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https://www.readbyqxmd.com/read/29453167/electrochemical-detection-of-methylated-dna-on-a-microfluidic-chip-with-nanoelectrokinetic-pre-concentration
#1
Sung A Hong, Yong-June Kim, Sung Jae Kim, Sung Yang
DNA methylation is considered to be a promising marker for the early diagnosis and prognosis of cancer. However, direct detection of the methylated DNAs in clinically relevant samples is still challenging because of its extremely low concentration (~fM). Here, an integrated microfluidic chip is reported, which is capable of pre-concentrating the methylated DNAs using ion concentration polarization (ICP) and electrochemically detecting the pre-concentrated DNAs on a single chip. The proposed chip is the first demonstration of an electrochemical detection of both level and concentration of the methylated DNAs by integrating a DNA pre-concentration unit without gene amplification...
February 1, 2018: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29452580/measuring-integrated-hiv-dna-ex-vivo-and-in-vitro-provides-insights-about-how-reservoirs-are-formed-and-maintained
#2
REVIEW
Marilia Rita Pinzone, Una O'Doherty
The identification of the most appropriate marker to measure reservoir size has been a great challenge for the HIV field. Quantitative viral outgrowth assay (QVOA), the reference standard to quantify the amount of replication-competent virus, has several limitations, as it is laborious, expensive, and unable to robustly reactivate every single integrated provirus. PCR-based assays have been developed as an easier, cheaper and less error-prone alternative to QVOA, but also have limitations. Historically, measuring integrated HIV DNA has provided insights about how reservoirs are formed and maintained...
February 17, 2018: Retrovirology
https://www.readbyqxmd.com/read/29452382/simulated-ablation-for-detection-of-cells-impacting-paracrine-signalling-in-histology-analysis
#3
Jake P Taylor-King, Etienne Baratchart, Andrew Dhawan, Elizabeth A Coker, Inga Hansine Rye, Hege Russnes, S Jon Chapman, David Basanta, Andriy Marusyk
Intra-tumour phenotypic heterogeneity limits accuracy of clinical diagnostics and hampers the efficiency of anti-cancer therapies. Dealing with this cellular heterogeneity requires adequate understanding of its sources, which is extremely difficult, as phenotypes of tumour cells integrate hardwired (epi)mutational differences with the dynamic responses to microenvironmental cues. The later comes in form of both direct physical interactions, as well as inputs from gradients of secreted signalling molecules. Furthermore, tumour cells can not only receive microenvironmental cues, but also produce them...
February 14, 2018: Mathematical Medicine and Biology: a Journal of the IMA
https://www.readbyqxmd.com/read/29452318/bone-metabolic-markers-in-the-clinical-assessment-of-patients-with-superior-semicircular-canal-dehiscence-treated-with-middle-fossa-craniotomy
#4
Thien Nguyen, Carlito Lagman, John P Sheppard, Courtney Duong, Vera Ong, Jessica Poon, Yasmine Alkhalid, Daniel Azzam, Prasanth Romiyo, Giyarpuram N Prashant, Quinton Gopen, Isaac Yang
BACKGROUND: Superior semicircular canal dehiscence (SSCD) is a bony defect in the osseous shell of the petrous temporal bone. The pathophysiological association between osteoporosis and SSCD remains poorly understood. We aim to investigate the relationships between serum calcium, 25-hydroxyvitamin D, and thyroid stimulating hormone levels, and symptoms in adult patients with SSCD treated through a middle fossa craniotomy. METHODS: Patient demographics and clinical parameters were collected...
February 13, 2018: World Neurosurgery
https://www.readbyqxmd.com/read/29452112/molecular-diagnosis-of-protozoan-parasites-by-recombinase-polymerase-amplification
#5
A Castellanos-Gonzalez, A C White, P Melby, B Travi
Infections caused by protozoan parasites affect millions of people around the world. Traditionally, diagnosis was made by microscopy, which is insensitive and in some cases not specific. Molecular methods are highly sensitive and specific, but equipment costs and personnel training limit its availability only to specialized centers, usually far from populations with the highest risk of infection. Inexpensive methods that can be applied at the point of care (POC), especially in places with limited health infrastructure, would be a major advantage...
February 13, 2018: Acta Tropica
https://www.readbyqxmd.com/read/29451896/hypomyelinating-disorders-in-china-the-clinical-and-genetic-heterogeneity-in-119-patients
#6
Haoran Ji, Dongxiao Li, Ye Wu, Quanli Zhang, Qiang Gu, Han Xie, Taoyun Ji, Huifang Wang, Lu Zhao, Haijuan Zhao, Yanling Yang, Hongchun Feng, Hui Xiong, Jinhua Ji, Zhixian Yang, Liping Kou, Ming Li, Xinhua Bao, Xingzhi Chang, Yuehua Zhang, Li Li, Huijuan Li, Zhengping Niu, Xiru Wu, Jiangxi Xiao, Yuwu Jiang, Jingmin Wang
OBJECTIVE: Hypomyelinating disorders are a group of clinically and genetically heterogeneous diseases characterized by neurological deterioration with hypomyelination visible on brain MRI scans. This study was aimed to clarify the clinical and genetic features of HMDs in Chinese population. METHODS: 119 patients with hypomyelinating disorders in Chinese population were enrolled and evaluated based on their history, clinical manifestation, laboratory examinations, series of brain MRI with follow-up, genetic etiological tests including chromosomal analysis, multiplex ligation probe amplification, Sanger sequencing, targeted enrichment-based next-generation sequencing and whole exome sequencing...
2018: PloS One
https://www.readbyqxmd.com/read/29451781/multiple-snps-detection-based-on-lateral-flow-assay-for-phenylketonuria-diagnostic
#7
Xiaonan Liu, Chao Zhang, Kewu Liu, Han Wang, Chaoxia Lu, Hang Li, Kai Hua, Juanli Zhu, Wenli Hui, Yali Cui, Xue Zhang
Single nucleotide polymorphisms (SNPs) are closely related to genetic diseases, but current SNP detection methods, such as DNA microarrays that include tedious procedures and expensive, sophisticated instruments, are unable to perform rapid SNPs detection in clinical practice, especially for those multiple SNPs related to genetic diseases. In this study, we report a sensitive, low cost, and easy-to-use point-of-care testing (POCT) system formed by combining amplification refractory mutation system (ARMS) polymerase chain reaction with gold magnetic nanoparticles (GMNPs) and lateral flow assay (LFA) noted as the ARMS-LFA system, which allow us to use a uniform condition for multiple SNPs detection simultaneously...
February 16, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29451375/-prevalence-and-phylogenetic-analysis-of-chlamydia-trachomatis-in-a-population-of-women-in-posadas-misiones
#8
G B Jordá, S E Hanke, J M Ramos-Rincón, J Mosmann, M L Lopéz, A C Entrocassi, C Cuffini
OBJECTIVE: Chlamydia trachomatis is the most prevalent bacteria causing sexually transmitted infections. In women, this infection can cause cervicitis and urethritis, although it's usually asymptomatic. The aim of this study was to investigate the prevalence of C. trachomatis in women attending the lab Instituto de Previsión Social and detect the genotypes. METHODS: Endocervical samples from 505 symptomatic and asymptomatic women were assayed. It was determined the presence of C...
February 16, 2018: Revista Española de Quimioterapia: Publicación Oficial de la Sociedad Española de Quimioterapia
https://www.readbyqxmd.com/read/29451302/comparing-cytotoxic-backbones-for-first-line-trastuzumab-containing-regimens-in-her2-positive-advanced-esophagogastric-cancer-a-meta-analysis
#9
Emil Ter Veer, Aafke Creemers, Laura de Waal, Martijn G H van Oijen, Hanneke W M van Laarhoven
According to the ToGA study, trastuzumab plus cisplatin and capecitabine/5-fluorouracil (5-FU) is standard first-line treatment for HER2-positive advanced esophagogastric cancer. We examined the relative efficacy and safety of alternative trastuzumab-based cytotoxic backbone regimens compared to the standard ToGA regimen using meta-analysis. We searched Medline, EMBASE, CENTRAL and ASCO and ESMO up to March 2017 for studies investigating alternative first-line trastuzumab-based regimens for HER2-positive esophagogastric cancer, defined as high protein expression IHC3+ or IHC2+ and gene amplification by in-situ-hybridisation...
February 16, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29451297/enhancement-of-the-conductivity-detection-signal-in-capillary-electrophoresis-systems-using-neutral-cyclodextrins-as-sweeping-agents
#10
Milan Boublík, Martina Riesová, Pavel Dubský, Bohuslav Gaš
Conductivity detection is a universal detection technique often encountered in electrophoretic separation systems, especially in modern chip-electrophoresis based devices. On the other hand, it is sparsely combined with another contemporary trend of enhancing limits of detection by means of various preconcentration strategies. This can be attributed to the fact that a preconcentration experimental setup usually brings about disturbances in a conductivity baseline. Sweeping with a neutral sweeping agent seems a good candidate for overcoming this problem...
February 16, 2018: Electrophoresis
https://www.readbyqxmd.com/read/29451144/moderate-dose-of-trolox-preventing-the-deleterious-effects-of-wi-fi-radiation-on-spermatozoa-in-vitro-through-reduction-of-oxidative-stress-damage
#11
Shang-Shu Ding, Ping Sun, Zhou Zhang, Xiang Liu, Hong Tian, Yong-Wei Huo, Li-Rong Wang, Yan Han, Jun-Ping Xing
Background: The worsening of semen quality, due to the application of Wi-Fi, can be ameliorated by Vitamin E. This study aimed to demonstrate whether a moderate dose of trolox, a new Vitamin E, inhibits oxidative damage on sperms in vitro after exposure to Wi-Fi radiation. Methods: Each of the twenty qualified semen, gathered from June to October 2014 in eugenics clinic, was separated into four aliquots, including sham, Wi-Fi-exposed, Wi-Fi plus 5 mmol/L trolox, and Wi-Fi plus 10 mmol/L trolox groups...
February 20, 2018: Chinese Medical Journal
https://www.readbyqxmd.com/read/29451063/epithelial-tumors-growing-from-within
#12
Mariana Muzzopappa, Marco Milán
The growth of epithelial tumors is often governed by cell interactions with the surrounding stroma. Drosophila has been instrumental in identifying the relevant molecular elements mediating these interactions. Of note is the role of the TNF ligand Eiger, released from recruited blood cells, in activating the JNK tumor-promoting pathway in epithelial tumors. JNK drives the transcriptional induction of mitogenic molecules, matrix metalloproteases and systemic signals that lead to tumor growth, tissue invasiveness and malignancy...
February 16, 2018: Fly
https://www.readbyqxmd.com/read/29450634/prevalence-genotypes-and-risk-factors-of-enterocytozoon-bieneusi-in-asiatic-black-bear-ursus-thibetanus-in-yunnan-province-southwestern-china
#13
Jie Wu, Jian-Qiang Han, Lian-Qin Shi, Yang Zou, Zhao Li, Jian-Fa Yang, Cui-Qin Huang, Feng-Cai Zou
Microsporidiosis is an important zoonotic disease, even leading to severe diarrhea. However, no information about prevalence and genotypes of Enterocytozoon bieneusi infection in Asiatic black bears in southwestern China is available. The objectives of the present study were to investigate the prevalence of E. bieneusi and to characterize their genotypes using the nested PCR amplification of the internal transcribed spacer region of the ribosomal RNA gene cluster and multilocus sequence typing (MLST). The overall prevalence of E...
February 15, 2018: Parasitology Research
https://www.readbyqxmd.com/read/29449965/genetic-diversity-and-cross-species-transmission-of-kobuviruses-in-vietnam
#14
Lu Lu, Nguyen Van Dung, Alasdair Ivens, Carlijn Bogaardt, Aine O'Toole, Juliet E Bryant, Juan Carrique-Mas, Nguyen Van Cuong, Pham Hong Anh, Maia A Rabaa, Ngo Tri Tue, Guy E Thwaites, Stephen Baker, Peter Simmonds, Mark Ej Woolhouse
Cross-species transmission of viruses poses a sustained threat to public health. Due to increased contact between humans and other animal species the possibility exists for cross-species transmissions and ensuing disease outbreaks. By using conventional PCR amplification and next generation sequencing, we obtained 130 partial or full genome kobuvirus sequences from humans in a sentinel cohort in Vietnam and various mammalian hosts including bats, rodents, pigs, cats, and civets. The evolution of kobuviruses in different hosts was analysed using Bayesian phylogenetic methods...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29449901/recently-integrated-alu-insertions-in-the-squirrel-monkey-saimiri-lineage-and-application-for-population-analyses
#15
Jasmine N Baker, Jerilyn A Walker, Michael W Denham, Charles D Loupe, Mark A Batzer
Background: The evolution of Alu elements has been ongoing in primate lineages and Alu insertion polymorphisms are widely used in phylogenetic and population genetics studies. Alu subfamilies in the squirrel monkey ( Saimiri ), a New World Monkey (NWM), were recently reported. Squirrel monkeys are commonly used in biomedical research and often require species identification. The purpose of this study was two-fold: 1) Perform locus-specific PCR analyses on recently integrated Alu insertions in Saimiri to determine their amplification dynamics, and 2) Identify a subset of Alu insertion polymorphisms with species informative allele frequency distributions between the Saimiri sciureus and Saimiri boliviensis groups...
2018: Mobile DNA
https://www.readbyqxmd.com/read/29449667/identification-of-g-quadruplex-clusters-by-high-throughput-sequencing-of-whole-genome-amplified-products-with-a-g-quadruplex-ligand
#16
Wataru Yoshida, Hiroki Saikyo, Kazuhiko Nakabayashi, Hitomi Yoshioka, Daniyah Habiballah Bay, Keisuke Iida, Tomoko Kawai, Kenichiro Hata, Kazunori Ikebukuro, Kazuo Nagasawa, Isao Karube
G-quadruplex (G4) is a DNA secondary structure that has been found to play regulatory roles in the genome. The identification of G4-forming sequences is important to study the specific structure-function relationships of such regions. In the present study, we developed a method for identification of G4 clusters on genomic DNA by high-throughput sequencing of genomic DNA amplified via whole-genome amplification (WGA) in the presence of a G4 ligand. The G4 ligand specifically bound to G4 structures on genomic DNA; thus, DNA polymerase was arrested on the G4 structures stabilised by G4 ligand...
February 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29449511/crispr-cas12a-target-binding-unleashes-indiscriminate-single-stranded-dnase-activity
#17
Janice S Chen, Enbo Ma, Lucas B Harrington, Maria Da Costa, Xinran Tian, Joel M Palefsky, Jennifer A Doudna
CRISPR-Cas12a (Cpf1) proteins are RNA-guided enzymes that bind and cut DNA as components of bacterial adaptive immune systems. Like CRISPR-Cas9, Cas12a has been harnessed for genome editing based on its ability to generate targeted, double-stranded DNA (dsDNA) breaks. Here we show that RNA-guided DNA binding unleashes indiscriminate single-stranded DNA (ssDNA) cleavage activity by Cas12a that completely degrades ssDNA molecules. We find that target-activated, non-specific ssDNase cleavage is also a property of other type V CRISPR-Cas12 enzymes...
February 15, 2018: Science
https://www.readbyqxmd.com/read/29449508/multiplexed-and-portable-nucleic-acid-detection-platform-with-cas13-cas12a-and-csm6
#18
Jonathan S Gootenberg, Omar O Abudayyeh, Max J Kellner, Julia Joung, James J Collins, Feng Zhang
Rapid detection of nucleic acids is integral for clinical diagnostics and biotechnological applications. We recently developed a platform termed SHERLOCK (<u>S</u>pecific<u>H</u>igh Sensitivity<u>E</u>nzymatic<u>R</u>eporter Un<u>LOCK</u>ing) that combines isothermal pre-amplification with Cas13 to detect single molecules of RNA or DNA. Through characterization of CRISPR enzymology and application development, we report here four advances integrated into SHERLOCKv2: 1) 4-channel single reaction multiplexing using orthogonal CRISPR enzymes; 2) quantitative measurement of input down to 2 aM; 3) 3...
February 15, 2018: Science
https://www.readbyqxmd.com/read/29449437/dynamic-clonal-progression-in-xenografts-of-acute-lymphoblastic-leukemia-with-intrachromosomal-amplification-of-chromosome-21
#19
Paul B Sinclair, Helen H Blair, Sarra L Ryan, Lars Buechler, Joanna Cheng, Jake Clayton, Rebecca Hanna, Shaun Hollern, Zoe Hawking, Matthew Bashton, Claire J Schwab, Lisa Jones, Lisa J Russell, Helen Marr, Peter Carey, Christina Halsey, Olaf Heidenreich, Anthony V Moorman, Christine J Harrison
Intrachromosomal amplification of chromosome 21 is a heterogeneous chromosomal rearrangement occurring in 2% of childhood precursor B-cell acute lymphoblastic leukemia. There are no cell lines with iAMP21 and these abnormalities are too complex to faithfully engineer in animal models. As a resource for future functional and pre-clinical studies, we have created xenografts from intrachromosomal amplification of chromosome 21 leukemia patient blasts and characterised them by in-vivo and ex-vivo luminescent imaging, FLOW immunophenotyping, and histological and ultrastructural analysis of bone marrow and the central nervous system...
February 15, 2018: Haematologica
https://www.readbyqxmd.com/read/29449271/targeted-therapies-for-targeted-populations-anti-egfr-treatment-for-egfr-amplified-gastroesophageal-adenocarcinoma
#20
Steven B Maron, Lindsay Alpert, Heewon A Kwak, Samantha Lomnicki, Leah Chase, David Xu, Emily O'Day, Rebecca J Nagy, Richard B Lanman, Fabiola Cecchi, Todd Hembrough, Alexa Schrock, John Hart, Shu-Yuan Xiao, Namrata Setia, Daniel V T Catenacci
Previous anti-EGFR trials in unselected gastroesophageal adenocarcinoma (GEA) patients were resoundingly negative. We identified EGFR amplification in 5% (19/363) of patients at the University of Chicago, including 6% (8/140) who were prospectively screened with intention-to-treat using anti-EGFR therapy. Seven pts received >1 dose of treatment: three first line FOLFOX plus ABT-806, one second line FOLFIRI plus cetuximab, and three third/fourth line cetuximab alone. Treatment achieved objective response in 58% (4/7) and disease control in 100% (7/7) with a median progression-free survival of 10 months...
February 15, 2018: Cancer Discovery
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