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https://www.readbyqxmd.com/read/28716000/quantiprot-a-python-package-for-quantitative-analysis-of-protein-sequences
#1
Bogumił M Konopka, Marta Marciniak, Witold Dyrka
BACKGROUND: The field of protein sequence analysis is dominated by tools rooted in substitution matrices and alignments. A complementary approach is provided by methods of quantitative characterization. A major advantage of the approach is that quantitative properties defines a multidimensional solution space, where sequences can be related to each other and differences can be meaningfully interpreted. RESULTS: Quantiprot is a software package in Python, which provides a simple and consistent interface to multiple methods for quantitative characterization of protein sequences...
July 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28714233/bioinspired-size-tunable-self-assembly-of-polymer-lipid-bilayer-nanodiscs
#2
Thirupathi Ravula, Sudheer Ramadugu, Giacomo Di Mauro, Ayyalusamy Ramamoorthy
Polymer-based nanodiscs are valuable tools in biomedical research that can offer a detergent-free solubilization of membrane proteins maintaining their native lipid environment. Here, we introduce a novel ~1.6 kDa SMA-based polymer with styrene:maleic acid moieties that can form nanodiscs containing a planar lipid bilayer which are useful to reconstitute membrane proteins for structural and functional studies. The physicochemical properties and the mechanism of formation of polymer-based nanodiscs are characterized by light scattering, NMR, FT-IR, and TEM imaging experiments...
July 16, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28710838/enzyme-free-ligation-of-5-phosphorylated-oligodeoxynucleotides-in-a-dna-nanostructure
#3
Markus Kramer, Clemens Richert
Multicomponent reactions are difficult synthetic transformations. For DNA, there is a special opportunity to align multiple strands in a folded nanostructure, so that they are preorganized to give a specific sequence. Multistrand reactions in DNA origami structures have previously been performed using photochemical crosslinking, 1,3-diploar cycloadditions or phosphoramidate-forming reactions. Here we report carbodiimide-driven phosphodiester formation in a small origami sheet that produces DNA strands up to 600 nucleotides in length in a single step...
July 15, 2017: Chemistry & Biodiversity
https://www.readbyqxmd.com/read/28702013/nitrogen-fixation-aligns-with-nifh-abundance-and-expression-in-two-coral-trophic-functional-groups
#4
Claudia Pogoreutz, Nils Rädecker, Anny Cárdenas, Astrid Gärdes, Christian Wild, Christian R Voolstra
Microbial nitrogen fixation (diazotrophy) is a functional trait widely associated with tropical reef-building (scleractinian) corals. While the integral role of nitrogen fixation in coral nutrient dynamics is recognized, its ecological significance across different coral functional groups remains yet to be evaluated. Here we set out to compare molecular and physiological patterns of diazotrophy (i.e., nifH gene abundance and expression as well as nitrogen fixation rates) in two coral families with contrasting trophic strategies: highly heterotrophic, free-living members of the family Fungiidae (Pleuractis granulosa, Ctenactis echinata), and mostly autotrophic coral holobionts with low heterotrophic capacity (Pocilloporidae: Pocillopora verrucosa, Stylophora pistillata)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28699920/systematic-periodicity-in-waviness-of-vertically-aligned-carbon-nanotubes-explained-by-helical-buckling
#5
Mehdi Jahangiri
A hypothesis is proposed in this work to account for the geometry of individual vertically aligned carbon nanotubes (VACNTs) that not only justifies the directionality of their growth, but also explains the origin of the waviness frequently reported for these nanotube forests. Such waviness has fundamental effects on the transport/conduction properties of VACNTs, either through or along them, regarding phenomena such as mass, stress, heat and electricity. Despite the general opinion about randomness of CNTs tortuosity, we demonstrate here that rules of helical buckling of tubular strings is applicable to VACNTs, based on which a regular 3D helical geometry is proposed for VACNTs, with a 2D sine wave shape side-profile...
July 12, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28699698/reduced-dosing-and-liability-in-methadone-maintenance-treatment-by-targeting-oestrogen-signal-for-morphine-addiction
#6
Yao-Chang Chiang, Ruey-Yun Wang, Chieh-Liang Huang, Shue-Hwa Chen, Wen-Jing Ho, Hsien-Yuan Lane, Ing-Kang Ho, Hwei-Ting Yang, Wen-Lung Ma
Methadone maintenance treatment (MMT) is the major tapering therapy for morphine addictive patients. There have gender differences reported in response to MMT. This study discovered that the estrogen-response element single nucleotide polymorphism (ERE-SNP; rs16974799, C/T) of cytochrome 2B6 gene (cyp2b6; methadone catabolic enzyme) responded differently to MMT dosing. Oestradiol was associated with high MMT dosing, high enantiomer (R- or S-) of 2-ethylidene-1,5-dimethyl-3,3-dipheny-pyrrolidine (EDDP; methadone metabolite) to methadone ratio and increased drug-seeking behaviour, implicating oestradiol-CYP-EDDP/methadone axis decreasing MMT efficacy...
July 12, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/28697920/higher-plasma-corticosterone-is-associated-with-reduced-costs-of-infection-in-red-winged-blackbirds
#7
Laura A Schoenle, Ivana Schoepf, Nicole M Weinstein, Ignacio T Moore, Frances Bonier
Glucocorticoid hormones allow individuals to rapidly adjust their physiology and behavior to meet the challenges of a variable environment. An individual's baseline concentration of glucocorticoids can reflect shifts in life history stage and resource demands while mediating a suite of physiological and behavioral changes that include immune modulation and resource allocation. Thus, glucocorticoids could facilitate a response to parasites that is optimized for an individual's specific challenges and life history stage...
July 8, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28697544/embedded-vertically-aligned-cadmium-telluride-nanorod-arrays-grown-by-one-step-electrodeposition-for-enhanced-energy-conversion-efficiency-in-three-dimensional-nanostructured-solar-cells
#8
Jun Wang, Shurong Liu, Yannan Mu, Li Liu, Runa A, Jiandong Yang, Guijie Zhu, Xianwei Meng, Wuyou Fu, Haibin Yang
Vertically aligned CdTe nanorods (NRs) arrays are successfully grown by a simple one-step and template-free electrodeposition method, and then embedded in the CdS window layer to form a novel three-dimensional (3D) heterostructure on flexible substrates. The parameters of electrodeposition such as deposition potential and pH of the solution are varied to analyze their important role in the formation of high quality CdTe NRs arrays. The photovoltaic conversion efficiency of the solar cell based on the 3D heterojunction structure is studied in detail...
July 3, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28694453/portable-and-error-free-dna-based-data-storage
#9
S M Hossein Tabatabaei Yazdi, Ryan Gabrys, Olgica Milenkovic
DNA-based data storage is an emerging nonvolatile memory technology of potentially unprecedented density, durability, and replication efficiency. The basic system implementation steps include synthesizing DNA strings that contain user information and subsequently retrieving them via high-throughput sequencing technologies. Existing architectures enable reading and writing but do not offer random-access and error-free data recovery from low-cost, portable devices, which is crucial for making the storage technology competitive with classical recorders...
July 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28693570/an-analysis-of-free-choice-electives-in-an-undergraduate-medical-degree
#10
Catriona Daly, Jason Last
BACKGROUND: The University College Dublin Elective Programme was introduced in 2005 with the intention of broadening the learning of its undergraduate students. Undergraduate medical students undertake seven free-choice electives during their six-year degree programme. They are permitted to choose electives from any school in the University. Students also have the option of selecting 'In-Programme' electives, which are aligned to medical themes. The purpose of this study is to analyse the electives taken by medical students with a view to better understanding the factors that influence their choices...
July 11, 2017: BMC Medical Education
https://www.readbyqxmd.com/read/28690134/recent-advances-in-rna-folding
#11
Jörg Fallmann, Sebastian Will, Jan Engelhardt, Björn Grüning, Rolf Backofen, Peter F Stadler
In the realm of nucleic acid structures, secondary structure forms a conceptually important intermediate level of description and explains the dominating part of the free energy of structure formation. Secondary structures are well conserved over evolutionary time-scales and for many classes of RNAs evolve slower than the underlying primary sequences. Given the close link between structure and function, secondary structure is routinely used as a basis to explain experimental findings. Recent technological advances, finally, have made it possible to assay secondary structure directly using high throughput methods...
July 6, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28688450/alignment-orientation-and-coulomb-explosion-of-difluoroiodobenzene-studied-with-the-pixel-imaging-mass-spectrometry-pimms-camera
#12
Kasra Amini, Rebecca Boll, Alexandra Lauer, Michael Burt, Jason W L Lee, Lauge Christensen, Felix Brauβe, Terence Mullins, Evgeny Savelyev, Utuq Ablikim, Nora Berrah, Cédric Bomme, Stefan Düsterer, Benjamin Erk, Hauke Höppner, Per Johnsson, Thomas Kierspel, Faruk Krecinic, Jochen Küpper, Maria Müller, Erland Müller, Harald Redlin, Arnaud Rouzée, Nora Schirmel, Jan Thøgersen, Simone Techert, Sven Toleikis, Rolf Treusch, Sebastian Trippel, Anatoli Ulmer, Joss Wiese, Claire Vallance, Artem Rudenko, Henrik Stapelfeldt, Mark Brouard, Daniel Rolles
Laser-induced adiabatic alignment and mixed-field orientation of 2,6-difluoroiodobenzene (C6H3F2I) molecules are probed by Coulomb explosion imaging following either near-infrared strong-field ionization or extreme-ultraviolet multi-photon inner-shell ionization using free-electron laser pulses. The resulting photoelectrons and fragment ions are captured by a double-sided velocity map imaging spectrometer and projected onto two position-sensitive detectors. The ion side of the spectrometer is equipped with a pixel imaging mass spectrometry camera, a time-stamping pixelated detector that can record the hit positions and arrival times of up to four ions per pixel per acquisition cycle...
July 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28688430/imaging-of-rotational-wave-function-in-photodissociation-of-rovibrationally-excited-hcl-molecules
#13
K Grygoryeva, J Rakovský, O Votava, M Fárník
We demonstrate a visualization of quantum mechanical phenomena with the velocity map imaging (VMI) technique, combining vibrationally mediated photodissociation (VMP) of a simple diatomic HCl with the VMI of its H-photofragments. Free HCl molecules were excited by a pump infrared (IR) laser pulse to particular rotational J levels of the v = 2 vibrational state, and subsequently a probe ultraviolet laser photodissociated the molecule at a fixed wavelength of 243.07 nm where also the H-fragments were ionized...
July 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28686612/evaluating-phecodes-clinical-classification-software-and-icd-9-cm-codes-for-phenome-wide-association-studies-in-the-electronic-health-record
#14
Wei-Qi Wei, Lisa A Bastarache, Robert J Carroll, Joy E Marlo, Travis J Osterman, Eric R Gamazon, Nancy J Cox, Dan M Roden, Joshua C Denny
OBJECTIVE: To compare three groupings of Electronic Health Record (EHR) billing codes for their ability to represent clinically meaningful phenotypes and to replicate known genetic associations. The three tested coding systems were the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) codes, the Agency for Healthcare Research and Quality Clinical Classification Software for ICD-9-CM (CCS), and manually curated "phecodes" designed to facilitate phenome-wide association studies (PheWAS) in EHRs...
2017: PloS One
https://www.readbyqxmd.com/read/28686160/the-cyanobacterial-circadian-clock-follows-midday-in-vivo-and-in-vitro
#15
Eugene Leypunskiy, Jenny Lin, Haneul Yoo, UnJin Lee, Aaron R Dinner, Michael J Rust
Circadian rhythms are biological oscillations that schedule daily changes in physiology. Outside the laboratory, circadian clocks do not generally free-run, but are driven by daily cues whose timing varies with the seasons. The principles that determine how circadian clocks align to these external cycles are not well understood. Here we report experimental platforms for driving the cyanobacterial circadian clock both in vivo and in vitro. We find that the phase of the circadian rhythm follows a simple scaling law in light-dark cycles, tracking midday across conditions with variable day length...
July 7, 2017: ELife
https://www.readbyqxmd.com/read/28684712/decaf-discrimination-comparison-alignment-tool-for-2d-pharmacophores
#16
Marta M Stepniewska-Dziubinska, Piotr Zielenkiewicz, Pawel Siedlecki
Comparison of small molecules is a common component of many cheminformatics workflows, including the design of new compounds and libraries as well as side-effect predictions and drug repurposing. Currently, large-scale comparison methods rely mostly on simple fingerprint representation of molecules, which take into account the structural similarities of compounds. Methods that utilize 3D information depend on multiple conformer generation steps, which are computationally expensive and can greatly influence their results...
July 6, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28680687/a-facilitated-diffusion-model-constrained-by-the-probability-isotherm-a-pedagogical-exercise-in-intuitive-non-equilibrium-thermodynamics
#17
REVIEW
Brian Chapman
This paper seeks to develop a more thermodynamically sound pedagogy for students of biological transport than is currently available from either of the competing schools of linear non-equilibrium thermodynamics (LNET) or Michaelis-Menten kinetics (MMK). To this end, a minimal model of facilitated diffusion was constructed comprising four reversible steps: cis-substrate binding, cis→trans bound enzyme shuttling, trans-substrate dissociation and trans→cis free enzyme shuttling. All model parameters were subject to the second law constraint of the probability isotherm, which determined the unidirectional and net rates for each step and for the overall reaction through the law of mass action...
June 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28678704/auto-context-convolutional-neural-network-auto-net-for-brain-extraction-in-magnetic-resonance-imaging
#18
Seyed Sadegh Mohseni Salehi, Deniz Erdogmus, Ali Gholipour
Brain extraction or whole brain segmentation is an important first step in many of the neuroimage analysis pipelines. The accuracy and robustness of brain extraction, therefore, is crucial for the accuracy of the entire brain analysis process. State-of-the-art brain extraction techniques rely heavily on the accuracy of alignment or registration between brain atlases and query brain anatomy, and/or make assumptions about the image geometry; therefore have limited success when these assumptions do not hold or image registration fails...
June 28, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28674752/-operative-access-for-treatment-of-pilon-fractures
#19
REVIEW
K Klaue
BACKGROUND: Under optimal conditions, fractures of the tibial pilon can be definitively managed operatively within 6 h after the trauma. Under suboptimal conditions, preoperative antiphlogistic treatment, possibly after approximate correction and external fixation of the alignment, is a reasonable option. Osteosynthesis implies reconstruction of good joint congruency in anatomical orientation. The soft tissue coverage of the distal lower leg is relatively poorly constructed and there is a high risk of devascularization, necrosis and ensuing infection...
July 3, 2017: Der Unfallchirurg
https://www.readbyqxmd.com/read/28673025/alignment-free-inference-of-hierarchical-and-reticulate-phylogenomic-relationships
#20
Guillaume Bernard, Cheong Xin Chan, Yao-Ban Chan, Xin-Yi Chua, Yingnan Cong, James M Hogan, Stefan R Maetschke, Mark A Ragan
We are amidst an ongoing flood of sequence data arising from the application of high-throughput technologies, and a concomitant fundamental revision in our understanding of how genomes evolve individually and within the biosphere. Workflows for phylogenomic inference must accommodate data that are not only much larger than before, but often more error prone and perhaps misassembled, or not assembled in the first place. Moreover, genomes of microbes, viruses and plasmids evolve not only by tree-like descent with modification but also by incorporating stretches of exogenous DNA...
June 30, 2017: Briefings in Bioinformatics
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