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Dna shape

Jesse M Engreitz, Noah Ollikainen, Mitchell Guttman
Over the past decade, it has become clear that mammalian genomes encode thousands of long non-coding RNAs (lncRNAs), many of which are now implicated in diverse biological processes. Recent work studying the molecular mechanisms of several key examples - including Xist, which orchestrates X chromosome inactivation - has provided new insights into how lncRNAs can control cellular functions by acting in the nucleus. Here we discuss emerging mechanistic insights into how lncRNAs can regulate gene expression by coordinating regulatory proteins, localizing to target loci and shaping three-dimensional (3D) nuclear organization...
October 26, 2016: Nature Reviews. Molecular Cell Biology
Saminathan Ramakrishnan, Sivaraman Subramaniam, Adrian Francis Stewart, Guido Grundmeier, Adrian Keller
DNA origami has become a widely used method for synthesizing well-defined nanostructures with promising applications in various areas of nanotechnology, biophysics, and medicine. Recently, the possibility to transfer the shape of single DNA origami nanostructures into different materials via molecular lithography approaches has received growing interest due to the great structural control provided by the DNA origami technique. Here, we use ordered monolayers of DNA origami nanostructures with internal cavities on mica surfaces as molecular lithography masks for the fabrication of regular protein patterns over large surface areas...
October 25, 2016: ACS Applied Materials & Interfaces
Ziwen Dai, Qi Gao, Man Ching Cheung, Hoi Man Leung, Terrence Chi Kong Lau, Hanadi F Sleiman, King Wai Chiu Lai, Pik Kwan Lo
We develop a versatile recognition system based on 3D triangular-shaped DNA nanotubes by integrating three different aptamer sequences along the three edges. This would allow multiple binding activities to be combined into a single system. The versatility of this nanotube platform can also provide a framework for spatial orientation and positioning of different aptamer-binding ligands in a 'pea-pod' architecture.
October 24, 2016: Nanoscale
Tae Soup Shim, Zaki G Estephan, Zhaoxia Qian, Jacob H Prosser, Su Yeon Lee, David M Chenoweth, Daeyeon Lee, So-Jung Park, John C Crocker
Active materials that respond to physical and chemical stimuli can be used to build dynamic micromachines that lie at the interface between biological systems and engineered devices. In principle, the specific hybridization of DNA can be used to form a library of independent, chemically driven actuators for use in such microrobotic applications and could lead to device capabilities that are not possible with polymer- or metal-layer-based approaches. Here, we report shape changing films that are powered by DNA strand exchange reactions with two different domains that can respond to distinct chemical signals...
October 24, 2016: Nature Nanotechnology
Dmitry M Korzhnev, Dante Neculai, Sirano Dhe-Paganon, Cheryl H Arrowsmith, Irina Bezsonova
HLTF is a SWI2/SNF2-family ATP-dependent chromatin remodeling enzyme that acts in the error-free branch of DNA damage tolerance (DDT), a cellular mechanism that enables replication of damaged DNA while leaving damage repair for a later time. Human HLTF and a closely related protein SHPRH, as well as their yeast homologue Rad5, are multi-functional enzymes that share E3 ubiquitin-ligase activity required for activation of the error-free DDT. HLTF and Rad5 also function as ATP-dependent dsDNA translocases and possess replication fork reversal activities...
October 22, 2016: Journal of Biomolecular NMR
Jian Du, Liqing Wang, Yuanxian Wang, Jian Shen, Chuanyin Pan, Yan Meng, Changming Yang, Hong Ji, Wuzi Dong
The outbreak of Chinese Giant Salamander (Andrias davidianus, CGS) Iridovirus (CGSIV) caused massive death of CGSs. However, some CGSs with low level of CGSIV usually could survive. In our study, major capsid protein (MCP) DNA replicates of CGSIV in shedding skin were employed to assess the relative content of CGSIV in the living CGSs by qPCR. Furthermore, the examinations of autophagy and apoptosis in CGSs in vivo and in the primary renal cells in vitro were performed, respectively. The results showed that the relative contents of CGSIV in the shedding skin could reflect those in liver, spleen, and kidney of the CGSs...
November 15, 2016: Veterinary Microbiology
Yanfeng Zhang, Yong Xu, Wei Fang, Xiaotang Wang, Zemin Fang, Yazhong Xiao
A taxonomic study was carried out on a Gram-stain negative, rod-shaped, non-flagellated, and facultatively anaerobic bacterial strain designated as strain SF-16(T), which was isolated from an unidentified starfish in Sanya, China. Strain SF-16(T) was found to be 5.0-7.0 μm long, and oxidase and catalase positive. Cell growth was observed at pH 6.0-8.5 (optimum, 7.0-8.0), temperatures of 10-41 °C (optimum, 25-30 °C), and salinities of 0-12 % (optimum, 3.0-6.0 %). The predominant fatty acids (>20 %) were found to be C18:1 ω7c and/or C18:1 ω6c (summed feature 8)...
October 21, 2016: Antonie Van Leeuwenhoek
M Moradi, N Sattarahmady, A Rahi, G R Hatam, S M Rezayat Sorkhabadi, H Heli
Detection of leishmaniasis is important in clinical diagnoses. In the present study, identification of Leishmania parasites was performed by a label-free, PCR-free and signal-on ultrasensitive electrochemical DNA biosensor. Gold nanoleaves were firstly electrodeposited by an electrodeposition method using spermidine as a shape directing agent. The biosensor was fabricated by immobilization of a Leishmania major specific DNA probe onto gold nanoleaves, and methylene blue was employed as a marker. Hybridization of the complementary single stranded DNA sequence with the biosensor under the selected conditions was then investigated...
December 1, 2016: Talanta
Nicoletta Bobola, Samir Merabet
Homeodomain proteins are evolutionary conserved proteins present in the entire eukaryote kingdom. They execute functions that are essential for life, both in developing and adult organisms. Most homeodomain proteins act as transcription factors and bind DNA to control the activity of other genes. In contrast to their similar DNA binding specificity, homeodomain proteins execute highly diverse and context-dependent functions. Several factors, including genome accessibility, DNA shape, combinatorial binding and the ability to interact with many transcriptional partners, diversify the activity of homeodomain proteins and culminate in the activation of highly dynamic, context-specific transcriptional programs...
October 18, 2016: Current Opinion in Genetics & Development
Szu-I Yeh, Wei-Feng Fang, Chao-Jyun Huang, Tzu-Ming Wang, Jing-Tang Yang
A simple and visual method to detect multi-nucleotide polymorphism (MNP) was performed on a pneumatic droplet manipulation platform on an open surface. This approach to colorimetric DNA detection was based on the hybridization-mediated growth of gold nanoparticle probes (AuNP probes). The growth size and configuration of the AuNP are dominated by the number of DNA samples hybridized with the probes. Based on the specific size- and shape-dependent optical properties of the nanoparticles, the number of mismatches in a sample DNA fragment to the probes is able to be discriminated...
September 27, 2016: Journal of Visualized Experiments: JoVE
Jilun Hou, Guixing Wang, Xiaoyan Zhang, Yufen Wang, Zhaohui Sun, Fei Si, Xiufeng Jiang, Haijin Liu
Clonal fishes are useful tools in biology and aquaculture studies due to their isogenicity. In Japanese flounder (Paralichthys olivaceus), a group of homozygous clones was created by inducing meiogynogenesis in eggs from a mitogynogenetic homozygous diploid. As the clones reached sexual maturity, meiogynogenesis was again induced in order to produce a 2(nd) generation clonal group of Japanese flounder. After 3 months, there were 611 healthy, surviving individuals. Twenty-four microsatellite markers, that covered all the linkage groups of Japanese flounder, were used to identify the homozygosity of the 2(nd) generation clones; no heterozygous locus was detected...
October 21, 2016: Scientific Reports
Francesca Bomboi, Flavio Romano, Manuela Leo, Javier Fernandez-Castanon, Roberto Cerbino, Tommaso Bellini, Federico Bordi, Patrizia Filetici, Francesco Sciortino
DNA is acquiring a primary role in material development, self-assembling by design into complex supramolecular aggregates, the building block of a new-materials world. Using DNA nanoconstructs to translate sophisticated theoretical intuitions into experimental realizations by closely matching idealized models of colloidal particles is a much less explored avenue. Here we experimentally show that an appropriate selection of competing interactions enciphered in multiple DNA sequences results into the successful design of a one-pot DNA hydrogel that melts both on heating and on cooling...
October 21, 2016: Nature Communications
Hiroko Makita, Emiko Tanaka, Satoshi Mitsunobu, Masayuki Miyazaki, Takuro Nunoura, Katsuyuki Uematsu, Yoshihiro Takaki, Shinro Nishi, Shigeru Shimamura, Ken Takai
A novel iron-oxidizing chemolithoautotrophic bacterium, strain ET2(T), was isolated from a deep-sea sediment in a hydrothermal field of the Bayonnaise knoll of the Izu-Ogasawara arc. Cells were bean-shaped, curved short rods. Growth was observed at a temperature range of 15-30 °C (optimum 25 °C, doubling time 24 h) and a pH range of 5.8-7.0 (optimum pH 6.4) in the presence of NaCl at a range of 1.0-4.0 % (optimum 2.75 %). The isolate was a microaerophilic, strict chemolithoautotroph capable of growing using ferrous iron and molecular oxygen (O2) as the sole electron donor and acceptor, respectively; carbon dioxide as the sole carbon source; and either ammonium or nitrate as the sole nitrogen source...
October 20, 2016: Archives of Microbiology
Ilhem Guesmi-Mzoughi, Antonio Archidona-Yuste, Carolina Cantalapiedra-Navarrete, Hajer Regaieg, Najet Horrigue-Raouani, Juan E Palomares-Rius, Pablo Castillo
Spiral nematode species of the genus Rotylenchus have been reported on olive (Olea europaea L.) in several Mediterranean countries (Castillo et al., 2010; Ali et al., 2014). Nematological surveys for plant-parasitic nematodes on olive trees were carried out in Tunisia between 2013 and 2014, and two nematode species of Rotylenchus were collected from the rhizosphere of olive cv. Chemlali in several localities of Tunisia (Tables 1,2 [Table: see text] [Table: see text] ). Twenty-two soil samples of 3 to 4 kg were collected with a shovel from the upper 50 cm of soil from arbitrarily chosen olive trees...
September 2016: Journal of Nematology
Antonella Conforti, Nadia Starc, Simone Biagini, Luigi Tomao, Angela Pitisci, Mattia Algeri, Pietro Sirleto, Antonio Novelli, Giulia Grisendi, Olivia Candini, Cintia Carella, Massimo Dominici, Franco Locatelli, Maria Ester Bernardo
The risk of malignant transformation of ex-vivo expanded human mesenchymal stromal cells (huMSCs) has been debated in the last years; however, the biosafety of these cells after exposure to supramaximal physical and chemical stress has never been systematically investigated.We established an experimental in vitro model to induce supramaximal physical (ionizing radiation, IR) and chemical (starvation) stress on ex-vivo expanded bone marrow (BM)-derived huMSCs and investigated their propensity to undergo malignant transformation...
October 15, 2016: Oncotarget
Iva Přikrylová, Andrew P Shinn, Giuseppe Paladini
A new genus and species of monogenean belonging to the Gyrodactylidae, Citharodactylus gagei n. gen. et n. sp. (Plathyhelminthes, Monogenea), is described from the gills of the moon fish, Citharinus citharus (Geoffroy Saint-Hilaire), a characiform fish collected from Lake Turkana in northern Kenya. The new viviparous genus can be readily distinguished from the six other gyrodactylid genera recorded from Africa and from the other viviparous genera within the Gyrodactylidae based on the morphology of the male copulatory organ (MCO), which consists of a muscular ovate organ with an opening onto the tegument through which the narrow tapered end of a sclerotised curved cone-shaped structure protrudes...
October 19, 2016: Parasitology Research
Sophie C Warner, Ana M Valdes
PURPOSE OF REVIEW: Osteoarthritis is a common complex disorder with a strong genetic component. Other identified risk factors such as increasing age and overweight do not fully explain the risk of osteoarthritis. Here, we highlight the main findings from genetic association studies on osteoarthritis to date. RECENT FINDINGS: Currently, genetic association studies have identified 21 independent susceptibility loci for osteoarthritis. Studies have focused on hip, knee and hand osteoarthritis, as well as posttotal joint replacement and minimum joint space width, a proxy for cartilage thickness...
October 17, 2016: Current Opinion in Rheumatology
Y K Liu, X X Deng, H L Yang
OBJECTIVES: The cytotoxicity induced by cobalt ions (Co(2+)) and cobalt nanoparticles (Co-NPs) which released following the insertion of a total hip prosthesis, has been reported. However, little is known about the underlying mechanisms. In this study, we investigate the toxic effect of Co(2+) and Co-NPs on liver cells, and explain further the potential mechanisms. METHODS: Co-NPs were characterised for size, shape, elemental analysis, and hydrodynamic diameter, and were assessed by Transmission Electron Microscope, Scanning Electron Microscope, Energy Dispersive X-ray Spectroscopy and Dynamic Light Scattering...
October 2016: Bone & Joint Research
Stephen Harrap
Genetic discovery in blood pressure is generally referenced in relation to protein-coding genes, despite the fact that genes less than 2% of the genome. Recent exploration of the DNA sequences between genes, once called "junk" DNA, has revealed a wealth of transcripts for RNA species that do not encode protein. These non-coding RNAs (ncRNAs) have emerged as dynamic managers of the business of the genome, able to coordinate the expression of genes in time and space to achieve the complexities of normal development and growth...
September 2016: Journal of Hypertension
E Wardal, A Kuch, I Gawryszewska, D Żabicka, W Hryniewicz, E Sadowy
The objective of this study was to investigate the antimicrobial resistance, Tn1546 transposon variability and plasmid diversity among Polish vancomycin-resistant Enterococcus faecium (VREfm) isolates of VanA phenotype in the context of their clonal structure. Two hundred sixteen clinical VREfm isolates collected between 1997 and 2010 were studied by antimicrobial susceptibility testing, MLST, MLVA and detection of IS16, esp Efm, pilA, intA and plasmid-specific genes by PCR. Tn1546 structure was revealed by overlapping PCR and sequencing...
October 17, 2016: European Journal of Clinical Microbiology & Infectious Diseases
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