274 results match your criteria composed stretches

Role of Charge Transfer in Halogen Bonding.

J Phys Chem A 2021 Apr 2;125(14):2944-2953. Epub 2021 Apr 2.

Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States.

Halogen bonding has received intensive attention recently for its applications in the construction of supramolecular assemblies and crystal engineering and its implications and potentials in chemical and biological processes and rational drug design. Peculiarly, in intermolecular interactions, halogen atoms are known as electron-donating groups carrying partial negative charges in molecules due to its high electronegativity, but they can counterintuitively act as Lewis acids and bind with Lewis bases in the form of a halogen bond. The unsettling issue regarding the nature of the halogen bonding is whether the electrostatics or charge transfer interaction dominates. Read More

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Degradable and Removable Tough Adhesive Hydrogels.

Adv Mater 2021 Apr 24;33(17):e2008553. Epub 2021 Mar 24.

John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA.

The development of tough adhesive hydrogels has enabled unprecedented adhesion to wet and moving tissue surfaces throughout the body, but they are typically composed of nondegradable components. Here, a family of degradable tough adhesive hydrogels containing ≈90% water by incorporating covalently networked degradable crosslinkers and hydrolyzable ionically crosslinked main-chain polymers is developed. Mechanical toughness, adhesion, and degradation of these new formulations are tested in both accelerated in vitro conditions and up to 16 weeks in vivo. Read More

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Shape Programming by Modulating Actuation over Hierarchical Length Scales.

Adv Mater 2020 Nov 19;32(47):e2004515. Epub 2020 Oct 19.

PMMH, CNRS, ESPCI Paris, Université PSL, Sorbonne Université, Université de Paris, F-75005, Paris, France.

Many active materials used in shape-morphing respond to an external stimulus by stretching or contracting along a director field. The programming of such actuators remains complex because of the single degree of freedom (the orientation) in local actuation. Here, texturing this field in zigzag patterns is shown to provide an extended family of biaxial active stretches out of an otherwise single uniaxial active deformation, opening a larger parameter space. Read More

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November 2020

Identification and Characterization of a Pear Chlorotic Leaf Spot-Associated Virus, a Novel Emaravirus Associated with a Severe Disease of Pear Trees in China.

Plant Dis 2020 Nov 30;104(11):2786-2798. Epub 2020 Sep 30.

Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi 330200, China.

Pear chlorotic leaf spot (PCLS) is a recently emerged disease of commercially cultivated sandy pear () trees in central and southern China. By integrating high-throughput sequencing and conventional Sanger sequencing of reverse-transcription (RT)-PCR products, a novel emaravirus infecting pear trees was identified and molecularly characterized. The virus was provisionally named pear chlorotic leaf spot-associated virus (PCLSaV). Read More

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November 2020

Stability of the pH-Dependent Parallel-Stranded d(CGA) Motif.

Biophys J 2020 10 11;119(8):1580-1589. Epub 2020 Sep 11.

Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland. Electronic address:

Noncanonical DNA structures that retain programmability and structural predictability are increasingly being used in DNA nanotechnology applications, in which they offer versatility beyond traditional Watson-Crick interactions. The d(CGA) triplet repeat motif is structurally dynamic and can transition between parallel-stranded homo-base paired duplex and antiparallel unimolecular hairpin in a pH-dependent manner. Here, we evaluate the thermodynamic stability and nuclease sensitivity of oligonucleotides composed of the d(CGA) motif and several structurally related sequence variants. Read More

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October 2020

COMBinatorial Oligonucleotide FISH (COMBO-FISH) with Uniquely Binding Repetitive DNA Probes.

Methods Mol Biol 2020 ;2175:65-77

Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany.

During the last decade, genome sequence databases of many species have been more and more completed so that it has become possible to further develop a recently established technique of FISH (Fluorescence In Situ Hybridization) called COMBO-FISH (COMBinatorial Oligo FISH). In contrast to standard FISH techniques, COMBO-FISH makes use of a bioinformatic search in sequence databases for probe design, so that it can be done for any species so far sequenced. In the original approach, oligonucleotide stretches of typical lengths of 15-30 nucleotides were selected in such a way that they only co-localize at the given genome target. Read More

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Structural characteristics and anti-complement activities of polysaccharides from Sargassum hemiphyllum.

Glycoconj J 2020 10 2;37(5):553-563. Epub 2020 Jul 2.

College of Biotechnology and Bioengineering, Zhejiang University of Technology, 310014, Hangzhou, China.

Three polysaccharides (SH-1, SH-2 and SH-3) were purified from a brown macroalgea, Sargassum hemiphyllum. The autohydrolysis products from each polysaccharide were separated to three fractions (S fractions as oligomers, L fractions as low molecular weight polysaccharides and H fractions as high molecular weight polysaccharides). Mass spectroscopy of S fractions (SH-1-S, SH-2-S and SH-3-S) showed that these three polymers all contained short stretches of sulfated fucose. Read More

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October 2020

Finite strain parametric HFGMC micromechanics of soft tissues.

Biomech Model Mechanobiol 2020 Dec 9;19(6):2443-2453. Epub 2020 Jun 9.

School of Mechanical Engineering, Tel Aviv University, Tel Aviv-Yafo, Israel.

A micromechanical analysis is offered for the prediction of the global behavior of biological tissues. The analysis is based on the isotropic-hyperelastic behavior of the individual constituents (Collagen and Elastin), their volume fractions, and takes into account their detailed interactions. The present analysis predicts the instantaneous tensors from which the effective current first tangent tensor is established, thus providing the overall anisotropic constitutive behavior of the composite and the resulting field distribution in the composite. Read More

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December 2020

Molecular Dynamics Simulation of the Ionic Liquid 1-n-Butyl-3-Methylimidazolium Methylsulfate [Bmim][MeSO ]: Interfacial Properties at the Silica and Vacuum Interfaces.

Chemphyschem 2020 Jun 21;21(11):1134-1145. Epub 2020 Apr 21.

Department of Chemistry, College of Sciences, Persian Gulf University, Boushehr, 75168, Iran.

Molecular dynamics simulations are done to investigate the structure and dynamics of a thin [Bmim][MeO ] film in contact with a hydroxylated silica surface on one side and with vacuum on the other. An examination of the microscopic structure of ionic liquid (IL) film shows that strong layered anionic/cationic structures are formed at both interfaces. At the silica interface, the imidazolium rings are closer to the silica surface (compared to anions) and are coplanar with it. Read More

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Synthetic and genomic regulatory elements reveal aspects of -regulatory grammar in mouse embryonic stem cells.

Elife 2020 02 11;9. Epub 2020 Feb 11.

Edison Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, United States.

In embryonic stem cells (ESCs), a core transcription factor (TF) network establishes the gene expression program necessary for pluripotency. To address how interactions between four key TFs contribute to regulation in mouse ESCs, we assayed two massively parallel reporter assay (MPRA) libraries composed of binding sites for SOX2, POU5F1 (OCT4), KLF4, and ESRRB. Comparisons between synthetic -regulatory elements and genomic sequences with comparable binding site configurations revealed some aspects of a regulatory grammar. Read More

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February 2020

Structure of a Tc holotoxin pore provides insights into the translocation mechanism.

Proc Natl Acad Sci U S A 2019 11 30;116(46):23083-23090. Epub 2019 Oct 30.

Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany;

Tc toxins are modular toxin systems of insect and human pathogenic bacteria. They are composed of a 1.4-MDa pentameric membrane translocator (TcA) and a 250-kDa cocoon (TcB and TcC) encapsulating the 30-kDa toxic enzyme (C terminus of TcC). Read More

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November 2019

Analysis of α-Dystroglycan/LG Domain Binding Modes: Investigating Protein Motifs That Regulate the Affinity of Isolated LG Domains.

Front Mol Biosci 2019 29;6:18. Epub 2019 Mar 29.

School of Biochemistry, University of Bristol, Bristol, United Kingdom.

Dystroglycan (DG) is an adhesion complex that links the cytoskeleton to the surrounding extracellular matrix in skeletal muscle and a wide variety of other tissues. It is composed of a highly glycosylated extracellular α-DG associated noncovalently with a transmembrane β-DG whose cytodomain interacts with dystrophin and its isoforms. Alpha-dystroglycan (α-DG) binds tightly and in a calcium-dependent fashion to multiple extracellular proteins and proteoglycans, each of which harbors at least one, or, more frequently, tandem arrays of laminin-globular (LG) domains. Read More

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Cryo-EM structure of cardiac amyloid fibrils from an immunoglobulin light chain AL amyloidosis patient.

Nat Commun 2019 03 20;10(1):1269. Epub 2019 Mar 20.

Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy.

Systemic light chain amyloidosis (AL)  is a life-threatening disease caused by aggregation and deposition of monoclonal immunoglobulin light chains (LC) in target organs. Severity of heart involvement is the most important factor determining prognosis. Here, we report the 4. Read More

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Introduction of 'Generalized Genomic Signatures' for the quantification of neighbour preferences leads to taxonomy- and functionality-based distinction among sequences.

Sci Rep 2019 02 8;9(1):1700. Epub 2019 Feb 8.

Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos", 15310, Athens, Greece.

Analysis of DNA composition at several length scales constitutes the bulk of many early studies aimed at unravelling the complexity of the organization and functionality of genomes. Dinucleotide relative abundances are considered an idiosyncratic feature of genomes, regarded as a 'genomic signature'. Motivated by this finding, we introduce the 'Generalized Genomic Signatures' (GGSs), composed of over- and under-abundances of all oligonucleotides of a given length, thus filtering out compositional trends and neighbour preferences at any shorter range. Read More

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February 2019

Mutational mechanism for DAB1 (ATTTC) insertion in SCA37: ATTTT repeat lengthening and nucleotide substitution.

Hum Mutat 2019 04 9;40(4):404-412. Epub 2019 Jan 9.

Genetics of Cognitive Dysfunction Laboratory, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.

Dynamic mutations by microsatellite instability are the molecular basis of a growing number of neuromuscular and neurodegenerative diseases. Repetitive stretches in the human genome may drive pathogenicity, either by expansion above a given threshold, or by insertion of abnormal tracts in nonpathogenic polymorphic repetitive regions, as is the case in spinocerebellar ataxia type 37 (SCA37). We have recently established that this neurodegenerative disease is caused by an (ATTTC) insertion within an (ATTTT) in a noncoding region of DAB1. Read More

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Exploiting Stretchable Metallic Springs as Compliant Electrodes for Cylindrical Dielectric Elastomer Actuators (DEAs).

Micromachines (Basel) 2017 Nov 22;8(11). Epub 2017 Nov 22.

Department of Mechanical Engineering, National Taiwan University, Taipei 10617, Taiwan.

In recent years, dielectric elastomer actuators (DEAs) have been widely used in soft robots and artificial bio-medical applications. Most DEAs are composed of a thin dielectric elastomer layer sandwiched between two compliant electrodes. DEAs vary in their design to provide bending, torsional, and stretch/contraction motions under the application of high external voltages. Read More

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November 2017

Characterization of copy number variants in a large multibreed population of beef and dairy cattle using high-density single nucleotide polymorphism genotype data.

J Anim Sci 2018 Sep;96(10):4112-4124

Teagasc, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland.

Copy number variants (CNVs) are a form of genomic variation that changes the structure of the genome through deletion or duplication of stretches of DNA. The objective of the present study was to characterize CNVs in a large multibreed population of beef and dairy bulls. The CNVs were called on the autosomes of 5,551 cattle from 22 different beef and dairy breeds, using 2 freely available software suites, QuantiSNP and PennCNV. Read More

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September 2018

Proprioception from a neurally controlled lower-extremity prosthesis.

Sci Transl Med 2018 05;10(443)

Center for Extreme Bionics, Massachusetts Institute of Technology (MIT) Media Lab, Cambridge, MA 02139, USA.

Humans can precisely sense the position, speed, and torque of their body parts. This sense is known as proprioception and is essential to human motor control. Although there have been many attempts to create human-mechatronic interactions, there is still no robust, repeatable methodology to reflect proprioceptive information from a synthetic device onto the nervous system. Read More

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Quantitative Methods to Investigate the 4D Dynamics of Heterochromatic Repair Sites in Drosophila Cells.

Methods Enzymol 2018 26;601:359-389. Epub 2018 Feb 26.

University of Southern California, Los Angeles, CA, United States. Electronic address:

Heterochromatin is mostly composed of long stretches of repeated DNA sequences prone to ectopic recombination during double-strand break (DSB) repair. In Drosophila, "safe" homologous recombination (HR) repair of heterochromatic DSBs relies on a striking relocalization of repair sites to the nuclear periphery. Central to understanding heterochromatin repair is the ability to investigate the 4D dynamics (movement in space and time) of repair sites. Read More

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Production of recombinant human tektin 1, 2, and 4 and in vitro assembly of human tektin 1.

Cytoskeleton (Hoboken) 2018 01 2;75(1):3-11. Epub 2017 Dec 2.

Department of Cell Biology and Human Anatomy, School of Medicine, University of California, Davis, California, 95616.

Proteins predicted to be composed of large stretches of coiled-coil structure have often proven difficult to crystallize for structural determination. We have successfully applied EPR spectroscopic techniques to the study of the structure and assembly of full-length human vimentin assembled into native 11 nm filaments, in physiologic solution, circumventing the limitations of crystallizing shorter peptide sequences. Tektins are a small family of highly alpha helical filamentous proteins found in the doublet microtubules of cilia and related structures. Read More

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January 2018

Engineering multifunctional protein nanoparticles by in vitro disassembling and reassembling of heterologous building blocks.

Nanotechnology 2017 Dec;28(50):505102

Institut d'Investigacions Biomèdiques Sant Pau and Josep Carreras Research Institute, Hospital de la Santa Creu i Sant Pau, E-08025 Barcelona, Spain. CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Spain.

The engineering of protein self-assembling at the nanoscale allows the generation of functional and biocompatible materials, which can be produced by easy biological fabrication. The combination of cationic and histidine-rich stretches in fusion proteins promotes oligomerization as stable protein-only regular nanoparticles that are composed by a moderate number of building blocks. Among other applications, these materials are highly appealing as tools in targeted drug delivery once empowered with peptidic ligands of cell surface receptors. Read More

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December 2017

Insoluble (1 → 3), (1 → 4)-β-D-glucan is a component of cell walls in brown algae (Phaeophyceae) and is masked by alginates in tissues.

Sci Rep 2017 06 6;7(1):2880. Epub 2017 Jun 6.

Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France.

Brown algae are photosynthetic multicellular marine organisms. They belong to the phylum of Stramenopiles, which are not closely related to land plants and green algae. Brown algae share common evolutionary features with other photosynthetic and multicellular organisms, including a carbohydrate-rich cell-wall. Read More

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Near-neighbor interactions of the membrane-embedded subunits of the mitochondrial ATP synthase of a chlorophycean alga.

Biochim Biophys Acta Bioenerg 2017 Jul 1;1858(7):497-509. Epub 2017 May 1.

Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, México. Electronic address:

Mitochondrial FF-ATP synthase of the chlorophycean algae Polytomella sp. can be isolated as a highly stable dimeric complex of 1600kDa. It is composed of eight highly conserved orthodox subunits (α, β, γ, δ, ε, OSCP, a, and c) and nine subunits (Asa1-9) that are exclusive of chlorophycean algae. Read More

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A new parallel pipeline for DNA methylation analysis of long reads datasets.

BMC Bioinformatics 2017 Mar 9;18(1):161. Epub 2017 Mar 9.

Department of Computational Genomics, Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera, s/n, Valencia, Spain.

Background: DNA methylation is an important mechanism of epigenetic regulation in development and disease. New generation sequencers allow genome-wide measurements of the methylation status by reading short stretches of the DNA sequence (Methyl-seq). Several software tools for methylation analysis have been proposed over recent years. Read More

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Evaluation of the Ion Torrent PGM sequencing workflow for the routine rapid detection of BRCA1 and BRCA2 germline mutations.

Exp Mol Pathol 2017 04 2;102(2):314-320. Epub 2017 Mar 2.

Biotechnology Laboratory and Department of Diagnostics, Civic Hospital of Brescia, Brescia, Italy.

Purpose: Conventional methods used to identify BRCA1/2 germline mutations in hereditary cancers are time-consuming and expensive, due to the large size of the genes. The recent introduction of next generation sequencing (NGS) benchtop platforms is a great promise, which is rapidly revolutionizing genetic screening in diagnostic and clinical applications. We recently transferred our methodology for routine BRCA1/2 mutation screening (denaturing High Performance Liquid Chromatography plus Sanger sequencing) to the Ion Torrent PGM platform with the Ion Ampliseq BRCA1 and BRCA2 panel and tested the performance of the system. Read More

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A Unified Theory for the Blue- and Red-Shifting Phenomena in Hydrogen and Halogen Bonds.

J Chem Theory Comput 2017 Apr 14;13(4):1626-1637. Epub 2017 Mar 14.

Department of Chemistry, Western Michigan University , Kalamazoo, Michigan 49008, United States.

Typical hydrogen and halogen bonds exhibit red-shifts of their vibrational frequencies upon the formation of hydrogen and halogen bonding complexes (denoted as D···Y-A, Y = H and X). The finding of blue-shifts in certain complexes is of significant interest, which has led to numerous studies of the origins of the phenomenon. Because charge transfer mixing (i. Read More

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Prestretched airway smooth muscle response to length oscillation.

Physiol Rep 2017 Jan 26;5(2). Epub 2017 Jan 26.

Institute of Biomedical Technologies, Auckland University of Technology, Auckland, New Zealand.

Airway smooth muscle (ASM) hyperconstriction is the cause of many respiratory diseases including asthma. In vitro testing has demonstrated that the active forces of ASM are reduced by length oscillation (LO) mimicking tidal breathing. In a previous study, we demonstrated that this force reduction can be further enhanced when superimposing oscillations (with certain frequencies and amplitudes) on this LO In contrast, it has been reported that pressurizing the lung may help in relieving asthmatic airway constrictions. Read More

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January 2017

Polypurine reverse-Hoogsteen (PPRH) oligonucleotides can form triplexes with their target sequences even under conditions where they fold into G-quadruplexes.

Sci Rep 2017 01 9;7:39898. Epub 2017 Jan 9.

Structure et Instability of Genomes, Sorbonne Universités, Muséum National d'Histoire Naturelle, Inserm U 1154, CNRS UMR 7196, Paris, France.

Polypurine reverse-Hoogsteen (PPRH) oligonucleotides are non-modified DNA molecules composed of two mirror-symmetrical polypurine stretches linked by a five-thymidine loop. They can fold into reverse-Hoogsteen hairpins and bind to their polypyrimidine target sequence by Watson-Crick bonds forming a three-stranded structure. They have been successfully used to knockdown gene expression and to repair single-point mutations in cells. Read More

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January 2017