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Molecular and Cellular Probes

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https://www.readbyqxmd.com/read/29458177/colorimetric-detection-of-microrna-based-on-dnazyme-and-nuclease-assisted-catalytic-hairpin-assembly-signal-amplification
#1
Hongmei Zhang, Kuiyu Wang, Shengjun Bu, Zhongyi Li, Chuanjing Ju, Jiayu Wan
Accurate and quantitative analysis of microRNA (miRNA) expression is critical for the diagnostics and theranostics of a disease. Herein, a proof-of-concept of a colorimetric horseradish peroxidase-mimicking DNAzyme (HRP-DNAzyme) biosensor for miRNA assay based on nuclease-assisted catalytic hairpin assembly (CHA) signal amplification was demonstrated. Duplex-specific nuclease (DSN) was employed to cleave the single-stranded DNA (ssDNA) chimeric probe (CP) on the magnetic bead (MB) surface via hybridization of the CP and target miRNA...
February 16, 2018: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/29438773/peroxisomal-disorders-improved-laboratory-diagnosis-new-defects-and-the-complicated-route-to-treatment
#2
Ronald J A Wanders
Peroxisomes catalyze a number of essential metabolic functions of which fatty acid alpha- and beta-oxidation, ether phospholipid biosynthesis, glyoxylate detoxification and bile acid synthesis are the most important. The key role of peroxisomes in humans is exemplified by the existence of a group of peroxisomal disorders, caused by mutations in > 30 different genes which codes for proteins with a role in either peroxisome biogenesis or one of the metabolic pathways in peroxisomes. Technological advances in laboratory methods at the metabolite-, enzyme-, and molecular level has not only allowed the identification of a new peroxisomal disorder but also new phenotypes associated with already identified genetic defects thus extending the clinical spectrum...
February 10, 2018: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/29409673/ogg1-regulates-the-level-of-symmetric-dimethylation-of-histone-h4-arginine-3-by-interacting-with-prmt5
#3
Xiaolong Zhou, Wentao Wang, Chengtao Du, Feifei Yan, Songbai Yang, Ke He, Han Wang, Ayong Zhao
OGG1 is the first enzyme in the base excision repair pathway (BER) responsible for repairing 8-oxoguanine DNA lesions. Recent studies found that OGG1 may also be involved in epigenetic regulation. In this study, we focused on the roles of OGG1 in histone modification. First, to study the effects of OGG1 on histone modification, the protein levels of symmetric dimethylation of histone H4 arginine-3 (H4R3me2s) were determined by western blot analysis following the knockdown or overexpression of OGG1. Second, the molecular mechanisms by which OGG1 regulates H4R3me2s were assessed by co-immunoprecipitation (CO-IP) assays in mouse embryonic fibroblast (MEF) wild-type (WT) and Ogg-/- cells...
February 2, 2018: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/29307697/modeling-rare-diseases-with-induced-pluripotent-stem-cell-technology
#4
REVIEW
Ruthellen H Anderson, Kevin R Francis
Rare diseases, in totality, affect a significant proportion of the population and represent an unmet medical need facing the scientific community. However, the treatment of individuals affected by rare diseases is hampered by poorly understood mechanisms preventing the development of viable therapeutics. The discovery and application of cellular reprogramming to create novel induced pluripotent stem cell models of rare diseases has revolutionized the rare disease community. Through developmental and functional analysis of differentiated cell types, these stem cell models carrying patient-specific mutations have become an invaluable tool for rare disease research...
January 4, 2018: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/29305905/the-contribution-of-gtf2i-haploinsufficiency-to-williams-syndrome
#5
Thanathom Chailangkarn, Chalongrat Noree, Alysson R Muotri
Williams syndrome (WS) is a neurodevelopmental disorder involving hemideletion of as many as 26-28 genes, resulting in a constellation of unique physical, cognitive and behavior phenotypes. The haploinsufficiency effect of each gene has been studied and correlated with phenotype(s) using several models including WS subjects, animal models, and peripheral cell lines. However, links for most of the genes to WS phenotypes remains unclear. Among those genes, general transcription factor 2I (GTF2I) is of particular interest as its haploinsufficiency is possibly associated with hypersociability in WS...
January 3, 2018: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/29288049/development-of-a-recombinase-polymerase-amplification-combined-with-lateral-flow-dipstick-assay-for-detection-of-bovine-ephemeral-fever-virus
#6
Peili Hou, Guimin Zhao, Hongmei Wang, Chengqiang He, Yanjun Huan, Hongbin He
Bovine ephemeral fever virus (BEFV), identified as the causative pathogen of bovine ephemeral fever (BEF), is responsible for increasing numbers of epidemics/outbreaks and has a significant harmful effect on the livestock industry. Therefore, a rapid detection assay is imperative for BEFV diagnosis. In this study, we described the development of lateral-flow dipstick isothermal recombinase polymerase amplification (LFD-RPA) assays for detection of BEFV. RPA primers and LF probes were designed by targeting the specific G gene, and the amplification product can be visualized on a simple lateral flow dipstick with the naked eyes...
December 26, 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/29278748/protective-effect-of-berberine-against-cardiac-ischemia-reperfusion-injury-by-inhibiting-apoptosis-through-the-activation-of-smad7
#7
Weidong Yao, Xin Wang, Kun Xiao
Berberine (BBR) is an isoquinnoline derivative alkaloid extracted from Rhizoma Coptidis that has the potential to protect myocardial tissues from ischemia/reperfusion (I/R) injuries. We attempted to evaluate the effect of BBR on the proliferation and apoptosis of a hypoxia/reoxygenation (H/R) cell model and to reveal the mechanism driving the improving function of BBR myocardial tissues. The H/R cell model was established using H9c2 rat cardiac myoblasts. The cell viability, apoptotic rates, and cell cycle distribution were measured with CCK-8 assay and flow cytometry...
December 23, 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/29274826/structure-activity-modelling-of-essential-oils-their-components-and-key-molecular-parameters-and-descriptors
#8
Lucy Owen, Katie Laird, Philippe B Wilson
Many essential oil components are known to possess broad spectrum antimicrobial activity, including against antibiotic resistant bacteria. These compounds may be a useful source of new and novel antimicrobials. However, there is limited research on the structure-activity relationship (SAR) of essential oil compounds, which is important for target identification and lead optimization. This study aimed to elucidate SARs of essential oil components from experimental and literature sources. Minimum Inhibitory Concentrations (MICs) of essential oil components were determined against Escherichia coli and Staphylococcus aureus using a microdilution method and then compared to those in published in literature...
December 21, 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/29224776/development-of-a-sybr-green-i-real-time-pcr-for-detection-and-quantitation-of-orthopoxvirus-by-using-ectromelia-virus
#9
Wenyu Cheng, Xiaobing He, Huaijie Jia, Guohua Chen, Cong Wang, Jun Zhang, Zhizhong Jing
Ectromelia virus (ECTV) is the causative agent of mousepox, which has devastating effects in laboratory-mouse colonies and causes economic loss in biomedical research. More importantly, ECTV has been extensively used as an excellent model for studies of the pathogenesis and immunobiology of human smallpox. A rapid and sensitive SYBR Green I-based real-time PCR assay was developed and used for the detection and quantitation of orthopoxvirus by using ECTV in this study. Primers targeted to the highly conserved region of major core protein P4b gene of orthopoxvirus were designed and the standard plasmid was constructed...
December 7, 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/29050990/application-of-nucleic-acid-aptamers-for-detection-of-apple-stem-pitting-virus-isolates
#10
Beata Komorowska, Beata Hasiów-Jaroszewska, Julia Minicka
DNA aptamers (PSA-H and MT32) were applied for the detection of Apple stem pitting virus (ASPV) isolates using an Enzyme-Linked Oligonucleotide Assay (ELONA) and Western blot analysis. The specificity and effectiveness of aptamers were verified in comparison to a conventional Enzyme Linked Immunosorbent Assay (ELISA). A genetically diverse group of ASPV isolates was tested. The results showed that aptamer MT32 detected a wider range of ASPV isolates than an aptamer PSA-H and proved to be superior to commercially available monoclonal antibodies...
December 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/28958719/recombinase-polymerase-amplification-assay-for-rapid-detection-of-porcine-circovirus-3
#11
Jianchang Wang, Yongning Zhang, Ruoxi Zhang, Qingan Han, Jinfeng Wang, Libing Liu, Ruiwen Li, Wanzhe Yuan
The objective of this study was to develop a real-time recombinase polymerase amplification (rt-RPA) assay for the rapid detection of porcine circovirus 3 (PCV3). Specific RPA primers and exo probes were designed for the cap gene of PCV3 within the conserved region of viral genome. The amplification was performed at 38 °C for 20 min. The rt-RPA was specific for PCV3, as there was no cross-reaction with other pathogens tested. Using the recombinant plasmid pUC57-PCV3 as template, the analytical sensitivity was 23 copies...
December 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/28863892/simultaneous-detection-and-differentiation-of-human-parvovirus-b19-and-human-parvovirus-4-by-an-internally-controlled-multiplex-quantitative-real-time-pcr
#12
Junting Jia, Yadi Zhong, Yi Guo, Chaoji Huangfu, Xiong Zhao, Chi Fang, Rui Fan, Yuyuan Ma, Jingang Zhang
Human parvovirus B19 (B19V) and human parvovirus 4 (PARV4) are two parvoviruses known to infect humans and transmit through blood and plasma derived medicinal products (PDMPs). Inactivation of the two parvoviruses has proven to be difficult and nucleic acid testing (NAT) would be an efficient means to exclude viruses. In this study, an internally controlled multiplex quantitative real-time PCR (qPCR) assay for B19V and PARV4 simultaneous detection and quantification was established and evaluated. The optimized multiplex qPCR assay allowed for simultaneous detection of all of the genotypes (1-3) of B19V and PARV4, with equal limit of quantification (LOQ) of 5 copies/μL, rather than other blood-borne viruses...
December 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/28842221/rapid-and-visual-detection-of-mycobacterium-tuberculosis-complex-using-recombinase-polymerase-amplification-combined-with-lateral-flow-strips
#13
Qinglin Ma, Houming Liu, Feidi Ye, Guangxin Xiang, Wanshui Shan, Wanli Xing
To definitively diagnose active pulmonary Tuberculosis (TB), Mycobacterium tuberculosis complex (MTBC) bacilli must be identified within clinical specimens from patients. In this study, we introduced a rapid and visual detection method of MTBC using recombinase polymerase amplification (RPA) combined with lateral flow (LF) strips. The LF-RPA assay, read results with naked eyes, could detect as few as 5 genome copies of M. tuberculosis H37Rv (ATCC 27294) per reaction and had no cross-reactions with other control bacteria even using excessive amount of template DNA...
December 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/28826997/detection-of-skeletonema-costatum-based-on-loop-mediated-isothermal-amplification-combined-with-lateral-flow-dipstick
#14
Hai-Long Huang, Peng Zhu, Cheng-Xu Zhou, Xiao-Jun Yan, Yi-Xin Zou, Pei-Wen Lv
We developed a new assay method, which combines loop-mediated isothermal amplification (LAMP) with a chromatographic lateral flow dipstick (LFD) for the rapid and special detection of the diatom Skeletonema costatum. Four groups of LAMP primers were derived from a conserved DNA sequence unique to S. costatum. The amplifications were carried out at 61, 63, and 65 °C for 60 min in various combinations by the quantitative PCR thermal cycler to confirm optimal primers and reaction temperature. The LAMP-LFD detection limit was 0...
December 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/28803792/rapid-and-visual-detection-of-leptospira-in-urine-by-ligb-lamp-assay-with-pre-addition-of-dye
#15
Syed Atif Ali, Gurpreet Kaur, Nongthombam Boby, T Sabarinath, Khushal Solanki, Dheeraj Pal, Pallab Chaudhuri
Leptospirosis is considered to be the most widespread zoonotic disease caused by pathogenic species of Leptospira. The present study reports a novel set of primers targeting LigB gene for visual detection of pathogenic Leptospira in urine samples through Loop-mediated isothermal amplification (LAMP). The results were recorded by using Hydroxyl napthol blue (HNB), SYBR GREEN I and calcein. Analytical sensitivity of LAMP was as few as 10 leptospiral organisms in spiked urine samples from cattle and dog. LigB gene based LAMP, termed as LigB-LAMP, was found 10 times more sensitive than conventional PCR...
December 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/28668278/synthetic-scale-up-of-a-novel-fluorescent-probe-and-its-biological-evaluation-for-surface-detection-of-staphylococcus-aureus
#16
Luke Bywaters, Lauren Mulcahy-Ryan, Mark Fielder, Alex Sinclair, Adam Le Gresley
This paper reports on the LGX fluorometric test for enzymatic MRSA/MSSA detection. It highlights the reasons rhodamines have been overlooked and also strategies to improve the synthesis of rhodamine-peptide conjugates. Evaluation of the LGX test for detection of MRSA/MSSA on surfaces is undertaken in the presence of potentially confounding E. coli and S. epidermidis for the first time.
December 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/28666619/development-of-a-multiplex-pcr-for-identification-of-%C3%AE-hemolytic-streptococci-relevant-to-human-infections-and-serotype-distribution-of-invasive-streptococcus-agalactiae-in-thailand
#17
Anusak Kerdsin, Rujirat Hatrongjit, Shigeyuki Hamada, Yukihiro Akeda, Marcelo Gottschalk
A multiplex polymerase chain reaction (mPCR) was developed for simultaneous detection (single reaction) of genes specific to five frequent clinically relevant β-hemolytic streptococcal species: Streptococcus pyogenes (Spy1258), Streptococcus agalactiae (cfb and cpn60), Streptococcus dysgalactiae subsp. equisimilis (16S-23S intergenic spacer) , S. equi subsp. zooepidemicus (esaA and sorD), and Streptococcus anginosus group (moaC). No cross-reaction was observed with other bacterial species. This test was validated and successfully used with 725 clinical isolates involved in pathological conditions in Thailand and collected between March 2014 and December 2015...
December 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/29179987/identification-of-genes-involved-in-the-four-stages-of-colorectal-cancer-gene-expression-profiling
#18
Guiling Shi, Yijia Wang, Chunze Zhang, Zhenying Zhao, Xiuying Sun, Shiwu Zhang, Jinling Fan, Cunxia Zhou, Jihong Zhang, Huijuan Zhang, Jun Liu
BACKGROUND: Colorectal cancer (CRC) is a common cancer with high morbidity and mortality. However, its molecular mechanism is not clear, nor the genes related to CRC stages. METHODS: Gene expression data in CRC and healthy colorectal tissues were obtained from gene expression omnibus. Limma package was used to identify the differentially expressed genes (DEGs) between control and CRC (stage I, II, III, and IV), obtaining 4 DEG sets. VennPlex was utilized to find all DEGs and intersection DEGs...
November 24, 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/29175285/development-of-hybeacon%C3%A2-probes-for-specific-mrna-detection-using-body-fluids-as-a-model-system
#19
Beccy Stafford-Allen, Nick Dawnay, Erin K Hanson, Glyn Ball, Ambika Gupta, Stephen Blackman, David J French, Nicola Duxbury, Jack Ballantyne, Simon Wells
HyBeacons are linear oligonucleotides which incorporate fluorescent dyes covalently linked to internal nucleotides. They have previously been used with PCR and isothermal amplification to interrogate SNPs and STRs in fields as diverse as clinical diagnostics, food authentication, and forensic DNA profiling. This work explores their use for the identification of expressed gene sequences through mRNA profiling. The use of mRNA is becoming increasingly common in forensic casework to identify body fluids on evidence items, as it offers higher specificity and fewer false positives than current chemical presumptive testing methods...
November 22, 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/29170100/genetic-differentiation-and-phylogeny-of-27-sheep-populations-based-on-structural-gene-loci
#20
Mingxun Li, Hailei Xia, Dan Chen, Dejun Ji, Tsunoda Kenji, Rui Li, Xiangxiang Liao, Yongjiang Mao, Wei Sun, Rongqing Geng, Zhangping Yang
To explore the genetic divergence and phylogeny of Chinese indigenous sheep breeds, in the current study, we analyzed the polymorphisms of 5 structural loci in ten sheep populations, including Sishui Fur, Sunite, Wurank, Bayinbuluke, Altay, Small-Tailed Han, Wadi, Tan, Tong and Hu sheep. The data were then compared with those from an additional 13 Asian and 4 European sheep populations acquired by the same experimental method. Based on the genetic distance and the results of a cluster analysis, we constructed the phylogenetic relationship of 27 populations...
November 21, 2017: Molecular and Cellular Probes
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