bacterial, archaeal, and eukaryotic species are known for their resistance to ionizing radiation. One of the challenges these species face is a potent environmental source of DNA double-strand breaks, potential drivers of genome structure evolution. Efficient and accurate DNA double-strand break repair systems have been demonstrated in several unrelated radiation-resistant species and are putative adaptations to the DNA damaging environment. Such adaptations are expected to compensate for the genome-destabilizing effect of environmental DNA damage and may be expected to result in a more conserved gene order in radiation-resistant species...
February 10, 2017: Genetics
https://www.readbyqxmd.com/read/28187647/dna-barcoding-reveals-sexual-dimorphism-in-i-isotrias-i-i-penedana-i-trematerra-2013-lepidoptera-tortricidae-chlidanotinae
#18
Martin Francis Vanner Corley, Sónia Ferreira
Isotrias penedana Trematerra, 2013 was described from north Portugal based on males alone. Unidentified females were associated with the males using DNA barcoding, revealing sexual dimorphism in the species. Males and females differ in forewing shape, markings, and size, with females significantly smaller than males. The female is described and illustrated for the first time. We also document the species' occurrence in northern Spain.
January 20, 2017: Zootaxa
https://www.readbyqxmd.com/read/28186723/bioresponsive-dna-hydrogels-beyond-the-conventional-stimuli-responsiveness
#19
Dong Wang, Yue Hu, Peifeng Liu, Dan Luo
Bioresponsive hydrogels can respond to various biological stimuli by a macroscopic change of physical state or by converting biochemical inputs into biological or mechanical outputs. These materials are playing an increasingly important role in a wide variety of applications, especially in the biological and biomedical fields. However, the design and engineering of intriguing bioresponsive materials with adequate biocompatibility and biodegradability have proven to be a great challenge. DNA, on the other hand, possesses many unique and fascinating properties, including its indispensable genetic function, broad biocompatibility, precise molecular recognition capability, tunable multifunctionality, and convenient programmability...
February 10, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28186408/functional-microgels-and-microgel-systems
#20
Felix A Plamper, Walter Richtering
Microgels are macromolecular networks swollen by the solvent in which they are dissolved. They are unique systems that are distinctly different from common colloids, such as, e.g., rigid nanoparticles, flexible macromolecules, micelles, or vesicles. The size of the microgel networks is in the range of several micrometers down to nanometers (then sometimes called "nanogels"). In a collapsed state, they might resemble hard colloids but they can still contain significant amounts of solvent. When swollen, they are soft and have a fuzzy surface with dangling chains...
February 10, 2017: Accounts of Chemical Research
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