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https://www.readbyqxmd.com/read/28941453/development-of-a-dna-aptamer-for-screening-neisseria-meningitidis-serogroup-b-by-cell-selex
#1
Kimia Mirzakhani, Seyed Latif Mousavi Gargari, Iraj Rasooli, Samaneh Rasoulinejad
Background: Artificial oligonucleotides like DNA or RNA aptamers can be used as biodiagnostic alternatives for antibodies to detect pathogens. Comparing to antibodies, artificial oligonucleotides are produced easily at lower costs and are more stable. Neisseria meningitidis, the causative agent of meningitis, is responsible for about 1% of infections in an epidemic period. Specific DNA aptamers that bind to N. meningitidis serogroup B were identified by whole-cell Systemic Evolution of Ligands by EXponential Enrichment (SELEX)...
September 24, 2017: Iranian Biomedical Journal
https://www.readbyqxmd.com/read/28938575/down-regulation-of-microrna-155-promotes-selenium-deficiency-induced-apoptosis-by-tumor-necrosis-factor-receptor-superfamily-member-1b-in-the-broiler-spleen
#2
Ci Liu, Zhepeng Sun, Zhe Xu, Tianqi Liu, Tingru Pan, Shu Li
The aim of this work was to explore the microRNA profile and the effect of microRNA-155 on apoptosis in the spleen of selenium-deficient broilers. We replicated the splenic-apoptotic model in selenium-deficient broilers. In vitro, microRNA-155 oligonucleotides were transfected into lymphocytes and subsequently treated with H2O2. We observed that selenium deficiency altered the microRNA profile and decreased the expression of microRNA-155 in the broiler spleens. Tumor necrosis factor receptor superfamily member 1B was verified as a target of microRNA-155 in the splenocytes...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938065/in-vitro-selection-of-diversely-functionalized-aptamers
#3
Dehui Kong, Wayland Yeung, Ryan Hili
We describe the application of T4 DNA ligase-catalyzed DNA templated oligonucleotide polymerization toward the evolution of a diversely functionalized nucleic acid aptamer for human α-thrombin. Using a 256-membered ANNNN co-monomer library comprising 16 sub-libraries modi-fied with different functional groups, a highly-functionalized aptamer for thrombin was raised with a dissociation constant of 1.6 nM. The aptamer was found to be selective for thrombin, and re-quired the modifications for binding affinity...
September 22, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28937879/advax4-delta-inulin-combination-adjuvant-together-with-ecmx-a-fusion-construct-of-three-protective-mtb-antigens-induces-a-potent-th1-immune-response-and-protects-mice-against-mycobacterium-tuberculosis-infection
#4
Bruno de Paula Oliveira Santos, Monalisa Martins Trentini, Renato Beilner Machado, Mara Rúbia Nunes Celes, André Kipnis, Nikolai Petrovsky, Ana Paula Junqueira-Kipnis
Tuberculosis (TB) remains a main public health concern and 10.4 million new cases occurred in 2015 around the world. BCG is the only approved vaccine against TB, but has variable efficacy and new vaccines are needed. We developed two new mTB vaccine candidates based on the recombinant fusion proteins, rCMX and rECMXformulated with Advax4, a new combination adjuvant combining delta inulin, CpG oligonucleotide and murabutide. When BALB/c mice were immunized three times intramuscularly with these vaccine formulationsInjection of Advax4 alone increased the percentage of lymphatic endothelial cells and activated macrophages (F480/CD11b(+)) in the draining lymph nodes consistent with a chemotactic adjuvant effect...
September 22, 2017: Human Vaccines & Immunotherapeutics
https://www.readbyqxmd.com/read/28937734/discovery-of-oligonucleotide-signaling-mediated-by-crispr-associated-polymerases-solves-two-puzzles-but-leaves-an-enigma
#5
Eugene V Koonin, Kira S Makarova
The signature component of type III CRISPR-Cas systems is the Cas10 protein that consists of two Palm domains homologous to those of DNA and RNA polymerases, and nucleotide cyclases, and an HD nuclease domain. However, until very recently, the activity of the Palm domains and their role in CRISPR function have not been experimentally established. Most of the type III CRISPR-Cas systems and some type I systems also encompass proteins containing the CARF (CRISPR-associated Rossmann fold) domain that has been predicted to regulate CRISPR functions via nucleotide binding but its function in CRISPR-Cas remained obscure...
September 22, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28937703/synthesis-of-oligonucleotides-containing-2-n-heteroarylguanine-residues-and-their-effect-on-duplex-triplex-stability
#6
Takeshi Inde, Yoshiaki Masaki, Atsuya Maruyama, Yu Ito, Naoaki Makio, Yuya Miyatake, Takahito Tomori, Mitsuo Sekine, Kohji Seio
To systematically understand the effect of 2-N-heteroarylguanine (G(HA)) modification on the stability of higher-order DNA structures, nucleoside derivatives and oligodeoxyribonucleotides containing guanine residues modified with four kinds of hereroaryl groups on the 2-amino group were synthesized. The stabilities of the DNA duplex and the parallel-oriented DNA triplex containing these G(HA)s were studied by measuring their melting temperatures (Tm). Tm experiments and DFT calculations of the modified guanine nucleobases suggested that the base pair formation energy and stability of the two conformations, i...
September 22, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28936338/photochemically-active-dna-intercalating-ruthenium-and-related-complexes-insights-by-combining-crystallography-and-transient-spectroscopy
#7
Christine J Cardin, John M Kelly, Susan J Quinn
Recent research on the study of the interaction of ruthenium polypyridyl compounds and defined sequence nucleic acids is reviewed. Particular emphasis is paid to complexes [Ru(LL)2(Int)](2+) containing potentially intercalating ligands (Int) such as dipyridophenazine (dppz), which are known to display light-switching or photo-oxidising behaviour, depending on the nature of the ancillary ligands. X-ray crystallography has made a key contribution to our understanding, and the first complete survey of structural results is presented...
July 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28935773/a-randomized-double-blinded-phase-ii-trial-of-gemcitabine-and-nab-paclitaxel-plus-apatorsen-or-placebo-in-patients-with-metastatic-pancreatic-cancer-the-rainier-trial
#8
Andrew H Ko, Patrick B Murphy, James D Peyton, Dianna L Shipley, Ahmed Al-Hazzouri, Francisco A Rodriguez, Mark S Womack, Henry Q Xiong, David M Waterhouse, Margaret A Tempero, Shuangli Guo, Cassie M Lane, Chris Earwood, Laura M DeBusk, Johanna C Bendell
LESSONS LEARNED: The addition of the heat shock protein 27 (Hsp27)-targeting antisense oligonucleotide, apatorsen, to a standard first-line chemotherapy regimen did not result in improved survival in unselected patients with metastatic pancreatic cancer.Findings from this trial hint at the possible prognostic and predictive value of serum Hsp27 that may warrant further investigation. BACKGROUND: This randomized, double-blinded, phase II trial evaluated the efficacy of gemcitabine/nab-paclitaxel plus either apatorsen, an antisense oligonucleotide targeting heat shock protein 27 (Hsp27) mRNA, or placebo in patients with metastatic pancreatic cancer...
September 21, 2017: Oncologist
https://www.readbyqxmd.com/read/28935443/complex-formation-with-protamine-prolongs-the-thrombin-inhibiting-effect-of-dna-aptamer-in-vivo
#9
V A Spiridonova, T M Novikova, D M Nikulina, T A Shishkina, E V Golubkina, O S Dyukareva, N N Trizno
Antithrombin DNA aptamersRE31 are single-chain oligonucleotides that fold into three-dimensional forms allowing them to bind the enzyme with high affinity and inhibit its activity in vivo. They are rapidly degraded by a nonspecific nuclease, and, to prolong the lifetime of the aptamer DNA in the bloodstream, it is necessary to coat it with a polymer envelope. A new approach to solving this problem based on preparation of DNA-polyelectrolyte complexes with a minimal particle size that can circulate with blood flow...
September 18, 2017: Biochimie
https://www.readbyqxmd.com/read/28935260/insights-of-lr28-mediated-wheat-leaf-rust-resistance-transcriptomic-approach
#10
Dharmendra Singh, Dhananjay Kumar, Lopamudra Satapathy, Jyoti Pathak, Saket Chandra, Adnan Riaz, Govindraj Bhaganagre, Raman Dhariwal, Manish Kumar, Kumble Vinod Prabhu, Harindra Singh Balyan, Pushpendra Kumar Gupta, Kunal Mukhopadhyay
Leaf rust is a fungal disease that causes severe yield losses in wheat. Resistant varieties with major and quantitative resistance genes are the most effective method to control the disease. However, the main problem is inadequate information for understanding resistance mechanism and its usefulness. This paper presents Lr28 mediated genome-wide response of known and unknown genes during wheat-Puccinia triticina interaction. In this study, we prepared Serial Analysis of Gene Expression (SAGE) libraries using seedling wheat mRNA for infected and mock conditions...
September 18, 2017: Gene
https://www.readbyqxmd.com/read/28934982/mir-320-inhibits-the-growth-of-glioma-cells-through-downregulating-pbx3
#11
Cuicui Pan, Hua Gao, Ni Zheng, Qi Gao, Yuanquan Si, Yueran Zhao
BACKGROUND: MiR-320 is downregulated in multiple cancers, including glioma and acts as tumor suppressor through inhibiting tumor cells proliferation and inducing apoptosis. PBX3 (Pre-B cell leukemia homeobox 3), a putative target gene of miR-320, has been reported to be upregulated in various tumors and promote tumor cell growth through regulating MAKP/ERK pathway. This study aimed to verify whether miR-320 influences glioma cells growth through regulating PBX3. METHODS: Twenty-four human glioma and paired adjacent nontumorous tissues were collected for determination of miR-320 and PBX3 expression using RT-qPCR and western blot assays...
September 21, 2017: Biological Research
https://www.readbyqxmd.com/read/28934663/using-a-fluorescence-quenching-method-to-detect-dna-adsorption-onto-single-walled-carbon-nanotube-surfaces
#12
Kazuo Umemura, Shizuma Sato, Gilbert Bustamante, Jing Yong Ye
Surface modification of single-walled carbon nanotubes (SWNTs) with DNA molecules has attracted much attention in recent years to increase SWNT solubility and make various SWNT-based nanobiodevices. Therefore, there is a critical need to quantify the interaction between DNA molecules and SWNT surfaces, particularly the intermediate structures during DNA adsorption. In this study, we demonstrate the ability to detect the adsorption of DNA oligomers on SWNT surfaces by fluorescence spectroscopy. Fluorescein-labelled, 30mer, thymine oligonucleotides (F-T30) were employed as a fluorescent probe to study the interaction of DNA with SWNTs...
September 12, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28934489/antisense-oligonucleotides-targeting-translation-inhibitory-elements-in-5-utrs-can-selectively-increase-protein-levels
#13
Xue-Hai Liang, Hong Sun, Wen Shen, Shiyu Wang, Joyee Yao, Michael T Migawa, Huynh-Hoa Bui, Sagar S Damle, Stan Riney, Mark J Graham, Rosanne M Crooke, Stanley T Crooke
A variety of diseases are caused by deficiencies in amounts or activity of key proteins. An approach that increases the amount of a specific protein might be of therapeutic benefit. We reasoned that translation could be specifically enhanced using trans-acting agents that counter the function of negative regulatory elements present in the 5' UTRs of some mRNAs. We recently showed that translation can be enhanced by antisense oligonucleotides (ASOs) that target upstream open reading frames. Here we report the amount of a protein can also be selectively increased using ASOs designed to hybridize to other translation inhibitory elements in 5' UTRs...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28933412/genetic-substrate-reduction-therapy-a-promising-approach-for-lysosomal-storage-disorders
#14
REVIEW
Maria Francisca Coutinho, Juliana Inês Santos, Liliana Matos, Sandra Alves
Lysosomal storage diseases are a group of rare genetic disorders characterized by the accumulation of storage molecules in late endosomes/lysosomes. Most of them result from mutations in genes encoding for the catabolic enzymes that ensure intralysosomal digestion. Conventional therapeutic options include enzyme replacement therapy, an approach targeting the functional loss of the enzyme by injection of a recombinant one. Even though this is successful for some diseases, it is mostly effective for peripheral manifestations and has no impact on neuropathology...
November 9, 2016: Diseases (Basel)
https://www.readbyqxmd.com/read/28932996/what-hinders-electron-transfer-dissociation-etd-of-dna-cations
#15
Yvonne Hari, Christian J Leumann, Stefan Schürch
Radical activation methods, such as electron transfer dissociation (ETD), produce structural information complementary to collision-induced dissociation. Herein, electron transfer dissociation of 3-fold protonated DNA hexamers was studied to gain insight into the fragmentation mechanism. The fragmentation patterns of a large set of DNA hexamers confirm cytosine as the primary target of electron transfer. The reported data reveal backbone cleavage by internal electron transfer from the nucleobase to the phosphate linker leading either to a•/w or d/z• ion pairs...
September 20, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28932764/antisense-oligonucleotide-mediated-knockdown-in-mammary-tumor-organoids
#16
Sarah D Diermeier, David L Spector
Primary mammary tumor organoids grown in 3D are an excellent system to study tumor biology. They resemble the organization and physiology of native epithelia more closely than cancer cell lines grown in 2D, and additionally model interactions with the ECM (Boj et al., 2015; Clevers, 2016; Shamir and Ewald, 2014). Mammary tumor organoids are therefore a promising model system to identify and characterize novel drivers of breast cancer that would be unlikely to be identified using 2D cell lines. Antisense oligonucleotides can be used to efficiently and specifically knockdown target genes in the cell (Bennett et al...
August 20, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28931373/improving-contig-binning-of-metagenomic-data-using-formula-see-text-oligonucleotide-frequency-dissimilarity
#17
Ying Wang, Kun Wang, Yang Young Lu, Fengzhu Sun
BACKGROUND: Metagenomics sequencing provides deep insights into microbial communities. To investigate their taxonomic structure, binning assembled contigs into discrete clusters is critical. Many binning algorithms have been developed, but their performance is not always satisfactory, especially for complex microbial communities, calling for further development. RESULTS: According to previous studies, relative sequence compositions are similar across different regions of the same genome, but they differ between distinct genomes...
September 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28930591/lipoprotein-a-and-cardiovascular-disease-current-state-and-future-directions-for-an-enigmatic-lipoprotein
#18
Anum Saeed, Salim S Virani
Lipoprotein (a) (Lp (a)) is a complex polymorphic lipoprotein. Although structurally similar to low-density lipoprotein, Lp(a) has a glycoprotein, apolipoprotein(a) (apo(a)), attached to the apolipoprotein B-100 component. Several unique properties of Lp(a) can be attributed to the presence of apo(a). Several decades of research has improved our understanding of the structure, biochemistry, and pathophysiology of Lp(a) associated diseases. Genetic, epidemiological, and translational data indicate that elevated Lp(a) levels are likely in the causal pathway for atherosclerotic cardiovascular diseases as well as calcification of the aortic valves...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28930175/sensitive-genotyping-of-foodborne-associated-human-noroviruses-and-hepatitis-a-virus-using-an-array-based-platform
#19
Beatriz Quiñones, Bertram G Lee, Todd J Martinsky, Jaszemyn C Yambao, Paul K Haje, Mark Schena
Human noroviruses (NoV) are the leading cause of human gastroenteritis in populations of all ages and are linked to most of the foodborne outbreaks worldwide. Hepatitis A virus (HAV) is another important foodborne enteric virus and is considered the most common agent causing acute liver disease worldwide. In the present study, a focused, low-density DNA microarray was developed and validated for the simultaneous identification of foodborne-associated genotypes of NoV and HAV. By employing a novel algorithm, capture probes were designed to target variable genomic regions commonly used for typing these foodborne viruses...
September 20, 2017: Sensors
https://www.readbyqxmd.com/read/28929521/safety-tolerability-and-pharmacokinetics-of-radavirsen-avi-7100-an-antisense-oligonucleotide-targeting-influenza-a-m1-m2-translation
#20
John H Beigel, Jocelyn Voell, Paula Muñoz, Parag Kumar, Kristina M Brooks, Jianbo Zhang, Patrick Iversen, Alison Heald, Michael Wong, Richard T Davey
AIMS: To assess the safety, tolerability, and pharmacokinetics (PK) of radavirsen following single ascending doses and multiple doses given as IV infusions in healthy adults. METHODS: A Phase 1 safety and pharmacokinetic (PK) study of radavirsen was performed in healthy volunteers. The study was divided into 2 parts. The first was a single-ascending dose study of 5 cohorts of 8 subjects each, randomized 6:2 to receive single intravenous doses of radavirsen ranging from 0...
September 20, 2017: British Journal of Clinical Pharmacology
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