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https://www.readbyqxmd.com/read/28651329/high-speed-and-high-ratio-referential-genome-compression
#1
Yuansheng Liu, Hui Peng, Limsoon Wong, Jinyan Li
Motivation: The rapidly increasing number of genomes generated by high-throughput sequencing platforms and assembly algorithms is accompanied by problems in data storage, compression and communication. Traditional compression algorithms are unable to meet the demand of high compression ratio due to the intrinsic challenging features of DNA sequences such as small alphabet size, frequent repeats and palindromes. Reference-based lossless compression, by which only the differences between two similar genomes are stored, is a promising approach with high compression ratio...
June 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28651291/development-of-a-reference-standard-library-of-chloroplast-genome-sequences-genometrakrcp
#2
Ning Zhang, Padmini Ramachandran, Jun Wen, James A Duke, Helen Metzman, William McLaughlin, Andrea R Ottesen, Ruth E Timme, Sara M Handy
Precise, species-level identification of plants in foods and dietary supplements is difficult. While the use of DNA barcoding regions (short regions of DNA with diagnostic utility) has been effective for many inquiries, it is not always a robust approach for closely related species, especially in highly processed products. The use of fully sequenced chloroplast genomes, as an alternative to short diagnostic barcoding regions, has demonstrated utility for closely related species. The U. S. Food and Drug Administration (FDA) has also developed species-specific DNA-based assays targeting plant species of interest by utilizing chloroplast genome sequences...
June 26, 2017: Planta Medica
https://www.readbyqxmd.com/read/28651200/nanostructured-micro-raspberries-from-superparamagnetic-iron-oxide-nanoparticles-studying-agglomeration-degree-and-redispersibility-of-nanoparticulate-powders-via-magnetisation-measurements
#3
Claudia Stauch, Stephan Späth, Thomas Ballweg, Robert Luxenhofer, Karl Mandel
Surface modified superparamagnetic iron oxide nanoparticles are assembled into nanostructured micro-raspberry particles via spray drying. The micro-raspberry powder is readily redispersed to individual nanoparticles or nanostructured sub-units, depending on the initially adjusted nanoparticle modification. In this work, it is demonstrated how the technique of magnetic zero-field-cooled/field-cooled (ZFC/FC) measurements can be used to judge the degree of agglomeration, i.e. the extent of hard-agglomerates and soft-agglomerates in a system and predict the redispersibility of the powder particles...
June 16, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28651051/molecular-precision-at-micrometer-length-scales-hierarchical-assembly-of-dna-protein-nanostructures
#4
Daniel Schiffels, Veronika A Szalai, J Alexander Liddle
Robust self-assembly across length scales is a ubiquitous feature of biological systems, but remains challenging for synthetic structures. Taking a cue from biology - where disparate molecules work together to produce large, functional assemblies - we demonstrate how to engineer microscale structures with nanoscale features: Our self-assembly approach begins by using DNA polymerase to controllably create double-stranded DNA (dsDNA) sections on a single-stranded template. The single-stranded DNA (ssDNA) sections are then folded into a mechanically flexible skeleton by the origami method...
June 26, 2017: ACS Nano
https://www.readbyqxmd.com/read/28651046/a-heparan-sulfate-microarray-reveals-that-heparan-sulfate-protein-binding-exhibit-different-ligand-requirements
#5
Chengli Zong, Andre Venot, Xiuru Li, Weigang Lu, Wenyuan Xiao, Josetti Lynn Wilkes, Catherina L Salanga, Tracy M Handel, Lianchun Wang, Margreet A Wolfert, Geert-Jan Boons
Heparan sulfates (HS) are linear sulfated polysaccharides that modulate a wide range of physiological and disease-processes. Variations in HS epimerization and sulfation provide enormous structural diversity, which is believed to underpin protein binding and regulatory properties. The ligand requirements of HS-binding proteins have, however, been defined in only a few cases. We describe here a synthetic methodology that can rapidly provide a library of well-defined HS oligosaccharides. It is based on the use of modular disaccharides to assemble several selectively protected tetrasaccharides that were subjected to selective chemical modifications such as regioselective O- and N-sulfation and selective de-sulfation...
June 26, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28650998/functional-annotation-of-alzheimer-s-disease-associated-loci-revealed-by-gwass
#6
Zengpeng Han, Han Huang, Yue Gao, Qingyang Huang
Genome-wide association studies (GWASs) discovered a number of SNPs and genes associated with Alzheimer's disease (AD). However, how these SNPs and genes influence the liability to AD is not fully understood. We deployed computational approaches to explore the function and action mechanisms of AD -related SNPs and genes identified by GWASs, including the effects of 195 GWAS lead SNPs and 338 proxy SNPs on miRNAs binding and protein phosphorylation, their RegulomeDB and 3DSNP scores, and gene ontology, pathway enrichment and protein-protein interaction network of 126 AD-associated genes...
2017: PloS One
https://www.readbyqxmd.com/read/28650635/ternary-interactions-and-energy-transfer-between-fluorescein-isothiocyanate-adenosine-triphosphate-and-graphene-oxide-nanocarriers
#7
Katarzyna Ratajczak, Magdalena Stobiecka
The interactions of fluorescent probes and biomolecules with nanocarriers are of key importance to the emerging targeted drug delivery systems. Graphene oxide nanosheets (GONs) as the nanocarriers offer biocompatibility and robust drug binding capacity. The interactions of GONs with fluorophores lead to strong fluorescence quenching, which may interfere with fluorescence bioimaging and biodetection. Herein, we report on the interactions and energy transfers in a model ternary system: GONs-FITC-ATP, where FITC is a model fluorophore (fluorescein isothiocyanate) and ATP is a common biomolecule (adenosine-5'-triphosphate)...
June 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28650624/precise-steric-control-over-2d-versus-3d-self-assembly-of-antimony-iii-alkoxide-cages-through-strong-secondary-bonding-interactions
#8
Shiva Moaven, Jingze Yu, Jason Yasin, Daniel K Unruh, Anthony F Cozzolino
Antimony(III) alkoxide cages were designed as building blocks for predictable supramolecular self-assembly. Supramolecular synthons featuring two Sb···O secondary bonding interactions (SBIs), each SBI stronger than 30 kJ/mol, were used to drive the formation of the supramolecular architectures. Judicious choice of pendant groups provided predictable control over the formation of self-assembled 3D columnar helices, which crystallized with hollow morphologies, or a self-assembled 2D bilayer. The Sb-O stretching frequency provides a spectroscopic signature of Sb···O SBI formation...
June 26, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28650609/a-pom-constructed-from-super-sodalite-cage-with-extra-large-24-membered-channels-as-effective-sorbent-for-uranium-adsorption
#9
Yayu Dong, Zhimin Dong, Zhibin Zhang, Yunhai Liu, Weiwei Cheng, Hao Miao, Xingxiang He, Yan Xu
A novel POMs-based sorbent functionalized by phosphate groups: H33Na14MoV24MoVI2(PO4)11O73 has been successfully isolated under hydrothermal conditions. The cooperative assembly of the ring-shaped polyoxometalate structural building unit {P4Mo6} and MoO4 tetrahedra linkers gives rise to an unprecedented super-sodalite cage containing approximately spherical cavities with a 8.76 Å diameter. As POMs-based inorganic material, compound 1 was first applied as sorbent to adsorb U(VI) from aqueous solution, exhibiting good stability, high efficient and selectivity...
June 26, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28650493/liquid-crystalline-epoxy-networks-with-exchangeable-disulfide-bonds
#10
Yuzhan Li, Yuehong Zhang, Orlando Rios, Jong K Keum, Michael R Kessler
A liquid crystalline epoxy network (LCEN) with exchangeable disulfide bonds is synthesized by polymerizing a biphenyl-based epoxy monomer with an aliphatic dicarboxylic acid curing agent containing a disulfide bond. The effect of disulfide bonds on curing behavior and liquid crystalline (LC) phase formation of the LCEN is investigated. The presence of the disulfide bonds results in an increase in the reaction rate, leading to a reduction in liquid crystallinity of the LCEN. In order to promote LC phase formation and stabilize the self-assembled LC domains, a similar aliphatic dicarboxylic acid without the disulfide bond is used as a co-curing agent to reduce the amount of exchangeable disulfide bonds in the system...
June 26, 2017: Soft Matter
https://www.readbyqxmd.com/read/28650492/exploiting-the-biosynthetic-machinery-of-streptomyces-pilosus-to-engineer-a-water-soluble-zirconium-iv-chelator
#11
Tomas Richardson-Sanchez, William Tieu, Michael P Gotsbacher, Thomas J Telfer, Rachel Codd
The water solubility of a natural product-inspired octadentate hydroxamic acid chelator designed to coordinate Zr(iv)-89 has been improved by using a combined microbiological-chemical approach to engineer four ether oxygen atoms into the main-chain region of a methylene-containing analogue. First, an analogue of the trimeric hydroxamic acid desferrioxamine B (DFOB) that contained three main-chain ether oxygen atoms (DFOB-O3) was generated from cultures of the native DFOB-producer Streptomyces pilosus supplemented with oxybis(ethanamine) (OBEA), which competed against the native 1,5-diaminopentane (DP) substrate during DFOB assembly...
June 26, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28650469/a-compartmentalized-phosphoinositide-signaling-axis-at-cilia-is-regulated-by-inpp5e-to-maintain-cilia-and-promote-sonic-hedgehog-medulloblastoma
#12
S E Conduit, V Ramaswamy, M Remke, D N Watkins, B J Wainwright, M D Taylor, C A Mitchell, J M Dyson
Sonic Hedgehog (SHH) signaling at primary cilia drives the proliferation and progression of a subset of medulloblastomas, the most common malignant paediatric brain tumor. Severe side effects associated with conventional treatments and resistance to targeted therapies has led to the need for new strategies. SHH signaling is dependent on primary cilia for signal transduction suggesting the potential for cilia destabilizing mechanisms as a therapeutic target. INPP5E is an inositol polyphosphate 5-phosphatase that hydrolyses PtdIns(4,5)P2 and more potently, the phosphoinositide (PI) 3-kinase product PtdIns(3,4,5)P3...
June 26, 2017: Oncogene
https://www.readbyqxmd.com/read/28650463/type-vi-secretion-tssk-baseplate-protein-exhibits-structural-similarity-with-phage-receptor-binding-proteins-and-evolved-to-bind-the-membrane-complex
#13
Van Son Nguyen, Laureen Logger, Silvia Spinelli, Pierre Legrand, Thi Thanh Huyen Pham, Thi Trang Nhung Trinh, Yassine Cherrak, Abdelrahim Zoued, Aline Desmyter, Eric Durand, Alain Roussel, Christine Kellenberger, Eric Cascales, Christian Cambillau
The type VI secretion system (T6SS) is a multiprotein machine widespread in Gram-negative bacteria that delivers toxins into both eukaryotic and prokaryotic cells. The mechanism of action of the T6SS is comparable to that of contractile myophages. The T6SS builds a tail-like structure made of an inner tube wrapped by a sheath, assembled under an extended conformation. Contraction of the sheath propels the inner tube towards the target cell. The T6SS tail is assembled on a platform-the baseplate-which is functionally similar to bacteriophage baseplates...
June 26, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28650436/monitoring-the-orientation-of-rare-earth-doped-nanorods-for-flow-shear-tomography
#14
Jongwook Kim, Sébastien Michelin, Michiel Hilbers, Lucio Martinelli, Elodie Chaudan, Gabriel Amselem, Etienne Fradet, Jean-Pierre Boilot, Albert M Brouwer, Charles N Baroud, Jacques Peretti, Thierry Gacoin
Rare-earth phosphors exhibit unique luminescence polarization features originating from the anisotropic symmetry of the emitter ion's chemical environment. However, to take advantage of this peculiar property, it is necessary to control and measure the ensemble orientation of the host particles with a high degree of precision. Here, we show a methodology to obtain the photoluminescence polarization of Eu-doped LaPO4 nanorods assembled in an electrically modulated liquid-crystalline phase. We measure Eu(3+) emission spectra for the three main optical configurations (σ, π and α, depending on the direction of observation and the polarization axes) and use them as a reference for the nanorod orientation analysis...
June 19, 2017: Nature Nanotechnology
https://www.readbyqxmd.com/read/28650319/somatostatin-binds-to-the-human-amyloid-%C3%AE-peptide-and-favors-the-formation-of-distinct-oligomers
#15
Hansen Wang, Lisa D Muiznieks, Punam Ghosh, Declan Williams, Michael Solarski, Andrew Fang, Alejandro Ruiz-Riquelme, Régis Pomès, Joel C Watts, Avi Chakrabartty, Holger Wille, Simon Sharpe, Gerold Schmitt-Ulms
The amyloid β peptide (Aβ) is a key player in the etiology of Alzheimer disease (AD), yet a systematic investigation of its molecular interactions has not been reported. Here we identified by quantitative mass spectrometry proteins in human brain extract that bind to oligomeric Aβ1-42 (oAβ1-42) and/or monomeric Aβ1-42 (mAβ1-42) baits. Remarkably, the cyclic neuroendocrine peptide somatostatin-14 (SST14) was observed to be the most selectively enriched oAβ1-42 binder. The binding interface comprises a central tryptophan within SST14 and the N-terminus of Aβ1-42...
June 26, 2017: ELife
https://www.readbyqxmd.com/read/28650219/interrogating-cell-division-errors-using-random-and-chromosome-specific-missegregation-approaches
#16
Peter Ly, Don W Cleveland
Accurate segregation of the duplicated genome in mitosis is essential for maintaining genetic stability. Errors in this process can cause numerical and/or structural chromosome abnormalities - hallmark genomic features commonly associated with both tumorigenesis and developmental disorders. A cell-based approach was recently developed permitting inducible missegregation of the human Y chromosome by selectively disrupting kinetochore assembly onto the Y centromere. Although this strategy initially requires several steps of genetic manipulation, it is easy to use, highly efficient and specific for the Y without affecting the autosomes or the X, and does not require cell cycle synchronization or mitotic perturbation...
June 26, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28650175/bioactive-peptide-natural-products-as-lead-structures-for-medicinal-use
#17
Tam Dang, Roderich D Süssmuth
The need for new drugs for the treatment of various diseases is enormous. From the previous century until the present, numerous peptide and peptide-derived natural products have been isolated from bacteria and fungi. Hence, microorganisms play a pivotal role as sources for novel drugs with an emphasis on anti-infective agents. Various disciplines from biology, chemistry, and medicine are involved in early stages of the search for peptide natural products including taxonomy, microbiology, bioanalytics, bioinformatics, and medicinal chemistry...
June 26, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28650162/lamellar-liquid-crystalline-system-with-tunable-iridescent-color-by-ionic-surfactants
#18
Zhenhua Cong, Bowen Lin, Weiqing Li, Jian Niu, Feng Yan
Liquid crystals formed by the self-assembly of small molecules are very promising smart materials because of their unique properties, such as self-assembled multivalency, biocompatibility, and fast response to external stimuli. Here we report an iridescent liquid crystal system composed of water layers sandwiched by two bilayer membranes that consist of a self-assembled nonionic surfactant hexadecylglyceryl maleate (HGM) and a tiny amount of ionic surfactants. It is found the iridescent color of the liquid crystal system changes greatly with a trace of change of the ionic surfactants' concentration...
June 26, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28650156/discovery-of-a-glutamine-kinase-required-for-the-biosynthesis-of-the-o-methyl-phosphoramidate-modifications-found-in-the-capsular-polysaccharides-of-campylobacter-jejuni
#19
Zane W Taylor, Haley A Brown, Tamari Narindoshvili, Cory Q Wenzel, Christine Szymanski, Hazel M Holden, Frank M Raushel
Bacterial capsular polysaccharides (CPS) are complex carbohydrate structures that play a role in the overall fitness of the organism. Campylobacter jejuni, known for being a major cause of bacterial gastroenteritis worldwide, produces a CPS with a unique O-methyl phosphoramidate (MeOPN) modification on specific sugar residues. The formation of P-N bonds in nature is relatively rare and the pathway for the assembly of the phosphoramidate moiety in the CPS of C. jejuni is unknown. In this investigation we discovered that the initial transformation in the biosynthetic pathway for the MeOPN modification of the CPS involves the direct phosphorylation of the amide nitrogen of L-glutamine with ATP by the catalytic activity of Cj1418...
June 26, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28650147/structural-basis-for-aza-glycine-stabilization-of-collagen
#20
Alexander Kasznel, Yitao Zhang, Yang Hai, David M Chenoweth
Previously, we have demonstrated that replacement of the strictly conserved glycine in collagen with aza-glycine provides a general solution for stabilizing triple helical collagen peptides.1-2 The additional hydrogen bond and conformational constraints provided by aza-glycine increases the thermal stability and rate of folding in collagen peptides composed of Pro-Hyp-Gly triplet repeats, allowing for truncation to the smallest self-assembling peptide systems observed to date. Here we show that aza-glycine substitution enhances the stability of an arginine-containing collagen peptide and provide a structural basis for this stabilization with an atomic resolution crystal structure...
June 26, 2017: Journal of the American Chemical Society
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