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https://www.readbyqxmd.com/read/28094955/using-diffusion-to-characterize-interfacial-heterogeneity
#1
Krystyna Kijewska, Gary J Blanchard
We report on the use of molecular diffusional motion over a range of length scales to characterize compositional heterogeneity in monolayer structures. This work focuses on the diffusional motion of perylene in two types of films supported on functionalized silica surfaces; single component (stearic acid) and two-component (hydrocarbon/fluorocarbon) films. Langmuir-Blodgett (LB) monolayers were deposited directly on silica or were bound to surface-modified silica by means of metal ion complexation. The LB films were characterized by their π-A isotherms and by Brewster angle microscopy (BAM) during formation and deposition...
January 17, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28094344/estrogen-related-receptor-is-required-for-the-testicular-development-and-for-the-normal-sperm-axoneme-mitochondrial-derivatives-in-drosophila-males
#2
Snigdha Misra, Anuj Kumar Pandey, Snigdha Gupta, Ajay Kumar, Priyanka Khanna, Jai Shankar, Kristipati Ravi Ram
Estrogen related receptors (ERRs), categorized as orphan nuclear receptors, are critical for energy homeostasis and somatic development. However, significance of ERRs in the development of reproductive organs/organelles/cells remain poorly understood, albeit their homology to estrogen receptors. In this context, here, we show that knockdown of ERR in the testes leads to improperly developed testes with mis-regulation of genes (aly, mia, bruce, bam, bgcn, fzo and eya) involved in spermatogenesis, resulting in reduced male fertility...
January 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28093410/fastdoop-a-versatile-and-efficient-library-for-the-input-of-fasta-and-fastq-files-for-mapreduce-hadoop-bioinformatics-applications
#3
Umberto Ferraro Petrillo, Gianluca Roscigno, Giuseppe Cattaneo, Raffaele Giancarlo
: MapReduce Hadoop bioinformatics applications require the availability of special-purpose routines to manage the input of sequence files. Unfortunately, the Hadoop framework does not provide any built-in support for the most popular sequence file formats like FASTA or BAM. Moreover, the development of these routines is not easy, both because of the diversity of these formats and the need for managing efficiently sequence datasets that may count up to billions of characters. We present FASTdoop, a generic Hadoop library for the management of FASTA and FASTQ files...
January 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28091278/brief-activity-performance-measure-for-upper-limb-amputees-bam-ula
#4
Linda Resnik, Matthew Borgia, Frantzy Acluche
BACKGROUND: Measures of activity performance for adults with upper limb amputation are needed. The purposes of this study were to evaluate the measurement properties of a new measure of activity performance for adults with upper limb amputation, which we call the Brief Activity Measure for Upper Limb Amputees (BAM-ULA) and to compare BAM-ULA scores for users of different types of prostheses. METHODS: In all, 35 persons with upper limb amputation were administered the BAM-ULA, twice within 1 week...
January 1, 2017: Prosthetics and Orthotics International
https://www.readbyqxmd.com/read/28080912/comparison-of-medetomidine-ketamine-and-butorphanol-azaperone-medetomidine-in-captive-bennett-s-wallabies-macropus-rufogriseus
#5
Megan K Watson, Mary Thurber, Sathya K Chinnadurai
The objective of this study was to compare a traditional partially reversible medetomidine-ketamine sedation with a more reversible butorphanol-azaperone-medetomidine combination in Bennett's wallabies ( Macropus rufogriseus ) maintained in a zoological collection. Fourteen animals were divided into two treatment groups. Individuals in group 1 received an intramuscular (i.m.) injection of butorphanol (0.54 ± 0.05 mg/kg), azaperone (0.22 ± 0.02 mg/kg), and medetomidine (0.16 ± 0.02 mg/kg). Individuals in group 2 received an i...
December 2016: Journal of Zoo and Wildlife Medicine: Official Publication of the American Association of Zoo Veterinarians
https://www.readbyqxmd.com/read/28067911/de-novo-mutations-in-smchd1-cause-bosma-arhinia-microphthalmia-syndrome-and-abrogate-nasal-development
#6
Christopher T Gordon, Shifeng Xue, Gökhan Yigit, Hicham Filali, Kelan Chen, Nadine Rosin, Koh-Ichiro Yoshiura, Myriam Oufadem, Tamara J Beck, Ruth McGowan, Alex C Magee, Janine Altmüller, Camille Dion, Holger Thiele, Alexandra D Gurzau, Peter Nürnberg, Dieter Meschede, Wolfgang Mühlbauer, Nobuhiko Okamoto, Vinod Varghese, Rachel Irving, Sabine Sigaudy, Denise Williams, S Faisal Ahmed, Carine Bonnard, Mung Kei Kong, Ilham Ratbi, Nawfal Fejjal, Meriem Fikri, Siham Chafai Elalaoui, Hallvard Reigstad, Christine Bole-Feysot, Patrick Nitschké, Nicola Ragge, Nicolas Lévy, Gökhan Tunçbilek, Audrey S M Teo, Michael L Cunningham, Abdelaziz Sefiani, Hülya Kayserili, James M Murphy, Chalermpong Chatdokmaiprai, Axel M Hillmer, Duangrurdee Wattanasirichaigoon, Stanislas Lyonnet, Frédérique Magdinier, Asif Javed, Marnie E Blewitt, Jeanne Amiel, Bernd Wollnik, Bruno Reversade
Bosma arhinia microphthalmia syndrome (BAMS) is an extremely rare and striking condition characterized by complete absence of the nose with or without ocular defects. We report here that missense mutations in the epigenetic regulator SMCHD1 mapping to the extended ATPase domain of the encoded protein cause BAMS in all 14 cases studied. All mutations were de novo where parental DNA was available. Biochemical tests and in vivo assays in Xenopus laevis embryos suggest that these mutations may behave as gain-of-function alleles...
January 9, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28061865/proteomic-analysis-of-enterotoxigenic-escherichia-coli-etec-in-neutral-and-alkaline-conditions
#7
Lucia Gonzales-Siles, Roger Karlsson, Diarmuid Kenny, Anders Karlsson, Åsa Sjöling
BACKGROUND: Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhea in children and travelers to endemic areas. Secretion of the heat labile AB5 toxin (LT) is induced by alkaline conditions. In this study, we determined the surface proteome of ETEC exposed to alkaline conditions (pH 9) as compared to neutral conditions (pH 7) using a LPI Hexalane FlowCell combined with quantitative proteomics. Relative quantitation with isobaric labeling (TMT) was used to compare peptide abundance and their corresponding proteins in multiple samples at MS/MS level...
January 7, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28058425/structure-and-photoluminescence-properties-of-a-novel-apatite-green-phosphor-ba5-po4-2sio4-eu-2-excited-by-nuv-light
#8
Xin Ding, Yuhua Wang
A novel apatite mineral of Ba5(PO4)2SiO4 was synthesized successfully using a traditional high temperature solid-state reaction. Its structure was determined by high-resolution transmission electron microscopy, fast Fourier transform, energy dispersive X-ray spectroscopy, and X-ray powder diffraction Rietveld refinement, and this was found to be a hexagonal crystal system with the space group attributed to P63/m (176). Moreover, a series of Eu(2+) doped Ba5(PO4)2SiO4 phosphors were investigated. The photoluminescence (PL) properties of Ba5(PO4)2SiO4:Eu(2+) were investigated in detail by density functional theory calculations, diffuse reflection spectra, emission-excitation spectra, decay curves, and temperature dependence spectra...
January 18, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28040159/relative-effectiveness-of-selected-preenrichment-media-for-the-detection-of-salmonella-from-leafy-green-produce-and-herbs
#9
Andrew P Jacobson, Hua Wang, Vikas S Gill, Robert Duvall, Gabriela Arce, Stuart Chirtel, Thomas S Hammack
Four buffered preenrichment media (BAX(®) System MP Media (BAX)), Universal Preenrichment Broth (UPB), modified Buffered Peptone Water (mBPW), and Buffered Peptone Water (BPW)) were compared with lactose broth (LB) in the Bacteriological Analytical Manual's (BAM) Salmonella culture method for the analysis of 9 leafy green produce and herb types. Artificially contaminated test portions were pre-enriched in each medium and the results were analyzed statistically using Fisher's Exact 2-tailed F test (p < 0...
May 2017: Food Microbiology
https://www.readbyqxmd.com/read/28027645/biocarriers-improve-bioaugmentation-efficiency-of-a-rapid-sand-filter-for-the-treatment-of-2-6-dichlorobenzamide-contaminated-drinking-water
#10
Benjamin Horemans, Bart Raes, Johanna Vandermaesen, Yanti Simanjuntak, Hannelore Brocatus, Jeroen T'Syen, Julie Degryse, Jos Boonen, Janneke Wittebol, Ales Lapanje, Sebastian R Sørensen, Dirk Springael
Aminobacter sp. MSH1 immobilized in an alginate matrix in porous stones was tested in a pilot system as an alternative inoculation strategy to the use of free suspended cells for biological removal of micropollutant concentrations of 2,6-dichlorobenzamide (BAM) in drinking water treatment plants (DWTPs). BAM removal rates and MSH1 cell numbers were recorded during operation and assessed with specific BAM degradation rates obtained in lab conditions using either freshly grown cells or starved cells to explain reactor performance...
January 12, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28011768/seqlib-a-c%C3%A2-api-for-rapid-bam-manipulation-sequence-alignment-and-sequence-assembly
#11
Jeremiah Wala, Rameen Beroukhim
: We present SeqLib, a C ++ API and command line tool that provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C ++ sequence analysis APIs. We demonstrate an example of how minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM...
December 22, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28004824/high-performing-solution-coated-electrolyte-gated-organic-field-effect-transistors-for-aqueous-media-operation
#12
Qiaoming Zhang, Francesca Leonardi, Stefano Casalini, Inés Temiño, Marta Mas-Torrent
Since the first demonstration, the electrolyte-gated organic field-effect transistors (EGOFETs) have immediately gained much attention for the development of cutting-edge technology and they are expected to have a strong impact in the field of (bio-)sensors. However EGOFETs directly expose their active material towards the aqueous media, hence a limited library of organic semiconductors is actually suitable. By using two mostly unexplored strategies in EGOFETs such as blended materials together with a printing technique, we have successfully widened this library...
December 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27998487/molecularly-imprinted-phloroglucinol-formaldehyde-melamine-resin-prepared-in-a-deep-eutectic-solvent-for-selective-recognition-of-clorprenaline-and-bambuterol-in-urine
#13
Shiru Liang, Hongyuan Yan, Jiankun Cao, Yehong Han, Shigang Shen, Ligai Bai
A new molecularly imprinted phloroglucinol-formaldehyde-melamine resin (MIPFMR) was synthesized in a deep eutectic solvent (DES) using phenylephrine as a dummy template. The MIPFMR was used as a solid phase extraction (SPE) sorbent for the selective isolation and recognition of clorprenaline (CLP) and bambuterol (BAM) in urine. Phloroglucinol and melamine were used as double functional monomers that introduced abundant hydrophilic groups (such as hydroxyl groups, imino groups, and ether linkages) into the MIPFMR, making it compatible with aqueous solvents...
January 25, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/27994606/lineage-specific-evolutionary-histories-and-regulation-of-major-starch-metabolism-genes-during-banana-ripening
#14
Cyril Jourda, Céline Cardi, Olivier Gibert, Andrès Giraldo Toro, Julien Ricci, Didier Mbéguié-A-Mbéguié, Nabila Yahiaoui
Starch is the most widespread and abundant storage carbohydrate in plants. It is also a major feature of cultivated bananas as it accumulates to large amounts during banana fruit development before almost complete conversion to soluble sugars during ripening. Little is known about the structure of major gene families involved in banana starch metabolism and their evolution compared to other species. To identify genes involved in banana starch metabolism and investigate their evolutionary history, we analyzed six gene families playing a crucial role in plant starch biosynthesis and degradation: the ADP-glucose pyrophosphorylases (AGPases), starch synthases (SS), starch branching enzymes (SBE), debranching enzymes (DBE), α-amylases (AMY) and β-amylases (BAM)...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27993563/the-effect-of-repeated-lateral-compression-and-expansions-mimicking-blinking-on-selected-tear-film-polar-lipid-monofilms
#15
Matthew Patterson, Hans J Vogel, Elmar J Prenner
The tear film lipid layer is formed on the anterior surface of the eye, functioning as a barrier to excess evaporation and foreign particles, while also providing stability to the tear film. The lipid layer is organized into a polar lipid layer consisting of phospholipids, ceramides, and free fatty acids that act as a surfactant to a non-polar multilayer of wax and cholesterol esters. Due to shear forces from eye movement and the compression and expansion of blinking, the tear lipids are under constant stress...
December 16, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27989620/flexibility-in-the-periplasmic-domain-of-bama-is-important-for-function
#16
Lisa R Warner, Petia Z Gatzeva-Topalova, Pamela A Doerner, Arthur Pardi, Marcelo C Sousa
The β-barrel assembly machine (BAM) mediates the biogenesis of outer membrane proteins (OMPs) in Gram-negative bacteria. BamA, the central BAM subunit composed of a transmembrane β-barrel domain linked to five polypeptide transport-associated (POTRA) periplasmic domains, is thought to bind nascent OMPs and undergo conformational cycling to catalyze OMP folding and insertion. One model is that conformational flexibility between POTRA domains is part of this conformational cycling. Nuclear magnetic resonance (NMR) spectroscopy was used here to study the flexibility of the POTRA domains 1-5 in solution...
January 3, 2017: Structure
https://www.readbyqxmd.com/read/27987304/identification-of-lanthanum-specific-peptides-for-future-recycling-of-rare-earth-elements-from-compact-fluorescent-lamps
#17
Franziska L Lederer, Susan B Curtis, Stefanie Bachmann, W Scott Dunbar, Ross T A MacGillivray
As components of electronic scrap, rare earth minerals are an interesting but little used source of raw materials that are highly important for the recycling industry. Currently, there exists no cost-efficient technology to separate rare earth minerals from an electronic scrap mixture. In this study, phage surface display has been used as a key method to develop peptides with high specificity for particular inorganic targets in electronic scrap. Lanthanum phosphate doped with cerium and terbium as part of the fluorescent phosphors of spent compact fluorescent lamps (CFL) was used as a target material of economic interest to test the suitability of the phage display method to the separation of rare earth minerals...
December 17, 2016: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/27983723/viruses-and-the-origin-of-microbiome-selection-and-immunity
#18
Steven D Quistad, Juris A Grasis, Jeremy J Barr, Forest L Rohwer
The last common metazoan ancestor (LCMA) emerged over half a billion years ago. These complex metazoans provided newly available niche space for viruses and microbes. Modern day contemporaries, such as cnidarians, suggest that the LCMA consisted of two cell layers: a basal endoderm and a mucus-secreting ectoderm, which formed a surface mucus layer (SML). Here we propose a model for the origin of metazoan immunity based on external and internal microbial selection mechanisms. In this model, the SML concentrated bacteria and their associated viruses (phage) through physical dynamics (that is, the slower flow fields near a diffusive boundary layer), which selected for mucin-binding capabilities...
December 16, 2016: ISME Journal
https://www.readbyqxmd.com/read/27951697/experimental-modeling-of-flavonoid-biomembrane-interactions
#19
Didem Sanver, Brent S Murray, Amin Sadeghpour, Michael Rappolt, Andrew L Nelson
Nonspecific interactions of flavonoids with lipids can alter the membrane's features (e.g., thickness and fluctuations) as well as influence their therapeutic potentials. However, relatively little is known about the details of how flavonoids interact with lipid components. Structure-dependent interactions of a variety of flavonoids with phospholipid monolayers on a mercury (Hg) film electrode were established by rapid cyclic voltammetry (RCV). The data revealed that flavonoids adopting a planar configuration altered the membrane properties more significantly than nonplanar flavonoids...
December 13, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/27940082/sucrose-esters-as-biocompatible-surfactants-for-penetration-enhancement-an-insight-into-the-mechanism-of-penetration-enhancement-studied-using-stratumcorneum-model-lipids-and-langmuir-monolayers
#20
Marija N Todosijević, Gerald Brezesinski, Snežana D Savić, Reinhard H H Neubert
Up to now, the molecular mechanism of the penetration enhancing effect of sucrose esters (SEs) on stratumcorneum (SC) has not been explained in details. In this study, variety of surface sensitive techniques, including surface pressure-area (π-A) isotherms, infrared reflection-absorption spectroscopy (IRRAS), and Brewster angle microscopy (BAM), have been used to investigate interactions between SEs and SC intercellular lipids. A monolayer of the mixture of ceramide AS C18:18, stearic acid and cholesterol in the molar ratio of 1:1:0...
December 8, 2016: European Journal of Pharmaceutical Sciences
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