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https://www.readbyqxmd.com/read/27911407/preparation-of-cd4-t-cells-for-analysis-of-gd3-and-gd2-ganglioside-membrane-expression-by-microscopy
#1
Tania M Villanueva-Cabello, Iván Martinez-Duncker
The methods described herein for activation of naïve CD4(+) T cells in suspension and their adherence in coverslips for confocal microscopy analysis allow the spatial localization and visualization of gangliosides involved in CD4(+) T cell activation, that complement expression profiling experiments such as flow cytometry, western blotting or real-time PCR. The quantification of ganglioside expression through flow cytometry and their cellular localization through microscopy can be obtained by the use of anti-ganglioside antibodies with high affinity and specificity...
November 8, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911273/robust-detection-of-immune-transcripts-in-ffpe-samples-using-targeted-rna-sequencing
#2
Benjamin E Paluch, Sean T Glenn, Jeffrey M Conroy, Antonios Papanicolau-Sengos, Wiam Bshara, Angela R Omilian, Elizabeth Brese, Mary Nesline, Blake Burgher, Jonathan Andreas, Kunle Odunsi, Kevin Eng, Ji He, Maochun Qin, Mark Gardner, Lorenzo Galluzzi, Carl D Morrison
Current criteria for identifying cancer patients suitable for immunotherapy with immune checkpoint blockers (ICBs) are subjective and prone to misinterpretation, as they mainly rely on the visual assessment of CD274 (best known as PD-L1) expression levels by immunohistochemistry (IHC). To address this issue, we developed a RNA sequencing (RNAseq)-based approach that specifically measures the abundance of immune transcripts in formalin-fixed paraffin embedded (FFPE) specimens. Besides exhibiting superior sensitivity as compared to whole transcriptome RNAseq, our assay requires little starting material, implying that it is compatible with RNA degradation normally caused by formalin...
November 29, 2016: Oncotarget
https://www.readbyqxmd.com/read/27909734/klf4-inhibits-tumor-growth-and-metastasis-by-targeting-microrna-31-in-human-hepatocellular-carcinoma
#3
Chuan Tian, Shanshan Yao, Li Liu, Youcheng Ding, Qingwang Ye, Xiao Dong, Yong Gao, Ning Yang, Qi Li
MicroRNAs (miRNAs or miRs) are short, endogenous non-coding RNA molecules, demonstrating abnormal expression in cancer initiation and progression. In this study, we profiled 18 differentially regulated miRNAs, including miRNA‑31, using miRNA array. Kruppel (or Krüppel)-like factor 4 (Klf4) is a transcription factor and putative tumor suppressor. Both were found to be significantly downregulated in liver cancer tissues and cells. However, little is known about the correlation between Klf4 and miRNA‑31 in hepatocellular carcinoma (HCC)...
November 24, 2016: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/27909575/a-step-by-step-workflow-for-low-level-analysis-of-single-cell-rna-seq-data
#4
Aaron T L Lun, Davis J McCarthy, John C Marioni
Single-cell RNA sequencing (scRNA-seq) is widely used to profile the transcriptome of individual cells. This provides biological resolution that cannot be matched by bulk RNA sequencing, at the cost of increased technical noise and data complexity. The differences between scRNA-seq and bulk RNA-seq data mean that the analysis of the former cannot be performed by recycling bioinformatics pipelines for the latter. Rather, dedicated single-cell methods are required at various steps to exploit the cellular resolution while accounting for technical noise...
2016: F1000Research
https://www.readbyqxmd.com/read/27909446/functional-toxicogenomic-profiling-expands-insight-into-modulators-of-formaldehyde-toxicity-in-yeast
#5
Matthew North, Brandon D Gaytán, Carlos Romero, Vanessa Y De La Rosa, Alex Loguinov, Martyn T Smith, Luoping Zhang, Chris D Vulpe
Formaldehyde (FA) is a commercially important chemical with numerous and diverse uses. Accordingly, occupational and environmental exposure to FA is prevalent worldwide. Various adverse effects, including nasopharyngeal, sinonasal, and lymphohematopoietic cancers, have been linked to FA exposure, prompting designation of FA as a human carcinogen by U.S. and international scientific entities. Although the mechanism(s) of FA toxicity have been well studied, additional insight is needed in regard to the genetic requirements for FA tolerance...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27909445/identification-and-profiling-of-micrornas-expressed-in-elongating-cotton-fibers-using-small-rna-deep-sequencing
#6
Yanmei Wang, Yan Ding, Jin-Yuan Liu
Plant microRNAs (miRNAs) have been shown to play essential roles in the regulation of gene expression. In this study, small RNA deep sequencing was applied to explore novel miRNAs expressed in elongating cotton fibers. A total of 46 novel and 96 known miRNAs, primarily derived from the corresponding specific loci in genome of Gossypium arboreum, were identified. 64 miRNAs were shown to be differentially expressed during the fiber elongation process; 16 were predicted to be novel miRNAs while the remaining 48 belong to known miRNA families...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27908735/unr-csde1-drives-a-post-transcriptional-program-to-promote-melanoma-invasion-and-metastasis
#7
Laurence Wurth, Panagiotis Papasaikas, David Olmeda, Nadine Bley, Guadalupe T Calvo, Santiago Guerrero, Daniela Cerezo-Wallis, Javier Martinez-Useros, María García-Fernández, Stefan Hüttelmaier, Maria S Soengas, Fátima Gebauer
RNA binding proteins (RBPs) modulate cancer progression through poorly understood mechanisms. Here we show that the RBP UNR/CSDE1 is overexpressed in melanoma tumors and promotes invasion and metastasis. iCLIP sequencing, RNA sequencing, and ribosome profiling combined with in silico studies unveiled sets of pro-metastatic factors coordinately regulated by UNR as part of RNA regulons. In addition to RNA steady-state levels, UNR was found to control many of its targets at the level of translation elongation/termination...
November 14, 2016: Cancer Cell
https://www.readbyqxmd.com/read/27908420/biological-effects-of-tolerable-level-chronic-boron-intake-on-transcription-factors
#8
Seda Orenay Boyacioglu, Mehmet Korkmaz, Erkan Kahraman, Hatice Yildirim, Selin Bora, Osman Yavuz Ataman
The mechanism of boron effect on human transcription and translation has not been fully understood. In the current study it was aimed to reveal the role of boron on the expression of certain transcription factors that play key roles in many cellular pathways on human subjects chronically exposed to low amounts of boron. The boron concentrations in drinking water samples were 1.57±0.06mg/l for boron group while the corresponding value for the control group was 0.016±0.002mg/l. RNA isolation was performed using PAX gene RNA kit on the blood samples from the subjects...
January 2017: Journal of Trace Elements in Medicine and Biology
https://www.readbyqxmd.com/read/27907096/global-deletion-of-tspo-does-not-affect-the-viability-and-gene-expression-profile
#9
Huaishan Wang, Kangle Zhai, Yingchao Xue, Jia Yang, Qi Yang, Yi Fu, Yu Hu, Fang Liu, Weiqing Wang, Lianxian Cui, Hui Chen, Jianmin Zhang, Wei He
Translocator Protein (18kDa, TSPO) is a mitochondrial outer membrane transmembrane protein. Its expression is elevated during inflammation and injury. However, the function of TSPO in vivo is still controversial. Here, we constructed a TSPO global knockout (KO) mouse with a Cre-LoxP system that abolished TSPO protein expression in all tissues and showed normal phenotypes in the physiological condition. The birth rates of TSPO heterozygote (Het) x Het or KO x KO breeding were consistent with Mendel's Law, suggesting a normal viability of TSPO KO mice at birth...
2016: PloS One
https://www.readbyqxmd.com/read/27907090/forkhead-box-c1-regulates-human-primary-keratinocyte-terminal-differentiation
#10
Lianghua Bin, Liehua Deng, Hengwen Yang, Leqing Zhu, Xiao Wang, Michael G Edwards, Brittany Richers, Donald Y M Leung
The epidermis serves as a critical protective barrier between the internal and external environment of the human body. Its remarkable barrier function is established through the keratinocyte (KC) terminal differentiation program. The transcription factors specifically regulating terminal differentiation remain largely unknown. Using a RNA-sequencing (RNA-seq) profiling approach, we found that forkhead box c 1 (FOXC1) was significantly up-regulated in human normal primary KC during the course of differentiation...
2016: PloS One
https://www.readbyqxmd.com/read/27905870/transcriptomic-and-proteomic-approach-to-identify-differentially-expressed-genes-and-proteins-in-arabidopsis-thaliana-mutants-lacking-chloroplastic-1-and-cytosolic-fbpases-reveals-several-levels-of-metabolic-regulation
#11
Mauricio Soto-Suárez, Antonio J Serrato, José A Rojas-González, Rocío Bautista, Mariam Sahrawy
BACKGROUND: During the photosynthesis, two isoforms of the fructose-1,6-bisphosphatase (FBPase), the chloroplastidial (cFBP1) and the cytosolic (cyFBP), catalyse the first irreversible step during the conversion of triose phosphates (TP) to starch or sucrose, respectively. Deficiency in cyFBP and cFBP1 isoforms provokes an imbalance of the starch/sucrose ratio, causing a dramatic effect on plant development when the plastidial enzyme is lacking. RESULTS: We study the correlation between the transcriptome and proteome profile in rosettes and roots when cFBP1 or cyFBP genes are disrupted in Arabidopsis thaliana knock-out mutants...
December 1, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27905550/deep-sequencing-of-transcriptome-profiling-of-gstm2-knock-down-in-swine-testis-cells
#12
Yuqi Lv, Yi Jin, Yongqiang Zhou, Jianjun Jin, Zhenfa Ma, Zhuqing Ren
Glutathione-S-transferases mu 2 (GSTM2), a kind of important Phase II antioxidant enzyme of eukaryotes, is degraded by nonsense mediated mRNA decay due to a C27T substitution in the fifth exon of pigs. As a reproductive performance-related gene, GSTM2 is involved in embryo implantation, whereas, functional deficiency of GSTM2 induces pre- or post-natal death in piglets potentially. To have some insight into the role of GSTM2 in embryo development, high throughput RNA sequencing is performed using the swine testis cells (ST) with the deletion of GSTM2...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27903806/oschx14-is-involved-in-the-k-homeostasis-in-rice-oryza-sativa-flowers
#13
Yi Chen, Jingkun Ma, Anthony J Miller, Bingbing Luo, Mei Wang, Zhen Zhu, Pieter B F Ouwerkerk
Previously we showed in the osjar1 mutants that the lodicule senescence which controls the closing of rice flowers was delayed. This resulted in florets staying open longer when compared with the wild type. The gene OsJAR1 is silenced in osjar1 mutants and is a key member of the jasmonic acid (JA) signaling pathway. We found that K concentrations in lodicules and flowers of osjar1-2 were significantly elevated compared with the wild type, indicating that K(+) homeostasis may play a role in regulating the closure of rice flowers...
July 2016: Plant & Cell Physiology
https://www.readbyqxmd.com/read/27903111/electric-stimulation-enhances-cardiac-differentiation-of-human-induced-pluripotent-stem-cells-for-myocardial-infarction-therapy
#14
Ruilian Ma, Jialiang Liang, Wei Huang, Linlin Guo, WenFeng Cai, Lei Wang, Christian Paul, Huang-Tian Yang, Ha Won Kim, Yigang Wang
AIM: Electrical stimulation (EleS) can promote cardiac differentiation, but the underlying mechanism is not well known. This study investigated the effect of EleS on cardiomyocyte (CM) differentiation of human induced pluripotent stem cells (hiPSCs) and evaluated the therapeutic effects for the treatment of myocardial infarction (MI). RESULTS: Cardiac differentiation of hiPSCs was induced with EleS after embryoid body formation. Spontaneously beating hiPSCs were observed as early at 2 days when treated with EleS as compared to control treatment...
November 30, 2016: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/27902747/joint-profiling-of-mirnas-and-mrnas-reveals-mirna-mediated-gene-regulation-in-the-g%C3%A3-ttingen-minipig-obesity-model
#15
Caroline M Junker Mentzel, Ferhat Alkan, Helle Keinicke, Mette J Jacobsen, Jan Gorodkin, Merete Fredholm, Susanna Cirera
Obesity and its comorbidities are an increasing challenge for both affected individuals and health care systems, worldwide. In obese individuals, perturbation of expression of both protein-coding genes and microRNAs (miRNA) are seen in obesity-relevant tissues (i.e. adipose tissue, liver and skeletal muscle). miRNAs are small non-coding RNA molecules which have important regulatory roles in a wide range of biological processes, including obesity. Rodents are widely used animal models for human diseases including obesity...
2016: PloS One
https://www.readbyqxmd.com/read/27902466/long-non-coding-rna-urothelial-carcinoma-associated-1-uca1-mediates-radiation-response-in-prostate-cancer
#16
Alireza Fotouhi Ghiam, Samira Taeb, Xiaoyong Huang, Vincent Huang, Jessica Ray, Seville Scarcello, Christianne Hoey, Sahar Jahangiri, Emmanouil Fokas, Andrew Loblaw, Robert G Bristow, Danny Vesprini, Paul Boutros, Stanley K Liu
Radioresistance remains a significant obstacle in the treatment of Prostate Cancer (PCa). To simulate the clinical scenario of irradiation resistance (IRR), we created DU145-IRR PCa cell lines by treatment with 2 Gy daily IR for 59 fractions. DU145-IRR cells acquired an aggressive phenotype as evidenced by increased clonogenic survival, tumorigenic potential and invasiveness. We performed transcriptome profiling to discover dysregulated genes in DU145-IRR cells and identified the long non-coding RNA (lncRNA), Urothelial carcinoma-associated 1 (UCA1)...
November 24, 2016: Oncotarget
https://www.readbyqxmd.com/read/27902365/the-oral-cavities-of-healthy-infants-harbor-high-proportions-of-streptococcus-salivarius-strains-with-phenotypic-and-genotypic-resistance-to-multiple-classes-of-antibiotics
#17
Thaís H Palma, Erika Harth-Chú, Jodie Scott, Rafael N Stipp, Heike Boisvert, Mariana F Salomão, Jéssica D Theobaldo, Rosana F Possobon, Leandro C Nascimento, Jonathan W McCafferty, Lina Faller, Margaret J Duncan, Renata O Mattos-Graner
Emerging antibiotic resistance in the oropharyngeal microbiota, of which Streptococcus salivarius is a prominent species, represents a challenge for treating pediatric populations. In this study, we investigated the role of S. salivarius as a reservoir for antibiotic resistance genes (ARG) in the oral microbiota by analyzing 95 S. salivarius isolates from 22 healthy infants (2 to 16 months of age). Minimum inhibitory concentrations (MIC) of penicillin G, amoxicillin, erythromycin, tetracycline, doxycycline and streptomycin were determined...
October 24, 2016: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/27902344/pre-infection-transcript-levels-of-fam26f-in-pbmcs-inform-about-overall-plasma-viral-load-in-acute-and-postacute-phase-after-siv-infection
#18
Aneela Javed, Nicole Leuchte, Gabriela Salinas, Lennart Opitz, Christiane Stahl-Hennig, Sieghart Sopper, Ulrike Sauermann
CD8+ cells from simian immunodeficiency virus (SIV)-infected long-term non-progressors and some uninfected macaques can suppress viral replication in vitro without killing the infected cells. The aim of the study was to identify factors responsible for non-cytolytic viral suppression by transcriptional profiling and to investigate their potential impact on SIV-replication. Results of microarray experiments and further validation with cells from infected and uninfected macaques revealed that FAM26F RNA levels distinguished CD8+ cells of controllers and non-controllers (p=0...
October 18, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27901097/sequencing-based-breast-cancer-diagnostics-as-an-alternative-to-routine-biomarkers
#19
Mattias Rantalainen, Daniel Klevebring, Johan Lindberg, Emma Ivansson, Gustaf Rosin, Lorand Kis, Fuat Celebioglu, Irma Fredriksson, Kamila Czene, Jan Frisell, Johan Hartman, Jonas Bergh, Henrik Grönberg
Sequencing-based breast cancer diagnostics have the potential to replace routine biomarkers and provide molecular characterization that enable personalized precision medicine. Here we investigate the concordance between sequencing-based and routine diagnostic biomarkers and to what extent tumor sequencing contributes clinically actionable information. We applied DNA- and RNA-sequencing to characterize tumors from 307 breast cancer patients with replication in up to 739 patients. We developed models to predict status of routine biomarkers (ER, HER2,Ki-67, histological grade) from sequencing data...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27900684/dna-rna-and-protein-based-stable-isotope-probing-for-high-throughput-biomarker-analysis-of-active-microorganisms
#20
Eleanor Jameson, Martin Taubert, Sara Coyotzi, Yin Chen, Özge Eyice, Hendrik Schäfer, J Colin Murrell, Josh D Neufeld, Marc G Dumont
Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of (13)C, (18)O, or (15)N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labeled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labeled populations by targeted gene analysis...
2017: Methods in Molecular Biology
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