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1. The Cap-Snatching Mechanism of Bunyaviruses

Author:
Olschewski, Silke; Cusack, Stephen; Rosenthal, Maria
Source:
Trends in microbiology 2020 v.28 no.4 pp. 293-303
ISSN:
0966-842X
Subject:
messenger RNA,   etc   ; Orthobunyavirus; Orthomyxoviridae;     Show all 3 Subjects
Abstract:
... In common with all segmented negative-sense RNA viruses, bunyavirus transcripts contain heterologous sequences at their 5′ termini originating from capped host cell RNAs. These heterologous sequences are acquired by a so-called cap-snatching mechanism. Whereas for nuclear replicating influenza virus the source of capped primers as well as the cap-binding and endonuclease activities of the viral po ...
DOI:
10.1016/j.tim.2019.12.006

2. Antisense probing of dynamic RNA structures

Author:
Lukasiewicz, Alexandra J.; Contreras, Lydia M.
Source:
Methods 2020
ISSN:
1046-2023
Subject:
messenger RNA,   etc   ; Tetrahymena; introns; regulatory sequences;     Show all 4 Subjects
Abstract:
... RNA regulation is influenced by the dynamic changes in conformational accessibility on the transcript. Here we discuss the initial validation of a cell-free antisense probing method for structured RNAs, using the Tetrahymena group I intron as a control target. We observe changes in signal that qualitatively match prior traditional DMS footprinting experiments. Importantly, we have shown that appli ...
DOI:
10.1016/j.ymeth.2020.01.015

3. Multiplexed primer extension sequencing: A targeted RNA-seq method that enables high-precision quantitation of mRNA splicing isoforms and rare pre-mRNA splicing intermediates

Author:
Gildea, Michael A.; Dwyer, Zachary W.; Pleiss, Jeffrey A.
Source:
Methods 2020 v.176 pp. 34-45
ISSN:
1046-2023
Subject:
messenger RNA,   etc   ; alternative splicing; introns; loci; reverse transcription; sequence analysis;     Show all 6 Subjects
Abstract:
... The study of pre-mRNA splicing has been greatly aided by the advent of RNA sequencing (RNA-seq), which enables the genome-wide detection of discrete splice isoforms. Quantification of these splice isoforms requires analysis of splicing informative sequencing reads, those that unambiguously map to a single splice isoform, including exon-intron spanning alignments corresponding to retained introns, ...
DOI:
10.1016/j.ymeth.2019.05.013
PubMed:
31121301
PubMed Central:
PMC6868320

4. Recent advances in ribosome profiling for deciphering translational regulation

Author:
Wang, Yirong; Zhang, Hong; Lu, Jian
Source:
Methods 2020 v.176 pp. 46-54
ISSN:
1046-2023
Subject:
messenger RNA,   etc   ; computational methodology; gene expression; genomics; ribosomes; translation (genetics);     Show all 6 Subjects
Abstract:
... Messenger RNA (mRNA) translation is a central step of gene expression. Translational regulation plays essential roles in various biological processes. Ribosome profiling is a powerful technique to study genome-wide translational regulation at a single-codon resolution. Based on conventional ribosome profiling procedures, many new experimental methods have recently been developed to investigate the ...
DOI:
10.1016/j.ymeth.2019.05.011

5. Adjuvant incorporated lipid nanoparticles for enhanced mRNA-mediated cancer immunotherapy

Author:
Lee, Kyuri; Kim, Soo Young; Seo, Yunmi; Kim, Myung Hee; Chang, Jun; Lee, Hyukjin
Source:
Biomaterials science 2020 v.8 no.4 pp. 1101-1105
ISSN:
2047-4849
Subject:
messenger RNA,   etc   ; adjuvants; antigens; immunotherapy; lipids; nanoparticles; neoplasms; vaccines;     Show all 8 Subjects
Abstract:
... For mRNA mediated cancer immunotherapy, Pam3 was incorporated as an adjuvant within lipid nanoparticles (LNPs) with OVA mRNA. The developed Pam3 incorporated LNPs showed successful expression of tumor antigens with enhanced immune stimulation. We demonstrated that the synergies of Pam3 LNPs could greatly improve the efficacy of tumor prevention by mRNA vaccines. ...
DOI:
10.1039/c9bm01564g

6. Challenges in detecting and quantifying intron retention from next generation sequencing data

Author:
Broseus, Lucile; Ritchie, William
Source:
Computational and Structural Biotechnology Journal 2020 v.18 pp. 501-508
ISSN:
2001-0370
Subject:
messenger RNA,   etc   ; high-throughput nucleotide sequencing; introns; transcription (genetics);     Show all 4 Subjects
Abstract:
... Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. An increasing body of literature has demonstrated a major role for IR in numerous biological functions and in disease. Here we give an overview of the different computational approaches for detecting IR events from sequencing data. We show that these are based on different biological and computa ...
DOI:
10.1016/j.csbj.2020.02.010
PubMed:
32206209
PubMed Central:
PMC7078297

7. Method for RNA extraction and transcriptomic analysis of single fungal spores

Author:
Geoghegan, Ivey A.; Emes, Richard D.; Archer, David B.; Avery, Simon V.
Source:
MethodsX 2020 v.7 pp. 100760
ISSN:
2215-0161
Subject:
messenger RNA,   etc   ; Aspergillus niger; DNA; conidia; fungi; mammals; phenotype; transcriptomics;     Show all 8 Subjects
Abstract:
... Transcriptomic analysis of single cells has been increasingly in demand in recent years, thanks to technological and methodological advances as well as growing recognition of the importance of individuals in biological systems. However, the majority of these studies have been performed in mammalian cells, due to their ease of lysis and high RNA content. No single cell transcriptomic analysis has y ...
DOI:
10.1016/j.mex.2019.12.002
PubMed:
31908984
PubMed Central:
PMC6938798

8. Comprehensive comparison and applications of different sections in investigating the microstructure and histochemistry of cereal kernels

Author:
Xu, Ahui; Wei, Cunxu
Source:
Plant methods 2020 v.16 no.1 pp. 8
ISSN:
1746-4811
Subject:
messenger RNA,   etc   ; immunohistochemistry; in situ hybridization; iodine; microstructure; protein bodies; resins; seeds; starch granules;     Show all 9 Subjects
Abstract:
... This review summarizes the main applications of different sections and some improved sectioning methods in investigating the microstructure and histochemistry of cereal kernels. Thick sections of developing kernels prepared by free-hand and sliding microtome-aided sectioning method can be employed to elucidate tissue anatomy and histochemistry. The thin sections of mature kernels prepared by ultra ...
DOI:
10.1186/s13007-020-0558-x
PubMed:
32021644
PubMed Central:
PMC6995210

9. DDX11-AS1 contributes to osteosarcoma progression via stabilizing DDX11

Author:
Zhang, Hui; Lin, Jiangtao; Chen, Junjun; Gu, Wenqi; Mao, Yanjie; Wang, Haixia; Zhang, Yahui; Liu, Wanjun
Source:
Life sciences 2020 v.254 pp. 117392
ISSN:
0024-3205
Subject:
messenger RNA,   etc   ; carcinogenesis; cell proliferation; genes; loss-of-function mutation; metastasis; non-coding RNA; osteosarcoma;     Show all 8 Subjects
Abstract:
... Increasing evidence has uncovered that long noncoding RNAs (lncRNAs) play extremely important roles in numerous steps of gene regulation concerning the progression of tumors. Defined as a kind of lncRNA, DDX11-AS1 has been considered to be closely related to the tumorigenesis of malignancies. Nevertheless, the underlying regulatory role of it in osteosarcoma remains to be analyzed and elucidated. ...
DOI:
10.1016/j.lfs.2020.117392

10. Effects of high intensity interval training (up & downward running) with BCAA/nano chitosan on Foxo3 and SMAD soleus muscles of aging rat

Author:
Sadri, Salimeh; Sharifi, Gholamreza; Jalali Dehkordi, Khosro
Source:
Life sciences 2020 v.252 pp. 117641
ISSN:
0024-3205
Subject:
messenger RNA,   etc   ; atrophy; chitosan; diet; energy; exercise; gene expression; males; muscles; nanoparticles; rats; transcription factors;     Show all 12 Subjects
Abstract:
... The aim of this study was investigate the effects of 8 weeks of high intensity interval training (HIIT, up & downward running) with BCAA/nano chitosan on Foxo3 and SMAD soleus muscles of aging rats.In this experimental study thirty male rats were randomly divided into six groups of control, BCAA with Nano chitosan (Supplement, (Sup)), upslope running, downslope running, upslope running+Sup, and do ...
DOI:
10.1016/j.lfs.2020.117641

11. The RALF1–FERONIA Complex Phosphorylates eIF4E1 to Promote Protein Synthesis and Polar Root Hair Growth

Author:
Zhu, Sirui; Estévez, José Manuel; Liao, Hongdong; Zhu, Yonghua; Yang, Tao; Li, Chiyu; Wang, Yichuan; Li, Lan; Liu, Xuanming; Pacheco, Javier Martinez; Guo, Hongwei; Yu, Feng
Source:
Molecular plant 2020 v.13 no.5 pp. 698-716
ISSN:
1674-2052
Subject:
messenger RNA,   etc   ; Arabidopsis thaliana; cell polarity; enzymes; genes; peptides; phosphorylation; protein synthesis; root hairs; translation (genetics);     Show all 10 Subjects
Abstract:
... The molecular links between extracellular signals and the regulation of localized protein synthesis in plant cells are poorly understood. Here, we show that in Arabidopsis thaliana, the extracellular peptide RALF1 and its receptor, the FERONIA receptor kinase, promote root hair (RH) tip growth by modulating protein synthesis. We found that RALF1 promotes FERONIA-mediated phosphorylation of eIF4E1, ...
DOI:
10.1016/j.molp.2019.12.014

12. Purification and characterization of theobromine synthase in a Theobromine-Enriched wild tea plant (Camellia gymnogyna Chang) from Dayao Mountain, China

Author:
Teng, Jie; Yan, Changyu; Zeng, Wen; Zhang, Yuqian; Zeng, Zhen; Huang, Yahui
Source:
Food chemistry 2020 v.311 pp. 125875
ISSN:
0308-8146
Subject:
messenger RNA,   etc   ; Camellia; caffeine; chromatography; enzymes; germplasm; leaves; molecular weight; pH; tea; temperature; theobromine; China;     Show all 13 Subjects
Abstract:
... Camellia gymnogyna Chang (CgC), a wild tea plant, was discovered on Dayao Mountain, China. However, research regarding this tea plant is limited. Our study found that CgC contains theobromine, caffeine, and theacrine, among which theobromine content was the highest (14.37–39.72 mg/g). In addition, theobromine synthase (TS) was partially purified from CgC leaves, up to 35.87-fold, with consecutive ...
DOI:
10.1016/j.foodchem.2019.125875

13. A novel Xist RNA-mediated chromosome inactivation model using a mouse artificial chromosome

Author:
Inaoka, Daigo; Sunamura, Naohiro; Ohira, Takahito; Nakayama, Yuji; Kugoh, Hiroyuki
Source:
Biotechnology letters 2020 v.42 no.5 pp. 697-705
ISSN:
0141-5492
Subject:
messenger RNA,   etc   ; X chromosome; embryonic stem cells; epigenetics; genes; males; mice; models; proteins; screening;     Show all 10 Subjects
Abstract:
... OBJECTIVE: To develop a mouse artificial chromosome (MAC) carrying the mouse Xist gene (X-inactive specific transcript; Xist-MAC) as a systematic in vitro approach for investigating Xist RNA-mediated chromosome inactivation. RESULTS: Ectopic expression of the Xist gene in CHO cells led to the accumulation of Xist RNA in cis on the MAC. In addition, the introduction of Xist-MAC to embryonic stem ce ...
DOI:
10.1007/s10529-020-02826-z

14. Effect of cluster zone leaf removal on monoterpene profiles of Sauvignon Blanc grapes and wines

Author:
Yue, Xiaofeng; Ma, Xin; Tang, Yali; Wang, Ying; Wu, Bowen; Jiao, Xuliang; Zhang, Zhenwen; Ju, Yanlun
Source:
Food research international 2020 v.131 pp. 109028
ISSN:
0963-9969
Subject:
messenger RNA,   etc   ; biosynthesis; defoliation; genes; grapes; leaves; monoterpenoids; odors; pH; tartaric acid; wines;     Show all 11 Subjects
Abstract:
... Monoterpenes contribute to the varietal aromas of grapes and wines. We determined the effects of cluster zone leaf removal on the monoterpene profiles of Sauvignon Blanc grape berries and wines, and on the expression of key genes in the terpenoid pathway. Leaf removal at two intensities (half basic, 50%; full basic, 100%) was conducted at two weeks before veraison, veraison, and two weeks after ve ...
DOI:
10.1016/j.foodres.2020.109028

15. Small heat shock protein genes are developmentally regulated during stress and non-stress conditions in Blastocladiella emersonii

Author:
Georg, Raphaela Castro; Oshiquiri, Letícia Harumi; Barbosa-Filho, Jomal Rodrigues; Gomes, Suely Lopes
Source:
Fungal biology 2020 v.124 no.5 pp. 482-489
ISSN:
1878-6146
Subject:
messenger RNA,   etc   ; fungi; genes; germination; heat shock proteins; heat stress; molecular weight; protein content; sporulation; temperature;     Show all 10 Subjects
Abstract:
... Small heat shock proteins (sHsps) are molecular chaperones of low molecular weight involved in an early association with misfolded proteins. In response to heat shock, B. emersonii induces the synthesis of a number of proteins. As sHsps are still poorly studied in B. emersonii and in fungi overall, the aim of this work was to carry out a in-depth characterization of sHsps during B. emersonni life ...
DOI:
10.1016/j.funbio.2020.02.009

16. Extensive Inter-plant Protein Transfer between Cuscuta Parasites and Their Host Plants

Author:
Liu, Nian; Shen, Guojing; Xu, Yuxing; Liu, Hui; Zhang, Jingxiong; Li, Shalan; Li, Jing; Zhang, Cuiping; Qi, Jinfeng; Wang, Lei; Wu, Jianqiang
Source:
Molecular plant 2020 v.13 no.4 pp. 573-585
ISSN:
1674-2052
Subject:
messenger RNA,   etc   ; Arabidopsis; Cuscuta; host plants; parasites; protein transport; proteins; proteome; seeds; soybeans;     Show all 10 Subjects
Abstract:
... Cuscuta species (dodders) are holoparasites that totally rely on host plants to survive. Although various mobile proteins have been identified to travel within a plant, whether and to what extent protein transfer between Cuscuta and host plants remain unclear. We found that hundreds to more than 1500 proteins were transferred between Cuscuta and the host plants Arabidopsis and soybean, and hundred ...
DOI:
10.1016/j.molp.2019.12.002

17. Effect of Downregulating the Hippo Pathway Members YAP1 and LATS2 Transcripts on Early Development and Gene Expression Involved in Differentiation in Porcine Embryos

Author:
Emura, Natsuko; Saito, Yuriko; Miura, Ruri; Sawai, Ken
Source:
Cellular reprogramming 2020 v.22 no.2 pp. 62-70
ISSN:
2152-4998
Subject:
messenger RNA,   etc   ; RNA interference; blastocyst; early development; embryogenesis; gene expression; genes; neoplasms; oocytes; swine; transcription factors;     Show all 11 Subjects
Abstract:
... In mouse development, differentiation of the inner cell mass (ICM) and trophectoderm (TE) during the transition from the morula to blastocyst stage is regulated by the Hippo pathway; however, the functions of the Hippo pathway in porcine embryogenesis have not been investigated. In the present study, we examined the gene expression patterns of the Hippo pathway members yes-associated protein 1 (YA ...
DOI:
10.1089/cell.2019.0082

18. IMD/ADM21-47, a factor that improves embryo quality

Author:
García-Hernández, J.; Castro-Valenzuela, B.E.; Rodríguez-Borbón, A.; Grado-Ahuir, J.A.; Burrola-Barraza, M.E.
Source:
Theriogenology 2020 v.146 pp. 1-13
ISSN:
0093-691X
Subject:
messenger RNA,   etc   ; apoptosis; blastocyst; cattle; culture media; in vitro culture; in vitro fertilization; metaphase; oocytes; peptides;     Show all 10 Subjects
Abstract:
... Starting in vitro fertilization process with competent oocytes that may endure first cellular divisions is a critical step for obtaining an embryo. To obtain in vitro competent oocytes, culture conditions should emulate the in vivo microenvironment as close as possible. With the aim of improving the in vitro culture medium, the present study evaluated the IMD/ADM2₁₋₄₇ peptide as a factor that prom ...
DOI:
10.1016/j.theriogenology.2020.01.049

19. Next-generation transcriptome assembly and analysis: Impact of ploidy

Author:
Voshall, Adam; Moriyama, Etsuko N.
Source:
Methods 2020 v.176 pp. 14-24
ISSN:
1046-2023
Subject:
messenger RNA,   etc   ; allopolyploidy; bioinformatics; chromosomes; data collection; diploidy; gene expression regulation; genes; transcriptome;     Show all 9 Subjects
Abstract:
... Whole genome duplications (WGD) occur widely in plants, but the effects of these events impact all branches of life. WGD events have major evolutionary impacts, often leading to major structural changes within the chromosomes and massive changes in gene expression that facilitate rapid speciation and gene diversification. Even for species that currently have diploid genomes, the impact of ancestra ...
DOI:
10.1016/j.ymeth.2019.06.001

20. Methyl-indole inhibits pancreatic cancer cell viability by down-regulating ZFX expression

Author:
Qin, Xueliang; Cui, Xiaopeng
Source:
3 Biotech 2020 v.10 no.4 pp. 187
ISSN:
2190-572X
Subject:
messenger RNA,   etc   ; apoptosis; cell viability; neoplasm cells; pancreatic neoplasms; protein synthesis; therapeutics; zinc finger motif;     Show all 8 Subjects
Abstract:
... This study explored the effect of methyl-indole on pancreatic cancer cell viability and investigated the mechanism involved. The viability of pancreatic cells showed a significant suppression on treatment with methyl-indole in dose-based manner. Treatment with 5 µM methyl-indole suppressed Capan-1 cell viability to 23%. The viability of Aspc-1 cells was reduced to 20% and those of MIApaCa-2 cells ...
DOI:
10.1007/s13205-020-02179-4
PubMed:
32257743
PubMed Central:
PMC7109247