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https://www.readbyqxmd.com/read/28107435/peptide-targeted-by-human-antibodies-associated-with-hiv-vaccine-associated-protection-assumes-a-dynamic-%C3%AE-helical-structure
#1
Mohammed S Aiyegbo, Evgeny Shmelkov, Lorenzo Dominguez, Michael Goger, Shibani Battacharya, Allan C deCamp, Peter B Gilbert, Phillip W Berman, Timothy Cardozo
The only evidence of vaccine-induced protection from HIV acquisition in humans was obtained in the RV144 HIV vaccine clinical trial. One immune correlate of risk in RV144 was observed to be higher titers of vaccine-induced antibodies (Abs) reacting with a 23-mer non-glycosylated peptide with the same amino acid sequence as a segment in the second variable (V2) loop of the MN strain of HIV. We used NMR to analyze the dynamic 3D structure of this peptide. Distance restraints between spatially proximate inter-residue protons were calculated from NOE cross peak intensities and used to constrain a thorough search of all possible conformations of the peptide...
2017: PloS One
https://www.readbyqxmd.com/read/28105744/multiclass-hcv-resistance-to-direct-acting-antiviral-failure-in-real-life-patients-advocates-for-tailored-second-line-therapies
#2
Velia C Di Maio, Valeria Cento, Ilaria Lenci, Marianna Aragri, Piera Rossi, Silvia Barbaliscia, Michela Melis, Gabriella Verucchi, Carlo F Magni, Elisabetta Teti, Ada Bertoli, FrancescoPaolo Antonucci, Maria C Bellocchi, Valeria Micheli, Chiara Masetti, Simona Landonio, Simona Francioso, Francesco Santopaolo, Adriano M Pellicelli, Vincenza Calvaruso, Laura Gianserra, Massimo Siciliano, Dante Romagnoli, Raffaele Cozzolongo, Antonio Grieco, Jacopo Vecchiet, Filomena Morisco, Manuela Merli, Giuseppina Brancaccio, Antonio Di Biagio, Elisabetta Loggi, Claudio M Mastroianni, Valeria Pace Palitti, Pierluigi Tarquini, Massimo Puoti, Gloria Taliani, Loredana Sarmati, Antonino Picciotto, Vincenzo Vullo, Nicola Caporaso, Maurizio Paoloni, Caterina Pasquazzi, Giuliano Rizzardini, Giustino Parruti, Antonio Craxì, Sergio Babudieri, Massimo Andreoni, Mario Angelico, Carlo F Perno, Francesca Ceccherini-Silberstein
BACKGROUND & AIMS: Despite the excellent efficacy of direct-acting antivirals (DAA) reported in clinical trials, virological failures can occur, often associated with the development of resistance-associated substitutions (RASs). This study aimed to characterize the presence of clinically relevant RASs to all classes in real-life DAA failures. METHODS: Of the 200 virological failures that were analyzed in 197 DAA-treated patients, 89 with pegylated-interferon+ribavirin (PegIFN+RBV) and 111 without (HCV-1a/1b/1g/2/3/4=58/83/1/6/24/25; 56...
January 20, 2017: Liver International: Official Journal of the International Association for the Study of the Liver
https://www.readbyqxmd.com/read/28105556/chikungunya-infection-presenting-as-mild-encephalitis-with-a-reversible-lesion-in-the-splenium-a-case-report
#3
Kadam Nagpal, Puneet Agarwal, Amit Kumar, Rajashekhar Reddi
Chikungunya fever is an Aedes mosquito-transmitted infection caused by chikungunya virus, an RNA virus in the family Togaviridae. The disease is characteristically manifested as fever, arthralgia, and/or rash. Various neurological manifestations like meningoencephalitis, myelitis, and myeloneuropathy have been mentioned in various reports. We present a rare case of chikungunya fever presenting with mild encephalitis with a reversible lesion of the splenium (MERS), which showed complete clinical and radiological recovery...
January 19, 2017: Journal of Neurovirology
https://www.readbyqxmd.com/read/28104327/clinical-validation-of-3-commercial-real-time-reverse-transcriptase-polymerase-chain-reaction-assays-for-the-detection-of-middle-east-respiratory-syndrome-coronavirus-from-upper-respiratory-tract-specimens
#4
Deqa H Mohamed, AbdulKarim F AlHetheel, Hanat S Mohamud, Kamel Aldosari, Fahad A Alzamil, Ali M Somily
Since discovery of Middle East respiratory syndrome coronavirus (MERS-CoV), a novel betacoronavirus first isolated and characterized in 2012, MERS-CoV real-time reverse transcriptase polymerase chain reaction (rRT-PCR) assays represent one of the most rapidly expanding commercial tests. However, in the absence of extensive evaluations of these assays on positive clinical material of different sources, evaluating their diagnostic effectiveness remains challenging. We describe the diagnostic performance evaluation of 3 common commercial MERS-CoV rRT-PCR assays on a large panel (n = 234) of upper respiratory tract specimens collected during an outbreak episode in Saudi Arabia...
January 10, 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/28102365/viral-phylogenomics-using-an-alignment-free-method-a-three-step-approach-to-determine-optimal-length-of-k-mer
#5
Qian Zhang, Se-Ran Jun, Michael Leuze, David Ussery, Intawat Nookaew
The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral "tree of life". However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28101187/severe-pneumonia-due-to-infection-with-candida-krusei-in-a-case-of-suspected-middle-east-respiratory-syndrome-a-case-report-and-literature-review
#6
Mingming Tan, Junwei Wang, Peiyang Hu, Bin Wang, Wanghua Xu, Jiao Chen
Candida krusei (C. krusei) pneumonia is a rare infection that is frequently associated with a poor outcome. The present study reports an unusual case of C. krusei pneumonia that was initially suspected to be a Middle East respiratory syndrome (MERS) case. A 64-year-old Saudi Arabian male patient was admitted to our hospital with complaints of cough and dyspnea that persisted for 6 days. The patient presented fever (oral temperature, 38.5°C) and slight tachypnea (25 respirations/min). A chest computerized tomography demonstrated unclear lung fields, diffuse pathological changes in the two lungs and multiple lymphadenectasis in the retrocaval and para-aortic arch area...
December 2016: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28100698/cdc45-induced-loading-of-human-rpa-onto-single-stranded-dna
#7
Anna Szambowska, Ingrid Tessmer, Piotr Prus, Bernhard Schlott, Helmut Pospiech, Frank Grosse
Cell division cycle protein 45 (Cdc45) is an essential component of the eukaryotic replicative DNA helicase. We found that human Cdc45 forms a complex with the single-stranded DNA (ssDNA) binding protein RPA. Moreover, it actively loads RPA onto nascent ssDNA. Pull-down assays and surface plasmon resonance studies revealed that Cdc45-bound RPA complexed with ssDNA in the 8-10 nucleotide binding mode, but dissociated when RPA covered a 30-mer. Real-time analysis of RPA-ssDNA binding demonstrated that Cdc45 catalytically loaded RPA onto ssDNA...
January 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28099008/critical-analysis-of-rate-constants-and-turnover-frequency-in-nucleic-acid-templated-reactions-reaching-terminal-velocity
#8
Dalu Chang, Eric Lindberg, Nicolas Winssinger
Nucleic acid-templated reactions have attracted significant attention for nucleic acid sensing and imaging. The level of signal amplification obtained from templated reactions is a function of the template turnover, wherein the template acts as the catalyst. Herein, we report the application of a pyridinium linker that immolates upon photocatalytic reduction with a ru-thenium complex to yield the fastest nucleic acid tem-plated reaction reported to date. We show that the tem-plated reaction turnover is limited by the duplex dissoci-ation kinetics beyond probes longer than a 6-mer and proceeded fastest for a 5-mer PNA probe...
January 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28095683/colorimetric-detection-of-staphylococcus-aureus-contaminated-solutions-without-purification
#9
Pamela Tiet, Karen C Clark, James O McNamara, Jacob M Berlin
Current water quality monitoring methods rely on growth-based measurements to detect fecal indicator bacteria, such as Escherichia coli and enterococci, and Staphylococcus aureus (S. aureus). These growth-based measurements, however, can take days to complete. This is a significant limitation in the evaluation of contaminated food and water sources. Various methods for selective in vitro detection of S. aureus have also been reported; however, these strategies, such as ELISA, agar-diffusion, PCR, or liquid chromatography-tandem mass spectrometry, all require overnight culturing or sophisticated instrumentation...
January 18, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28094979/photo-induced-cross-linking-of-short-furan-modified-dna-on-surfaces
#10
Cinthya Yamila Véliz Montes, Henry Memczak, Ellen Gyssels, Tomas Torres, Annemieke Madder, Rudolf J Schneider
We report for the first time the formation of site-specifically interstrand cross-linked (ICL) surface-immobilized furan-modified DNA duplexes via singlet oxygen. 1O2, necessary for effecting furan-mediated ICL formation, was produced in situ using methylene blue or a zinc phthalocyanine derivative (TT1) as photosensitizers. Via surface plasmon resonance spectroscopy we show that surface ICL was achieved and established a robust link which enhances the stability of the 12-mer duplex even after surface regeneration...
January 17, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28094516/designed-dna-crystal-habit-modifiers
#11
Diana Zhang, Paul J Paukstelis
DNA is now one of the most widely used molecules for programmed self-assembly of discrete nanostructures. One of the long-standing goals of the DNA nanotechnology field has been the assembly of periodic, macroscopic 3D DNA crystals for controlled positioning of guest molecules to be used in a variety of applications. With continuing successes in assembling DNA crystals there is an enhanced need to tailor macroscopic crystal properties - including morphology - to enable their integration into more complex systems...
January 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28094182/dna-duplex-linker-for-afm-selex-of-dna-aptamer-against-human-serum-albumin
#12
Musashi Takenaka, Yuzo Okumura, Tomokazu Amino, Yusuke Miyachi, Chiaki Ogino, Akihiko Kondo
DNA-duplex interactions in thymines and adenins are used as a linker for the novel methodology of Atomic Force Microscope-Systematic Evolution of Ligands by EXpotential enrichment (AFM-SELEX). This study used the hydrogen bonds in 10 mer of both thymines (T10) and adenines (A10). Initially, the interactive force in T10-A10 was measured by AFM, which returned an average interactive force of approximately 350pN. Based on this result, DNA aptamers against human serum albumin could be selected in the 4th round, and 15 different clones could be sequenced...
January 7, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28093876/development-of-poly-lactide-co-glycolide-nanoparticles-functionalized-with-a-mitochondria-penetrating-peptide
#13
Francesca Selmin, Giulia Magri, Chiara G M Gennari, Silvia Marchianò, Nicola Ferri, Sara Pellegrino
The development of mitochondria-targeting cell permeable vectors represents a promising therapeutic approach for several diseases, such as cancer and oxidative pathologies. Nevertheless, access to mitochondria can be difficult. A new hybrid material composed by poly(lactide-co-glycolide) (PLGA) functionalized with a 6-mer mitochondria penetrating peptide (MPP), consisting in alternating arginine and unnatural cyclohexylalanine, was developed. Circular dichroism, FT-IR and DSC studies indicated that the conjugation of the peptide with the polymer led to the obtainment of a more rigid material with respect to both PLGA and MPP as such...
January 17, 2017: Journal of Peptide Science: An Official Publication of the European Peptide Society
https://www.readbyqxmd.com/read/28093818/intraoperative-microstimulation-predicts-outcome-of-postoperative-macrostimulation-in-subthalamic-nucleus-deep-brain-stimulation-for-parkinson-s-disease
#14
Raja Mehanna, Andre G Machado, John E Connett, Faisal Alsaloum, Scott E Cooper
BACKGROUND: In deep brain stimulation (DBS) of the subthalamic nucleus for treatment of Parkinson's Disease, a commonly encountered stimulation side effect is involuntary muscle contractions from spread of electrical current to cortico-spinal and cortico-bulbar fibers in the internal capsule. During surgery, a variety of techniques, including microelectrode recording (MER), are used to avoid positioning the DBS electrode too close to the internal capsule. At some centers, MER includes stimulating through the microelectrode (microstimulation)...
January 17, 2017: Neuromodulation: Journal of the International Neuromodulation Society
https://www.readbyqxmd.com/read/28093125/hairpin-stabilized-fluorescent-silver-nanoclusters-for-quantitative-detection-of-nad-and-monitoring-nad-nadh-based-enzymatic-reactions
#15
Priyamvada Jain, Babina Chakma, Sanjukta Patra, Pranab Goswami
A set of 90 mer long ssDNA candidates, with different degrees of cytosine (C-levels) (% and clusters) was analyzed for their function as suitable Ag-nanocluster (AgNC) nucleation scaffolds. The sequence (P4) with highest C-level (42.2%) emerged as the only candidate supporting the nucleation process as evident from its intense fluorescence peak at λ660 nm. Shorter DNA subsets derived from P4 with only stable hairpin structures could support the AgNC formation. The secondary hairpin structures were confirmed by PAGE, and CD studies...
March 1, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28091625/mplex-a-method-for-simultaneous-pathogen-inactivation-and-extraction-of-samples-for-multi-omics-profiling
#16
Kristin E Burnum-Johnson, Jennifer E Kyle, Amie J Eisfeld, Cameron P Casey, Kelly G Stratton, Juan F Gonzalez, Fabien Habyarimana, Nicholas M Negretti, Amy C Sims, Sadhana Chauhan, Larissa B Thackray, Peter J Halfmann, Kevin B Walters, Young-Mo Kim, Erika M Zink, Carrie D Nicora, Karl K Weitz, Bobbie-Jo M Webb-Robertson, Ernesto S Nakayasu, Brian Ahmer, Michael E Konkel, Vladimir Motin, Ralph S Baric, Michael S Diamond, Yoshihiro Kawaoka, Katrina M Waters, Richard D Smith, Thomas O Metz
The continued emergence and spread of infectious agents is of great concern, and systems biology approaches to infectious disease research can advance our understanding of host-pathogen relationships and facilitate the development of new therapies and vaccines. Molecular characterization of infectious samples outside of appropriate biosafety containment can take place only subsequent to pathogen inactivation. Herein, we describe a modified Folch extraction using chloroform/methanol that facilitates the molecular characterization of infectious samples by enabling simultaneous pathogen inactivation and extraction of proteins, metabolites, and lipids for subsequent mass spectrometry-based multi-omics measurements...
January 16, 2017: Analyst
https://www.readbyqxmd.com/read/28088012/new-4-4-chlorophenyl-2-2-6-2%C3%A2-terpyridine-ruthenium-ii-complexes-synthesis-characterization-interaction-with-dna-bsa-and-cytotoxicity-studies
#17
Milan M Milutinović, Ana Rilak, Ioannis Bratsos, Olivera Klisurić, Milan Vraneš, Nevenka Gligorijević, Siniša Radulović, Živadin D Bugarčić
In this study, we have developed a series of new monofunctional Ru(II) complexes of the general formula mer-[Ru(Cl-Ph-tpy)(N-N)Cl]Cl in which Cl-Ph-tpy is 4'-(4-chlorophenyl)-2,2':6',2″-terpyridine, N-N is a bidentate chelating ligand (1,2-diaminoethane (en, 1), 1,2-diaminocyclohexane (dach, 2) or 2,2'-bipyridine (bpy, 3)). All complexes were fully characterized by elemental analysis and spectroscopic techniques (IR, UV-Vis, 1D and 2D NMR). Their chemical behavior in aqueous solution was studied by UV-Vis and NMR spectroscopy showing that all compounds are relatively labile leading to the formation of the corresponding aqua species 1aq-3aq...
October 14, 2016: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28087693/de-novo-genome-and-transcriptome-assembly-of-the-canadian-beaver-castor-canadensis
#18
Si Lok, Tara A Paton, Zhuozhi Wang, Gaganjot Kaur, Susan Walker, Ryan K C Yuen, Wilson W L Sung, Joseph Whitney, Janet A Buchanan, Brett Trost, Naina Singh, Beverly Apresto, Nan Chen, Matthew Coole, Travis J Dawson, Karen Y Ho, Zhizhou Hu, Sanjeev Pullenayegum, Kozue Samler, Arum Shipstone, Fiona Tsoi, Ting Wang, Sergio L Pereira, Pirooz Rostami, Carol Ann Ryan, Amy Hin Yan Tong, Karen Ng, Yogi Sundaravadanam, Jared T Simpson, Burton K Lim, Mark D Engstrom, Christopher J Dutton, Kevin C R Kerr, Maria Franke, William Rapley, Richard F Wintle, Stephen W Scherer
The Canadian beaver (Castor canadensis) is the largest indigenous rodent in North America. We report a draft annotated assembly of the beaver genome, the first for a large rodent and the first mammalian genome assembled directly from uncorrected and moderate coverage (< 30 ×) long-reads generated by single-molecule sequencing. The genome size is 2.7 Gb estimated by k-mer analysis. We assembled the beaver genome using the new Canu assembler optimized for noisy reads. The resulting assembly was refined using Pilon supported by shortreads (80 ×) and checked for accuracy by congruency against an independent short-read assembly...
January 13, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28087531/salivary-gluten-degradation-and-oral-microbial-profiles-in-health-and-celiac-disease
#19
Na Tian, Lina Faller, Daniel A Leffler, Ciaran P Kelly, Joshua Hansen, Jos A Bosch, Guoxian Wei, Bruce J Paster, Detlef Schuppan, Eva J Helmerhorst
: Celiac disease (CD) is a chronic immune-mediated enteropathy induced by dietary gluten in genetically predisposed individuals. Saliva harbors the second highest bacterial load of the GI tract after the colon. Moreover, saliva contains gluten-degrading enzymes produced by oral bacteria that may modify gluten processing in the intestine and susceptibility to celiac disease (CD). AIM: To investigate salivary enzymatic activities and oral microbial profiles in healthy subjects vs patients with classical and refractory CD...
January 13, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28087520/atheroprotective-vaccination-with-mhc-ii-restricted-apob-peptides-induces-peritoneal-il-10-producing-cd4-t-cells
#20
Takayuki Kimura, Kevin Tse, Sara McArdle, Teresa Gerhardt, Jacqueline Miller, Zbigniew Mikulski, John Sidney, Alessandro Sette, Dennis Wolf, Klaus Ley
Although immunization with MHC class II-restricted ApoB peptides has been shown to be atheroprotective, the mechanism is unclear. Here, we investigated CD4(+) T cell populations in immunized atherosclerotic mice. Peptides (16-mers) from mouse ApoB, the core protein of low-density lipoprotein (LDL), were screened for binding to I-A(b) by computer prediction and confirmed by radiolabeled peptide competition. Three new peptides, P101 (FGKQGFFPDSVNKALY, 5.5 nM IC50), P102 (TLYALSHAVNSYFDVD, 6.8 nM), and P103 (LYYKEDKTSLSASAAS, 95 nM) were tested in an atherosclerosis model (Apoe(-/-) mice on western diet)...
January 13, 2017: American Journal of Physiology. Heart and Circulatory Physiology
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