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https://www.readbyqxmd.com/read/29330168/mrb7260-is-essential-for-productive-protein-rna-interactions-within-the-rna-editing-substrate-binding-complex-during-trypanosome-rna-editing
#1
Natalie M McAdams, Rachel M Simpson, Runpu Chen, Yijun Sun, Laurie Read
The trypanosome RNA Editing Substrate Binding Complex (RESC) acts as the platform for mitochondrial uridine insertion/deletion RNA editing and facilitates the protein-protein and protein-RNA interactions required for the editing process. RESC is broadly comprised of two subcomplexes: GRBC (Guide RNA Binding Complex) and REMC (RNA Editing Mediator Complex). Here, we characterize the function and position in RESC organization of a previously unstudied RESC protein, MRB7260. We show that MRB7260 forms numerous RESC-related complexes, including a novel, small complex with the guide RNA binding protein, GAP1, which is a canonical GRBC component, and REMC components MRB8170 and TbRGG2...
January 12, 2018: RNA
https://www.readbyqxmd.com/read/29329439/conserved-proteins-of-the-rna-interference-system-in-the-arbuscular-mycorrhizal-fungus-rhizoglomus-irregulare-provide-new-insight-into-the-evolutionary-history-of-glomeromycota
#2
Soon-Jae Lee, Mengxuan Kong, Paul Harrison, Mohamed Hijri
Horizontal gene transfer (HGT) is an important mechanism in the evolution of many living organisms particularly in Prokaryotes where genes are frequently dispersed between taxa. Although, HGT has been reported in Eukaryotes, its accumulative effect and its frequency has been questioned. Arbuscular mycorrhizal fungi (AMF) are an early diverged fungal lineage belonging to phylum Glomeromycota, whose phylogenetic position is still under debate. The history of AMF and land plant symbiosis dates back to at least 460 million years ago...
January 10, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29328372/differential-microrna-expression-profiles-and-bioinformatics-analysis-between-young-and-aging-spontaneously-hypertensive-rats
#3
Jingfeng Wang, Jingjing Zhang, Xuefeng Ding, Yanyan Wang, Zhiming Li, Weipeng Zhao, Jianguo Jia, Jingmin Zhou, Junbo Ge
MicroRNAs (miRNAs/miRs) serve a role as important regulators in cardiac hypertrophy. The present study aimed to reveal the differential expression profile of miRNAs between young and aging spontaneously hypertensive rats (SHRs) and studied the functional annotation of predicted targets. Briefly, 3‑month‑old and 12‑month‑old SHRs (n=3/group) were subjected to echocardiography, histopathological analysis and dihydroethidium staining. Subsequently, small RNA sequencing and data processing was conducted to identify the differentially expressed miRNAs between these two groups...
January 9, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29327716/genomic-heterogeneity-of-alk-fusion-breakpoints-in-non-small-cell-lung-cancer
#4
Jason N Rosenbaum, Ryan Bloom, Jason T Forys, Jeff Hiken, Jon R Armstrong, Julie Branson, Samantha McNulty, Priya D Velu, Kymberlie Pepin, Haley Abel, Catherine E Cottrell, John D Pfeifer, Shashikant Kulkarni, Ramaswamy Govindan, Eric Q Konnick, Christina M Lockwood, Eric J Duncavage
In lung adenocarcinoma, canonical EML4-ALK inversion results in a fusion protein with a constitutively active ALK kinase domain. Evidence of ALK rearrangement occurs in a minority (2-7%) of lung adenocarcinoma, and only ~60% of these patients will respond to targeted ALK inhibition by drugs such as crizotinib and ceritinib. Clinically, targeted anti-ALK therapy is often initiated based on evidence of an ALK genomic rearrangement detected by fluorescence in situ hybridization (FISH) of interphase cells in formalin-fixed, paraffin-embedded tissue sections...
January 12, 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/29327641/generation-of-an-arrayed-crispr-cas9-library-targeting-epigenetic-regulators-from-high-content-screens-to-in-vivo-assays
#5
Tristan Henser-Brownhill, Josep Monserrat, Paola Scaffidi
The CRISPR-Cas9 system has revolutionized genome engineering, allowing precise modification of DNA in various organisms. The most popular method for conducting CRISPR-based functional screens involves the use of pooled lentiviral libraries in selection screens coupled with next-generation sequencing. Screens employing genome-scale pooled small guide RNA (sgRNA) libraries are demanding, particularly when complex assays are used. Furthermore, pooled libraries are not suitable for microscopy-based high-content screens or for systematic interrogation of protein function...
January 12, 2018: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29325388/-the-research-advances-of-microrna-184-and-related-ocular-diseases
#6
R R Zong, Y P Zhou, Z G Liu
microRNA-184 (miR-184) is a small, non-coding, endogenic RNA molecule of 22 nucleotides in length. It is a highly conserved sequence throughout many different species. Multiple studies have demonstrated that miR-184 is an important factor in regulating gene expression at the post-transcriptional level. miR-184 plays vital roles in many biological processes, including development and differentiation in many tissues and organs. Meanwhile, the research on the physiological and pathological role of miR-184 in eyes draws more and more attention lately...
December 11, 2017: [Zhonghua Yan Ke za Zhi] Chinese Journal of Ophthalmology
https://www.readbyqxmd.com/read/29322778/using-genome-sequence-to-enable-the-design-of-medicines-and-chemical-probes
#7
Alicia J Angelbello, Jonathan L Chen, Jessica L Childs-Disney, Peiyuan Zhang, Zi-Fu Wang, Matthew D Disney
Rapid progress in genome sequencing technology has put us firmly into a postgenomic era. A key challenge in biomedical research is harnessing genome sequence to fulfill the promise of personalized medicine. This Review describes how genome sequencing has enabled the identification of disease-causing biomolecules and how these data have been converted into chemical probes of function, preclinical lead modalities, and ultimately U.S. Food and Drug Administration (FDA)-approved drugs. In particular, we focus on the use of oligonucleotide-based modalities to target disease-causing RNAs; small molecules that target DNA, RNA, or protein; the rational repurposing of known therapeutic modalities; and the advantages of pharmacogenetics...
January 11, 2018: Chemical Reviews
https://www.readbyqxmd.com/read/29322298/a-new-microsporidium-fibrillaspora-daphniae-g-n-sp-n-infecting-daphnia-magna-crustacea-cladocera-in-siberia-and-its-taxonomic-placing-within-a-new-family-fibrillasporidae-and-new-superfamily-tubulinosematoidea-opisthosporidia-microsporidia
#8
Anastasia V Simakova, Yuri S Tokarev, Irma V Issi
Infection with a new microsporidium, Fibrillaspora daphniae g. n. sp. n., was found in a local Daphnia magna population in Tomsk region (Western Siberia, Russia) at the prevalence rate of 52%. Histological sections showed parasite cells entirely encompassing the host haemocoel. Methanol-fixed spores were elongate, oval, 4.8 ± 0.3 μm × 2.3 ± 0.2 μm in size. All developmental stages were in direct contact with the host cell cytoplasm, with single nuclei, and division by binary fission. The sporont surface was covered with an additional outer layer composed of fine tubules...
January 10, 2018: Parasitology Research
https://www.readbyqxmd.com/read/29321960/the-clinical-value-of-mir-193a-3p-in-non-small-cell-lung-cancer-and-its-potential-molecular-mechanism-explored-in-silico-using-rna-sequencing-and-microarray-data
#9
Xiang Gao, Rui-Xue Tang, Qiong-Ni Xie, Jia-Ying Lin, Hong-Lan Shi, Gang Chen, Zu-Yun Li
miR-193a-3p is a tumor-related miRNA playing an essential role in tumorigenesis and progression of non-small cell lung cancer (NSCLC). The objective of the present study was to investigate the relationship between miR-193a-3p expression and clinical value and to further explore the potential signaling of miR-193a-3p in the carcinogenesis of NSCLC. RNA-sequencing and microarray data were collected from the databases GEO, ArrayExpress and The Cancer Genome Atlas (TCGA). Furthermore, in silico assessments were performed to analyze the prospective pathways and networks of the target genes of miR-193a-3p...
January 2018: FEBS Open Bio
https://www.readbyqxmd.com/read/29321591/respiratory-syncytial-virus-infection-changes-cargo-composition-of-exosome-released-from-airway-epithelial-cells
#10
Harendra Singh Chahar, Tiziana Corsello, Andrzej S Kudlicki, Narayana Komaravelli, Antonella Casola
Exosomes are microvesicles known to carry biologically active molecules, including RNA, DNA and proteins. Viral infections can induce profound changes in exosome composition, and exosomes have been implicated in viral transmission and pathogenesis. No information is current available regarding exosome composition and function during infection with Respiratory Syncytial Virus (RSV), the most important cause of lower respiratory tract infections in children. In this study, we characterized exosomes released from RSV-infected lung carcinoma-derived A549 cells...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29320577/genome-wide-profiling-of-the-piwi-interacting-rna-mrna-regulatory-networks-in-epithelial-ovarian-cancers
#11
Garima Singh, Jyoti Roy, Pratiti Rout, Bibekanand Mallick
PIWI-interacting (piRNAs), ~23-36 nucleotide-long small non-coding RNAs (sncRNAs), earlier believed to be germline-specific, have now been identified in somatic cells, including cancer cells. These sncRNAs impact critical biological processes by fine-tuning gene expression at post-transcriptional and epigenetic levels. The expression of piRNAs in ovarian cancer, the most lethal gynecologic cancer is largely uncharted. In this study, we investigated the expression of PIWILs by qRT-PCR and western blotting and then identified piRNA transcriptomes in tissues of normal ovary and two most prevalent epithelial ovarian cancer subtypes, serous and endometrioid by small RNA sequencing...
2018: PloS One
https://www.readbyqxmd.com/read/29320459/the-landscape-of-small-non-coding-rnas-in-triple-negative-breast-cancer
#12
Yan Guo, Hui Yu, Jing Wang, Quanhu Sheng, Shilin Zhao, Ying-Yong Zhao, Brian D Lehmann
Triple-negative breast cancer (TNBC) is an operational term for breast cancers lacking targetable estrogen receptor expression and HER2 amplifications. TNBC is, therefore, inherently heterogeneous, and is associated with worse prognosis, greater rates of metastasis, and earlier onset. TNBC displays mutational and transcriptional diversity, and distinct mRNA transcriptional subtypes exhibiting unique biology. High-throughput sequencing has extended cancer research far beyond protein coding regions that include non-coding small RNAs, such as miRNA, isomiR, tRNA, snoRNAs, snRNA, yRNA, 7SL, and 7SK...
January 10, 2018: Genes
https://www.readbyqxmd.com/read/29317883/the-distribution-of-blastocystis-subtypes-among-school-aged-children-in-mugla-turkey
#13
Funda Sankur, Seniz Ayturan, Erdogan Malatyali, Hatice Ertabaklar, Sema Ertug
Background: Blastocystis is a common protozoon that inhabits human intestinal tract and has a worldwide distribution. This study aimed to determine subtype (ST) distribution of Blastocystis among school-aged children in a western city of Turkey between Mar and Jun 2014. Methods: This cross-sectional study was conducted among primary school children in Mugla between Mar and Jun 2014. Overall, 468 stool samples from children were examined by direct microscopy and inoculated into Jones medium...
October 2017: Iranian Journal of Parasitology
https://www.readbyqxmd.com/read/29317776/non-coding-rnas-in-hepatocellular-carcinoma-molecular-functions-and-pathological-implications
#14
REVIEW
Chun-Ming Wong, Felice Ho-Ching Tsang, Irene Oi-Lin Ng
Hepatocellular carcinoma (HCC) is a leading lethal malignancy worldwide. However, the molecular mechanisms underlying liver carcinogenesis remain poorly understood. Over the past two decades, overwhelming evidence has demonstrated the regulatory roles of different classes of non-coding RNAs (ncRNAs) in liver carcinogenesis related to a number of aetiologies, including HBV, HCV and NAFLD. Among the ncRNAs, microRNAs, which belong to a distinct class of small ncRNAs, have been proven to play a crucial role in the post-transcriptional regulation of gene expression...
January 10, 2018: Nature Reviews. Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/29317697/physiological-response-and-microrna-expression-profiles-in-head-kidney-of-genetically-improved-farmed-tilapia-gift-oreochromis-niloticus-exposed-to-acute-cold-stress
#15
Jun Qiang, Yan T Cui, Fan Y Tao, Wen J Bao, Jie He, Xia H Li, Pao Xu, Lan Y Sun
Cold stress has a serious impact on the overwintering survival and yield of genetically improved farmed tilapia (GIFT, Oreochromis niloticus). Understanding the physiological and molecular regulation mechanisms of low-temperature adaptation is necessary to help breed new tolerant strains. The semi-lethal low temperature of juvenile GIFT at 96 h was determined as 9.4 °C. We constructed and sequenced two small RNA libraries from head kidney tissues, one for the control (CO) group and one for the 9.4 °C-stressed (LTS) group, and identified 1736 and 1481 known microRNAs (miRNAs), and 164 and 152 novel miRNAs in the CO and LTS libraries, respectively...
January 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29316045/redescription-of-tintinnopsis-everta-kofoid-campbell-1929-alveolata-ciliophora-tintinnina-based-on-taxonomic-and-genetic-analyses-discovery-of-a-new-complex-ciliary-pattern
#16
Michael S Gruber, Michaela Strüder-Kypke, Sabine Agatha
The about 1,000 species of tintinnid ciliates are identified and classified almost exclusively based on their lorica features, although the shortcomings of this structure are well-known, e.g., causing uncertain species limitations and non-monophyletic taxa. Hence, the present redescription of Tintinnopsis everta Kofoid and Campbell, 1929 considers not only the lorica characteristics, but focuses on cell and genetic features. The species is redescribed from the North Atlantic and adjacent sea areas, namely the east coast of the USA, using live observation, protargol-stained material, scanning electron microscopy, and genetic analyses...
January 5, 2018: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/29313485/biological-and-molecular-characterization-of-trypanosoma-cruzi-strains-from-four-states-of-brazil
#17
Aline Rimoldi Ribeiro, Luciana Lima, Larissa Aguiar de Almeida, Joana Monteiro, Cláudia Jassica Gonçalves Moreno, Juliana Damieli Nascimento, Renato Freitas de Araújo, Fernanda Mello, Luciamáre Perinetti Alves Martins, Márcia Aparecida Silva Graminha, Marta Maria Geraldes Teixeira, Marcelo Sousa Silva, Mário Steindel, João Aristeu da Rosa
Chagas disease affects between six and seven million people. Its etiological agent, Trypanosoma cruzi, is classified into six discrete typing units (DTUs). The biological study of 11 T. cruzi strains presented here included four parameters: growth kinetics, parasitemia curves, rate of macrophage infection, and serology to evaluate IgM, total IgG, IgG1, IgG2a, and IgG3. Sequencing of small subunit of ribosomal RNA (SSU rRNA)was performed and the T. cruzi strains were classified into three DTUs. When their growth in liver infusion tryptose medium was represented in curves, differences among the strains could be noted...
January 8, 2018: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/29310260/luminescent-quantum-dots-for-mirna-detection
#18
REVIEW
O A Goryacheva, P K Mishra, I Yu Goryacheva
MicroRNAs (miRNAs) are a class of small non-coding RNAs that are involved in nearly all developmental processes and human pathologies. MiRNAs are considered to be promising biomarkers, since their dysregulation correlates with the development and progress of many diseases. Short length, sequence homology among family members, susceptibility to degradation, and low abundance in total RNA samples make miRNA analysis a challenging task. Photoluminescent semiconductor nanoparticles (quantum dots, QDs) possess unique properties such as bright photoluminescence, photostability and narrow emission peaks, wide possibilities for surface modification and bioconjugation, which serve as the basis for the development of different analytical methods for variety of analytes...
March 1, 2018: Talanta
https://www.readbyqxmd.com/read/29305975/identification-and-expression-analysis-of-micrornas-in-medaka-gonads
#19
Weiwei Qiu, Yefei Zhu, Yun Wu, Cancan Yuan, Kerang Chen, Mingyou Li
Gonad development is a highly regulated, coordinated biological process and increasing evidences have indicated that microRNA (miRNA) may be involved in this dynamic program. Medaka (Oryzias latipes) is a good model for reproductive research as it has distinct sex determining genes, however, research in gonadal miRNAs is lacked. In this study, two small RNA libraries from the ovaries and testes were constructed and sequenced. A total of 285 conserved and 388 novel miRNAs were obtained, among which, 142 mature miRNAs were significantly (> two-fold change) up or down regulated in the testis compared to the ovary...
January 3, 2018: Gene
https://www.readbyqxmd.com/read/29305331/differential-expression-of-micrornas-in-hemocytes-from-white-shrimp-litopenaeus-vannamei-under-copper-stress
#20
Hui Guo, Zhi-Cheng Lu, Xiao-Wen Zhu, Chun-Hua Zhu, Cheng-Gui Wang, Yu-Chun Shen, Wei Wang
MicroRNAs (miRNAs) are small noncoding RNAs that regulate diverse cellular processes, including organismal stress response, through posttranscriptional repression of gene transcripts. They are known to have antiviral functions in aquatic crustacean species, but little is known about the role of miRNAs against environmental stress caused by Cu, a common chemical contaminant in aquatic environment. We performed small RNA sequencing to characterize the differentially expressed microRNAs in Cu exposed shrimp. A total of 4524 known miRNAs and 73 novel miRNAs were significantly (P < ...
January 2, 2018: Fish & Shellfish Immunology
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