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https://www.readbyqxmd.com/read/28531156/molecular-techniques-for-the-detection-of-organisms-in-aquatic-environments-with-emphasis-on-harmful-algal-bloom-species
#1
REVIEW
Linda K Medlin, Jahir Orozco
Molecular techniques to detect organisms in aquatic ecosystems are being gradually considered as an attractive alternative to standard laboratory methods. They offer faster and more accurate means of detecting and monitoring species, with respect to their traditional homologues based on culture and microscopic counting. Molecular techniques are particularly attractive when multiple species need to be detected and/or are in very low abundance. This paper reviews molecular techniques based on whole cells, such as microscope-based enumeration and Fluorescence In-Situ Hybridization (FISH) and molecular cell-free formats, such as sandwich hybridization assay (SHA), biosensors, microarrays, quantitative polymerase chain reaction (qPCR) and real time PCR (RT-PCR)...
May 22, 2017: Sensors
https://www.readbyqxmd.com/read/28529717/gene-length-and-detection-bias-in-single-cell-rna-sequencing-protocols
#2
Belinda Phipson, Luke Zappia, Alicia Oshlack
Background: Single cell RNA sequencing (scRNA-seq) has rapidly gained popularity for profiling transcriptomes of hundreds to thousands of single cells. This technology has led to the discovery of novel cell types and revealed insights into the development of complex tissues. However, many technical challenges need to be overcome during data generation. Due to minute amounts of starting material, samples undergo extensive amplification, increasing technical variability. A solution for mitigating amplification biases is to include unique molecular identifiers (UMIs), which tag individual molecules...
2017: F1000Research
https://www.readbyqxmd.com/read/28529576/increased-mir31hg-lncrna-expression-increases-gefitinib-resistance-in-non-small-cell-lung-cancer-cell-lines-through-the-egfr-pi3k-akt-signaling-pathway
#3
Bing Wang, Hong Jiang, Limin Wang, Xueqin Chen, Kan Wu, Shirong Zhang, Shenglin Ma, Bing Xia
The aim of the present study was to gain insight into the molecular mechanism of gefitinib resistance in non-small cell lung cancer (NSCLC), and demonstrate whether long noncoding RNA (lncRNA) expression signatures differ between gefitinib-sensitive PC9 and gefitinib-resistant PC9 (PC9-R) cell lines. PC9 and PC9-R cells were treated with gefitinib and, after 48 h, proliferation and apoptosis were analyzed using a Cell Counting Kit-8 (CCK-8) assay and flow cytometry. Microarray expression profiling of lncRNAs was undertaken in both PC9 and PC9-R cells, and the expression profiles were verified by reverse transcription quantitative-polymerase chain reaction...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28524835/collapsin-response-mediator-protein-2-induced-retinal-ischemic-injury-in-a-novel-mice-model-of-ocular-ischemia-syndrome
#4
Yu Wang, Xiao-Lei Wang, Guo-Li Xie, Hong-Yang Li, Yan-Ling Wang
BACKGROUND: Collapsin response mediator protein-2 (CRMP2) has been shown to be involved in ischemia/hypoxia (IH) injury. We determined whether CRMP2 modulates ischemic injury in the retinal of Ocular ischemic syndrome (OIS). This study was to explore the molecular mechanisms underlying OIS in a novel mice model. METHODS: Experiments were performed on adult male C57/BL6 mice that received bilateral internal carotid arteries ligation for 1, 2, or 4 weeks. The mice received injection of calpeptin group before occlusion for 4 weeks or not...
June 5, 2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28522800/single-cell-single-mrna-analysis-of-ccnb1-promoter-regulation
#5
Nidhi Vishnoi, Jie Yao
Promoter activation drives gene transcriptional output. Here we report generating site-specifically integrated single-copy promoter transgenes and measuring their expression to indicate promoter activities at single-mRNA level. mRNA counts, Pol II density and Pol II firing rates of the Ccnb1 promoter transgene resembled those of the native Ccnb1 gene both among asynchronous cells and during the cell cycle. We observed distinct activation states of the Ccnb1 promoter among G1 and G2/M cells, suggesting cell cycle-independent origin of cell-to-cell variation in Ccnb1 promoter activation...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28522576/natural-killer-cell-counts-are-associated-with-molecular-relapse-free-survival-after-imatinib-discontinuation-in-chronic-myeloid-leukemia-the-immunostim-study
#6
Delphine Rea, Guylaine Henry, Zena Khaznadar, Gabriel Etienne, François Guilhot, Franck Nicolini, Joelle Guilhot, Philippe Rousselot, Françoise Huguet, Laurence Legros, Martine Gardembas, Viviane Dubruille, Agnès Guerci-Bresler, Aude Charbonnier, Frédéric Maloisel, Jean-Christophe Ianotto, Bruno Villemagne, François-Xavier Mahon, Hélène Moins-Teisserenc, Nicolas Dulphy, Antoine Toubert
Despite leukemic stem cell persistence, patients with chronic myeloid leukemia who achieve and maintain deep molecular responses may successfully stop the tyrosine kinase inhibitor imatinib. However, questions remain unanswered regarding the biological basis of molecular relapse after imatinib cessation. In IMMUNOSTIM, we monitored 51 patients from the French Stop IMatinib trial for peripheral blood T-cells and natural killer-cells. Molecular relapse-free survival at 24 months was 45.1% (95% CI: 31.44%-58.75%)...
May 18, 2017: Haematologica
https://www.readbyqxmd.com/read/28521487/microrna-29a-functions-as-a-potential-tumor-suppressor-through-directly-targeting-cdc42-in-non-small-cell-lung-cancer
#7
Yongqiang Li, Zhi Wang, Yijiang Li, Ruijun Jing
The expression and function of microRNA-29a (miR-29a) have been investigated in various types of cancer. In the present study, the expression, function and underlying molecular mechanism of miR-29a were investigated in non-small cell lung cancer (NSCLC). The expression level of miR-29a in NSCLC was determined using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Cell proliferation, migration and invasion ability were determined using Cell Counting Kit-8, cell migration and invasion assays, respectively...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28520430/fluorescence-dynamics-of-a-fret-probe-designed-for-crowding-studies
#8
Megan Currie, Hannah Leopold, Jacob Schwarz, Arnold J Boersma, Erin D Sheets, Ahmed A Heikal
Living cells are crowded with macromolecules and organelles. As a result, there is an urgent need for molecular sensors for quantitative, site-specific assessment of the macromolecular crowding effects on a myriad of biochemical processes towards quantitative cell biology and biophysics. Here we investigate the excited-state dynamics and translational diffusion of a novel FRET sensor (mCerulean-linker-mCitrine) in a buffer (PBS, pH 7.4) at room temperature. Complementary experiments were carried out on free CFP, YFP, and the cleaved FRET probe as controls...
May 18, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28518172/super-resolution-microscopy-with-dna-paint
#9
Joerg Schnitzbauer, Maximilian T Strauss, Thomas Schlichthaerle, Florian Schueder, Ralf Jungmann
Super-resolution techniques have begun to transform biological and biomedical research by allowing researchers to observe structures well below the classic diffraction limit of light. DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) offers an easy-to-implement approach to localization-based super-resolution microscopy, owing to the use of DNA probes. In DNA-PAINT, transient binding of short dye-labeled ('imager') oligonucleotides to their complementary target ('docking') strands creates the necessary 'blinking' to enable stochastic super-resolution microscopy...
June 2017: Nature Protocols
https://www.readbyqxmd.com/read/28515471/clinical-and-molecular-investigation-of-14-japanese-patients-with-complete-tfp-deficiency-a-comparison-with-caucasian-cases
#10
Ryosuke Bo, Kenji Yamada, Hironori Kobayashi, Purevsuren Jamiyan, Yuki Hasegawa, Takeshi Taketani, Seiji Fukuda, Ikue Hata, Yo Niida, Yosuke Shigematsu, Kazumoto Iijima, Seiji Yamaguchi
Mitochondrial trifunctional protein (TFP) deficiency is an inherited metabolic disorder of mitochondrial fatty-acid oxidation. Isolated long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency is often reported in Caucasian countries due to a common mutation. However, the molecular and clinical basis of complete TFP deficiency has not been extensively reported. In this study, 14 Japanese cases (13 families) with complete TFP deficiency, including 9 previously reported cases, were analyzed to clarify the clinical and molecular characteristics of TFP deficiency...
May 18, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28515464/systems-immunology-of-diabetes-tuberculosis-comorbidity-reveals-signatures-of-disease-complications
#11
Cesar A Prada-Medina, Kiyoshi F Fukutani, Nathella Pavan Kumar, Leonardo Gil-Santana, Subash Babu, Flávio Lichtenstein, Kim West, Shanmugam Sivakumar, Pradeep A Menon, Vijay Viswanathan, Bruno B Andrade, Helder I Nakaya, Hardy Kornfeld
Comorbid diabetes mellitus (DM) increases tuberculosis (TB) risk and adverse outcomes but the pathological interactions between DM and TB remain incompletely understood. We performed an integrative analysis of whole blood gene expression and plasma analytes, comparing South Indian TB patients with and without DM to diabetic and non-diabetic controls without TB. Luminex assay of plasma cytokines and growth factors delineated a distinct biosignature in comorbid TBDM in this cohort. Transcriptional profiling revealed elements in common with published TB signatures from cohorts that excluded DM...
May 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28513096/is-the-oral-fungal-pathogen-candida-albicans-a-cariogen
#12
REVIEW
Daniel Freitas Alves Pereira, Chaminda Jayampath Seneviratne, Cristiane Yumi Koga-Ito, Lakshman Perera Samaranayake
Pathobiology of dental caries is complex. Data from recent molecular microbiologic studies have further redefined the role of the oral microbiome in the etiology of dental caries. This new information challenges the conventional view on the hegemony of classic cariogenic prokaryotes such as Streptococcus mutans in caries aetiology, and raises the intriguing possibility of the participation of the eukaryotic oral fungal pathogen Candida in the caries process. The virulence attributes of Candida species such as their acidogenicity and aciduric nature, the ability to develop profuse biofilms, ferment and assimilate dietary sugars, and produce collagenolytic proteinases are all indicative of their latent cariogenic potential...
May 17, 2017: Oral Diseases
https://www.readbyqxmd.com/read/28512371/first-report-of-the-spiral-nematode-helicotylenchus-microlobus-infecting-soybean-in-north-dakota
#13
Guiping Yan, Addison Plaisance, Danqiong Huang, Zafar A Handoo
Spiral nematodes (Helicotylenchus spp.) are common plant-parasitic nematodes in fields of many crops. In June 2015, two soil samples were collected from a soybean field in Richland County, ND. Nematodes were extracted from soil using the sugar centrifugal flotation method (Jenkins, 1964). Plant-parasitic nematodes were identified to genus based on morphological features and counted. Both samples contained spiral nematodes from 1,500 to 3,300 per kilogram of soil. In June and August 2016, 10 soil samples were collected from the same field...
March 2017: Journal of Nematology
https://www.readbyqxmd.com/read/28507795/digital-analysis-and-epigenetic-regulation-of-the-signature-of-rejection-in-colorectal-cancer
#14
Viktor H Koelzer, Lena Sokol, Stefan Zahnd, Lucine Christe, Heather Dawson, Martin D Berger, Daniel Inderbitzin, Inti Zlobec, Alessandro Lugli
The immune system plays a pivotal role in the development and progression of colorectal cancer (CRC). Tumor immune rejection has been previously linked to the activation of the interferon-stimulated genes (ISG) STAT1, IRF-5 and IRF-1. Specific immunoregulatory microRNAs (miRNAs) may impact the expression of these ISG in the tumor microenvironment. In this translational study, we develop a digital image analysis protocol to identify the ISG-gene expression signature and investigate miRNA expression in the immediate environment of invading cancer cells...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28504144/low-molecular-weight-xanthan-gum-suppresses-oxidative-stress-induced-apoptosis-in-rabbit-chondrocytes
#15
Qixin Chen, Xintian Shao, Peixue Ling, Fei Liu, Huarong Shao, Aibin Ma, Jixu Wu, Wei Zhang, Fuyan Liu, Guanying Han, Fengshan Wang
We have previously reported the application of low molecular weight XG(LM-XG), with molecular weights ranging from 1×10(6)Da to 1.5×10(6)Da for treating osteoarthritis. In this study, we investigated the anti-apoptotic activity of LM-XG under oxidative stress conditions, activated by hydrogen peroxide (H2O2)-treated chondrocytes in vitro. Chondrocytes were pretreated with various doses of LM-XG (0, 10, 100, 500, or 1000μg/mL) or 1000μg/mL sodium hyaluronate for 12h, and then exposed to 0.5mmol/L H2O2 for another 12h...
August 1, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28503134/aquaporin-4-mediated-glutamate-induced-astrocyte-swelling-is-partially-mediated-through-metabotropic-glutamate-receptor-5-activation
#16
Zhongfang Shi, Wei Zhang, Yang Lu, Yi Lu, Lixin Xu, Qing Fang, Min Wu, Mei Jia, Yujiao Wang, Liping Dong, Xu Yan, Shaohua Yang, Fang Yuan
Astrocytes are one of the most abundant cell types in the mammalian central nervous system (CNS), and astrocyte swelling is the primary event associated with brain edema. Glutamate, the principal excitatory amino acid neurotransmitter in the CNS, is released at high levels after brain injury including cerebral ischemia. This leads to astrocyte swelling, which we previously demonstrated is related to metabotropic glutamate receptor (mGluR) activation. Aquaporin 4 (AQP4), the predominant water channel in the brain, is expressed in astrocyte endfeet and plays an important role in brain edema following ischemia...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28502292/-autophagy-modulates-the-levels-of-inflammatory-cytokines-in-macrophages-induced-by-lipopolysaccharide
#17
Caiyuan Ren, Xiangying Zhang, Hongbo Shi, Dexi Chen, Zhongping Duan, Huanhu Zhang, Feng Ren
Objective To analyze the effect of autophagy on inflammatory response in macrophages induced by lipopolysaccharide (LPS) and investigate its molecular mechanism. Methods Bone marrow mesenchymal stem cells, which were separated from the femora of mice, were cultured and induced to differentiate into primary macrophages in vitro. The inflammatory cell model was established by stimulating the primary macrophages with LPS. Autophagy was inhibited by 3-methyladenine (3-MA) or promoted by rapamycin. Green fluorescent protein-microtubule associated protein 1 light chain 3 (GFP-LC3) plasmid was used to transfect primary macrophages and the percentage of cells with GFP-LC3 puncta were counted in the different groups...
May 2017: Xi Bao Yu Fen Zi Mian Yi Xue za Zhi, Chinese Journal of Cellular and Molecular Immunology
https://www.readbyqxmd.com/read/28501728/effects-of-fine-air-particulates-on-gene-expression-in-non-small-cell-lung-cancer
#18
Biao Yang, Xinming Li, Dongmei Chen, Chunling Xiao
PURPOSE: Airborne particulate matter smaller than 2.5μm (PM2.5) has been shown to induce adverse health effects through various mechanisms. However, its effects on gene expression in non-small-cell lung cancer (NSCLC) remain undefined. The aim of this study was to analyze the expression profile of PM2.5-induced adverse health effects on human. MATERIALS AND METHODS: We performed RNA sequencing to elucidate key molecular effects of PM2.5 collected from Shenyang China, to identify potential diagnostic markers or therapeutic targets, and further validated these differences in gene expression by using quantitative PCR in A549 and H1299 human non-small-cell lung cancer cell lines...
May 11, 2017: Advances in Medical Sciences
https://www.readbyqxmd.com/read/28499226/effectiveness-of-a-full-scale-horizontal-slow-sand-filter-for-controlling-phytopathogens-in-recirculating-hydroponics-from-microbial-isolation-to-full-microbiome-assessment
#19
Francesc X Prenafeta-Boldú, Isabel Trillas, Marc Viñas, Miriam Guivernau, Rafaela Cáceres, Oriol Marfà
The microbial disinfestation efficiency of an innovative horizontal-flow slow sand filter (HSSF) for treating nutrient solution spent from an experimental closed-loop nursery was evaluated by means of a combination of culture-dependent and independent molecular techniques. A dense inoculum of the fungal plant pathogen Fusarium oxysporum f.sp. lycopersici was applied in the fertigation system (10(6) cells per mL). Indigenous and introduced populations of eubacteria and fungi were assessed in the nutrient solution, the HSSF influent/effluent, and a sand bed transect by isolation on selective media, as well as by quantitative qPCR and next-generation sequencing (NGS) on target ribosomal genes...
May 9, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28497843/heart-failure-pilot-transcriptomic-analysis-of-cardiac-tissue-by-rna-sequencing
#20
Concetta Schiano, Valerio Costa, Marianna Aprile, Vincenzo Grimaldi, Ciro Maiello, Roberta Esposito, Andrea Soricelli, Vittorio Colantuoni, Francesco Donatelli, Alfredo Ciccodicola, Claudio Napoli
BACKGROUND: Despite left ventricular (LV) dysfunction contributing to mortality in chronic heart failure (HF), the molecular mechanisms of LV failure continues to remain poorly understood and myocardial biomarkers have yet to be identified. The aim of this pilot study was to investigate specific transcriptome changes occurring in cardiac tissues of patients with HF compared to healthy condition patients to improve diagnosis and possible treatment of affected subjects. METHODS: Unlike other studies, only dilated cardiomyopathy (DCM) (n = 2) and restrictive cardiomyopathy (RCM) (n = 2) patients who did not report family history of the disease were selected with the aim of obtaining a homogeneous population for the study...
May 12, 2017: Cardiology Journal
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