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https://www.readbyqxmd.com/read/29158498/activity-dependent-expression-of-channelrhodopsin-at-neuronal-synapses
#1
Francesco Gobbo, Laura Marchetti, Ajesh Jacob, Bruno Pinto, Noemi Binini, Federico Pecoraro Bisogni, Claudia Alia, Stefano Luin, Matteo Caleo, Tommaso Fellin, Laura Cancedda, Antonino Cattaneo
Increasing evidence points to the importance of dendritic spines in the formation and allocation of memories, and alterations of spine number and physiology are associated to memory and cognitive disorders. Modifications of the activity of subsets of synapses are believed to be crucial for memory establishment. However, the development of a method to directly test this hypothesis, by selectively controlling the activity of potentiated spines, is currently lagging. Here we introduce a hybrid RNA/protein approach to regulate the expression of a light-sensitive membrane channel at activated synapses, enabling selective tagging of potentiated spines following the encoding of a novel context in the hippocampus...
November 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/29155068/a-noncanonical-poly-a-rna-polymerase-gene-affects-morphology-in-phoma-medicaginis
#2
Kihyuck Choi, Stephen M Marek
Phoma medicaginis (syn. Ascochyta medicaginicola Qchen &L. Cai) causes spring black stem and leaf spot, an important disease of alfalfa and annual medics. P. medicaginis forms uninucleate conidia in melanized pycnidia and is genetically tractable using Agrobacterium mediated transformation (ATMT), resulting in random integration of T-DNA that occasionally generates pycnidial mutants. The T-DNA tagged mutant, P265 displayed smaller pycnidia and more aerial hyphae than the wild type. A single T-DNA disrupted a putative noncanonical poly(A) RNA polymerase gene, Pmncpap1, which in yeast interacts with ribonucleotide reductase (RNR)...
November 15, 2017: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/29151891/the-exon-junction-complex-factor-y14-is-dynamic-in-the-nucleus-of-the-beetle-tribolium-castaneum-during-late-oogenesis
#3
Artem M Kiselev, Irina S Stepanova, Leonid S Adonin, Florina M Batalova, Vladimir N Parfenov, Dmitry S Bogolyubov, Olga I Podgornaya
Background: The oocyte chromosomes of the red flour beetle, Tribolium castaneum, are gathered into a knot, forming a karyosphere at the diplotene stage of meiotic prophase. Chromatin rearrangement, which is a characteristic feature of oocyte maturation, is well documented. The T. castaneum karyosphere is surrounded by a complex extrachromosomal structure termed the karyosphere capsule. The capsule contains the vast majority of oocyte RNA. We have previously shown using a BrUTP assay that oocyte chromosomes in T...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/29149037/development-of-novel-polymorphic-est-ssr-markers-in-bailinggu-pleurotus-tuoliensis-for-crossbreeding
#4
Yueting Dai, Wenying Su, Chentao Yang, Bing Song, Yu Li, Yongping Fu
Identification of monokaryons and their mating types and discrimination of hybrid offspring are key steps for the crossbreeding of Pleurotus tuoliensis (Bailinggu). However, conventional crossbreeding methods are troublesome and time consuming. Using RNA-seq technology, we developed new expressed sequence tag-simple sequence repeat (EST-SSR) markers for Bailinggu to easily and rapidly identify monokaryons and their mating types, genetic diversity and hybrid offspring. We identified 1110 potential EST-based SSR loci from a newly-sequenced Bailinggu transcriptome and then randomly selected 100 EST-SSRs for further validation...
November 17, 2017: Genes
https://www.readbyqxmd.com/read/29146194/association-analyses-of-genetic-variants-in-long-non-coding-rna-malat1-with-breast-cancer-susceptibility-and-mrna-expression-of-malat1-in-chinese-han-population
#5
Rui Peng, Chenglin Luo, Qiaoyun Guo, Jingjing Cao, Qian Yang, Kaiyan Dong, Shuaibing Wang, Kaijuan Wang, Chunhua Song
The long non-coding RNA (lncRNA) Metastasis-associated lung adenocarcinoma transcript 1(MALAT1) has been implicated in breast cancer (BC). Polymorphisms in MALAT1 may play a vital role in the progress of breast cancer by its regulation function. However, potential genetic variants in MALAT1 affecting the development of BC is rarely explored. In our current molecular epidemiology study, all three tagging SNPs (rs3200401, rs619586 and rs7927113) in lncRNA MALAT1 were selected for genotyping in 487BCE patients and 489 cancer-free controls in Chinese Han population, and futher experiment of quantitative real-time (qRT) PCR was conducted to examine the relative expression of MALAT1...
November 13, 2017: Gene
https://www.readbyqxmd.com/read/29144390/rna-sequencing-and-coexpression-analysis-reveal-key-genes-involved-in-%C3%AE-linolenic-acid-biosynthesis-in-perilla-frutescens-seed
#6
Tianyuan Zhang, Chi Song, Li Song, Zhiwei Shang, Sen Yang, Dong Zhang, Wei Sun, Qi Shen, Degang Zhao
Perillafrutescen is used as traditional food and medicine in East Asia. Its seeds contain high levels of α-linolenic acid (ALA), which is important for health, but is scarce in our daily meals. Previous reports on RNA-seq of perilla seed had identified fatty acid (FA) and triacylglycerol (TAG) synthesis genes, but the underlying mechanism of ALA biosynthesis and its regulation still need to be further explored. So we conducted Illumina RNA-sequencing in seven temporal developmental stages of perilla seeds...
November 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29136179/fluorescently-tagged-human-eif3-for-single-molecule-spectroscopy
#7
Alex G Johnson, Alexey N Petrov, Gabriele Fuchs, Karim Majzoub, Rosslyn Grosely, Junhong Choi, Joseph D Puglisi
Human translation initiation relies on the combined activities of numerous ribosome-associated eukaryotic initiation factors (eIFs). The largest factor, eIF3, is an ∼800 kDa multiprotein complex that orchestrates a network of interactions with the small 40S ribosomal subunit, other eIFs, and mRNA, while participating in nearly every step of initiation. How these interactions take place during the time course of translation initiation remains unclear. Here, we describe a method for the expression and affinity purification of a fluorescently-tagged eIF3 from human cells...
November 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29131585/antibody-templated-assembly-of-an-rna-mimic-of-green-fluorescent-protein
#8
Alessandro Bertucci, Alessandro Porchetta, Francesco Ricci
One of the most intriguing ways through which Nature achieves regulation of biological pathways encompasses the coordination of non-covalent interactions that bring biomolecules to be co-localized in a designated restricted space. This nano-confinement leads to a drastic increase in the effective local concentration of the species involved, which ultimately triggers reactions that would otherwise not occur at the low concentrations found in cells. Inspired by this mechanism, we have explored the possibility of using antibodies as bivalent biomolecular substrates for the templated assembly of a functional RNA structure...
November 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29131164/an-improved-ms2-system-for-accurate-reporting-of-the-mrna-life-cycle
#9
Evelina Tutucci, Maria Vera, Jeetayu Biswas, Jennifer Garcia, Roy Parker, Robert H Singer
The MS2-MCP system enables researchers to image multiple steps of the mRNA life cycle with high temporal and spatial resolution. However, for short-lived mRNAs, the tight binding of the MS2 coat protein (MCP) to the MS2 binding sites (MBS) protects the RNA from being efficiently degraded, and this confounds the study of mRNA regulation. Here, we describe a reporter system (MBSV6) with reduced affinity for the MCP, which allows mRNA degradation while preserving single-molecule detection determined by single-molecule FISH (smFISH) or live imaging...
November 13, 2017: Nature Methods
https://www.readbyqxmd.com/read/29130966/itraq-based-proteomic-analysis-of-neonatal-kidney-from-offspring-of-protein-restricted-rats-reveals-abnormalities-in-intraflagellar-transport-proteins
#10
Xiaomei Liu, Jun Wang, Linlin Gao, Hao Liu, Caixia Liu
BACKGROUND: It is well recognized that adverse events in utero can impair fetal development and lead to the development of kidney injury and hypertension in adulthood. We previously reported a lower kidney index, glomeruli number, and decreased glomerular filtration rate in intrauterine growth restriction (IUGR) offspring induced by maternal protein malnutrition. To explore the molecular mechanisms linking impaired fetal growth to renal diseases, we investigated differentially expressed proteins (DEPs) in the IUGR neonatal kidneys by isobaric tags for relative and absolute quantitation (iTRAQ) analysis...
November 6, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29130216/rna-tagging-preparation-of-high-throughput-sequencing-libraries
#11
Christopher P Lapointe, Marvin Wickens
Protein-RNA networks, in which a single protein binds and controls multiple mRNAs, are central in biological control. As a result, methods to identify protein-RNA interactions that occur in vivo are valuable. The "RNA Tagging" approach enables the investigator to unambiguously identify global protein-RNA interactions in vivo and is independent of protein purification, cross-linking, and radioactive labeling steps. Here, we provide a protocol to prepare high-throughput sequencing libraries for RNA Tagging experiments...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29130205/visualizing-rna-in-live-bacterial-cells-using-fluorophore-and-quencher-binding-aptamers
#12
Murat Sunbul, Ankita Arora, Andres Jäschke
To elucidate the roles, dynamics, and regulation of RNAs, it is vital to be able to visualize the RNA of interest (ROI) in living cells noninvasively. Here, we describe a novel live-cell RNA imaging method using fluorophore- and quencher-binding aptamers, which can be genetically fused to the ROI. In this method, new membrane permeable and nonfluorescent fluorophore-quencher conjugates were utilized, and we showed that their fluorescence increases dramatically upon binding to fluorophore- or quencher-binding aptamers...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29130197/detection-of-mrna-and-associated-molecules-by-ish-iem-on-frozen-sections
#13
Catherine Rabouille
The use of tagged RNA probes to directly hybridize frozen sections of chemically fixed tissues, followed by the tag detection with specific antibodies and gold conjugates form the core of the in situ hybridization (ISH)-immunoelectron microscopy (IEM) method that we have developed and successfully used to detect endogenous gurken and bicoid mRNAs in Drosophila oocytes.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29126834/low-expression-of-nkd2-is-associated-with-enhanced-cell-proliferation-and-poor-prognosis-in-human-hepatocellular-carcinoma
#14
Dongzhi Wang, Shusen Zhang, Yuyan Chen, Baoying Hu, Cuihua Lu
NKD2 is a member of the Naked cuticle (Nkd) protein family and functions as a negative regulator of the Wnt signaling pathway. We investigated the prognostic value of NKD2 expression in hepatocellular carcinoma (HCC). Western blot and immunohistochemical analyses revealed that NKD2 was significantly downregulated in HCC specimens compared with adjacent non-tumorous tissues. Next, we found that NKD2 expression correlated significantly with several clinicopathologic features, such as tumor grade, tumor size, and Ki-67 expression...
November 7, 2017: Human Pathology
https://www.readbyqxmd.com/read/29126204/proteomic-analysis-of-germinal-vesicles-in-the-domestic-cat-model-reveals-candidate-nuclear-proteins-involved-in-oocyte-competence-acquisition
#15
P-C Lee, D E Wildt, P Comizzoli
STUDY QUESTION: Do nuclear proteins in the germinal vesicle (GV) contribute to oocyte competence acquisition during folliculogenesis? SUMMARY ANSWER: Proteomic analysis of GVs identified candidate proteins for oocyte competence acquisition, including a key RNA processing protein - heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNPA2B1). WHAT IS KNOWN ALREADY: The domestic cat GV, which is physiologically similar to the human GV, gains the intrinsic ability to resume meiosis and support early embryo development during the pre-antral-to-antral follicle transition...
November 8, 2017: Molecular Human Reproduction
https://www.readbyqxmd.com/read/29093094/characterization-of-recombinant-flaviviridae-viruses-possessing-a-small-reporter-tag
#16
Tomokazu Tamura, Takasuke Fukuhara, Takuro Uchida, Chikako Ono, Hiroyuki Mori, Asuka Sato, Yuzy Fauzyah, Toru Okamoto, Takeshi Kurosu, Yin Xiang Setoh, Michio Imamura, Norbert Tautz, Yoshihiro Sakoda, Alexander A Khromykh, Kazuaki Chayama, Yoshiharu Matsuura
The family Flaviviridae consists of four genera, Flavivirus, Pestivirus, Pegivirus, and Hepacivirus, and comprises important pathogens of human and animals. Although the construction of recombinant viruses carrying reporter genes including fluorescent and bioluminescent proteins has been reported, the stable insertion of foreign genes into viral genomes retaining infectivity remains difficult. Here, we applied the 11-amino-acid subunit derived from NanoLuc luciferase to the engineering of the Flaviviridae viruses, and then examined the biological characteristics of the viruses...
November 1, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29089383/herg1a-and-herg1b-potassium-channel-subunits-directly-interact-and-preferentially-form-heteromeric-channels
#17
Beth A McNally, Zeus Pendon, Matthew C Trudeau
Voltage-activated human ether-a-go-go related gene (hERG) potassium channels are critical for the repolarization of cardiac action potentials and tune-spike frequency adaptation in neurons. Two isoforms of mammalian ERG1 channel subunits, ERG1a and ERG1b, are the principal subunits that conduct the IKr current in the heart and are also broadly expressed in the nervous system. However, there is little direct evidence that ERG1a and ERG1b form heteromeric channels. Here, using electrophysiology, biochemistry, and fluorescence approaches, we systematically tested for direct interactions between hERG1a and hERG1b subunits...
October 31, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29081948/fluorescent-turn-on-probes-for-wash-free-mrna-imaging-via-covalent-site-specific-enzymatic-labeling
#18
Cun Yu Zhou, Seth C Alexander, Neal K Devaraj
Investigating the many roles RNA plays in cellular regulation and function has increased demand for tools to explore RNA tracking and localization within cells. Our recently reported RNA-TAG (transglycosylation at guanine) approach uses an RNA-modifying enzyme, tRNA-guanine transglycosylase (TGT), to accomplish covalent labeling of an RNA of interest with fluorescent tracking agents in a highly selective and efficient manner. Unfortunately, labeling by this method currently suffers from a high nonspecific fluorescent background and is currently unsuitable for imaging RNA within complex cellular environments...
October 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29078784/dynamic-changes-in-eif4f-mrna-interactions-revealed-by-global-analyses-of-environmental-stress-responses
#19
Joseph L Costello, Christopher J Kershaw, Lydia M Castelli, David Talavera, William Rowe, Paul F G Sims, Mark P Ashe, Christopher M Grant, Simon J Hubbard, Graham D Pavitt
BACKGROUND: Translation factors eIF4E and eIF4G form eIF4F, which interacts with the messenger RNA (mRNA) 5' cap to promote ribosome recruitment and translation initiation. Variations in the association of eIF4F with individual mRNAs likely contribute to differences in translation initiation frequencies between mRNAs. As translation initiation is globally reprogrammed by environmental stresses, we were interested in determining whether eIF4F interactions with individual mRNAs are reprogrammed and how this may contribute to global environmental stress responses...
October 27, 2017: Genome Biology
https://www.readbyqxmd.com/read/29078406/site-directed-rna-repair-of-endogenous-mecp2-rna-in-neurons
#20
John R Sinnamon, Susan Y Kim, Glen M Corson, Zhen Song, Hiroyuki Nakai, John P Adelman, Gail Mandel
Rett syndrome (RTT) is a debilitating neurological disorder caused by mutations in the gene encoding the transcription factor Methyl CpG Binding Protein 2 (MECP2). A distinct disorder results from MECP2 gene duplication, suggesting that therapeutic approaches must restore close to normal levels of MECP2. Here, we apply the approach of site-directed RNA editing to repair, at the mRNA level, a disease-causing guanosine to adenosine (G > A) mutation in the mouse MeCP2 DNA binding domain. To mediate repair, we exploit the catalytic domain of Adenosine Deaminase Acting on RNA (ADAR2) that deaminates A to inosine (I) residues that are subsequently translated as G...
October 31, 2017: Proceedings of the National Academy of Sciences of the United States of America
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