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Dna shape

Sophie Desset, Axel Poulet, Christophe Tatout
Image analysis is a classical way to study nuclear organization. While nuclear organization used to be investigated by colorimetric or fluorescent labeling of DNA or specific nuclear compartments, new methods in microscopy imaging now enable qualitative and quantitative analyses of chromatin pattern, and nuclear size and shape. Several procedures have been developed to prepare samples in order to collect 3D images for the analysis of spatial chromatin organization, but only few preserve the positional information of the cell within its tissue context...
2018: Methods in Molecular Biology
Dhiraj Kumar Chaudhary, Sang Don Lee, Jaisoo Kim
Strain K-4-11-1(T), a psychrotolerant, light salmon-coloured, Gram-stain-negative, non-motile and rod-shaped bacterium, was isolated from forest soil of Kyonggi University, Suwon, South Korea. It was able to grow at 0-32 °C, at pH 5.0-10.0 and with 0-1.5 % (w/v) NaCl. This strain was taxonomically characterized by a polyphasic approach. Based on 16S rRNA gene sequence analysis, strain K-4-11-1(T) belongs to the genus Pedobacter and is closely related to Pedobacter ginsenosidimutans THG-45(T) (98.75 % sequence similarity), Pedobacter borealis G-1(T) (98...
October 19, 2017: International Journal of Systematic and Evolutionary Microbiology
Masayuki Endo, Elena M Willner, Yuu Kamada, Yuki Suzuki, Tomoko Emura, Kumi Hidaka, Hendrik Dietz, Hiroshi Sugiyama
We demonstrate direct observation of the dynamic opening and closing behavior of photo-controllable DNA origami nanoscissors (NS) using high-speed AFM. First the conformational change between the open and closed state controlled by adjustment of salt concentration could be directly observed during AFM scanning. Then light-responsive moieties were incorporated into the NS to control the structural changes by irradiation. Using photo-switchable DNA strands, we created a photoresponsive NS variant and were able to distinguish between the open and closed conformations after respective irradiation with UV and visible (Vis) light via gel electrophoresis and AFM imaging...
October 17, 2017: Angewandte Chemie
Noelia Fonseca Balvís, Soledad Garcia-Martinez, Serafín Pérez-Cerezales, Elena Ivanova, Isabel Gomez-Redondo, Meriem Hamdi, Dimitrios Rizos, Pilar Coy, Gavin Kelsey, Alfonso Gutierrez-Adan
A major limitation of embryo epigenotyping by chromatin immunoprecipitation analysis is the reduced amount of sample available from an embryo biopsy. We developed an in vitro system to expand trophectoderm cells from an embryo biopsy to overcome this limitation. This work analyzes whether expanded trophectoderm (EX) is representative of the trophectoderm (TE) methylation or adaptation to culture has altered its epigenome. We took a small biopsy from the trophectoderm (30-40 cells) of in vitro produced bovine-hatched blastocysts and cultured it on fibronectin-treated plates until we obtained ∼4 × 104 cells...
August 1, 2017: Biology of Reproduction
Ling-Yun Guo, Si-Kai Ling, Chang-Ming Li, Guan-Jun Chen, Zong-Jun Du
A novel Gram-stain-negative, moderately halophilic, motile, facultatively anaerobic and rod-shaped strain, designated WDN1C137(T), was isolated from a marine saltern at Wendeng, PR China. Optimal growth occurred at 40 °C, pH 7.5 and with 7.0 % (w/v) NaCl. Q-10 was the sole respiratory quinone. The major cellular fatty acids (>10.0 %) in WDN1C137(T) were C18 : 1ω7c (46.2 %), cyclo C19 : 0ω8c (18.7 %) and C16 : 0 (12.3 %). The major polar lipids were phosphatidylglycerol, phosphoglycolipid, phosphatidylcholine, one unidentified glycolipid, one unidentified lipid, one unidentified aminolipid and two unidentified phospholipids...
October 18, 2017: International Journal of Systematic and Evolutionary Microbiology
Zhen-Xing Xu, Pei Yu, Da-Shuai Mu, Yan Liu, Zong-Jun Du
A novel Gram-stain-negative, aerobic, rod-shaped, non-flagellated and agar-digesting marine bacterium, designated as HZ1(T), was isolated from the marine alga Porphyra yezoensis Ueda (AST58-103) collected from the coastal area of Weihai, PR China. Phylogenetic analysis based on 16S rRNA gene sequences placed HZ1(T) in the genus Tenacibaculum, and it formed a distinct clade in the phylogenetic tree with the type strains of Tenacibaculum amylolyticum and Tenacibaculum skagerrakense, with 97.0 % and 96.7 % 16S rRNA gene sequence similarities, respectively...
October 18, 2017: International Journal of Systematic and Evolutionary Microbiology
Hu Liao, Yuqian Li, Xintong Guo, Xiaolan Lin, Qiliang Lai, Hong Xu, Tianling Zheng, Yun Tian
A Gram-stain-negative, facultative anaerobic and oligotrophic, rod-shaped, and motile with single polar flagellum bacterial strain, designed M11-4(T) was isolated from mangrove sediment in Yunxiao Mangrove National Nature Reserve, China. Growth was observed at temperatures from 10 to 40 °C (optimum 30 °C), at salinities from 0.5 to 6 % (optimum 2-3 %), and at pH from 5 to 8 (optimum 6). Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain M11-4(T) shared highest sequence similarity with the genus Marinobacter(92...
October 18, 2017: International Journal of Systematic and Evolutionary Microbiology
Verónica Urdaneta, Josep Casadesús
Bile salts and bacteria have intricate relationships. The composition of the intestinal pool of bile salts is shaped by bacterial metabolism. In turn, bile salts play a role in intestinal homeostasis by controlling the size and the composition of the intestinal microbiota. As a consequence, alteration of the microbiome-bile salt homeostasis can play a role in hepatic and gastrointestinal pathological conditions. Intestinal bacteria use bile salts as environmental signals and in certain cases as nutrients and electron acceptors...
2017: Frontiers in Medicine
Stacy L Metivier, Jin-Hong Kim, Jason A Addison
Mitochondrial DNA analyses indicate that the Bay of Fundy population of the intertidal tellinid bivalve Macoma petalum is genetically divergent from coastal populations in the Gulf of Maine and Nova Scotia. To further examine the evolutionary forces driving this genetic break, we performed double digest genotype by sequencing (GBS) to survey the nuclear genome for evidence of both neutral and selective processes shaping this pattern. The resulting reads were mapped to a partial transcriptome of its sister species, M...
October 2017: Ecology and Evolution
Fernando Vargas-Lara, Ahmed M Hassan, Marc L Mansfield, Jack F Douglas
The Coulomb energy E C is defined by the energy required to charge a conductive object and scales inversely to the self-capacity C, a basic measure of object size and shape. It is known that C is minimized for a sphere for all objects having the same volume, and that C increases as the symmetry of an object is reduced at fixed volume. Mathematically similar energy functionals have been related to the average knot crossing number 〈m〉, a natural measure of knot complexity and, correspondingly, we find E C to be directly related to 〈m〉 of knotted DNA...
October 17, 2017: Scientific Reports
Tsu-Pei Chiu, Satyanarayan Rao, Richard S Mann, Barry Honig, Remo Rohs
Protein-DNA binding is a fundamental component of gene regulatory processes, but it is still not completely understood how proteins recognize their target sites in the genome. Besides hydrogen bonding in the major groove (base readout), proteins recognize minor-groove geometry using positively charged amino acids (shape readout). The underlying mechanism of DNA shape readout involves the correlation between minor-groove width and electrostatic potential (EP). To probe this biophysical effect directly, rather than using minor-groove width as an indirect measure for shape readout, we developed a methodology, DNAphi, for predicting EP in the minor groove and confirmed the direct role of EP in protein-DNA binding using massive sequencing data...
October 11, 2017: Nucleic Acids Research
Li-Li Guo, Yue-Hong Wu, Xiao-Wu Xu, Chao-Jie Huang, Yun-Yun Xu, Hong Cheng, Chun-Sheng Wang, Min Wu, Xue-Wei Xu
A Gram-stain-negative, non-motile, rod-shaped bacterium, designated JN33(T), was isolated from seawater collected from the western Pacific Ocean. Strain JN33(T) was positive for hydrolysis of aesculin and gelatin. On the basis of 16S rRNA gene sequence analysis, strain JN33(T) showed high 16S rRNA gene sequence similarity to Actibacterium atlanticum 22II-S11-z10(T) (97.3 %), A. mucosum KCTC 23349(T) (96.6 %) and A. ureilyticum LS-811(T) (95.7 %) and exhibited less than 97.0 % 16S rRNA gene sequence similarity with respect to the other type strains within the family Rhodobacteraceae...
October 17, 2017: International Journal of Systematic and Evolutionary Microbiology
Maria Fernanda Pérez Bernal, Elcia Margareth Souza Brito, Manon Bartoli, Johanne Aubé, Marie-Laure Fardeau, German Cuevas Rodriguez, Bernard Ollivier, Rémy Guyoneaud, Agnès Hirschler-Réa
Novel Gram-stain-negative, non-spore-forming, vibrio-shaped, anaerobic, alkaliphilic, sulfate-reducing bacteria, designated strains PAR180(T) and PAR190, were isolated from sediments collected at an alkaline crater lake in Guanajuato (Mexico). Strain PAR180(T) grew at temperatures between 15 and 40 °C (optimum 35 °C), and at pH between 8.3 and 10.4 (optimum 9). It was halotolerant, growing with up to 8 % (w/v) NaCl. Lactate, formate, pyruvate and ethanol were used as electron donors in the presence of sulfate and were incompletely oxidized to acetate and CO2...
October 17, 2017: International Journal of Systematic and Evolutionary Microbiology
Jingran Huang, Zhaobin Huang, Zongze Shao
Two strains, AFRC7-2-1(T) and CFD7-4-2, were isolated from the intestine of abalone, Haliotis discus hannai. The bacterial cells were Gram-stain-negative, stick-shaped and non-flagellated. They were facultative anaerobic bacteria and could reduce Fe(III) to Fe(II). The 16S rRNA genes of two strains shared 99.7 % sequence similarity, and had the highest similarity of 97.3-97.5 % with Paraferrimonas sedimenticola NBRC 101628(T), and of <94.0 % with other species. Phylogenetic relationship showed that the two strains formed a tight clade with an isolate Paraferrimonas sp...
October 17, 2017: International Journal of Systematic and Evolutionary Microbiology
B Golhasan, R Heydari, E Miraeiz, J Abolafia, R Peña-Santiago
A new species belonging to the genus Belondira is described from natural areas in Iran. Belondira coomansi n. sp. is characterized by its general size, the dimensions and appearance of its lip region, presence of distinct labial and post-labial sclerotization, the length of the odontostyle and its inconspicuous lumen and aperture, the length of the neck and its pharyngeal expansion, the reduction of the female anterior genital branch to a simple uterine sac, a very short posterior uterus, the anterior position of the vulva, the length and shape of the caudal region with distinctly thick cuticle at its tip, the length of the spicules, and the presence of only one pair of ventromedian supplements...
October 17, 2017: Journal of Helminthology
Yuanyuan Wang, Xiao Chen, Yalan Sheng, Yifan Liu, Shan Gao
DNA N6-methyladenine (6mA) is newly rediscovered as a potential epigenetic mark across a more diverse range of eukaryotes than previously realized. As a unicellular model organism, Tetrahymena thermophila is among the first eukaryotes reported to contain 6mA modification. However, lack of comprehensive information about 6mA distribution hinders further investigations into its function and regulatory mechanism. In this study, we provide the first genome-wide, base pair-resolution map of 6mA in Tetrahymena by applying single-molecule real-time (SMRT) sequencing...
October 3, 2017: Nucleic Acids Research
Soojin V Yi
Evolutionary studies of DNA methylation begin to provide insights into the underlying forces governing the variation of genomic DNA methylation across different species. Comparisons of gross levels of DNA methylation between distantly related species indicate that the size of the genome and the level of genomic DNA methylation are positively correlated. In plant genomes, this can be reliably explained by the contents of repetitive sequences, while the underlying driver of this correlation is less clear in animal genomes...
September 25, 2017: Genome Biology and Evolution
Robert Horvath, Tanja Slotte
To avoid negative effects of transposable element (TE) proliferation, plants epigenetically silence TEs using a number of mechanisms, including RNA-directed DNA methylation. These epigenetic modifications can extend outside the boundaries of TE insertions and lead to silencing of nearby genes, resulting in a trade-off between TE silencing and interference with nearby gene regulation. Therefore, purifying selection is expected to remove silenced TE insertions near genes more efficiently and prevent their accumulation within a population...
September 27, 2017: Genome Biology and Evolution
Ajasja Ljubetič, Fabio Lapenta, Helena Gradišar, Igor Drobnak, Jana Aupič, Žiga Strmšek, Duško Lainšček, Iva Hafner-Bratkovič, Andreja Majerle, Nuša Krivec, Mojca Benčina, Tomaž Pisanski, Tanja Ćirković Veličković, Adam Round, José María Carazo, Roberto Melero, Roman Jerala
Polypeptides and polynucleotides are natural programmable biopolymers that can self-assemble into complex tertiary structures. We describe a system analogous to designed DNA nanostructures in which protein coiled-coil (CC) dimers serve as building blocks for modular de novo design of polyhedral protein cages that efficiently self-assemble in vitro and in vivo. We produced and characterized >20 single-chain protein cages in three shapes-tetrahedron, four-sided pyramid, and triangular prism-with the largest containing >700 amino-acid residues and measuring 11 nm in diameter...
October 16, 2017: Nature Biotechnology
Liang Chi, Ridwan Mahbub, Bei Gao, Xiaoming Bian, Pengcheng Tu, Hongyu Ru, Kun Lu
As the primary active substance in tobacco, nicotine affects the activity of the central nervous system, and its effects are sex-dependent. There are complex interactions between the gut and brain, and the gut microbiome can influence neuronal activity and host behavior, with diverse chemical signaling being involved. However, it is unclear whether nicotine can affect the normal gut microbiome and associated chemical signaling of the gut-brain axis. Sex is an important factor that shapes the gut microbiome, but the role of sex in the interaction among nicotine, gut bacteria, and related metabolites remains unknown...
October 16, 2017: Chemical Research in Toxicology
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