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Hui Dong, Hao Sun, Jianping Zheng
With the development of large-scale biologic databases, precision medicine is becoming a frontier in biomedical research. As a main focus of precision medicine study, cancer has been widely accepted as a disease born out of inherited genetic variations or accumulating genomic damage. At the single-cell level, microfluidics or lab-on-a-chip technology for cancer study is an emerging tool for improving risk assessment, diagnostic categories and therapeutic strategies. This work presents a multi-layer microchip for single-cell gene expression profiling...
December 1, 2016: Talanta
Eun-Hee Shin, Ji-Hun Shin, You-Won Lee, Seung-Ha Lee, Chun-Feng Xin
Due to mixed use of shrimp in foodstuffs, it is important to distinguish Fenneropenaeus chinensis from other shrimp species, such as Litopenaeus vannamei and Penaeus monodon. For this purpose, we have developed a multiplex PCR method to detect the simultaneous presence of all three species. Universal primers specific to the 16S ribosomal RNA subunit were used to sequence and ascertain the species in the samples. In this study, specific primers were designed to result in a unique PCR product size (143, 260, and 348 bp for L...
October 19, 2016: Journal of AOAC International
Corinna La Rosa, Jeff Longmate, Joy Martinez, Qiao Zhou, Teodora I Kaltcheva, Weimin Tsai, Jennifer Drake, Mary Carroll, Felix Wussow, Flavia Chiuppesi, Nicola Hardwick, Sanjeet Dadwal, Ibrahim Aldoss, Ryotaro Nakamura, John A Zaia, Don J Diamond
Attenuated poxvirus Modified vaccinia Ankara (MVA) is a useful viral-based vaccine for clinical investigation, because of its excellent safety profile and property of inducing potent immune responses against recombinant (r) antigens. We developed Triplex by constructing an rMVA encoding three immunodominant CMV antigens which stimulates a host anti-viral response: UL83 (pp65), UL123 (IE1-exon4), and UL122 (IE2-exon5). We completed the first clinical evaluation of the Triplex vaccine in 24 healthy adults, with or without immunity to CMV and vaccinia virus (previous DryVax smallpox vaccination)...
October 19, 2016: Blood
Shradha Subedi, Fanrong Kong, Peter Jelfs, Timothy J Gray, Meng Xiao, Vitali Sintchenko, Sharon C-A Chen
Accurate identification of slowly growing nontuberculous mycobacteria (SG-NTM) of clinical significance remains problematic. This study evaluated a novel method of SG-NTM identification by amplification of the mycobacterial 16S-23S rRNA internal transcribed spacer (ITS) region followed by resolution of amplified fragments by sequencer-based capillary gel electrophoresis (SCGE). Fourteen American Type Culture Collection (ATCC) strains and 103 clinical/environmental isolates (total n = 24 species) of SG-NTM were included...
2016: PloS One
Samiksha Nayak, Archana Sridhara, Rita Melo, Luciana Richer, Natalie H Chee, Jiyoon Kim, Vincent Linder, David Steinmiller, Samuel K Sia, Maria Gomes-Solecki
Currently, diagnostic testing for Lyme disease is done by determination of the serologic responses to Borrelia burgdorferi antigens, with the exception of the early localized phase of disease where diagnosis must be done clinically. Here, we describe the use of microfluidics technology to develop a multiplexed rapid lab-on-a-chip point of care (POC) assay for the serologic diagnosis of human Lyme disease. Following ELISA screening of 12 candidate antigens, we tested 8 on a microfluidic diagnostic system, called mChip-Ld, using a set of 60 serological samples...
October 11, 2016: Scientific Reports
Erica Del Grosso, Andrea Idili, Alessandro Porchetta, Francesco Ricci
Here we demonstrate a general and modular approach to regulate the activity of target-responsive DNA-based nanoswitches. We do so by coupling together two DNA-based responsive elements: a triplex-forming clamp-like probe able to bind a specific DNA sequence and a split aptamer selected to bind a small molecule. In the presence of the specific target of one of the above responsive elements, the nanoswitch partially folds and its ability to bind the second target is restored. With this approach we can finely modulate the affinity of both DNA-recognition elements and aptamers using an external ligand...
September 21, 2016: Nanoscale
Ajay Kumar, Shilpa Jamwal, Mukul Kumar Midha, Baseerat Hamza, Suruchi Aggarwal, Amit Kumar Yadav, Kanury V S Rao
Here we provide data for SILAC and iTRAQ based hyperplexing combined with BONCAT based click chemistry for selective enrichment of newly synthesized proteins secreted by THP1 macrophages at various time points after infection with four different strains of Mycobacterium tuberculosis. The macrophages were infected with H37Ra, H37Rv, BND433 and JAL2287 strains of M. tuberculosis. Newly-synthesized secreted host proteins were observed, starting from six hours post-infection till 26 h, at 4 h intervals. We have combined BONCAT with hyperplexing (18-plex), which blends SILAC and iTRAQ, for the first time...
December 2016: Data in Brief
Reza Mirnejad, Nikta Sajjadi, Sara Masoumi Zavaryani, Vahhab Piranfar, Maryam Hajihosseini, Maliheh Roshanfekr
Early detection of antibiotic-resistant enterococci is an important part of patient treatment. Therefore, the aim of the present study was to evaluate the resistance patterns and simultaneously identify and characterise the resistance genes in Enterococcus spp. using a triplex polymerase chain reaction (PCR) method. In all, 150 consecutive Enterococcus spp were collected from several hospitals in Tehran (Iran) from January to December 2015. The Enterococcus species were identified by standard phenotypic/biochemical tests and PCR...
September 1, 2016: Le Infezioni in Medicina
Caili Fu, Chang Liu, Ying Li, Yajing Guo, Fang Luo, Peilong Wang, Longhua Guo, Bin Qiu, Zhenyu Lin
Abasic site (AP site) in the triplex structure can recognize specific target with high selectivity. In this study, this character was first applied to develop a simple, sensitive, and selective homogeneous electrochemical biosensor for melamine determination. The assay combines the advantage of the high selectivity of the DNA triplex structure containing an AP site to melamine and high efficiency of exonuclease (Exo) III-assisted recycling amplification. DNA-1 (T1), DNA-2 (T2), poly[dA] probe containing an AP site (8A) and methylene blue-labeled DNA probe (dMB probe) were carefully designed...
October 3, 2016: Analytical Chemistry
Amer F Saleh, Mick M Fellows, Liming Ying, Nigel J Gooderham, Catherine C Priestley
Triplex forming oligonucleotides (TFOs) bind in the major groove of DNA duplex in a sequence-specific manner imparted by Hoogsteen hydrogen bonds. There have been several reports demonstrating the ability of guanine-rich TFOs to induce targeted mutagenesis on an exogenous plasmid or an endogenous chromosomal locus. In particular, a 30mer guanine-rich triplex forming oligonucleotide, AG30, optimally designed to target the supFG1 reporter gene was reported to be mutagenic in the absence of DNA reactive agents in cultured cells and in vivo Here, we investigated the mutagenic potential of AG30 using the supFG1 shuttle vector forward mutation assay under physiological conditions...
September 21, 2016: Toxicological Sciences: An Official Journal of the Society of Toxicology
Yijun Fu, Bin Li, Jean-Michel Bourget, Olexandr Bondarenko, Jing Lin, Randolph Guzman, Royston Paynter, Denis Desaulniers, Boyin Qin, Lu Wang, Lucie Germain, Ze Zhang, Robert Guidoin
The Bentall procedure introduced in 1968 represents an undisputed cure to treat multiple pathologies involving the aortic valve and the ascending thoracic aorta. Over the years, multiple modifications have been introduced as well as a standardized approach to the operation with the goal to prevent long-term adverse events. The BioValsalva prosthesis provides a novel manner to more efficiently reconstruct the aortic valve together with the anatomy of the aortic root with the implantation of a valved conduit...
2016: Journal of Long-term Effects of Medical Implants
Marie Kalwa, Sonja Hänzelmann, Sabrina Otto, Chao-Chung Kuo, Julia Franzen, Sylvia Joussen, Eduardo Fernandez-Rebollo, Björn Rath, Carmen Koch, Andrea Hofmann, Shih-Han Lee, Andrew E Teschendorff, Bernd Denecke, Qiong Lin, Martin Widschwendter, Elmar Weinhold, Ivan G Costa, Wolfgang Wagner
There is a growing perception that long non-coding RNAs (lncRNAs) modulate cellular function. In this study, we analyzed the role of the lncRNA HOTAIR in mesenchymal stem cells (MSCs) with particular focus on senescence-associated changes in gene expression and DNA-methylation (DNAm). HOTAIR binding sites were enriched at genomic regions that become hypermethylated with increasing cell culture passage. Overexpression and knockdown of HOTAIR inhibited or stimulated adipogenic differentiation of MSCs, respectively...
September 14, 2016: Nucleic Acids Research
M Syed Ali, N Gunasekaran, Choon Ki Ahn, Peng Shi
This paper deals with the sampled-data stabilization problem for Takagi-Sugeno (T-S) fuzzy genetic regulatory networks with leakage delays. A novel Lyapunov-Krasovskii functional (LKF) is established by the non-uniform division of the delay intervals with triplex and quadruplex integral terms. Using such LKFs for constant and time-varying delay cases, new stability conditions are obtained in the T-S fuzzy framework. Based on this, a new condition for the sampled-data controller design is proposed using a linear matrix inequality representation...
September 7, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Kanti Pabbaraju, Sallene Wong, Kara Gill, Kevin Fonseca, Graham A Tipples, Raymond Tellier
BACKGROUND: In the recent past, arboviruses such as Chikungunya (CHIKV) and Zika (ZIKV) have increased their area of endemicity and presented as an emerging global public health threat. OBJECTIVES: To design an assay for the simultaneous detection of ZIKV, CHIKV and Dengue (DENV) 1-4 from patients with symptoms of arboviral infection. This would be advantageous because of the similar clinical presentation typically encountered with these viruses and their co-circulation in endemic areas...
October 2016: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
Maria-Bernadette Madel, Harald Niederstätter, Walther Parson
Sexing of biological evidence is an important aspect in forensic investigations. A routinely used molecular-genetic approach to this endeavour is the amelogenin sex test, which is integrated in most commercially available polymerase chain reaction (PCR) kits for human identification. However, this assay is not entirely effective in respect to highly degraded DNA samples. This study presents a homogeneous PCR assay for robust sex diagnosis, especially for the analysis of severely fragmented DNA. The introduced triplex for the X and Y chromosome (TriXY) is based on real-time PCR amplification of short intergenic sequences (<50bp) on both gonosomes...
September 3, 2016: Forensic Science International. Genetics
Desiree-Faye Kaixin Toh, Gitali Devi, Kiran M Patil, Qiuyu Qu, Manikantha Maraswami, Yunyun Xiao, Teck Peng Loh, Yanli Zhao, Gang Chen
RNA duplex regions are often involved in tertiary interactions and protein binding and thus there is great potential in developing ligands that sequence-specifically bind to RNA duplexes. We have developed a convenient synthesis method for a modified peptide nucleic acid (PNA) monomer with a guanidine-modified 5-methyl cytosine base. We demonstrated by gel electrophoresis, fluorescence and thermal melting experiments that short PNAs incorporating the modified residue show high binding affinity and sequence specificity in the recognition of an RNA duplex containing an internal inverted Watson-Crick C-G base pair...
September 4, 2016: Nucleic Acids Research
Natalia V Beloglazova, Astrid Foubert, Anna Gordienko, Mickael D Tessier, Tangi Aubert, Emile Drijvers, Irina Goryacheva, Zeger Hens, Sarah De Saeger
A sensitive tool for simultaneous quantitative determination of three analytes in one single well of a microtiter plate is shown for the first time. The developed technique is based on use of colloidal quantum dot enrobed into a silica shell (QD@SiO2) derivatives as a highly responsive label. Silica-coated quantum dots were prepared and subsequently modified via the co-hydrolysis with tetraethylorthosilicate (TEOS) and various organosilane reagents. Different surface modification schemes were compared in terms of applicability of the obtained particles for the multiplex immunoassay, e...
November 1, 2016: Talanta
Na Wu, Itamar Willner
Reversible pH-responsive dimer or trimer origami structures are assembled by bridging origami frames with pH-responsive units. The cyclic pH-stimulated separation and reassembly of dimer origami structures is demonstrated using i-motif or Hoogsteen-type (C-G·C(+) or T-A·T) interactions. The duplex-bridged dimer T1-T2 is separated by the pH-induced formation of an i-motif structure (pH = 4.5), and the dimer is reassembled at pH = 7.0. The duplex-bridged dimer, T3-T4, is separated at pH = 4.5 through the formation of C-G·C(+) triplex structures and is reassembled to the dimer at pH = 7...
October 12, 2016: Nano Letters
Chenli Liu, Claudia Danilowicz, Nancy Kleckner, Mara Prentiss
Long non-coding RNAs (lncRNAs) are prominently associated with chromosomes in an ever-increasing diversity of roles. To provide further insight into the potential nature of these associations, we have explored, for the first time, the interaction of long single-stranded (ss) RNAs with cognate homologous double-stranded (ds) DNA in vitro Using magnetic tweezers, we measured the effects of ssRNA on force extension curves for dsDNA. We observe that the presence of ssRNA impedes the extension of dsDNA, specifically at low forces, dependent on homology between the RNA and DNA species, and dependent on ssRNA lengths (≥1 kb)...
August 31, 2016: Nucleic Acids Research
Hidenori Okamura, Yosuke Taniguchi, Shigeki Sasaki
The sequence-specific formation of triplex DNA offers a potential basis for genome-targeting technologies. In an antiparallel triplex DNA, the sequence-specificity is established by the formation of specific base triplets (G-GC, A-AT, and T-AT) between a triplex-forming oligonucleotide (TFO) and a duplex DNA. However, there are no natural nucleosides that can selectively recognize the inverted CG and TA base pairs. Therefore, the recognition of the CG and TA inversion sites to form a stable triplex DNA has been a long-standing goal for the triplex-forming technology...
September 26, 2016: Angewandte Chemie
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