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nucleic acids

Joseph B DeShields, Rachel A Bomberger, James W Woodhall, David L Wheeler, Natalia Moroz, Dennis A Johnson, Kiwamu Tanaka
On-site diagnosis of plant diseases can be a useful tool for growers for timely decisions enabling the earlier implementation of disease management strategies that reduce the impact of the disease. Presently in many diagnostic laboratories, the polymerase chain reaction (PCR), particularly real-time PCR, is considered the most sensitive and accurate method for plant pathogen detection. However, laboratory-based PCRs typically require expensive laboratory equipment and skilled personnel. In this study, soil-borne pathogens of potato are used to demonstrate the potential for on-site molecular detection...
February 23, 2018: Journal of Visualized Experiments: JoVE
Saahir Khan, Audrey Nakasone, Minoo Ghajar, Mariam Zhowandai, Sunita Prabhu, Rick Alexander, Julie Low, Ellena Peterson, Lauri Thrupp
For 94 patients with culture-positive pulmonary tuberculosis, time-to-detection (TTD), acid-fast bacilli (AFB) smear, and nucleic acid amplification test (NAAT) results were reviewed. All 12 patients whose first specimen was negative by AFB smear and NAAT had prolonged TTD, indicating low transmissibility and supporting discontinuing isolation for low-risk patients. Infect Control Hosp Epidemiol 2018;1-3.
March 19, 2018: Infection Control and Hospital Epidemiology
Fei Yu, Ting Qiu, Ying Zeng, Yiyin Wang, Shufa Zheng, Xiao Chen, Yu Chen
Viscous sputum specimens usually cannot undergo automated extraction, and thus, a pre-homogenization process is desirable before isolating nucleic acids for real-time reverse transcription PCR. In this study, we compared three preprocessing methods [preprocessing with normal saline (NS), dithiothreitol (DTT), and proteinase K (PK)] of sputum specimens on the extraction and detection of influenza A virus (IAV) nucleic acids. Based on the experimental results of 217 specimens, we found that DTT and PK could be used to improve the homogenization effects of sputum and increase the positive rates by 5...
2018: Frontiers in Medicine
Jin-Peng Wang, Yan-Yan Tang, Chun-Mei Fan, Can Guo, Yan-Hong Zhou, Zheng Li, Xiao-Ling Li, Yong Li, Gui-Yuan Li, Wei Xiong, Zhao-Yang Zeng, Fang Xiong
An increasing number of studies has confirmed that many cells can secrete vesicles or exosomes in eukaryotes, which contain important nucleic acids, proteins and lipids and play important roles in cell communication and tumor metastasis. This paper summarizes the comprehensive function of exosomal non-coding RNAs. Although some studies have shown that exosomes mediate tumor signal transduction, the functional mechanism of the tumor metastasis remains to be elucidated. In this paper, we reviewed the role of exosomal non-coding RNAs in mediating cancer metastasis in the tumor microenvironment to provide new ideas for the study of tumor pathophysiology...
February 23, 2018: Oncotarget
Fan Fu, Hua Hu, Shuai Yang, Xiaoqiu Liang
TERF1-interacting nuclear factor 2 (TIN2) is a key member of the protein complexes that protect telomeres. TIN2 contributes an important role in biological processes. In a previous study by the present authors, an association was reported between high TIN2 protein expression and gastric cancer. Therefore, it was hypothesized that abnormal TIN2 expression may cause the development of malignancies, including, gastric carcinomas. To investigate this hypothesis, the present study employed peptide nucleic acid fluorescence in situ hybridization technology to analyze the human gastric epithelial GES-1 cells with high TIN2 expression or inhibited TIN2 expression...
April 2018: Oncology Letters
Hisako Ibaraki, Takanori Kanazawa, Yuuki Takashima, Hiroaki Okada, Yasuo Seta
Nucleic acid-based targeting of nuclear factor kappaB (NF-κB) is gaining attention as a treatment option for skin diseases like atopic dermatitis (AD). Transdermal administration improves patient quality of life because of non-invasive; however, siRNA delivery into the skin can be challenging owing to the barrier of tight junctions in the granular layer. Therefore, we aimed to develop a delivery system of siRNA for topical skin application using functional peptides. We previously reported that combined treatment with a cytoplasm-responsive stearylated-arginine-rich peptide (STR-CH2 R4 H2 C) and a tight junction opening peptide (AT1002) showed high siRNA permeability in the skin of AD-induced and normal mice...
March 15, 2018: International Journal of Pharmaceutics
Aigli G Vakrakou, Sorina Boiu, Panayiotis D Ziakas, Evangelia Xingi, Haralabia Boleti, Menelaos N Manoussakis
Sjögren's syndrome (SS) patients manifest high cell-free DNA (cf-DNA) levels in serum, associated with impaired DNaseI activity. Undegraded DNA may accumulate in tissues and act as an inflammasome-activating signal. Herein, we investigated the occurrence of aberrant DNA build-up in various biologic compartments of SS patients and its correlation with the activity of NLRP3 and AIM2 inflammasomes. For this purpose, we evaluated sera, PBMC, circulating monocytes and salivary glands (SG) from different SS patient subgroups and controls...
March 15, 2018: Journal of Autoimmunity
Atsushi Hirano, Kazuki Iwashita, Shun Sakuraba, Kentaro Shiraki, Tsutomu Arakawa, Tomoshi Kameda
Ion-exchange chromatography and multimodal ion-exchange chromatography are widely used for the separation of small molecules, peptides and proteins. Salts generally attenuate the electrostatic interactions between charged moieties of solutes and those of resins through electrostatic screening. However, little is known about how salts affect the interaction between the uncharged moieties of the solutes, such as aromatic moieties, and the charged moieties of the resins. In this study, we used alkyl gallates as model aromatic solutes to investigate the interaction mechanism of aromatic moieties with multimodal and conventional ion-exchange resins...
March 6, 2018: Journal of Chromatography. A
Anouk S Lubbe, Qing Liu, Sanne J Smith, Jan Willem de Vries, Jos C M Kistemaker, Alex H De Vries, Ignacio Faustino, Zhuojun Meng, Wiktor Szymanski, Andreas Herrmann, Ben L Feringa
Reversible control over the functionality of biological systems via external triggers may be used in future medicine to reduce the need for invasive procedures. Additionally, externally regulated biomacromolecules are now considered as particularly attractive tools in nanoscience and the design of smart materials, due to their highly programmable nature and complex functionality. Incorporation of photoswitches into biomolecules, such as peptides, antibiotics and nucleic acids, has generated exciting results in the past few years...
March 18, 2018: Journal of the American Chemical Society
Karteek Kadimisetty, Jinzhao Song, Aoife M Doto, Young Hwang, Jing Peng, Michael G Mauk, Frederic D Bushman, Robert Gross, Joseph N Jarvis, Changchun Liu
Molecular diagnostics that involve nucleic acid amplification tests (NAATs) are crucial for prevention and treatment of infectious diseases. In this study, we developed a simple, inexpensive, disposable, fully 3D printed microfluidic reactor array that is capable of carrying out extraction, concentration and isothermal amplification of nucleic acids in variety of body fluids. The method allows rapid molecular diagnostic tests for infectious diseases at point of care. A simple leak-proof polymerization strategy was developed to integrate flow-through nucleic acid isolation membranes into microfluidic devices, yielding a multifunctional diagnostic platform...
March 10, 2018: Biosensors & Bioelectronics
Elnaz Bagheri, Legha Ansari, Khalil Abnous, Seyed Mohammad Taghdisi, Fahimeh Charbgoo, Mohammad Ramezani, Mona Alibolandi
Silica hybrid materials play an important role in improvement of novel progressive functional nanomaterials. Study in silica hybrid functional materials is supported by growing interest in providing intelligent materials that combine best of the inorganic silica structure along with organic or biological realms. Hybrid silica materials do not only provide fantastic opportunities for the design of novel materials for research but their represented unique properties open versatile applications specifically in nanomedicine since it was recognized by US FDA as a safe material for human trials...
March 14, 2018: Journal of Controlled Release: Official Journal of the Controlled Release Society
Ibtehaj Naqvi, Ruwan Gunaratne, Jessica E McDade, Angelo Moreno, Rachel E Rempel, Douglas C Rouse, Silvia Gabriela Herrera, David S Pisetsky, Jaewoo Lee, Rebekah R White, Bruce A Sullenger
Nucleic acid binding polymers (NABPs) have been extensively used as vehicles for DNA and RNA delivery. More recently, we discovered that a subset of these NABPs can also serve as anti-inflammatory agents by capturing pro-inflammatory extracellular nucleic acids and associated protein complexes that promote activation of toll-like receptors (TLRs) in diseases such as lupus erythematosus. Nucleic-acid-mediated TLR signaling also facilitates tumor progression and metastasis in several cancers, including pancreatic cancer (PC)...
February 23, 2018: Molecular Therapy: the Journal of the American Society of Gene Therapy
Robert Sidney Cox, Curtis Madsen, James McLaughlin, Tramy Nguyen, Nicholas Roehner, Bryan Bartley, Swapnil Bhatia, Mike Bissell, Kevin Clancy, Thomas Gorochowski, Raik Grünberg, Augustin Luna, Nicolas Le Novere, Matthew Pocock, Herbert Sauro, John T Sexton, Guy-Bart Stan, Jeffrey J Tabor, Christopher A Voigt, Zach Zundel, Chris Myers, Jacob Beal, Anil Wipat
People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard for organizing and systematizing such conventions in order to produce a coherent language for expressing the structure and function of genetic designs...
March 19, 2018: Journal of Integrative Bioinformatics
Susan K Seo, Zivile Gedrimaite, Alla Paskovaty, Kenneth Seier, Sejal Morjaria, Nina Cohen, Elyn Riedel, Yi-Wei Tang, N Esther Babady
OBJECTIVE: To evaluate the impact of rapidly identifying coagulase-negative staphylococci (CoNS) from positive blood cultures (BC) combined with an established antimicrobial stewardship (AS) program at a tertiary cancer center. METHODS: Cancer patients >=18 years with >=1 positive CoNS BC identified by Staphylococcus QuickFISH®, a peptide nucleic acid fluorescence in situ hybridization assay, between 01/1/13 and 12/31/13 (QuickFISH) were compared to cancer patients >=18 years with CoNS identified via standard microbiologic techniques between 01/01/11 and 12/31/11 (baseline)...
March 13, 2018: Clinical Microbiology and Infection
Qisen Xiang, Xiufang Liu, Junguang Li, Shengnan Liu, Hua Zhang, Yanhong Bai
This work aimed to evaluate the effects of dielectric barrier discharge (DBD) plasma on inactivation of spoilage yeast Zygosaccharomyces rouxii (Z. rouxii), in apple juice. Results showed that DBD plasma treatment at 90 W for 140 s resulted in about 5-log reduction of Z. rouxii in apple juice. The levels of extracellular nucleic acids and proteins as well as contents of H2 O2 and NO2 - in yeast extract-peptone-dextrose (YPD) medium increased significantly after DBD plasma treatment at 90 W for 40-200 s...
July 15, 2018: Food Chemistry
Aykut Erbaş, Monica Olvera de la Cruz, John F Marko
We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics simulations are suggested by single-molecule studies of protein-DNA interactions. We consider univalent salt concentrations spanning roughly a 1000-fold range, together with various concentrations of excess ligands in solution. To reveal the ionic effects on unbinding kinetics of spontaneous and facilitated dissociation mechanisms, we treat electrostatic interactions both at a Debye-Hückel (DH) (or implicit ions, i...
February 2018: Physical Review. E
Pei-Hui Wang, Sin-Yee Fung, Wei-Wei Gao, Jian-Jun Deng, Yun Cheng, Vidyanath Chaudhary, Kit-San Yuen, Ting-Hin Ho, Ching-Ping Chan, Yan Zhang, Kin-Hang Kok, Wanling Yang, Chi-Ping Chan, Dong-Yan Jin
STING is a core adaptor in innate nucleic acid sensing in mammalian cells, on which different sensing pathways converge to induce type I interferon (IFN) production. Particularly, STING is activated by 2'3'-cGAMP, a cyclic dinucleotide containing mixed phosphodiester linkages and produced by cytoplasmic DNA sensor cGAS. Here, we reported on a novel transcript isoform of STING designated STING-β that dominantly inhibits innate nucleic acid sensing. STING-β without transmembrane domains was widely expressed at low levels in various human tissues and viral induction of STING-β correlated inversely with IFN-β production...
March 14, 2018: Nucleic Acids Research
Aloma L D'Souza, John R Chevillet, Pejman Ghanouni, Xinrui Yan, Muneesh Tewari, Sanjiv S Gambhir
We have previously shown that low frequency ultrasound can release biomarkers from cells into the murine circulation enabling an amplification and localization of the released biomarker that could be used as a blood-based method to detect cancer earlier and monitor therapy. In this study, we further demonstrate that this technique could be used for characterization of tumors and/or identification of cellular masses of unknown origin due to the release of multiple protein and nucleic acid biomarkers in cells in culture, mice and patients...
2018: PloS One
Jejoong Yoo, Aleksei Aksimentiev
In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly ordered three-dimensional structures that define their functions. The key to folding of a biopolymer into a unique 3D structure or to an assembly of several biopolymers into a functional unit is a delicate balance between the attractive and repulsive forces that also makes such self-assembly reversible under physiological conditions. The all-atom molecular dynamics (MD) method has emerged as a powerful tool for studies of individual biomolecules and their functional assemblies, encompassing systems of ever increasing complexity...
March 16, 2018: Physical Chemistry Chemical Physics: PCCP
Donatella Pietraforte, Eleonora Paulicelli, Clarice Patrono, Lucrezia Gambardella, Giuseppe Scorza, Antonella Testa, Paola Fattibene
Reactive oxygen species (ROS) are important mediators of the cytotoxicity induced by the direct reaction of ionising radiation (IR) with all critical cellular components, such as proteins, lipids, and nucleic acids. The derived oxidative damage may propagate in exposed tissues in a dose- and spatiotemporal dependent manner to other cell compartments, affecting intracellular signalling, and cell fate. To understand how cell damage is induced, we studied the oxidative events occurring immediately after cell irradiation by analysing the fate of IR-derived ROS, the intracellular oxidative damage, and the modification of redox environment accumulating in Chinese hamster ovary (CHO) within 1 h after cell irradiation (dose range 0-10 Gy)...
March 16, 2018: Free Radical Research
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