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https://www.readbyqxmd.com/read/27904893/assay-for-listeria-monocytogenes-cells-in-whole-blood-using-isotachophoresis-and-recombinase-polymerase-amplification
#1
Charbel Eid, Juan G Santiago
We present a new approach which enables lysis, extraction, and detection of inactivated Listeria monocytogenes cells from blood using isotachophoresis (ITP) and recombinase polymerase amplification (RPA). We use an ITP-compatible alkaline and proteinase K approach for rapid and effective lysis. We then perform ITP purification to separate bacterial DNA from whole blood contaminants using a microfluidic device that processes 25 μL sample volume. Lysis, mixing, dispensing, and on-chip ITP purification are completed in a total of less than 50 min...
December 1, 2016: Analyst
https://www.readbyqxmd.com/read/27903974/lncrnas-are-altered-in-lung-squamous-cell-carcinoma-and-lung-adenocarcinoma
#2
Bing Liu, Yifei Chen, Jiong Yang
Long non-coding RNAs (lncRNAs) have been implicated in pathogenesis of various cancers, including lung squamous cell carcinoma (LUSC) and lung adenocarcinoma (LUAD). We used cBioPortal to analyze lncRNA alteration frequencies and their ability to predict overall survival (OS) using 504 LUSC and 522 LUAD samples from The Cancer Genome Atlas (TCGA) database. In LUSC, 624 lncRNAs had alteration rates > 1% and 64 > 10%. In LUAD 625 lncRNAs had alteration rates > 1% and 36 > 10%. Among those, 620 lncRNAs had alteration frequencies > 1% in both LUSC and LUAD, while 22 were LUSC-specific and 23 were LUAD-specific...
November 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/27902940/a-novel-lab-on-chip-platform-with-integrated-solid-phase-pcr-and-supercritical-angle-fluorescence-saf-microlens-array-for-highly-sensitive-and-multiplexed-pathogen-detection
#3
Tran Quang Hung, Wai Hoe Chin, Yi Sun, Anders Wolff, Dang Duong Bang
Solid-phase PCR (SP-PCR) has become increasingly popular for molecular diagnosis and there have been a few attempts to incorporate SP-PCR into lab-on-a-chip (LOC) devices. However, their applicability for on-line diagnosis is hindered by the lack of sensitive and portable on-chip optical detection technology. In this paper, we addressed this challenge by combining the SP-PCR with super critical angle fluorescence (SAF) microlens array embedded in a microchip. We fabricated miniaturized SAF microlens array as part of a microfluidic chamber in thermoplastic material and performed multiplexed SP-PCR directly on top of the SAF microlens array...
November 12, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27900430/visible-and-red-emissive-molecular-beacons-for-optical-temperature-measurements-and-quality-control-in-diagnostic-assays-utilizing-temperature-dependent-amplification-reactions
#4
Zerrin Fidan, Andy Wende, Ute Resch-Genger
Quality control requirements imposed on assays used in clinical diagnostics and point-of-care-diagnostic testing (POCT), utilizing amplification reactions performed at elevated temperatures of 35 to 95 °C are very stringent. As the temperature of a reaction vessel has a large impact on the specificity and sensitivity of the amplification reaction, simple tools for local in situ temperature sensing and monitoring are required for reaction and assay control. We describe here a platform of stem-and-loop structured DNA hairpins (molecular beacons, MBs), absorbing and emitting in the visible and red spectral region, rationally designed for precise temperature measurements in microfluidic assays for POCT, and their application for temperature measurements in a common DNA-based molecular biological assay utilizing thermophilic helicase-dependent amplification (tHDA)...
November 29, 2016: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/27899623/combining-transcription-factor-binding-affinities-with-open-chromatin-data-for-accurate-gene-expression-prediction
#5
Florian Schmidt, Nina Gasparoni, Gilles Gasparoni, Kathrin Gianmoena, Cristina Cadenas, Julia K Polansky, Peter Ebert, Karl Nordström, Matthias Barann, Anupam Sinha, Sebastian Fröhler, Jieyi Xiong, Azim Dehghani Amirabad, Fatemeh Behjati Ardakani, Barbara Hutter, Gideon Zipprich, Bärbel Felder, Jürgen Eils, Benedikt Brors, Wei Chen, Jan G Hengstler, Alf Hamann, Thomas Lengauer, Philip Rosenstiel, Jörn Walter, Marcel H Schulz
The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899259/overexpression-of-the-long-non-coding-rna-spry4-it1-promotes-tumor-cell-proliferation-and-invasion-by-activating-ezh2-in-hepatocellular-carcinoma
#6
Meng Zhou, Xiao-Yu Zhang, Xi Yu
BACKGROUND: Increasing evidences have demonstrated that the dysregulation of long non-coding RNAs (lncRNAs) may act as an important role in tumor progression. The long non-coding RNA SPRY4 intronic transcript 1 (SPRY4-IT1) has been reported in some cancer including regulating cell growth, differentiation, apoptosis, and cancer progression. However, the expression and function of SPRY4-IT1 in the progression of hepatocellular carcinoma (HCC) remain largely unknown. METHODS: The lncRNA SPRY4-IT1 was detected by quantitative real time PCR (qRT-PCR) in HCC cell lines, CCK8 cell proliferation and transwell invasion assays were performed to detect the GC cell proliferation and invasion abilities...
November 26, 2016: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/27898713/peg3-interacts-with-kap1-through-krab-a
#7
Hongzhi He, An Ye, Hana Kim, Joomyeong Kim
Peg3 (Paternally Expressed Gene 3) is an imprinted gene that encodes a zinc finger DNA-binding protein. Peg3 itself is localized in the middle of a KRAB-A (Kruppel-Associated Box) zinc finger gene cluster. The amino acid sequence encoded by its exon 7 also shows sequence similarity to that of KRAB-A, suggesting Peg3 as a KRAB-containing zinc finger gene. As predicted, the PEG3 protein was co-immunoprecipitated with KAP1, a co-repressor that interacts with KRAB-A. A series of follow-up experiments further demonstrated that the exon 7 of PEG3 is indeed responsible for its physical interaction with KAP1...
2016: PloS One
https://www.readbyqxmd.com/read/27898347/human-amniotic-epithelial-cells-inhibit-cd4-t-cell-activation-in-acute-kidney-injury-patients-by-influencing-the-mir-101-c-rel-il-2-pathway
#8
Junfeng Liu, Rong Hua, Zhangbin Gong, Bin Shang, Yongyi Huang, Lihe Guo, Te Liu, Jun Xue
In the pathogenesis of acute kidney injury (AKI), the release of multiple interleukins can lead to increased kidney damage. Human amniotic epithelial cells (HuAECs) can inhibit immune cell activation in vivo and in vitro. We hypothesized that HuAECs could weaken patient-derived peripheral blood CD4+ T-cell activation and decreasing the ability of these cells to express and release IL-2. -Cell proliferation assay revealed that under the same culture conditions, activated AKI patient-derived CD4+ T cells had a significantly reduced proliferation rate when were co-cultured with HuAECs...
November 26, 2016: Molecular Immunology
https://www.readbyqxmd.com/read/27897418/suppression-of-muscle-wasting-by-the-plant-derived-compound-ursolic-acid-in-a-model-of-chronic-kidney-disease
#9
Rizhen Yu, Ji-An Chen, Jing Xu, Jin Cao, Yanlin Wang, Sandhya S Thomas, Zhaoyong Hu
BACKGROUND: Muscle wasting in chronic kidney disease (CKD) and other catabolic disorders contributes to morbidity and mortality, and there are no therapeutic interventions that regularly and safely block losses of muscle mass. We have obtained evidence that impaired IGF-1/insulin signalling and increases in glucocorticoids, myostatin and/or inflammatory cytokines that contribute to the development of muscle wasting in catabolic disorders by activating protein degradation. METHODS: Using in vitro and in vivo models of muscle wasting associated with CKD or dexamethasone administration, we measured protein synthesis and degradation and examined mechanisms by which ursolic acid, derived from plants, could block the loss of muscle mass stimulated by CKD or excessive levels of dexamethasone...
November 17, 2016: Journal of Cachexia, Sarcopenia and Muscle
https://www.readbyqxmd.com/read/27896778/lab-on-a-chip-multiplex-assays
#10
Harald Peter, Julia Wienke, Frank F Bier
Lab-on-a-chip multiplex assays allow a rapid identification of multiple parameters in an automated manner. Here we describe a lab-based preparation followed by a rapid and fully automated DNA microarray hybridization and readout in less than 10 min using the Fraunhofer in vitro diagnostics (ivD) platform to enable rapid identification of bacterial species and detection of antibiotic resistance. The use of DNA microarrays allows a fast adaptation of new biomarkers enabling the identification of different genes as well as single-nucleotide-polymorphisms (SNPs) within these genes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896251/combined-sybr-green-real-time-polymerase-chain-reaction-and-microarray-method-for-the-simultaneous-determination-of-human-papillomavirus-loads-and-genotypes
#11
Hyun Hee Seo, Young Jun Kim, Mi Seon Jeong, Sung Ran Hong, In Ho Lee, Kyeong A So, Mi-Kyung Kim, Yoo Kyung Lee, Ki Heon Lee, Juree Kim, Sung Jae Kim, Tae Jin Kim
OBJECTIVE: The aim of this study was to describe the principle of the Cheil HPV DNA Chip assay and evaluate its accuracy. In order to quantify the human papillomavirus (HPV) load and identify HPV genotypes simultaneously, this assay combined the two methods: SYBR Green quantitative real-time polymerase chain reaction (PCR) and DNA microarray. METHODS: We designed novel consensus primer sets that target the conserved region of the HPV L1 gene for quantifying and detecting a broad range of HPV types by quantitative real-time PCR...
November 2016: Obstetrics & Gynecology Science
https://www.readbyqxmd.com/read/27895806/genome-wide-epigenomic-profiling-for-biomarker-discovery
#12
REVIEW
René A M Dirks, Hendrik G Stunnenberg, Hendrik Marks
A myriad of diseases is caused or characterized by alteration of epigenetic patterns, including changes in DNA methylation, post-translational histone modifications, or chromatin structure. These changes of the epigenome represent a highly interesting layer of information for disease stratification and for personalized medicine. Traditionally, epigenomic profiling required large amounts of cells, which are rarely available with clinical samples. Also, the cellular heterogeneity complicates analysis when profiling clinical samples for unbiased genome-wide biomarker discovery...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27895756/role-of-microrna-4458-in-patients-with-non-small-cell-lung-cancer
#13
Lidao Bao, Linlin Wang, Guomin Wei, Yuehong Wang, Gerile Wuyun, Agula Bo
Incidence and progression of non-small-cell lung cancer (NSCLC) is a multi-factor, multi-step process. The present study investigated the association between the expression level of microRNA (miR)-4458 in NSCLC and paracarcinoma liver tissues and survival rates, and studied the biological functions of miR-4458 at the cellular and protein level. NSCLC and paracarcinoma tissues were sequenced using a miR expression chip. The association between miR-4458 expression and tumor-node-metastasis staging, total survival rate and relapse-free survival rate was analyzed...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27894866/transcriptional-regulation-of-the-sodium-channel-gene-scn5a-by-gata4-in-human-heart
#14
Anna Tarradas, Mel Lina Pinsach-Abuin, Carlos Mackintosh, Oriol Llorà-Batlle, Alexandra Pérez-Serra, Montserrat Batlle, Félix Pérez-Villa, Thomas Zimmer, Ivan Garcia-Bassets, Ramon Brugada, Pedro Beltran-Alvarez, Sara Pagans
Aberrant expression of the sodium channel gene (SCN5A) has been proposed to disrupt cardiac action potential and cause human cardiac arrhythmias, but the mechanisms of SCN5A gene regulation and dysregulation still remain largely unexplored. To gain insight into the transcriptional regulatory networks of SCN5A, we surveyed the promoter and first intronic regions of the SCN5A gene, predicting the presence of several binding sites for GATA transcription factors (TFs). Consistent with this prediction, chromatin immunoprecipitation (ChIP) and sequential ChIP (Re-ChIP) assays show co-occupancy of cardiac GATA TFs GATA4 and GATA5 on promoter and intron 1 SCN5A regions in fresh-frozen human left ventricle samples...
November 25, 2016: Journal of Molecular and Cellular Cardiology
https://www.readbyqxmd.com/read/27892506/negative-feedback-regulation-of-aba-biosynthesis-in-peanut-arachis-hypogaea-a-transcription-factor-complex-inhibits-ahnced1-expression-during-water-stress
#15
Shuai Liu, Meijuan Li, Liangchen Su, Kui Ge, Limei Li, Xiaoyun Li, Xu Liu, Ling Li
Abscisic acid (ABA), a key plant stress-signaling hormone, is produced in response to drought and counteracts the effects of this stress. The accumulation of ABA is controlled by the enzyme 9-cis-epoxycarotenoid dioxygenase (NCED). In Arabidopsis, NCED3 is regulated by a positive feedback mechanism by ABA. In this study in peanut (Arachis hypogaea), we demonstrate that ABA biosynthesis is also controlled by negative feedback regulation, mediated by the inhibitory effect on AhNCED1 transcription of a protein complex between transcription factors AhNAC2 and AhAREB1...
November 28, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27890615/egr2-is-a-gonadotropin-induced-survival-factor-that-controls-the-expression-of-ier3-in-ovarian-granulosa-cells
#16
Hanyong Jin, Miae Won, Eunkyoung Shin, Hong-Man Kim, Kangseok Lee, Jeehyeon Bae
Pituitary gonadotropins are key hormones that orchestrate the growth and development of ovarian follicles. However, limited information is available on intra-ovarian factors that mediate the actions of gonadotropins. In this study, we identified that the early growth response 2 gene (EGR2) is a gonadotropin-inducible gene in granulosa cells of rats and humans. Analysis of consensus EGR-binding elements (EBEs) showed that the immediate early response 3 gene (IER3) is a novel transcriptional target gene of EGR2 as confirmed by the luciferase assay, electrophoretic mobility-shift assay (EMSA), chromatin immunoprecipitation (ChIP), and western blot analysis...
November 24, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27889620/the-fli-1-transcription-factor-is-a-critical-regulator-for-controlling-the-expression-of-chemokine-c-x-c-motif-ligand-2-cxcl2
#17
Ning Lou, Mara L Lennard Richard, Jin Yu, Mark Kindy, Xian K Zhang
Mammalian cells produce inflammatory cytokines and chemokines in response to innate immune signals and their expression is tightly regulated. Chemokine (C-X-C motif) ligand 2 (CXCL2), also known as macrophage inflammatory protein 2-alpha (MIP2-alpha), is an inflammatory chemokine belonging to the CXC chemokine family. CXCL2 is chemotactic for neutrophils and elevated expression of CXCL2 is associated with many inflammatory and autoimmune diseases. The Fli-1 gene belongs to the large Ets transcription factor family, whose members regulate a wide variety of cellular functions including the immune response...
November 24, 2016: Molecular Immunology
https://www.readbyqxmd.com/read/27889568/fosb-regulates-expression-of-mir-22-during-pma-induced-differentiation-of-k562-cells-to-megakaryocytes
#18
Hafiz M Ahmad, Pamchui Muiwo, Rohini Muthuswami, Alok Bhattacharya
Expression of many miRNAs is altered in different cancers and these changes are thought to play a key role in formation and progression of cancer. In chronic myelogenous leukemia (CML) a number of miRNAs are known to be down regulated as compared to normal cells. In this report we have investigated the mechanism of this down regulation by using PMA induced differentiation of CML cell line K562 to megakaryocytes as an experimental system. On treatment with PMA, expression of many down regulated miRNAs including miR-22 is induced...
November 23, 2016: Biochimie
https://www.readbyqxmd.com/read/27883226/the-circadian-gene-clock-regulates-bone-formation-via-pdia3
#19
Gongsheng Yuan, Bingxuan Hua, Yang Yang, Lirong Xu, Tingting Cai, Ning Sun, Zuoqin Yan, Chao Lu, Ruizhe Qian
The expression patterns of clock-controlled genes (ccgs) are regulated by circadian rhythm, which is a major regulatory and physiological mechanism tied to the solar day. Disruptions in circadian rhythm contribute to the development of cardiovascular diseases, cancer, metabolic syndromes and aging. It has been reported that bone remodeling is also regulated by circadian rhythm. However, the molecular mechanism by which the circadian gene Clock regulates bone remodeling has yet to be elucidated. Here, we show that Clock mutant mice exhibit a significant reduction in bone density as well as increased apoptosis...
November 24, 2016: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/27883216/long-non-coding-rna-uc-187-is-upregulated-in-preeclampsia-and-modulates-proliferation-apoptosis-and-invasion-of-htr-8-svneo-trophoblast-cells
#20
Chunyu Cao, Jingyun Li, Jun Li, Lan Liu, Xiaoyan Cheng, Ruizhe Jia
Among the preeclampsia-related long non-cording RNAs (lncRNAs) screened with a gene chip in our preliminary study, uc.187 attracted our attention because of its high conservation across different species and significant positive correlation with preeclampsia (PE). The literature and bioinformatics analysis suggested that lncRNA uc.187 might be associated with cell growth, invasion, and apoptosis. The expression of uc.187 in severe preeclamptic placentas (n = 31) and normal placentas (n = 18) was evaluated by real-time reverse transcription polymerase chain reaction (qRT-PCR)...
November 24, 2016: Journal of Cellular Biochemistry
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