keyword
MENU ▼
Read by QxMD icon Read
search

RNA-seq

keyword
https://www.readbyqxmd.com/read/29778014/expression-of-grape-acs1-in-tomato-decreases-ethylene-and-alters-the-balance-between-auxin-and-ethylene-during-shoot-and-root-formation
#1
Xia Ye, Mengmeng Fu, Yu Liu, Dongliang An, Xianbo Zheng, Bin Tan, Jidong Li, Jun Cheng, Wei Wang, Jiancan Feng
Ethylene plays an important role in the grape rachis, where its production can be 10 times higher than in the berry. VvACS1 is the only rachis-specific ACC synthase (ACS) gene, and its expression is coincident with ethylene production in the rachis of Vitis vinifera 'Thompson seedless'. VvACS1 was cloned and ectopically expressed in tomato (Solanum lycopersicum 'Moneymaker'). Lateral buds were increased in two- or four-week-old 35s∷VvACS1 transgenic tomato plants after transplanting. Compared with wild-type (WT) plants, the transgenic tomato plants showed higher expression of the VvACS1 gene in the flowers, leaves, rachis, and fruits...
May 4, 2018: Journal of Plant Physiology
https://www.readbyqxmd.com/read/29777802/derivation-and-characterization-of-a-ucp1-reporter-human-es-cell-line
#2
Suranjit Mukherjee, Tuo Zhang, Lauretta A Lacko, Lei Tan, Jenny Zhaoying Xiang, Jason M Butler, Shuibing Chen
Interest in human brown fat as a novel therapeutic target to tackle the growing obesity and diabetes epidemic has increased dramatically in recent years. While much insight into brown fat biology has been gained from murine cell lines and models, few resources are available to study human brown fat in vitro, which makes the need for new ways to derive and study human brown adipocytes imperative. Human ES cell based reporter systems present an excellent tool to identify, mark, and purify cell populations of choice...
April 22, 2018: Stem Cell Research
https://www.readbyqxmd.com/read/29777657/mcv-mir-m1-targets-the-host-cell-immune-response-resulting-in-the-attenuation-of-neutrophil-chemotaxis
#3
P Akhbari, D Tobin, K Poterlowicz, W Roberts, J R Boyne
Virus-encoded miRNAs are emerging as key regulators of persistent infection and host-cell immune evasion. Merkel cell polyomavirus (MCPyV), the predominant aetiological agent of Merkel cell carcinoma (MCC), encodes a single miRNA, MCV-miR-M1, which targets the oncogenic MCPyV large T antigen (LT). MCV-miR-M1 has previously been shown to play an important role in establishment of long-term infection, however, the underlying mechanism is not fully understood. A key unanswered question is whether, in addition to auto-regulating LT, MCV-miR-M1 also targets cellular transcripts to orchestrate an environment conducive for persistent infection...
May 16, 2018: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/29777364/cell-division-and-turgor-mediate-enhanced-plant-growth-in-arabidopsis-plants-treated-with-the-bacterial-signalling-molecule-lumichrome
#4
Motlalepula Pholo, Beatrix Coetzee, Hans J Maree, Philip R Young, James R Lloyd, Jens Kossmann, Paul N Hills
Transcriptomic analysis indicates that the bacterial signalling molecule lumichrome enhances plant growth through a combination of enhanced cell division and cell enlargement, and possibly enhances photosynthesis. Lumichrome (7,8 dimethylalloxazine), a novel multitrophic signal molecule produced by Sinorhizobium meliloti bacteria, has previously been shown to elicit growth promotion in different plant species (Phillips et al. in Proc Natl Acad Sci USA 96:12275-12280, https://doi.org/10.1073/pnas.96.22.12275 , 1999)...
May 17, 2018: Planta
https://www.readbyqxmd.com/read/29777235/response-of-skeletal-muscle-ucp2-expression-during-metabolic-adaptation-to-caloric-restriction
#5
Sascha Heinitz, Paolo Piaggi, Shanshan Yang, Susan Bonfiglio, Jason Steel, Jonathan Krakoff, Susanne B Votruba
BACKGROUND/OBJECTIVES: Spendthrift vs. thrifty individuals expend more energy and experience greater weight loss during caloric restriction (CR). Adaptive mechanisms in skeletal muscle, adipose tissue, and on hormone level modulate energy expenditure (EE) during weight loss. Metabolic mechanisms underlying the variability in EE during CR are unclear. The present study explored whether during long-term CR (i) gene expression changes in skeletal muscle and adipose tissue relate with the individual EE response and weight loss, and (ii) altered catecholamine and FGF21-concentrations are associated with measures of metabolic adaptation...
May 17, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29776334/swi-snf-regulates-half-of-its-targets-without-the-need-of-atp-driven-nucleosome-remodeling-by-brahma
#6
Antonio Jordán-Pla, Simei Yu, Johan Waldholm, Thomas Källman, Ann-Kristin Östlund Farrants, Neus Visa
BACKGROUND: Brahma (BRM) is the only catalytic subunit of the SWI/SNF chromatin-remodeling complex of Drosophila melanogaster. The function of SWI/SNF in transcription has long been attributed to its ability to remodel nucleosomes, which requires the ATPase activity of BRM. However, recent studies have provided evidence for a non-catalytic function of BRM in the transcriptional regulation of a few specific genes. RESULTS: Here we have used RNA-seq and ChIP-seq to identify the BRM target genes in S2 cells, and we have used a catalytically inactive BRM mutant (K804R) that is unable to hydrolyze ATP to investigate the magnitude of the non-catalytic function of BRM in transcription regulation...
May 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29776333/transcriptomic-analysis-of-genes-in-soybean-in-response-to-peronospora-manshurica-infection
#7
Hang Dong, Shuangfeng Shi, Chong Zhang, Sihui Zhu, Mei Li, Jie Tan, Yue Yu, Liping Lin, Shirong Jia, Xujing Wang, Yuanhua Wu, Yuhui Liu
BACKGROUND: Soybean downy mildew (SDM), caused by Peronospora manshurica (Pm), is a major fungal disease in soybean. To date, little is known regarding the defense mechanism at molecular level and how soybean plants response to Pm infection. In this study, differential gene expression in SDM-resistant (HR) and SDM-susceptible (HS) genotype was analyzed by RNA-seq to identify differentially expressed genes (DEGs) following Pm infection. RESULTS: Of a total of 55,017 genes mapped to the soybean reference genome sequences, 2581 DEGs were identified...
May 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29775224/circular-rnas-are-differentially-expressed-in-liver-ischemia-reperfusion-injury-model
#8
Zhiqiang Ye, Qinglei Kong, Jianhua Han, Jingyi Deng, Miaolue Wu, Hong Deng
Liver ischemia/reperfusion (I/R) injury has high mortality due to the intense inflammatory process occurs in the liver. However, the pathological mechanism underlying I/R injury is still not clear. Recent works showed that circular RNAs play critical roles in many human diseases. In this study, the occurrence of liver I/R injury was validated by an analysis of the blood samples and hematoxylin-eosin (HE) staining of liver tissues. Total RNA was purified and followed by RNA-seq in the purpose of screening the circRNAs in significant differentially expression, which were validated by quantitative PCR...
May 18, 2018: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29774201/investigation-of-experimental-factors-that-underlie-brca1-2-mrna-isoform-expression-variation-recommendations-for-utilizing-targeted-rna-sequencing-to-evaluate-potential-spliceogenic-variants
#9
Vanessa L Lattimore, John F Pearson, Margaret J Currie, Amanda B Spurdle, Bridget A Robinson, Logan C Walker
PCR-based RNA splicing assays are commonly used in diagnostic and research settings to assess the potential effects of variants of uncertain clinical significance in BRCA1 and BRCA2 . The Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium completed a multicentre investigation to evaluate differences in assay design and the integrity of published data, raising a number of methodological questions associated with cell culture conditions and PCR-based protocols. We utilized targeted RNA-seq to re-assess BRCA1 and BRCA2 mRNA isoform expression patterns in lymphoblastoid cell lines (LCLs) previously used in the multicentre ENIGMA study...
2018: Frontiers in Oncology
https://www.readbyqxmd.com/read/29774046/identification-of-rice-genes-associated-with-enhanced-cold-tolerance-by-comparative-transcriptome-analysis-with-two-transgenic-rice-plants-overexpressing-dacbf4-or-dacbf7-isolated-from-antarctic-flowering-plant-deschampsia-antarctica
#10
Mi Young Byun, Li Hua Cui, Jungeun Lee, Hyun Park, Andosung Lee, Woo Taek Kim, Hyoungseok Lee
Few plant species can survive in Antarctica, the harshest environment for living organisms. Deschampsia antarctica is the only natural grass species to have adapted to and colonized the maritime Antarctic. To investigate the molecular mechanism of the Antarctic adaptation of this plant, we identified and characterized D. antarctica C-repeat binding factor 4 ( DaCBF4 ), which belongs to monocot CBF group IV. The transcript level of DaCBF4 in D. antarctica was markedly increased by cold and dehydration stress...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29774030/changes-in-the-tcr%C3%AE-repertoire-and-tumor-immune-signature-from-a-cutaneous-melanoma-patient-immunized-with-the-csf-470-vaccine-a-case-report
#11
Mariana Aris, Alicia Inés Bravo, María Betina Pampena, Paula Alejandra Blanco, Ibel Carri, Daniel Koile, Patricio Yankilevich, Estrella Mariel Levy, María Marcela Barrio, José Mordoh
The allogeneic therapeutic vaccine CSF-470 has demonstrated a significant benefit over medium-dose IFNα2b in the distant metastasis-free survival for stages IIB-IIC-III cutaneous melanoma patients in a randomized phase II/III clinical trial (CASVAC-0401, NCT01729663). At the end of the 2-year CSF-470 immunization protocol, patient #006 developed several lung and one subcutaneous melanoma metastases; this later was excised. In this report, we analyzed the changes throughout vaccination of immune populations in blood and in the tumor tissue, with special focus on the T-cell repertoire...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29774021/mitotic-spindle-organizing-protein-mzta-mediates-septation-signaling-by-suppressing-the-regulatory-subunit-of-protein-phosphatase-2a-para-in-aspergillus-nidulans
#12
Ping Jiang, Shujun Zheng, Ling Lu
The proper timing and positioning of cytokinesis/septation is crucial for hyphal growth and conidiation in Aspergillus nidulans . The septation initiation network (SIN) components are a conserved spindle pole body (SPB) localized signaling cascade and the terminal kinase complex SidB-MobA, which must localize on the SPB in this pathway to trigger septation/cytokinesis. The regulatory subunit of phosphatase PP2A-ParA has been identified to be a negative regulator capable of inactivating the SIN. However, little is known about how ParA regulates the SIN pathway and whether ParA regulates the septum formation process through affecting the SPB-localized SIN proteins...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29773903/circadian-regulator-nr1d2-regulates-glioblastoma-cell-proliferation-and-motility
#13
Min Yu, Wenjing Li, Qianqian Wang, Yan Wang, Fei Lu
Nuclear receptor NR1D2 is originally characterized as the repressor of genes involved in circadian rhythm. Recently, it is documented that NR1D2 is overexpressed in various cancers. However, the pathways and biological functions that NR1D2 involved in cancers remain poorly understood. Here, we reported that NR1D2 was abundant in human glioblastoma (GBM) tissue and cell lines but not primary human astrocytes. Silencing of NR1D2 changed the morphology of GBM cells, inhibited cell proliferation and motility, whereas had no effects on apoptosis...
May 18, 2018: Oncogene
https://www.readbyqxmd.com/read/29773840/rna-seq-and-uhplc-q-tof-ms-based-lipidomics-study-in-lysiphlebia-japonica
#14
Xueke Gao, Junyu Luo, Limin Lü, LiJuan Zhang, Shuai Zhang, Jinjie Cui
Lipids play an important role in energy storage, membrane structure stabilization and signaling. Parasitoids are excellent models to study lipidomics because a majority of them do not accumulate during their free-living life-stage. Studies on parasitoids have mostly focused on the changes in the lipids and gene transcripts in hosts and little attention has been devoted to lipidomics and transcriptomics changes in parasitoids. In this study, a relative quantitative analysis of lipids and their gene transcripts in 3-days-old Lysiphlebia japonica larva (3 days after spawning) and pupae were performed using liquid chromatography, mass spectrometry and RNA-seq...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29773832/distinct-epigenetic-landscapes-underlie-the-pathobiology-of-pancreatic-cancer-subtypes
#15
Gwen Lomberk, Yuna Blum, Rémy Nicolle, Asha Nair, Krutika Satish Gaonkar, Laetitia Marisa, Angela Mathison, Zhifu Sun, Huihuang Yan, Nabila Elarouci, Lucile Armenoult, Mira Ayadi, Tamas Ordog, Jeong-Heon Lee, Gavin Oliver, Eric Klee, Vincent Moutardier, Odile Gayet, Benjamin Bian, Pauline Duconseil, Marine Gilabert, Martin Bigonnet, Stephane Garcia, Olivier Turrini, Jean-Robert Delpero, Marc Giovannini, Philippe Grandval, Mohamed Gasmi, Veronique Secq, Aurélien De Reyniès, Nelson Dusetti, Juan Iovanna, Raul Urrutia
Recent studies have offered ample insight into genome-wide expression patterns to define pancreatic ductal adenocarcinoma (PDAC) subtypes, although there remains a lack of knowledge regarding the underlying epigenomics of PDAC. Here we perform multi-parametric integrative analyses of chromatin immunoprecipitation-sequencing (ChIP-seq) on multiple histone modifications, RNA-sequencing (RNA-seq), and DNA methylation to define epigenomic landscapes for PDAC subtypes, which can predict their relative aggressiveness and survival...
May 17, 2018: Nature Communications
https://www.readbyqxmd.com/read/29773173/gene-expression-in-adverse-reaction-to-metal-debris-around-metal-on-metal-arthroplasty-an-rna-seq-based-study
#16
Antti Pemmari, Tiina Leppänen, Erja-Leena Paukkeri, Antti Eskelinen, Teemu Moilanen, Eeva Moilanen
Joint replacement surgery is a standard treatment of advanced osteoarthritis (OA). Since 2000, cobalt-chromium (CoCr) metal-on-metal (MoM) implants were widely used in hip arthroplasties. Some patients developed "adverse reaction to metal debris" (ARMD) around the prosthesis, resulting in a need for revision surgery. In the present study, we addressed the pathogenesis of ARMD by genome-wide expression analysis. Pseudosynovial ARMD tissue was obtained from revision surgery of Articular Surface Replacement (ASR, DePuy, Warsaw, IN, USA) hip arthroplasties...
July 2018: Journal of Trace Elements in Medicine and Biology
https://www.readbyqxmd.com/read/29772705/b-myb-mediates-proliferation-and-migration-of-non-small-cell-lung-cancer-via-suppressing-igfbp3
#17
Xiaoyan Fan, Yitao Wang, Tinghui Jiang, Wei Cai, Yuelei Jin, Yulong Niu, Huifang Zhu, Youquan Bu
B-Myb has been shown to play an important oncogenic role in several types of human cancers, including non-small-cell lung cancer (NSCLC). We previously found that B-Myb is aberrantly upregulated in NSCLC, and overexpression of B-Myb can significantly promote NSCLC cell growth and motility. In the present study, we have further investigated the therapeutic potential of B-Myb in NSCLC. Kaplan⁻Meier and Cox proportional hazards analysis indicated that high expression of B-Myb is significantly associated with poor prognosis in NSCLC patients...
May 16, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29771332/mechanisms-of-skeletal-muscle-wasting-in-a-mouse-model-for-myotonic-dystrophy-type-1
#18
Ginny R Morriss, Kimal Rajapakshe, Shixia Huang, Cristian Coarfa, Thomas A Cooper
Myotonic dystrophy type 1 (DM1) is a multisystemic disease resulting in severe muscle weakening and wasting. DM1 is caused by expansion of CTG repeats in the 3'-UTR of the DMPK gene. We have developed an inducible, skeletal muscle-specific mouse model of DM1 (CUG960) that expresses 960 CUG repeats in the context of human DMPK exons 11-15. CUG960 RNA-expressing mice induced at PN1, as well as adult-onset animals, show clear, measurable muscle wasting accompanied by severe histological defects including central myonuclei, reduced fiber cross sectional area, increased percentage of oxidative myofibers, and the presence of nuclear RNA foci that colocalize with Mbnl1 protein...
May 16, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29770209/cell-specific-cis-natural-antisense-transcripts-cis-nats-in-the-sperm-and-the-pollen-vegetative-cells-of-arabidopsis-thaliana
#19
Peng Qin, Ann E Loraine, Sheila McCormick
Background: cis-NATs ( cis-natural antisense transcripts ) are transcribed from opposite strands of adjacent genes and have been shown to regulate gene expression by generating small RNAs from the overlapping region. cis-NATs are important for plant development and resistance to pathogens and stress. Several genome-wide investigations identified a number of cis-NAT pairs, but these investigations predicted cis-NATS using expression data from bulk samples that included lots of cell types. Some cis-NAT pairs identified from those investigations might not be functional, because both transcripts of cis-NAT pairs need to be co-expressed in the same cell...
2018: F1000Research
https://www.readbyqxmd.com/read/29769607/facs-seq-analysis-of-pax3-derived-cells-identifies-non-myogenic-lineages-in-the-embryonic-forelimb
#20
Arun J Singh, Chih-Ning Chang, Hsiao-Yen Ma, Stephen A Ramsey, Theresa M Filtz, Chrissa Kioussi
Skeletal muscle in the forelimb develops during embryonic and fetal development and perinatally. While much is known regarding the molecules involved in forelimb myogenesis, little is known about the specific mechanisms and interactions. Migrating skeletal muscle precursor cells express Pax3 as they migrate into the forelimb from the dermomyotome. To compare gene expression profiles of the same cell population over time, we isolated lineage-traced Pax3+ cells (Pax3 EGFP ) from forelimbs at different embryonic days...
May 16, 2018: Scientific Reports
keyword
keyword
6912
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"