keyword
MENU ▼
Read by QxMD icon Read
search

nucleic acids

keyword
https://www.readbyqxmd.com/read/28646675/conformational-regulation-of-crispr-associated-nucleases
#1
REVIEW
Ryan N Jackson, Paul Bg van Erp, Samuel H Sternberg, Blake Wiedenheft
Adaptive immune systems in bacteria and archaea rely on small CRISPR-derived RNAs (crRNAs) to guide specialized nucleases to foreign nucleic acids. The activation of these nucleases is controlled by a series of molecular checkpoints that ensure precise cleavage of nucleic acid targets, while minimizing toxic off-target cleavage events. In this review, we highlight recent advances in understanding regulatory mechanisms responsible for controlling the activation of these nucleases and identify emerging regulatory themes conserved across diverse CRISPR systems...
June 21, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28646234/electroporation-as-a-vaccine-delivery-system-and-a-natural-adjuvant-to-intradermal-administration-of-plasmid-dna-in-macaques
#2
Biliana Todorova, Lucille Adam, Slobodan Culina, Raphaël Boisgard, Frédéric Martinon, Antonio Cosma, Mart Ustav, Thierry Kortulewski, Roger Le Grand, Catherine Chapon
In vivo electroporation (EP) is used to enhance the uptake of nucleic acids and its association with DNA vaccination greatly stimulates immune responses to vaccine antigens delivered through the skin. However, the effect of EP on cutaneous cell behavior, the dynamics of immune cell recruitment and local inflammatory factors, have not been fully described. Here, we show that intradermal DNA vaccination combined with EP extends antigen expression to the epidermis and the subcutaneous skin muscle in non-human primates...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28646219/efficient-and-unbiased-metagenomic-recovery-of-rna-virus-genomes-from-human-plasma-samples
#3
Carmen F Manso, David F Bibby, Jean L Mbisa
RNA viruses cause significant human pathology and are responsible for the majority of emerging zoonoses. Mainstream diagnostic assays are challenged by their intrinsic diversity, leading to false negatives and incomplete characterisation. New sequencing techniques are expanding our ability to agnostically interrogate nucleic acids within diverse sample types, but in the clinical setting are limited by overwhelming host material and ultra-low target frequency. Through selective host RNA depletion and compensatory protocol adjustments for ultra-low RNA inputs, we are able to detect three major blood-borne RNA viruses - HIV, HCV and HEV...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28645658/spacer-structure-and-hydrophobicity-influences-transfection-activity-of-novel-polycationic-gemini-amphiphiles
#4
Pavel A Puchkov, Irina A Kartashova, Elena V Shmendel, Anastasya S Luneva, Nina G Morozova, Marina A Zenkova, Mikhail A Maslov
Three novel polycationic gemini amphiphiles with different spacers were developed and evaluated in terms of their physiochemical properties and transfection efficiencies. Cationic liposomes formed by these amphiphiles and the helper lipid DOPE were able to successfully condense DNA, as shown by gel mobility shift and ethidium bromide intercalation assays. Transfection activity of the liposomes was superior to Lipofectamine(®) 2000 and was dependent on spacer structure, hydrophobicity, and nucleic acid type (pDNA or siRNA)...
June 10, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28645373/strategies-and-methods-of-transcription-coupled-repair-studies-in-vitro-and-in-vivo
#5
Vitaly Epshtein, Venu Kamarthapu, Evgeny Nudler
Transcription-coupled repair (TCR) serves an important role in preserving genome integrity and maintaining fidelity of replication. Coupling transcription to DNA repair requires a coordinated action of several factors, including transcribing RNA polymerase and various transcription modulators and repair proteins. To study TCR in molecular detail, it is important to employ defined protein complexes in vitro and defined genetic backgrounds in vivo. In this chapter, we present methods to interrogate various aspects of TCR at different stages of repair...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28645097/raman-spectroscopy-differentiates-between-sensitive-and-resistant-multiple-myeloma-cell-lines
#6
Domenico Franco, Sebastiano Trusso, Enza Fazio, Alessandro Allegra, Caterina Musolino, Antonio Speciale, Francesco Cimino, Antonella Saija, Fortunato Neri, Marco S Nicolò, Salvatore P P Guglielmino
Current methods for identifying neoplastic cells and discerning them from their normal counterparts are often nonspecific and biologically perturbing. Here, we show that single-cell micro-Raman spectroscopy can be used to discriminate between resistant and sensitive multiple myeloma cell lines based on their highly reproducible biomolecular spectral signatures. In order to demonstrate robustness of the proposed approach, we used two different cell lines of multiple myeloma, namely MM.1S and U266B1, and their counterparts MM...
June 15, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28644690/advances-in-the-development-of-human-protein-microarrays
#7
Jessica Duarte, Jonathan M Blackburn
High-content protein microarrays in principle enable the functional interrogation of the human proteome in a broad range of applications, including biomarker discovery, profiling of immune responses, identification of enzyme substrates, and quantifying protein-small molecule, protein-protein and protein-DNA/RNA interactions. As with other microarrays, the underlying proteomic platforms are under active technological development and a range of different protein microarrays are now commercially available. However, deciphering the differences between these platforms to identify the most suitable protein microarray for the specific research question is not always straightforward...
June 23, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28644608/targeting-cpg-adjuvant-to-lymph-node-via-dextran-conjugate-enhances-anti-tumor-immunotherapy
#8
Weidong Zhang, Myunggi An, Jingchao Xi, Haipeng Liu
Nucleic acids based adjuvants recognized by Toll-like receptors (TLR) are potent immune system stimulants that can augment the anti-tumor immune responses in an antigen-specific manner. However, their clinical uses as vaccine adjuvants are limited primarily due to lack of accumulation in the lymph nodes, the anatomic sites where the immune responses are initiated. Here, we showed that chemical conjugation of type B CpG DNA, a TLR9 agonist to dextran polymer dramatically enhanced CpG's lymph node accumulation in mice...
June 23, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28644540/cytokeratin-19-expression-in-early-oral-squamous-cell-carcinoma-and-their-metastasis-inadequate-biomarker-for-one-step-nucleic-acid-amplification-implementation-in-sentinel-lymph-node-biopsy-procedure
#9
Rob Noorlag, Robert J J van Es, Remco de Bree, Stefan M Willems
BACKGROUND: Intraoperative analysis of lymph nodes during a sentinel lymph node biopsy (SLNB) procedure could result in one-step surgery for early oral squamous cell carcinoma (OSCC) with an occult nodal metastasis. One-step nucleic acid amplification rapidly detects cytokeratin 19 (CK19) RNA with high accuracy. Sensitivity and specificity of CK19 expression in OSCC was evaluated. METHODS: Immunohistochemical CK19 expression was done in 207 patients with OSCC with 65 cases of paired nodal metastases...
June 23, 2017: Head & Neck
https://www.readbyqxmd.com/read/28644423/probing-the-interaction-of-dielectric-nanoparticles-with-supported-lipid-membrane-coatings-on-nanoplasmonic-arrays
#10
Abdul Rahim Ferhan, Gamaliel Junren Ma, Joshua A Jackman, Tun Naw Sut, Jae Hyeon Park, Nam-Joon Cho
The integration of supported lipid membranes with surface-based nanoplasmonic arrays provides a powerful sensing approach to investigate biointerfacial phenomena at membrane interfaces. While a growing number of lipid vesicles, protein, and nucleic acid systems have been explored with nanoplasmonic sensors, there has been only very limited investigation of the interactions between solution-phase nanomaterials and supported lipid membranes. Herein, we established a surface-based localized surface plasmon resonance (LSPR) sensing platform for probing the interaction of dielectric nanoparticles with supported lipid bilayer (SLB)-coated, plasmonic nanodisk arrays...
June 23, 2017: Sensors
https://www.readbyqxmd.com/read/28643940/proteomic-profiling-of-extracellular-vesicles-secreted-from-toxoplasma-gondii
#11
Pryscilla Fanini Wowk, Maria Luisa Zardo, Halisson Tesseroli Miot, Samuel Goldenberg, Paulo Costa Carvalho, Patricia Alves Mörking
Toxoplasma gondii infects a wide range of hosts worldwide, including humans and domesticated animals causing toxoplasmosis disease. Recently, exosomes, small extracellular vesicles (EV) that contain nucleic acids, proteins, and lipids derived from their original cells were linked with disease protection. The effect of EVs derived from T. gondii on the immune response and its relevance in a physiological context is unknown. Here we disclose the first proteomic profiling of T. gondii EVs compared to EVs isolated from a human foreskin fibroblast infected cell line cultured in a vesicle- free medium...
June 23, 2017: Proteomics
https://www.readbyqxmd.com/read/28643380/microscopy-visualisation-confirms-multi-species-biofilms-are-ubiquitous-in-diabetic-foot-ulcers
#12
Khalid Johani, Matthew Malone, Slade Jensen, Iain Gosbell, Hugh Dickson, Honhua Hu, Karen Vickery
Increasing evidence within the literature has identified the presence of biofilms in chronic wounds and proposed that they contribute to delayed wound healing. This research aimed to investigate the presence of biofilm in diabetic foot ulcers (DFUs) using microscopy and molecular approaches and define if these are predominantly mono- or multi-species. Secondary objectives were to correlate wound observations against microscopy results in ascertaining if clinical cues are useful in detecting wound biofilm. DFU tissue specimens were obtained from 65 subjects...
June 23, 2017: International Wound Journal
https://www.readbyqxmd.com/read/28643063/intraoperative-identification-and-analysis-of-lymph-nodes-at-laparoscopic-colorectal-cancer-surgery-using-fluorescence-imaging-combined-with-rapid-osna-pathological-assessment
#13
Trevor M Yeung, Lai Mun Wang, Richard Colling, Rebecca Kraus, Ronan Cahill, Roel Hompes, Neil J Mortensen
BACKGROUND: Standard surgical practice for colorectal cancer involves resection of the primary lesion and all draining lymph nodes. Accurate intraoperative assessment of nodal status could allow stratified resectional extent. One-step nucleic acid (OSNA) can provide a rapid method of interrogating nodal tissue, whilst near-infrared (NIR) laparoscopy together with indocyanine green (ICG) can identify relevant nodal tissue intraoperatively. METHODS: ICG was administered around the tumour endoscopically prior to the operation...
June 22, 2017: Surgical Endoscopy
https://www.readbyqxmd.com/read/28642967/strategies-for-characterization-of-enzymatic-nucleic-acids
#14
Fatemeh Javadi-Zarnaghi, Claudia Höbartner
Practical application of enzymatic nucleic acids has received more attention in recent years. Understanding the mechanism of catalysis and availability of information on potentials and limitations of these enzymes expands their application scope. A general approach for characterization of functional macromolecules including enzymatic nucleic acids is to perturb a specific set of condition and to follow the perturbation effect by biophysical and biochemical methods. This chapter reviews several perturbation strategies for functional nucleic acids, including deletion, mutation, and modifications of backbone and nucleobases, and consequent kinetic analysis, spectroscopic investigations, and probing assays...
June 23, 2017: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/28642882/tumor-related-exosomes-contribute-to-tumor-promoting-microenvironment-an-immunological-perspective
#15
REVIEW
Wuzhen Chen, Jingxin Jiang, Wenjie Xia, Jian Huang
Exosomes are a kind of cell-released membrane-form structures which contain proteins, lipids, and nucleic acids. These vesicular organelles play a key role in intercellular communication. Numerous experiments demonstrated that tumor-related exosomes (TEXs) can induce immune surveillance in the microenvironment in vivo and in vitro. They can interfere with the maturation of DC cells, impair NK cell activation, induce myeloid-derived suppressor cells, and educate macrophages into protumor phenotype. They can also selectively induce effector T cell apoptosis via Fas/FasL interaction and enhance regulatory T cell proliferation and function by releasing TGF-β...
2017: Journal of Immunology Research
https://www.readbyqxmd.com/read/28642152/g-quadruplex-dynamics
#16
REVIEW
Robert W Harkness, Anthony K Mittermaier
G-quadruplexes (GQs) are four-stranded nucleic acid secondary structures formed by guanosine (G)-rich DNA and RNA sequences. It is becoming increasingly clear that cellular processes including gene expression and mRNA translation are regulated by GQs. GQ structures have been extensively characterized, however little attention to date has been paid to their conformational dynamics, despite the fact that many biological GQ sequences populate multiple structures of similar free energies, leading to an ensemble of exchanging conformations...
June 19, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28642036/transcription-factor-decoy-technology-a-therapeutic-update
#17
REVIEW
Markus Hecker, Andreas H Wagner
Targeting transcription factors represents one possibility to interfere with a known activated regulatory pathway that promotes disease. Double-stranded transcription factor decoy (TFD) oligodeoxynucleotides (ODN) are therapeutic drug candidates, which are able to specifically target and neutralize key transcription factors involved in the pathogenesis of a given disease. These short double-stranded TFD molecules mimic the consensus DNA binding site of a specific transcription factor in the promoter region of its target genes...
June 19, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28641500/levels-of-8-oxo-dgsn-and-8-oxo-gsn-in-random-urine-are-consistent-with-24%C3%A2-h-urine-in-healthy-subjects-and-patients-with-renal-disease
#18
Yong-Hui Mao, Qing-Hua Weng, Leng-Nan Xu, Xiang-Yu Li, Ban Zhao, Ying Sun, Jing-Jing Nie, Ji-Hong Hu, Qi Zhou, Li-Qun Zhang, Jian Guo, Ming-Zhang Zuo, Sadayoshi Ito, Jian-Ping Cai
Oxidatively generated damage to nucleic acids may play an important role in the pathophysiological processes of a variety of diseases. 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dGsn) and 8-oxo-7,8-dihydroguanosine (8-oxo-Gsn) are oxidatively generated products of DNA and RNA, respectively. Our previous studies have suggested that the amounts of 8-oxo-dGsn and 8-oxo-Gsn in urine were considerably higher than other body fluid or tissue. The aim of this study was to investigate whether 8-oxo-dGsn and 8-oxo-Gsn levels in random urine samples are consistent with those in 24 h urine samples in healthy subjects and patients with renal disease...
June 23, 2017: Free Radical Research
https://www.readbyqxmd.com/read/28641400/cytosolic-delivery-of-sirna-by-ultra-high-affinity-dsrna-binding-proteins
#19
Nicole J Yang, Monique J Kauke, Fangdi Sun, Lucy F Yang, Katie F Maass, Michael W Traxlmayr, Yao Yu, Yingda Xu, Robert S Langer, Daniel G Anderson, K Dane Wittrup
Protein-based methods of siRNA delivery are capable of uniquely specific targeting, but are limited by technical challenges such as low potency or poor biophysical properties. Here, we engineered a series of ultra-high affinity siRNA binders based on the viral protein p19 and developed them into siRNA carriers targeted to the epidermal growth factor receptor (EGFR). Combined in trans with a previously described endosome-disrupting agent composed of the pore-forming protein Perfringolysin O (PFO), potent silencing was achieved in vitro with no detectable cytotoxicity...
June 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28640876/reliability-and-performance-of-commercial-rna-and-dna-extraction-kits-for-ffpe-tissue-cores
#20
Palak G Patel, Shamini Selvarajah, Karl-Philippe Guérard, John M S Bartlett, Jacques Lapointe, David M Berman, John B A Okello, Paul C Park
Cancer biomarker studies often require nucleic acid extraction from limited amounts of formalin-fixed, paraffin-embedded (FFPE) tissues, such as histologic sections or needle cores. A major challenge is low quantity and quality of extracted nucleic acids, which can limit our ability to perform genetic analyses, and have a significant influence on overall study design. This study was aimed at identifying the most reliable and reproducible method of obtaining sufficient high-quality nucleic acids from FFPE tissues...
2017: PloS One
keyword
keyword
22731
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"