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https://www.readbyqxmd.com/read/28317902/a-natural-tandem-array-alleviates-epigenetic-repression-of-ipa1-and-leads-to-superior-yielding-rice
#1
Lin Zhang, Hong Yu, Bin Ma, Guifu Liu, Jianjun Wang, Junmin Wang, Rongcun Gao, Jinjun Li, Jiyun Liu, Jing Xu, Yingying Zhang, Qun Li, Xuehui Huang, Jianlong Xu, Jianming Li, Qian Qian, Bin Han, Zuhua He, Jiayang Li
Super hybrid rice varieties with ideal plant architecture (IPA) have been critical in enhancing food security worldwide. However, the molecular mechanisms underlying their improved yield remain unclear. Here, we report the identification of a QTL, qWS8/ipa1-2D, in the super rice Yongyou12 (YY12) and related varieties. In-depth genetic molecular characterization of qWS8/ipa1-2D reveals that this newly identified QTL results from three distal naturally occurring tandem repeats upstream of IPA1, a key gene/locus previously shown to shape rice ideal plant architecture and greatly enhance grain yield...
March 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28317184/self-assembled-multivalent-samul-polyanion-binding-impact-of-hydrophobic-modifications-in-the-micellar-core-on-dna-and-heparin-binding-at-the-peripheral-cationic-ligands
#2
Buthaina Albanyan, Erik Laurini, Paola Posocco, Sabrina Pricl, David K Smith
This paper reports a small family of cationic surfactants designed to bind polyanions such as DNA and heparin. Each molecule has the same hydrophilic cationic ligand, and a hydrophobic aliphatic group with eighteen carbon atoms with either one, two or three alkene groups within the hydrophobic chain (C18-1, C18-2 and C18-3). Dynamic light scattering indicates that more alkenes lead to geometric distortion, giving rise to larger self-assembled multivalent (SAMul) nanostructures. Mallard Blue and Ethidium Bromide dye displacement assays demonstrate that heparin and DNA have markedly different binding preferences, with heparin binding most effectively to C18-1, and DNA to C18-3, even though the molecular structural differences of these SAMul systems are buried in the hydrophobic core...
March 20, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28316324/spatial-organization-of-dna-sequences-directs-the-assembly-of-bacterial-chromatin-by-a-nucleoid-associated-protein
#3
Aleksandre Japarize, Sylvain Renevey, Parick Sobetzko, Liubov Stoliar, William Nasser, Giovanni Dietler, Georgi Muskhelishvili
Structural differentiation of bacterial chromatin depends on cooperative binding of abundant nucleoid-associated proteins at numerous genomic DNA sites and stabilization of distinct long-range nucleoprotein structures. Histone-like nucleoid-structuring protein (H-NS) is an abundant DNA-bridging, nucleoid-associated protein that binds to an AT rich conserved DNA sequence motif and regulates both the shape and the genetic expression of the bacterial chromosome. Although there is ample evidence that the mode of H-NS binding depends on environmental conditions, the role of the spatial organization of H-NS binding sequences in the assembly of long-range nucleoprotein structures remains unknown...
March 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28316119/animal-tracking-meets-migration-genomics-transcriptomic-analysis-of-a-partially-migratory-bird-species
#4
Paolo Franchini, Iker Irisarri, Adam Fudickar, Andreas Schmidt, Axel Meyer, Martin Wikelski, Jesko Partecke
Seasonal migration is a widespread phenomenon, which is found in many different lineages of animals. This spectacular behaviour allows animals to avoid seasonally adverse environmental conditions to exploit more favourable habitats. Migration has been intensively studied in birds, which display astonishing variation in migration strategies, thus providing a powerful system for studying the ecological and evolutionary processes that shape migratory behaviour. Despite intensive research, the genetic basis of migration remains largely unknown...
March 17, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28316093/morphology-heterogeneity-within-a-campylobacter-jejuni-helical-population-the-use-of-calcofluor-white-to-generate-rod-shaped-c-jejuni-81-176-clones-and-the-genetic-determinants-responsible-for-differences-in-morphology-within-11168-strains
#5
Emilisa Frirdich, Jacob Biboy, Steven Huynh, Craig T Parker, Waldemar Vollmer, Erin C Gaynor
Campylobacter jejuni helical shape is important for colonization and host interactions with straight mutants having altered biological properties. Passage on calcofluor white (CFW) resulted in C. jejuni 81-176 isolates with morphology changes: either a straight morphology from frameshift mutations and single nucleotide polymorphisms in peptidoglycan hydrolase genes pgp1 or pgp2 or a reduction in curvature due a frameshift mutation in cjj81176_1105, a putative peptidoglycan endopeptidase. Shape defects were restored by complementation...
March 18, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28304272/vagococcus-humatus-sp-nov-isolated-from-soil-beneath-a-decomposing-pig-carcass
#6
Aravind Sundararaman, Sathiyaraj Srinivasan, Sang-Seob Lee
A Gram-stain-positive, non-motile, coccus-shaped bacterium, designated strain C25T, was isolated from the soil beneath a decomposing pig carcass in Korea and was characterized using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain C25T belongs to the genus Vagococcus in the family Enterococcaceae of the Lactobacillales. 16S rRNA gene sequence analysis showed that strain C25T was closely related to Vagococcus lutrae CCUG 39187T (96.5 % similarity) and Enterococcus termitis LMG 8895T (95...
February 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28303594/the-analysis-of-the-different-functions-of-starch-phosphorylating-enzymes-during-the-development-of-arabidopsis-thaliana-plants-discloses-an-unexpected-role-for-the-cytosolic-isoform-gwd2
#7
Claudia Pirone, Libero Gurrieri, Ivan Gaiba, Alessio Adamiano, Francesco Valle, Paolo Trost, Francesca Sparla
The genome of Arabidopsis thaliana encodes three glucan, water dikinases. Glucan, water dikinase 1 (GWD1; EC 2.7.9.4) and phosphoglucan, water dikinase (PWD; EC 2.7.9.5) are chloroplastic enzymes, while glucan, water dikinase 2 (GWD2) is cytosolic. Both GWDs and PWD catalyze the addition of phosphate groups to amylopectin chains at the surface of starch granules, changing its physicochemical properties. As a result, GWD1 and PWD have a positive effect on transitory starch degradation at night. Because of its cytosolic localization, GWD2 does not have the same effect...
March 17, 2017: Physiologia Plantarum
https://www.readbyqxmd.com/read/28301470/pleistocene-refugia-and-genetic-diversity-patterns-in-west-africa-insights-from-the-liana-chasmanthera-dependens-menispermaceae
#8
Andrew Chibuzor Iloh, Marco Schmidt, Alexandra Nora Muellner-Riehl, Oluwatoyin Temitayo Ogundipe, Juraj Paule
Processes shaping the African Guineo-Congolian rain forest, especially in the West African part, are not well understood. Recent molecular studies, based mainly on forest tree species, confirmed the previously proposed division of the western African Guineo-Congolian rain forest into Upper Guinea (UG) and Lower Guinea (LG) separated by the Dahomey Gap (DG). Here we studied nine populations in the area of the DG and the borders of LG and UG of the widespread liana species, Chasmanthera dependens (Menispermaceae) by amplified fragment length polymorphism (AFLP), a chloroplast DNA sequence marker, and modelled the distribution based on current as well as paleoclimatic data (Holocene Climate Optimum, ca...
2017: PloS One
https://www.readbyqxmd.com/read/28299702/optical-and-electrochemical-aptasensors-for-sensitive-detection-of-streptomycin-in-blood-serum-and-milk
#9
Mohammad Ramezani, Khalil Abnous, Seyed Mohammad Taghdisi
Detection and quantitation of antibiotic residues in blood serum and foodstuffs are in great demand. We have developed aptasensors for detection of streptomycin using electrochemical and optical methods. In the first method, an electrochemical aptasensor was developed for sensitive and selective detection of streptomycin, based on combination of exonuclease I (Exo I), complementary strand of aptamer (CS), arch shaped structure of aptamer (Apt)-CS conjugate, and gold electrode. The designed electrochemical aptasensor exhibited high selectivity toward streptomycin with a limit of detection (LOD) as low as 11...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28299670/roles-of-runx-complexes-in-immune-cell-development
#10
Takashi Ebihara, Wooseok Seo, Ichiro Taniuchi
During hematopoiesis, a variety of cells are generated from stem cells through successive rounds of cell fate determination processes. Studies in the last two decades have demonstrated the involvement of Runx transcription factor family members in differentiation of multiple types of hematopoietic cells. Along with evolutionary conservation, the Runx family is considered to be one of the ancestral regulators of hematopoiesis. It is conceivable that the Runx family is involved in shaping the immune system, which is then comprised of innate and acquired lymphoid cells in vertebrates...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28298479/cyst-nematode-parasitism-induces-dynamic-changes-in-the-root-epigenome
#11
Tarek Hewezi, Thomas Lane, Sarbottam Piya, Aditi Rambani, J Hollis Rice, Meg Staton
A growing body of evidence indicates that epigenetic modifications can provide efficient, dynamic, and reversible cellular responses to a wide range of environmental stimuli. However, the significance of epigenetic modifications in plant-pathogen interactions remains largely unexplored. In this study, we provide a comprehensive analysis of epigenome changes during the compatible interaction between the beet cyst nematode Heterodera schachtii and Arabidopsis (Arabidopsis thaliana). Whole genome bisulfite sequencing was conducted to assess the dynamic changes in the methylome of Arabidopsis roots in response to H schachtii infection...
March 15, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28298347/distinctive-fungal-communities-in-an-obligate-african-ant-plant-mutualism
#12
Christopher C M Baker, Dino J Martins, Julianne N Pelaez, Johan P J Billen, Anne Pringle, Megan E Frederickson, Naomi E Pierce
Three ant species nest obligately in the swollen-thorn domatia of the African ant-plant Vachellia (Acacia) drepanolobium, a model system for the study of ant-defence mutualisms and species coexistence. Here we report on the characteristic fungal communities generated by these ant species in their domatia. First, we describe behavioural differences between the ant species when presented with a cultured fungal isolate in the laboratory. Second, we use DNA metabarcoding to show that each ant species has a distinctive fungal community in its domatia, and that these communities remain characteristic of the ant species over two Kenyan sampling locations separated by 190 km...
March 15, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28297560/an-investigation-of-the-potential-effect-of-sperm-nuclear-vacuoles-in-human-spermatozoa-on-dna-fragmentation-using-a-neutral-and-alkaline-comet-assay
#13
E Pastuszek, J Kiewisz, P Skowronska, J Liss, M Lukaszuk, A Bruszczynska, G Jakiel, K Lukaszuk
Presence of vacuoles and degree of sperm DNA damage are considered to be the basic factors used for the assessment of sperm fertilization capacity. We aimed to investigate the link between these two parameters. According to our knowledge, this is the first study where the Comet assay was used to assess the degree of DNA fragmentation of sperm categorized by Motile Sperm Organelle Morphology Examination (MSOME) Grades. Semen samples from 10 patients were assessed. Spermatozoa were graded into four MSOME groups according to the Vanderzwalmen's criteria...
March 2017: Andrology
https://www.readbyqxmd.com/read/28294640/evoligo-a-novel-software-to-design-and-group-libraries-of-oligonucleotides-applicable-for-nucleic-acid-based-experiments
#14
Marek C Milewski, Karol Kamel, Anna Kurzynska-Kokorniak, Marcin K Chmielewski, Marek Figlerowicz
Experimental methods based on DNA and RNA hybridization, such as multiplex polymerase chain reaction, multiplex ligation-dependent probe amplification, or microarray analysis, require the use of mixtures of multiple oligonucleotides (primers or probes) in a single test tube. To provide an optimal reaction environment, minimal self- and cross-hybridization must be achieved among these oligonucleotides. To address this problem, we developed EvOligo, which is a software package that provides the means to design and group DNA and RNA molecules with defined lengths...
March 15, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28294638/potential-targetability-of-multi-walled-carbon-nanotube-loaded-with-silver-nanoparticles-photosynthesized-from-ocimum-tenuiflorum-tulsi-extract-in-fertility-diagnosis
#15
Pradeep K Jha, Rakhi K Jha, Dilip Rout, Sathishkumar Gnanasekar, Suresh Vs Rana, Maidul Hossain
Nanocarrier mediated targeted delivery and biosensing in reproductive health care is a major exploratory domain. This work demonstrates the loading of silver nanoparticle (AgNP) inside the multiwalled Carbon nanotube(MWCNT) and their targetability to the intracellular part of the sperm cell for its further application in biosensing based infertility diagnosis. Ocimum tenuiflorum (tulsi extract) mediated photosynthesized AgNP exhibited spherical shape, 5-40nm size and surface plasmonic resonance at 430 nm...
March 15, 2017: Journal of Drug Targeting
https://www.readbyqxmd.com/read/28290215/genetic-assessment-of-leech-species-from-yak-bos-grunniens-in-the-tract-of-northeast-india
#16
Nilkantha Chatterjee, Bishal Dhar, Debasis Bhattarcharya, Sourabh Deori, Juwar Doley, Joken Bam, Pranab J Das, Asit K Bera, Sitangshu M Deb, Ningthoujam Neelima Devi, Rajesh Paul, Sorokhaibam Malvika, Sankar Kumar Ghosh
Yak is an iconic symbol of Tibet and high altitudes of Northeast India. It is highly cherished for milk, meat, and skin. However, yaks suffer drastic change in milk production, weight loss, etc, when infested by parasites. Among them, infestation by leeches is a serious problem in the Himalayan belt of Northeast India. The parasite feeds on blood externally or from body orifices, like nasopharynx, oral, rectum, etc. But there has been limited data about the leech species infesting the yak in that region because of the difficulties in morphological identification due to plasticity of the body, changes in shape, and surface structure and thus, warrants for the molecular characterization of leech...
March 14, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28289836/prokaryotic-abundance-and-activity-in-permafrost-of-the-northern-victoria-land-and-upper-victoria-valley-antarctica
#17
Rosabruna La Ferla, Maurizio Azzaro, Luigi Michaud, Gabriella Caruso, Angelina Lo Giudice, Rodolfo Paranhos, Anderson S Cabral, Antonella Conte, Alessandro Cosenza, Giovanna Maimone, Maria Papale, Alessandro Ciro Rappazzo, Mauro Guglielmin
Victoria Land permafrost harbours a potentially large pool of cold-affected microorganisms whose metabolic potential still remains underestimated. Three cores (BC-1, BC-2 and BC-3) drilled at different depths in Boulder Clay (Northern Victoria Land) and one sample (DY) collected from a core in the Dry Valleys (Upper Victoria Valley) were analysed to assess the prokaryotic abundance, viability, physiological profiles and potential metabolic rates. The cores drilled at Boulder Clay were a template of different ecological conditions (different temperature regime, ice content, exchanges with atmosphere and with liquid water) in the same small basin while the Dry Valleys site was very similar to BC-2 conditions but with a complete different geological history and ground ice type...
March 13, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28289084/control-of-recombination-directionality-by-the-listeria-phage-a118-protein-gp44-and-the-coiled-coil-motif-of-its-serine-integrase
#18
Sridhar Mandali, Kushol Gupta, Anthony R Dawson, Gregory D Van Duyne, Reid C Johnson
The serine integrase of phage A118 catalyzes integrative recombination between attP on the phage and a specific attB locus on the chromosome of Listeriamonocytogenes but is unable to promote excisive recombination between the hybrid attL and attR sites found on the integrated prophage without assistance from a Recombination Directionality Factor (RDF). We have identified and characterized the phage-encoded RDF, Gp44, which activates the A118 integrase for excision and inhibits integration. Gp44 binds to the C-terminal DNA binding domain of integrase, and we have localized the primary binding site to be within the mobile coiled-coil (CC) motif but distinct from the distal tip of the CC that is required for recombination...
March 13, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28287243/models-of-amphibian-myogenesis-the-case-of-bombina-variegata
#19
Leokadia Kiełbwna, Marta Migocka-Patrzałek
Several different models of myogenesis describing early stages of amphibian paraxial myotomal myogenesis are known. Myoblasts of Xenopus laevis and Hymenochirus boettgeri change their position from perpendicular to parallel, in relation to axial organs, and differentiate into mononucleate myotubes. In Bombina variegate the myotomal myoblasts change their shape from round to elongate and then differentiate into mononuclear, morphologically mature myotubes. In Pelobates fuscus and Triturus vulgaris, myoblasts fuse into multinuclear myotubes...
2017: International Journal of Developmental Biology
https://www.readbyqxmd.com/read/28284913/higher-order-assembly-folding-the-chromosome
#20
REVIEW
Sven A Sewitz, Zahra Fahmi, Karen Lipkow
The linear molecules of DNA that constitute a eukaryotic genome have to be carefully organised within the nucleus to be able to correctly direct gene expression. Microscopy and chromosome capture methods have revealed a hierarchical organisation into territories, domains and subdomains that ensure the accessibility of expressed genes and eventually chromatin loops that serve to bring gene enhancers into proximity of their target promoters. A rapidly growing number of genome-wide datasets and their analyses have given detailed information into the conformation of the entire genome, allowing evolutionary insights, observations of genome rearrangements during development and the identification of new gene-to-disease associations...
March 8, 2017: Current Opinion in Structural Biology
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