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https://www.readbyqxmd.com/read/28922553/programmable-nucleic-acid-based-polygons-with-controlled-neuroimmunomodulatory-properties-for-predictive-qsar-modeling
#1
Morgan Brittany Johnson, Justin R Halman, Emily Satterwhite, Alexey V Zakharov, My N Bui, Kheiria Benkato, Victoria Goldsworthy, Taejin Kim, Enping Hong, Marina A Dobrovolskaia, Emil F Khisamutdinov, Ian Marriott, Kirill A Afonin
In the past few years, the study of therapeutic RNA nanotechnology has expanded tremendously to encompass a large group of interdisciplinary sciences. It is now evident that rationally designed programmable RNA nanostructures offer unique advantages in addressing contemporary therapeutic challenges such as distinguishing target cell types and ameliorating disease. However, to maximize the therapeutic benefit of these nanostructures, it is essential to understand the immunostimulatory aptitude of such tools and identify potential complications...
September 18, 2017: Small
https://www.readbyqxmd.com/read/28922385/metabolomics-analyses-identify-platelet-activating-factors-and-heme-breakdown-products-as-lassa-fever-biomarkers
#2
Trevor V Gale, Timothy M Horton, Donald S Grant, Robert F Garry
Lassa fever afflicts tens of thousands of people in West Africa annually. The rapid progression of patients from febrile illness to fulminant syndrome and death provides incentive for development of clinical prognostic markers that can guide case management. The small molecule profile of serum from febrile patients triaged to the Viral Hemorrhagic Fever Ward at Kenema Government Hospital in Sierra Leone was assessed using untargeted Ultra High Performance Liquid Chromatography Mass Spectrometry. Physiological dysregulation resulting from Lassa virus (LASV) infection occurs at the small molecule level...
September 18, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28922030/rapid-detection-and-classification-of-salmonella-enterica-shedding-in-feedlot-cattle-utilizing-the-roka-bioscience-atlas-salmonella-detection-assay-for-the-analysis-of-rectoanal-mucosal-swabs
#3
W Evan Chaney, Getahun E Agga, Scott V Nguyen, Terrance M Arthur, Joseph M Bosilevac, Erin Dreyling, Anantharama Rishi, Dayna Brichta-Harhay
With an increasing focus on preharvest food safety, rapid methods are required for the detection and quantification of foodborne pathogens such as Salmonella enterica in beef cattle. We validated the Atlas Salmonella Detection Assay (SEN), a nucleic acid amplification technology that targets Salmonella rRNA, for the qualitative detection of S. enterica with sample enrichment using immunomagnetic separation as a reference test, and we further evaluated its accuracy to predict pathogen load using SEN signal-to-cutoff (SCO) values from unenriched samples to classify animals as high or nonhigh shedders...
September 18, 2017: Journal of Food Protection
https://www.readbyqxmd.com/read/28921499/synthesis-of-the-phosphoramidite-units-for-benzene-glycol-nucleic-acid
#4
Yusuke Maeda, Nazuki Niwa, Yoshihito Ueno
Benzene-glycol nucleic acid-DNA chimeras form thermally and thermodynamically stable duplexes with complementary RNAs, and have base-discriminating abilities. This unit describes the synthesis of four nucleoside analogs, an adenine, cytosine, thymine, and guanine analogs with base-benzene-glycol structure. The synthesis starts with conversion of (S)-mandelic acid in arylboronic acid derivative, common intermediate. Nucleobase coupling of the intermediate and phosphitylation afford to phosphoroamidite units...
September 18, 2017: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/28921497/quantitative-analysis-of-nucleic-acid-stability-with-ligands-under-high-pressure-to-design-novel-drugs-targeting-g-quadruplexes
#5
Shuntaro Takahashi, Naoki Sugimoto
Nucleic acids (DNA and RNA) can form various non-canonical structures. Because some serious diseases are caused by the conformational change of G-quadruplex DNA structures, the development of ligands that bind and stabilize G-quadruplex DNA is of interest to the field of nucleic acid chemistry. Volumetric changes (ΔV) in the biomolecular reaction include the structural change of biomolecules and hydration behaviors, which provide information about the tertiary interaction between G-quadruplex DNA and ligands...
September 18, 2017: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/28921124/droplet-volume-variability-as-a-critical-factor-for-accuracy-of-absolute-quantification-using-droplet-digital-pcr
#6
Alexandra Bogožalec Košir, Carla Divieto, Jernej Pavšič, Stefano Pavarelli, David Dobnik, Tanja Dreo, Roberto Bellotti, Maria Paola Sassi, Jana Žel
Accurate and precise nucleic-acid quantification is crucial for clinical and diagnostic decisions, as overestimation or underestimation can lead to misguided treatment of a disease or incorrect labelling of the products. Digital PCR is one of the best tools for absolute nucleic-acid copy-number determination. However, digital PCR needs to be well characterised in terms of accuracy and sources of uncertainty. With droplet digital PCR, discrepancies between the droplet volume assigned by the manufacturer and measured by independent laboratories have already been shown in previous studies...
September 18, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28921104/development-of-constant-ph-simulation-methods-in-implicit-solvent-and-applications-in-biomolecular-systems
#7
REVIEW
Fernando Luís Barroso daSilva, Luis Gustavo Dias
pH is a critical parameter for biological and technological systems directly related with electrical charges. It can give rise to peculiar electrostatic phenomena, which also makes them more challenging. Due to the quantum nature of the process, involving the forming and breaking of chemical bonds, quantum methods should ideally by employed. Nevertheless, due to the very large number of ionizable sites, different macromolecular conformations, salt conditions, and all other charged species, the CPU time cost simply becomes prohibitive for computer simulations, making this a quite complex problem...
September 18, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28920452/challenges-and-opportunities-in-bioanalytical-support-for-gene-therapy-medicinal-product-development
#8
Mark Ma, Nanda Balasubramanian, Robert Dodge, Yan Zhang
Gene and nucleic acid therapies have demonstrated patient benefits to address unmet medical needs. Beside considerations regarding the biological nature of the gene therapy, the quality of bioanalytical methods plays an important role in ensuring the success of these novel therapies. Inconsistent approaches among bioanalytical labs during preclinical and clinical phases have been observed. There are many underlying reasons for this inconsistency. Various platforms and reagents used in quantitative methods, lacking of detailed regulatory guidance on method validation and uncertainty of immunogenicity strategy in supporting gene therapy may all be influential...
September 18, 2017: Bioanalysis
https://www.readbyqxmd.com/read/28920443/four-fallacies-and-an-oversight-searching-for-martian-life
#9
J D Rummel, C A Conley
While it is anticipated that future human missions to Mars will increase the amount of biological and organic contamination that might be distributed on that planet, robotic missions continue to grow in capability and complexity, requiring precautions to be taken now to protect Mars, and particularly areas of Mars that might be Special Regions. Such precautionary cleanliness requirements for spacecraft have evolved over the course of the space age, as we have learned more about planetary environments, and are the subject of regular deliberations and decisions sponsored by the Committee on Space Research (COSPAR)...
September 16, 2017: Astrobiology
https://www.readbyqxmd.com/read/28920119/synthesis-and-thermal-stabilities-of-oligonucleotides-containing-2-o-4-c-methylene-bridged-nucleic-acid-with-a-phenoxazine-base
#10
Yuki Kishimoto, Akane Fujii, Osamu Nakagawa, Tetsuya Nagata, Takanori Yokota, Yoshiyuki Hari, Satoshi Obika
We designed and synthesized a novel artificial 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA/LNA) with a phenoxazine nucleobase and named this compound BNAP. Oligodeoxynucleotide (ODN) containing BNAP showed higher binding affinities toward complementary DNA and RNA as compared to ODNs bearing 2',4'-BNA/LNA with 5-methylcytosine or 2'-deoxyribonucleoside with phenoxazine. Thermodynamic analysis revealed that BNAP exhibits properties associated with the phenoxazine moiety in DNA/DNA duplexes and characteristics associated with the 2',4'-BNA/LNA moiety in DNA/RNA duplexes...
September 18, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28919833/conventional-culture-versus-nucleic-acid-amplification-tests-for-screening-of-urethral-neisseria-gonorrhea-infection-among-asymptomatic-men-who-have-sex-with-men
#11
Jiratha Budkaew, Bandit Chumworathayi, Chamsai Pientong, Tipaya Ekalaksananan
BACKGROUND: Many methods are used to detect urethral Neisseria gonorrhea (NG) infection among asymptomatic men who have sex with men (MSM). The objective of this study was to define the performance of conventional culture compared to real-time polymerase chain reaction (PCR) for diagnosis of asymptomatic urethral gonorrhea among MSM. METHODS: In this cross-sectional study, 147 clinical specimens for NG testing from asymptomatic participants were evaluated. MSM >18 years old who consented to undergo urethral swab and collection of urine samples from two clinics (one was the sexually transmitted diseases (STDs) mobile clinic and the second was the antiretroviral clinic) located in Khon Kaen, Thailand, were recruited...
2017: Pragmatic and Observational Research
https://www.readbyqxmd.com/read/28919362/a-homozygote-trex1-mutation-in-two-siblings-with-different-phenotypes-chilblains-and-cerebral-vasculitis
#12
Rabia Miray Kisla Ekinci, Sibel Balci, Atil Bisgin, Derya Ufuk Altintas, Mustafa Yılmaz
Three prime repair exonuclease 1 degrades single and double stranded DNA with 3'-5' nuclease activity and its mutations are related to type 1 IFN mediated autoinflammation due to accumulated intracellular nucleic acids. To date, several cases of systemic lupus erythematosus, Aicardi-Goutieres syndrome, familial chilblain lupus, retinal vasculopathy-cerebral leukodystrophy have been reported with TREX1 mutations. Chilblain lupus is a skin disease characterized by blue-reddish coloring, swelling or ulcers on acral regions of body such as fingertips, heels, nose and auricles...
September 12, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28919361/molecular-characterisation-ontogeny-and-expression-analysis-of-melanoma-differentiation-associated-factor-5-mda5-from-asian-seabass-lates-calcarifer
#13
Anutosh Paria, M Makesh, Aparna Chaudhari, C S Purushothaman, K V Rajendran
MDA5 is the pivotal member of the retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) and is reported to play a crucial role in type I IFN-mediated responses against pathogen-associated molecular patterns (PAMPs), especially nucleic acids. In this study, we have identified and cloned the full-length cDNA sequence of MDA5, which comprises 3398 nucleotides and encodes for a putative protein of 978 AA length, in Asian seabass, Lates calcarifer. From the putative amino acid sequence of AsMDA5, four different conserved domains could be predicted: two N-terminal CARD domains, a DExDc domain, a HELICc domain and a C-terminal RIG-1_C-RD domain...
September 15, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28918972/-mycological-and-parasitological-examinations-in-the-management-of-lung-infections
#14
REVIEW
L Lachaud, J P Gangneux
Pulmonary parasitic diseases are rare whereas pulmonary fungal infections are increasing. The diversity of clinical presentations requires laboratory tests to confirm the diagnosis. Direct examination of lung samples and antibody detection are the basis of parasitological diagnosis. With regard to mycoses, the range of biological tests is broader. The conventional mycological examination allows identification of any type of fungus except Pneumocystis jirovecii. Its specificity is excellent but it lacks sensitivity...
September 14, 2017: Revue des Maladies Respiratoires
https://www.readbyqxmd.com/read/28918740/methylglyoxal-and-small-heat-shock-proteins
#15
REVIEW
M V Sudnitsyna, N B Gusev
Methylglyoxal is a highly reactive dicarbonyl compound formed during glucose metabolism and able to modify phospholipids, nucleic acids, and proteins belonging to the so-called dicarbonyl proteome. Small heat shock proteins participating in protection of the cell against different unfavorable conditions can be modified by methylglyoxal. The probability of methylglyoxal modification is increased in the case of distortion of glucose metabolism (diabetes), in the case of utilization of glycolysis as the main source of energy (malignancy), and/or at low rate of modified protein turnover...
July 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/28918528/signaling-of-the-complement-cleavage-product-anaphylatoxin-c5a-through-c5ar-cd88-contributes-to-pharmacological-hematopoietic-stem-cell-mobilization
#16
Kamila Bujko, Sylwia Rzeszotek, Kai Hoehlig, Jun Yan, Axel Vater, Mariusz Z Ratajczak
Several mechanisms have been postulated for orchestrating the mobilization of hematopoietic stem/progenitor cells (HSPCs), and we previously proposed that activation of the complement cascade plays a crucial role in the initiation and execution of the egress of HSPCs from bone marrow (BM) into peripheral blood (PB). In support of this notion, we demonstrated that mice deficient in the mannan-binding lectin (MBL) pathway, which activates the proximal part of the complement cascade, as well as mice deficient in the fifth component of the complement cascade (C5), which is part of the distal part of the complement cascade, are poor mobilizers...
September 16, 2017: Stem Cell Reviews
https://www.readbyqxmd.com/read/28918196/expression-and-purification-of-human-and-saccharomyces-cerevisiae-equilibrative-nucleoside-transporters
#17
Rebba C Boswell-Casteel, Jennifer M Johnson, Zygy Roe-Žurž, Kelli D Duggan, Hannah Schmitz, Franklin A Hays
Nucleosides play an essential role in the physiology of eukaryotes by acting as metabolic precursors in de novo nucleic acid synthesis and energy metabolism. Nucleosides also act as ligands for purinergic receptors. Equilibrative nucleoside transporters (ENTs) are polytopic integral membrane proteins that aid in regulating plasmalemmal flux of purine and pyrimidine nucleosides and nucleobases. ENTs exhibit broad substrate selectivity across different isoforms and utilize diverse mechanisms to drive substrate flux across membranes...
September 13, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28918068/a-simple-and-rapid-dna-extraction-method-for-chlamydia-trachomatis-detection-from-urogenital-swabs
#18
Matthew A Butzler, Jennifer L Reed, Sally M McFall
A highly sensitive and specific Chlamydia trachomatis (CT) diagnostic test was developed by combining filtration isolation of nucleic acid (FINA) extraction with quantitative polymerase chain reaction including an internal control to identify test inhibition. A pilot study of 40 clinical specimens yielded 100% sensitivity and specificity.
August 17, 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/28918054/rapid-and-sensitive-detection-of-breast-cancer-cells-in-patient-blood-with-nuclease-activated-probe-technology
#19
Sven Kruspe, David D Dickey, Kevin T Urak, Giselle N Blanco, Matthew J Miller, Karen C Clark, Elliot Burghardt, Wade R Gutierrez, Sneha D Phadke, Sukriti Kamboj, Timothy Ginader, Brian J Smith, Sarah K Grimm, James Schappet, Howard Ozer, Alexandra Thomas, James O McNamara, Carlos H Chan, Paloma H Giangrande
A challenge for circulating tumor cell (CTC)-based diagnostics is the development of simple and inexpensive methods that reliably detect the diverse cells that make up CTCs. CTC-derived nucleases are one category of proteins that could be exploited to meet this challenge. Advantages of nucleases as CTC biomarkers include: (1) their elevated expression in many cancer cells, including cells implicated in metastasis that have undergone epithelial-to-mesenchymal transition; and (2) their enzymatic activity, which can be exploited for signal amplification in detection methods...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28918042/electronic-structures-of-lna-phosphorothioate-oligonucleotides
#20
Henrik G Bohr, Irene Shim, Cy Stein, Henrik Ørum, Henrik F Hansen, Troels Koch
Important oligonucleotides in anti-sense research have been investigated in silico and experimentally. This involves quantum mechanical (QM) calculations and chromatography experiments on locked nucleic acid (LNA) phosphorothioate (PS) oligonucleotides. iso-potential electrostatic surfaces are essential in this study and have been calculated from the wave functions derived from the QM calculations that provide binding information and other properties of these molecules. The QM calculations give details of the electronic structures in terms of e...
September 15, 2017: Molecular Therapy. Nucleic Acids
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