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https://www.readbyqxmd.com/read/28346704/the-chloroplast-rna-helicase-ise2-is-required-for-multiple-chloroplast-rna-processing-steps-in-arabidopsis-thaliana
#1
Krzysztof Bobik, Tyra N McCray, Ben Ernest, Jessica C Fernandez, Katharine A Howell, Thomas Lane, Margaret Staton, Tessa M Burch-Smith
INCREASED SIZE EXCLUSION LIMIT2 (ISE2) is a chloroplast-localized RNA helicase that is indispensable for proper plant development. Chloroplasts in leaves with reduced ISE2 expression have previously been shown to exhibit reduced thylakoid contents and increased stromal volume, indicative of defective development. It has recently been reported that ISE2 is required for the splicing of group II introns from chloroplast transcripts. The current study extends these findings, and presents evidence for ISE2's role in multiple aspects of chloroplast RNA processing beyond group II intron splicing...
March 27, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28346477/disruption-of-sorcs2-reveals-differences-in-the-regulation-of-stereociliary-bundle-formation-between-hair-cell-types-in-the-inner-ear
#2
Andrew Forge, Ruth R Taylor, Sally J Dawson, Michael Lovett, Daniel J Jagger
Behavioural anomalies suggesting an inner ear disorder were observed in a colony of transgenic mice. Affected animals were profoundly deaf. Severe hair bundle defects were identified in all outer and inner hair cells (OHC, IHC) in the cochlea and in hair cells of vestibular macular organs, but hair cells in cristae were essentially unaffected. Evidence suggested the disorder was likely due to gene disruption by a randomly inserted transgene construct. Whole-genome sequencing identified interruption of the SorCS2 (Sortilin-related VPS-10 domain containing protein) locus...
March 27, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28346474/the-microrna-205-5p-is-correlated-to-metastatic-potential-of-21t-series-a-breast-cancer-progression-model
#3
L Stankevicins, A Barat, P Dessen, Y Vassetzky, C V de Moura Gallo
MicroRNA is a class of noncoding RNAs able to base pair with complementary messenger RNA sequences, inhibiting their expression. These regulatory molecules play important roles in key cellular processes including cell proliferation, differentiation and response to DNA damage; changes in miRNA expression are a common feature of human cancers. To gain insights into the mechanisms involved in breast cancer progression we conducted a microRNA global expression analysis on a 21T series of cell lines obtained from the same patient during different stages of breast cancer progression...
2017: PloS One
https://www.readbyqxmd.com/read/28346370/de-novo-assembly-annotation-and-characterization-of-root-transcriptomes-of-three-caladium-cultivars-with-a-focus-on-necrotrophic-pathogen-resistance-defense-related-genes
#4
Zhe Cao, Zhanao Deng
Roots are vital to plant survival and crop yield, yet few efforts have been made to characterize the expressed genes in the roots of non-model plants (root transcriptomes). This study was conducted to sequence, assemble, annotate, and characterize the root transcriptomes of three caladium cultivars (Caladium × hortulanum) using RNA-Seq. The caladium cultivars used in this study have different levels of resistance to Pythiummyriotylum, the most damaging necrotrophic pathogen to caladium roots. Forty-six to 61 million clean reads were obtained for each caladium root transcriptome...
March 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28346055/a-to-i-editing-in-disease-is-not-fake-news
#5
Prajakta Bajad, Michael F Jantsch, Liam Keegan, Mary O'Connell
Adenosine deaminases acting on RNA (ADARs) are zinc-containing enzymes that deaminate adenosine bases to inosines within dsRNA regions in transcripts. In short, structured dsRNA hairpins individual adenosine bases may be targeted specifically and edited with up to one hundred percent efficiency, leading to the production of alternative protein variants. However, the majority of editing events occur within longer stretches of dsRNA formed by pairing of repetitive sequences. Here, many different adenosine bases are potential targets but editing efficiency is usually much lower...
March 27, 2017: RNA Biology
https://www.readbyqxmd.com/read/28345912/fluorogenic-templated-reaction-cascades-for-rna-detection
#6
Willem A Velema, Eric T Kool
Nucleic acids detection is essential to the study of biological processes and to diagnosis of pathological states. Although PCR is highly effective in vitro, methods that can function without prior sample preparation, thermal cycling, or enzymes are of interest due to their simplicity. Most current non-PCR detection methods rely on linear signal amplification, which hinders the detection of small amounts of genetic material. To address this limitation, we tested a new strategy for attaining higher-order signal amplification, in which a target sequence templates a chemical ligation and the product of this reaction is in turn detected with a second templated reaction...
March 27, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28345896/transcriptomics-and-lipidomics-of-the-environmental-strain-rhodococcus-ruber-point-out-consumption-pathways-and-potential-metabolic-bottlenecks-for-polyethylene-degradation
#7
Kevin Gravouil, Romain Ferru-Clement, Steven Colas, Reynald Helye, Linette Kadri, Ludivine Bourdeau, Bouziane Moumen, Anne Mercier, Thierry Ferreira
Polyethylene (PE), one of the most prominent synthetic polymer used worldwide, is very poorly biodegradable in the natural environment. Consequently, PE represents by itself more than half of all plastic wastes. PE biodegradation is achieved through the combination of abiotic and biotic processes. Several microorganisms have been shown to grow on the surface of PE materials, among which are the species of the Rhodococcus genus, suggesting a potent ability of these microorganisms to use, at least partly, PE as a potent carbon source...
March 27, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28345805/promoter-hypermethylation-mediated-downregulation-of-mir-770-and-its-host-gene-meg3-a-long-non-coding-rna-in-the-development-of-gastric-cardia-adenocarcinoma
#8
Wei Guo, Zhiming Dong, Shengnan Liu, Yiling Qiao, Gang Kuang, Yanli Guo, Supeng Shen, Jia Liang
Maternally expressed gene 3 (MEG3) is an imprinted gene located at 14q32 which encodes an lncRNA and is downregulated in an expanding list of cancer cell lines and primary human cancers. The miR-770 is transcribed from the intronic sequence of MEG3 and MEG3 may be the host gene for miR-770. However, the biological role of MEG3 and miR-770 in gastric cardia adenocarcinoma (GCA) development and prognosis is poorly defined. The present study was to investigate the function and methylation status of MEG3 in GCA, and further to detect the functional association of miR-770 and its host gene MEG3 in GCA carcinogenesis and prognosis...
March 27, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28345687/recent-advances-in-high-performance-fluorescent-and-bioluminescent-rna-imaging-probes
#9
REVIEW
Yuqiong Xia, Ruili Zhang, Zhongliang Wang, Jie Tian, Xiaoyuan Chen
RNA plays an important role in life processes. Imaging of messenger RNAs (mRNAs) and micro-RNAs (miRNAs) not only allows us to learn the formation and transcription of mRNAs and the biogenesis of miRNAs involved in various life processes, but also helps in detecting cancer. High-performance RNA imaging probes greatly expand our view of life processes and enhance the cancer detection accuracy. In this review, we summarize the state-of-the-art high-performance RNA imaging probes, including exogenous probes that can image RNA sequences with special modification and endogeneous probes that can directly image endogenous RNAs without special treatment...
March 27, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/28345652/synergistic-infection-of-bryv-and-pemv-2-increases-the-accumulations-of-both-bryv-and-bryv-derived-sirnas-in-nicotiana-benthamiana
#10
Cui-Ji Zhou, Xiao-Yan Zhang, Song-Yu Liu, Ying Wang, Da-Wei Li, Jia-Lin Yu, Cheng-Gui Han
Viral synergism is caused by co-infection of two unrelated viruses, leading to more severe symptoms or increased titres of one or both viruses. Synergistic infection of phloem-restricted poleroviruses and umbraviruses has destructive effects on crop plants. The mechanism underlying this synergy remains elusive. In our study, synergism was observed in co-infections of a polerovirus Brassica yellows virus (BrYV) and an umbravirus Pea enation mosaic virus 2 (PEMV 2) on Nicotiana benthamiana, which led to (1) increased titres of BrYV, (2) appearance of severe symptoms, (3) gain of mechanical transmission capacity of BrYV, (4) broader distribution of BrYV to non-vascular tissues...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28345582/enhancing-titres-of-therapeutic-viral-vectors-using-the-transgene-repression-in-vector-production-trip-system
#11
H E Maunder, J Wright, B R Kolli, C R Vieira, T T Mkandawire, S Tatoris, V Kennedy, S Iqball, G Devarajan, S Ellis, Y Lad, N G Clarkson, K A Mitrophanous, D C Farley
A key challenge in the field of therapeutic viral vector/vaccine manufacturing is maximizing production. For most vector platforms, the 'benchmark' vector titres are achieved with inert reporter genes. However, expression of therapeutic transgenes can often adversely affect vector titres due to biological effects on cell metabolism and/or on the vector virion itself. Here, we exemplify the novel 'Transgene Repression In vector Production' (TRiP) system for the production of both RNA- and DNA-based viral vectors...
March 27, 2017: Nature Communications
https://www.readbyqxmd.com/read/28345074/single-cell-rna-seq-and-computational-analysis-using-temporal-mixture-modelling-resolves-th1-tfh-fate-bifurcation-in-malaria
#12
Tapio Lönnberg, Valentine Svensson, Kylie R James, Daniel Fernandez-Ruiz, Ismail Sebina, Ruddy Montandon, Megan S F Soon, Lily G Fogg, Arya Sheela Nair, Urijah Liligeto, Michael J T Stubbington, Lam-Ha Ly, Frederik Otzen Bagger, Max Zwiessele, Neil D Lawrence, Fernando Souza-Fonseca-Guimaraes, Patrick T Bunn, Christian R Engwerda, William R Heath, Oliver Billker, Oliver Stegle, Ashraful Haque, Sarah A Teichmann
Differentiation of naïve CD4(+) T cells into functionally distinct T helper subsets is crucial for the orchestration of immune responses. Due to extensive heterogeneity and multiple overlapping transcriptional programs in differentiating T cell populations, this process has remained a challenge for systematic dissection in vivo. By using single-cell transcriptomics and computational analysis using a temporal mixtures of Gaussian processes model, termed GPfates, we reconstructed the developmental trajectories of Th1 and Tfh cells during blood-stage Plasmodium infection in mice...
March 3, 2017: Science Immunology
https://www.readbyqxmd.com/read/28344865/identification-of-genetic-determinants-of-breast-cancer-immune-phenotypes-by-integrative-genome-scale-analysis
#13
Wouter Hendrickx, Ines Simeone, Samreen Anjum, Younes Mokrab, François Bertucci, Pascal Finetti, Giuseppe Curigliano, Barbara Seliger, Luigi Cerulo, Sara Tomei, Lucia Gemma Delogu, Cristina Maccalli, Ena Wang, Lance D Miller, Francesco M Marincola, Michele Ceccarelli, Davide Bedognetti
Cancer immunotherapy is revolutionizing the clinical management of several tumors, but has demonstrated limited activity in breast cancer. The development of more effective treatments is hindered by incomplete knowledge of the genetic determinant of immune responsiveness. To fill this gap, we mined copy number alteration, somatic mutation, and expression data from The Cancer Genome Atlas (TCGA). By using RNA-sequencing data from 1,004 breast cancers, we defined distinct immune phenotypes characterized by progressive expression of transcripts previously associated with immune-mediated rejection...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28344583/rbm25-mediates-abiotic-responses-in-plants
#14
Chunhong Cheng, Zhijuan Wang, Bingjian Yuan, Xia Li
Alternative splicing (AS) of pre-mRNAs is one of the most important post-transcriptional regulations that enable a single gene to code for multiple proteins resulting in the biodiversity of proteins in eukaryotes. Recently, we have shown that an Arabidopsis thaliana RNA recognition motif-containing protein RBM25 is a novel splicing factor to modulate plant response to ABA during seed germination and post-germination through regulating HAB1 pre-mRNA AS. Here, we show that RBM25 is preferentially expressed in stomata and vascular tissues in Arabidopsis and is induced by ABA and abiotic stresses...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28344045/ezh2-mediated-%C3%AE-actin-methylation-needs-lncrna-tug1-and-promotes-the-cortex-cytoskeleton-formation-in-vsmcs
#15
Rong Chen, Peng Kong, Fan Zhang, Ya-Nan Shu, Xi Nie, Li-Hua Dong, Yan-Ling Lin, Xiao-Li Xie, Li-Li Zhao, Xiang-Jian Zhang, Mei Han
Recent studies have revealed that long non-coding RNAs (lncRNAs) participate in vascular homeostasis and pathophysiological conditions development. But still very few literatures elucidate the regulatory mechanism of non-coding RNAs in this biological process. Here we identified lncRNA taurine up-regulated gene 1 (TUG1) in rat vascular smooth muscle cells (VSMCs), and got 4612bp nucleotide sequence. The expression level of TUG1 RNA was increased in synthetic VSMCs by real-time PCR analysis. Meanwhile, the expression of enhancer of zeste homolog 2 (EZH2) (TUG1 binding protein) increased in cytoplasm of VSMCs under the same conditions...
March 23, 2017: Gene
https://www.readbyqxmd.com/read/28344037/methods-for-decoding-cas9-protospacer-adjacent-motif-pam-sequences-a-brief-overview
#16
REVIEW
Tautvydas Karvelis, Giedrius Gasiunas, Virginijus Siksnys
Recently the Cas9, an RNA guided DNA endonuclease, emerged as a powerful tool for targeted genome manipulations. Cas9 protein can be reprogrammed to cleave, bind or nick any DNA target by simply changing crRNA sequence, however a short nucleotide sequence, termed PAM, is required to initiate crRNA hybridization to the DNA target. PAM sequence is recognized by Cas9 protein and must be determined experimentally for each Cas9 variant. Exploration of Cas9 orthologs could offer a diversity of PAM sequences and novel biochemical properties that may be beneficial for genome editing applications...
March 23, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28343999/a-genome-wide-analysis-of-human-pluripotent-stem-cell-derived-endothelial-cells-in-2d-or-3d-culture
#17
Jue Zhang, Michael P Schwartz, Zhonggang Hou, Yongsheng Bai, Hamisha Ardalani, Scott Swanson, John Steill, Victor Ruotti, Angela Elwell, Bao Kim Nguyen, Jennifer Bolin, Ron Stewart, James A Thomson, William L Murphy
A defined protocol for efficiently deriving endothelial cells from human pluripotent stem cells was established and vascular morphogenesis was used as a model system to understand how synthetic hydrogels influence global biological function compared with common 2D and 3D culture platforms. RNA sequencing demonstrated that gene expression profiles were similar for endothelial cells and pericytes cocultured in polyethylene glycol (PEG) hydrogels or Matrigel, while monoculture comparisons identified distinct vascular signatures for each cell type...
March 10, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28343963/maternally-inherited-stable-intronic-sequence-rna-triggers-a-self-reinforcing-feedback-loop-during-development
#18
Mandy Li-Ian Tay, Jun Wei Pek
Maternally inherited noncoding RNAs (ncRNAs) can regulate zygotic gene expression across generations [1-4]. Recently, many stable intronic sequence RNAs (sisRNAs), which are byproducts of pre-mRNA splicing, were found to be maternally deposited and persist till zygotic transcription in Xenopus and Drosophila [5-7]. In various organisms, sisRNAs can be in linear or circular conformations, and they have been suggested to regulate host gene expression [5-10]. It is unknown whether maternally deposited sisRNAs can regulate zygotic gene expression in the embryos...
March 17, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28343791/androgen-receptor-deficient-islet-%C3%AE-cells-exhibit-alteration-in-genetic-markers-of-insulin-secretion-and-inflammation-a-transcriptome-analysis-in-the-male-mouse
#19
Weiwei Xu, Tianhua Niu, Beibei Xu, Guadalupe Navarro, Matthew J Schipma, Franck Mauvais-Jarvis
AIMS: Testosterone action is mediated via the androgen receptor (AR). We have reported that male mice lacking AR selectively in β-cells (βARKO(-/y)) develop decreased glucose-stimulated insulin secretion (GSIS), producing glucose intolerance. We showed that testosterone action on AR in β-cells amplifies the insulinotropic action of GLP-1 on its receptor via a cAMP-dependent protein kinase-A pathway. METHODS: To investigate AR-dependent gene networks in β-cells, we performed a high throughput whole transcriptome sequencing (RNA-Seq) in islets from male βARKO(-/y) and control mice...
March 9, 2017: Journal of Diabetes and its Complications
https://www.readbyqxmd.com/read/28343104/localized-surface-plasmon-resonance-mediated-fluorescence-signals-in-plasmonic-nanoparticle-quantum-dot-hybrids-for-ultrasensitive-zika-virus-rna-detection-via-hairpin-hybridization-assays
#20
Oluwasesan Adegoke, Masahiro Morita, Tatsuya Kato, Masahito Ito, Tetsuro Suzuki, Enoch Y Park
The current epidemic caused by the Zika virus (ZIKV) and the devastating effects of this virus on fetal development, which result in an increased incidence of congenital microcephaly symptoms, have prompted the World Health Organization (WHO) to declare the ZIKV a public health issue of global concern. Efficient probes that offer high detection sensitivity and specificity are urgently required to aid in the point-of-care treatment of the virus. In this study, we show that localized surface plasmon resonance (LSPR) signals from plasmonic nanoparticles (NPs) can be used to mediate the fluorescence signal from semiconductor quantum dot (Qdot) nanocrystals in a molecular beacon (MB) biosensor probe for ZIKV RNA detection...
March 22, 2017: Biosensors & Bioelectronics
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