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https://www.readbyqxmd.com/read/28339741/shear-stress-regulated-mir-27b-controls-pericyte-recruitment-by-repressing-sema6a-and-sema6d
#1
Shemsi Demolli, Anuradha Doddaballapur, Kavi Devraj, Konstantin Stark, Yosif Manavski, Annekathrin Eckart, Christoph Zehendner, Tina Lucas, Thomas Korff, Markus Hecker, Steffen Massberg, Stefan Liebner, David Kaluza, Reinier A Boon, Stefanie Dimmeler
Aims: Vessel maturation involves the recruitment of mural cells such as pericytes and smooth muscle cells. Laminar shear stress is a major trigger for vessel maturation, but the molecular mechanisms by which shear stress affects recruitment of pericytes are unclear. MicroRNAs (miRs) are small non-coding RNAs, which post-transcriptionally control gene expression. The aim of the present study was to unveil the mechanism by which shear stress-regulated microRNAs contribute to vessel maturation...
February 23, 2017: Cardiovascular Research
https://www.readbyqxmd.com/read/28339732/exploring-the-in-vivo-digestion-of-plant-proteins-in-broiler-chickens
#2
E Recoules, H Sabboh-Jourdan, A Narcy, M Lessire, G Harichaux, V Labas, M J Duclos, S Réhault-Godbert
The use of various protein sources (industry by-products, proteaginous) in poultry diets requires a greater understanding of protein digestion mechanisms. The aim of this study was to characterize the molecular actors required for protein digestion in broilers fed 4 different diets containing soybean meal, rapeseed meal, pea, or corn distiller's dried grain with solubles as the only protein source. The digesta of the digestive tract segments were collected and soluble proteins were analyzed by SDS-PAGE. SDS-PAGE analyses revealed 5 ubiquitous bands in digesta of all digestive tract segments regardless of the diet, whereas 3 bands were diet-specific...
February 23, 2017: Poultry Science
https://www.readbyqxmd.com/read/28339458/rapid-surveillance-for-vector-presence-rsvp-development-of-a-novel-system-for-detecting-aedes-aegypti-and-aedes-albopictus
#3
Brian L Montgomery, Martin A Shivas, Sonja Hall-Mendelin, Jim Edwards, Nicholas A Hamilton, Cassie C Jansen, Jamie L McMahon, David Warrilow, Andrew F van den Hurk
BACKGROUND: The globally important Zika, dengue and chikungunya viruses are primarily transmitted by the invasive mosquitoes, Aedes aegypti and Aedes albopictus. In Australia, there is an increasing risk that these species may invade highly urbanized regions and trigger outbreaks. We describe the development of a Rapid Surveillance for Vector Presence (RSVP) system to expedite presence- absence surveys for both species. METHODOLOGY/PRINCIPAL FINDINGS: We developed a methodology that uses molecular assays to efficiently screen pooled ovitrap (egg trap) samples for traces of target species ribosomal RNA...
March 24, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28338690/a-viscous-solvent-enables-information-transfer-from-gene-length-nucleic-acids-in-a-model-prebiotic-replication-cycle
#4
Christine He, Isaac Gállego, Brandon Laughlin, Martha A Grover, Nicholas V Hud
Many hypotheses concerning the nature of early life assume that genetic information was once transferred through the template-directed synthesis of RNA, before the emergence of coded enzymes. However, attempts to demonstrate enzyme-free, template-directed synthesis of nucleic acids have been limited by 'strand inhibition', whereby transferring information from a template strand in the presence of its complementary strand is inhibited by the stability of the template duplex. Here, we use solvent viscosity to circumvent strand inhibition, demonstrating information transfer from a gene-length template (>300 nt) within a longer (545 bp or 3 kb) duplex...
April 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28338689/a-prebiotically-plausible-synthesis-of-pyrimidine-%C3%AE-ribonucleosides-and-their-phosphate-derivatives-involving-photoanomerization
#5
Jianfeng Xu, Maria Tsanakopoulou, Christopher J Magnani, Rafał Szabla, Judit E Šponer, Jiří Šponer, Robert W Góra, John D Sutherland
Previous research has identified ribose aminooxazoline as a potential intermediate in the prebiotic synthesis of the pyrimidine nucleotides with remarkable properties. It crystallizes spontaneously from reaction mixtures, with an enhanced enantiomeric excess if initially enantioenriched, which suggests that reservoirs of this compound might have accumulated on the early Earth in an optically pure form. Ribose aminooxazoline can be converted efficiently into α-ribocytidine by way of 2,2'-anhydroribocytidine, although anomerization to β-ribocytidine by ultraviolet irradiation is extremely inefficient...
April 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28338682/simple-peptides-derived-from-the-ribosomal-core-potentiate-rna-polymerase-ribozyme-function
#6
Shunsuke Tagami, James Attwater, Philipp Holliger
The emergence of functional interactions between nucleic acids and polypeptides was a key transition in the origin of life and remains at the heart of all biology. However, how and why simple non-coded peptides could have become critical for RNA function is unclear. Here, we show that putative ancient peptide segments from the cores of both ribosomal subunits enhance RNA polymerase ribozyme (RPR) function, as do derived homopolymeric peptides comprising lysine or the non-proteinogenic lysine analogues ornithine or, to a lesser extent, diaminobutyric acid, irrespective of chirality or chiral purity...
April 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28338097/the-cellular-protein-hnrnp-a2-b1-enhances-hiv-1-transcription-by-unfolding-ltr-promoter-g-quadruplexes
#7
Matteo Scalabrin, Ilaria Frasson, Emanuela Ruggiero, Rosalba Perrone, Elena Tosoni, Sara Lago, Martina Tassinari, Giorgio Palù, Sara N Richter
G-quadruplexes are four-stranded conformations of nucleic acids that act as cellular epigenetic regulators. A dynamic G-quadruplex forming region in the HIV-1 LTR promoter represses HIV-1 transcription when in the folded conformation. This activity is enhanced by nucleolin, which induces and stabilizes the HIV-1 LTR G-quadruplexes. In this work by a combined pull-down/mass spectrometry approach, we consistently found hnRNP A2/B1 as an additional LTR-G-quadruplex interacting protein. Surface plasmon resonance confirmed G-quadruplex specificity over linear sequences and fluorescence resonance energy transfer analysis indicated that hnRNP A2/B1 is able to efficiently unfold the LTR G-quadruplexes...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28338022/alizarin-red-s-for-online-pyrophosphate-detection-identified-by-a-rapid-screening-method
#8
Jens Fischbach, Qiuting Loh, Frank F Bier, Theam Soon Lim, Marcus Frohme, Jörn Glökler
We identified Alizarin Red S and other well known fluorescent dyes useful for the online detection of pyrophosphate in enzymatic assays, including the loop mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR) assays. An iterative screening was used for a selected set of compounds to first secure enzyme compatibility, evaluate inorganic pyrophosphate sensitivity in the presence of manganese as quencher and optimize conditions for an online detection. Of the selected dyes, the inexpensive alizarin red S was found to selectively detect pyrophosphate under LAMP and PCR conditions and is superior with respect to its defined red-shifted spectrum, long shelf life and low toxicity...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28337468/comparative-analysis-data-of-sf1-and-sf2-helicases-from-three-domains-of-life
#9
Wafi Chaar, Hiba Ibrahim, Juliana Kozah, Hala Chamieh
SF1 and SF2 helicases are important molecular motors that use the energy of ATP to unwind nucleic acids or nucleic-acid protein complexes. They are ubiquitous enzymes and found in almost all organisms sequenced to date. This article provides a comparative analysis for SF1 and SF2 helicase families from three domains of life archaea, human, bacteria. Seven families are conserved in these three representatives and includes Upf1-like, UvrD-like, Rad3-like, DEAD-box, RecQ-like. Snf2 and Ski2-like. The data highlight conservation of the helicase core motifs for each of these families...
April 2017: Data in Brief
https://www.readbyqxmd.com/read/28337070/genomic-methods-and-microbiological-technologies-for-profiling-novel-and-extreme-environments-for-the-extreme-microbiome-project-xmp
#10
Scott Tighe, Ebrahim Afshinnekoo, Tara M Rock, Ken McGrath, Noah Alexander, Alexa McIntyre, Sofia Ahsanuddin, Daniela Bezdan, Stefan J Green, Samantha Joye, Sarah Stewart Johnson, Don A Baldwin, Nathan Bivens, Nadim Ajami, Joseph R Carmical, Ian Charold Herriott, Rita Colwell, Mohamed Donia, Jonathan Foox, Nick Greenfield, Tim Hunter, Jessica Hoffman, Joshua Hyman, Ellen Jorgensen, Diana Krawczyk, Jodie Lee, Shawn Levy, Natàlia Garcia-Reyero, Matthew Settles, Kelley Thomas, Felipe Gómez, Lynn Schriml, Nikos Kyrpides, Elena Zaikova, Jon Penterman, Christopher E Mason
The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines...
March 10, 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28336071/sensitive-protein-detection-and-quantification-in-paper-based-microfluidics-for-the-point-of-care
#11
Caitlin E Anderson, Kamal G Shah, Paul Yager
The design of appropriate diagnostic assays for the point of care requires development of suitable biosensors, detection methods, and diagnostic platforms for sensitive, quantitative detection of biological analytes. Protein targets in particular are especially challenging to detect quantitatively and sensitively due to the lack of amplification strategies akin to nucleic acid amplification. However, recent advances in transducer and biosensor design, new detection labels, and paper-based microfluidics may realize the goal of sensitive, fast, portable, and low-cost protein detection...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28335682/effect-of-lipophilicity-of-amylamine-and-amylglycine-ligands-on-biological-activity-of-new-anticancer-cisplatin-analog
#12
Fatemeh Safa Shams Abyaneh, Mahboube Eslami Moghadam, Moayyed Hoseini Sadr, Adeleh Divsalar
Investigation of side effects and solubility of anticancer drugs is a major challenge in chemotherapy science. Thus, design and synthesis of cisplatin analogs with higher lipophilicity as novel water-soluble anticancer drugs is valuable. In this work, two new Pt (II) complexes were synthesized with formula cis-[Pt (NH3)2(amylgly)] NO3 and cis-[Pt (amylamine)2(amylgly)]NO3; where gly is penthyl glycine as an amino acid. The new compounds were synthesized and extensively characterized using analytical techniques; spectroscopic methods and conductivity measurement...
March 23, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28335433/evaluation-and-adaptation-of-a-laboratory-based-cdna-library-preparation-protocol-for-retrospective-sequencing-of-archived-micrornas-from-up-to-35-year-old-clinical-ffpe-specimens
#13
Olivier Loudig, Tao Wang, Kenny Ye, Juan Lin, Yihong Wang, Andrew Ramnauth, Christina Liu, Azadeh Stark, Dhananjay Chitale, Robert Greenlee, Deborah Multerer, Stacey Honda, Yihe Daida, Heather Spencer Feigelson, Andrew Glass, Fergus J Couch, Thomas Rohan, Iddo Z Ben-Dov
Formalin-fixed paraffin-embedded (FFPE) specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years...
March 14, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28335314/effects-of-g-quadruplex-topology-on-electronic-transfer-integrals
#14
Wenming Sun, Daniele Varsano, Rosa Di Felice
G-quadruplex is a quadruple helical form of nucleic acids that can appear in guanine-rich parts of the genome. The basic unit is the G-tetrad, a planar assembly of four guanines connected by eight hydrogen bonds. Its rich topology and its possible relevance as a drug target for a number of diseases have stimulated several structural studies. The superior stiffness and electronic π-π overlap between consecutive G-tetrads suggest exploitation for nanotechnologies. Here we inspect the intimate link between the structure and the electronic properties, with focus on charge transfer parameters...
October 15, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28335269/galactosylated-liposomes-for-targeted-co-delivery-of-doxorubicin-vimentin-sirna-to-hepatocellular-carcinoma
#15
Hea Ry Oh, Hyun-Young Jo, James S Park, Dong-Eun Kim, Je-Yoel Cho, Pyung-Hwan Kim, Keun-Sik Kim
The combination of therapeutic nucleic acids and chemotherapeutic drugs has shown great promise for cancer therapy. In this study, asialoglycoprotein receptors (ASGPR) targeting-ligand-based liposomes were tested to determine whether they can co-deliver vimentin siRNA and doxorubicin to hepatocellular carcinoma (HCC) selectively. To achieve this goal, we developed an ASGPR receptor targeted co-delivery system called gal-doxorubicin/vimentin siRNA liposome (Gal-DOX/siRNA-L). The Gal-DOX/siRNA-L was created via electrostatic interaction of galactose linked-cationic liposomal doxorubicin (Gal-DOX-L) on vimentin siRNA...
July 30, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28335224/structural-changes-induced-in-grapevine-vitis-vinifera-l-dna-by-femtosecond-ir-laser-pulses-a-surface-enhanced-raman-spectroscopic-study
#16
Nicoleta E Dina, Cristina M Muntean, Nicolae Leopold, Alexandra Fălămaș, Adela Halmagyi, Ana Coste
In this work, surface-enhanced Raman spectra of ten genomic DNAs extracted from leaf tissues of different grapevine (Vitis vinifera L.) varieties, respectively, are analyzed in the wavenumber range 300-1800 cm(-1). Furthermore, structural changes induced in grapevine genomic nucleic acids upon femtosecond (170 fs) infrared (IR) laser pulse irradiation (λ = 1100 nm) are discussed in detail for seven genomic DNAs, respectively. Surface-enhanced Raman spectroscopy (SERS) signatures, vibrational band assignments and structural characterization of genomic DNAs are reported for each case...
May 25, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28334941/rna-protein-interactions-govern-antiviral-specificity-and-encapsidation-of-broad-spectrum-anti-hiv-reverse-transcriptase-aptamers
#17
Margaret J Lange, Phuong D M Nguyen, Mackenzie K Callaway, Marc C Johnson, Donald H Burke
RNA aptamers that bind HIV-1 reverse transcriptase (RT) inhibit HIV-1 replication, but little is known about potential aptamer-specific viral resistance. During replication, RT interacts with diverse nucleic acids. Thus, the genetic threshold for eliciting resistance may be high for aptamers that make numerous contacts with RT. To evaluate the impact of RT-aptamer binding specificity on replication, we engineered proviral plasmids encoding diverse RTs within the backbone of HIV-1 strain NL4-3. Viruses inhibited by pseudoknot aptamers were rendered insensitive by a naturally occurring R277K variant, providing the first demonstration of aptamer-specific resistance in cell culture...
March 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334877/iron-mediates-catalysis-of-nucleic-acid-processing-enzymes-support-for-fe-ii-as-a-cofactor-before-the-great-oxidation-event
#18
C Denise Okafor, Kathryn A Lanier, Anton S Petrov, Shreyas S Athavale, Jessica C Bowman, Nicholas V Hud, Loren Dean Williams
Life originated in an anoxic, Fe2+-rich environment. We hypothesize that on early Earth, Fe2+ was a ubiquitous cofactor for nucleic acids, with roles in RNA folding and catalysis as well as in processing of nucleic acids by protein enzymes. In this model, Mg2+ replaced Fe2+ as the primary cofactor for nucleic acids in parallel with known metal substitutions of metalloproteins, driven by the Great Oxidation Event. To test predictions of this model, we assay the ability of nucleic acid processing enzymes, including a DNA polymerase, an RNA polymerase and a DNA ligase, to use Fe2+ in place of Mg2+ as a cofactor during catalysis...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334258/review-and-comparative-assessment-of-sequence-based-predictors-of-protein-binding-residues
#19
Jian Zhang, Lukasz Kurgan
Understanding of molecular mechanisms that govern protein-protein interactions and accurate modeling of protein-protein docking rely on accurate identification and prediction of protein-binding partners and protein-binding residues. We review over 40 methods that predict protein-protein interactions from protein sequences including methods that predict interacting protein pairs, protein-binding residues for a pair of interacting sequences and protein-binding residues in a single protein chain. We focus on the latter methods that provide residue-level annotations and that can be broadly applied to all protein sequences...
March 1, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28334006/assessing-various-infrared-ir-microscopic-imaging-techniques-for-post-mortem-interval-evaluation-of-human-skeletal-remains
#20
Claudia Woess, Seraphin Hubert Unterberger, Clemens Roider, Monika Ritsch-Marte, Nadin Pemberger, Jan Cemper-Kiesslich, Petra Hatzer-Grubwieser, Walther Parson, Johannes Dominikus Pallua
Due to the influence of many environmental processes, a precise determination of the post-mortem interval (PMI) of skeletal remains is known to be very complicated. Although methods for the investigation of the PMI exist, there still remains much room for improvement. In this study the applicability of infrared (IR) microscopic imaging techniques such as reflection-, ATR- and Raman- microscopic imaging for the estimation of the PMI of human skeletal remains was tested. PMI specific features were identified and visualized by overlaying IR imaging data with morphological tissue structures obtained using light microscopy to differentiate between forensic and archaeological bone samples...
2017: PloS One
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