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https://www.readbyqxmd.com/read/29455023/an-innovative-paradigm-of-methods-in-micrornas-detection-highlighting-dnazymes-the-illuminators
#1
REVIEW
Mojdeh Mahdiannasser, Zahra Karami
miRNAs are short regulatory sequences that monitor gene expression at post-transcriptional level. miRNAs play outstanding roles in cellular processes and their altered expression or aberrant function has been reported in diseases such as cancer. Furthermore, some of them serve as biomarkers for prognosis, diagnosis, and prediction of drug effectiveness as well as probable utility in the field of personalized medicine. As a result, proper and sensitive detection of miRNAs is a crucial matter. Traditional approaches including Northern blotting, Microarray, and Quantitative reverse transcription polymerase chain reaction have been extensively employed by means of miRNA detection for decades...
February 8, 2018: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29453091/identification-of-mirnas-and-their-targets-in-maize-in-response-to-sugarcane-mosaic-virus-infection
#2
Zihao Xia, Zhenxing Zhao, Mingjun Li, Ling Chen, Zhiyuan Jiao, Yuanhua Wu, Tao Zhou, Weichang Yu, Zaifeng Fan
MicroRNAs (miRNAs) are endogenous non-coding small RNAs that play essential regulatory roles in plant development and environmental stress responses. Maize (Zea mays L.) is a global economically important food and forage crop. To date, a number of maize miRNAs have been identified as being involved in plant development and stress responses. However, the miRNA-mediated gene regulatory networks responsive to virus infections in maize remain largely unknown. In this study, the profiles of small RNAs in buffer- and Sugarcane mosaic virus (SCMV)-inoculated maize plants were obtained by high-throughput sequencing, respectively...
January 31, 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29441981/long-non-coding-rna-sox4-promotes-proliferation-and-migration-by-activating-wnt-%C3%AE-catenin-signaling-pathway-in-osteosarcoma
#3
Zhoubin Tian, Guang Yang, Peng Jiang, Laibo Zhang, Jian Wang, Shui Sun
Osteosarcoma is a bone tumor without effective treatment in the world. Recently, long non-coding RNAs (lncRNAs) are considered as essential regulators in cancer progression. LncSox4 plays crucial roles in liver tumor-initiating cells self-renewal and tumor initiation. However, the effect of lncSox4 in osteosarcoma remains largely unclear. Quantitative real-time PCR (qRT-PCR) and Northern blot were performed to detect lncSox4 expressions in osteosarcoma. The functions of lncSox4 in osteosarcoma were determined using cell viability and migration assays...
September 1, 2017: Die Pharmazie
https://www.readbyqxmd.com/read/29440670/characterization-of-conserved-and-novel-micrornas-in-lilium-lancifolium-thunb-by-high-throughput-sequencing
#4
Xiangfeng He, Awraris Getachew Shenkute, Wenhe Wang, Shufa Xu
MicroRNAs (miRNAs) are among the class of noncoding small RNA molecules and play a crucial role in post-transcriptional regulation in plants. Although Lilium is one of the most popular ornamental flowers worldwide, however, there is no report on miRNAs identification. In the present study, therefore, miRNAs and their targets were identified from flower, leaf, bulblet and bulb of Lilium lancifolium Thunb. by high-throughput sequencing and bioinformatics analysis. In this study, a total of 38 conserved miRNAs belonging to 17 miRNA families and 44 novel miRNAs were identified...
February 13, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29440318/monitoring-the-5-methoxycarbonylmethyl-2-thiouridine-mcm5s2u-modification-in-eukaryotic-trnas-via-the-gamma-toxin-endonuclease
#5
Jenna M Lentini, Jillian Ramos, Dragony Fu
The post-transcriptional modification of tRNA at the wobble position is a universal process occurring in all domains of life. In eukaryotes, the wobble uridine of particular tRNAs is transformed to the 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) modification which is critical for proper mRNA decoding and protein translation. However, current methods to detect mcm5s2U are technically challenging and/or require specialized instrumental expertise. Here, we show that gamma-toxin endonuclease from the yeast Kluyveromyces lactis can be used as a probe for assaying mcm5s2U status in the tRNA of diverse eukaryotic organisms ranging from protozoans to mammalian cells...
February 13, 2018: RNA
https://www.readbyqxmd.com/read/29434609/frg3-a-target-of-slmir482e-3p-provides-resistance-against-the-fungal-pathogen-fusarium-oxysporum-in-tomato
#6
Hui-Min Ji, Min Zhao, Ying Gao, Xin-Xin Cao, Hui-Ying Mao, Yi Zhou, Wen-Yu Fan, Katherine A Borkovich, Shou-Qiang Ouyang, Peng Liu
The vast majority of plant disease resistance (R) genes encode nucleotide binding site-leucine-rich repeat (NBS-LRR) proteins, which specifically determine the plant immune response and have been demonstrated to be targets of several microRNA (miRNA) families. The fungus Fusarium oxysporum f. sp. lycopersici (FOL) causes vascular wilt disease in tomato worldwide. Here, we explored a possible role for FGR3 in tomato defense against FOL. FRG3 is a predicted NBS-LRR like gene that is targeted by slmiR482e-3p, a member of slmiR482 miRNA family...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29433022/the-aldehyde-dehydrogenase-alda-contributes-to-the-hypochlorite-defense-and-is-redox-controlled-by-protein-s-bacillithiolation-in-staphylococcus-aureus
#7
Marcel Imber, Vu Van Loi, Sylvia Reznikov, Verena Nadin Fritsch, Agnieszka J Pietrzyk-Brzezinska, Janek Prehn, Chris Hamilton, Markus C Wahl, Agnieszka K Bronowska, Haike Antelmann
Staphylococcus aureus produces bacillithiol (BSH) as major low molecular weight (LMW) thiol which functions in thiol-protection and redox-regulation by protein S-bacillithiolation under hypochlorite stress. The aldehyde dehydrogenase AldA was identified as S-bacillithiolated at its active site Cys279 under NaOCl stress in S. aureus. Here, we have studied the expression, function, redox regulation and structural changes of AldA of S. aureus. Transcription of aldA was previously shown to be regulated by the alternative sigma factor SigmaB...
February 5, 2018: Redox Biology
https://www.readbyqxmd.com/read/29431851/stress-induced-trna-cleavage-and-tirna-generation-in-rat-neuronal-pc12-cells
#8
Elkordy Alaa, Eikan Mishima, Kuniyasu Niizuma, Yasutoshi Akiyama, Miki Fujimura, Teiji Tominaga, Takaaki Abe
Transfer RNA (tRNA) plays a role in stress response programs involved in various pathological conditions including neurological diseases. Under cell stress conditions, intracellular tRNA is cleaved by a specific ribonuclease, angiogenin, generating tRNA-derived fragments or tRNA-derived stress-induced RNA (tiRNA). Generated tiRNA contributes to the cell stress response and has potential cell protective effects. However, tiRNA generation under stress conditions in neuronal cells has not been fully elucidated...
February 12, 2018: Journal of Neurochemistry
https://www.readbyqxmd.com/read/29425878/the-klotho-related-protein-klph-lctl-has-preferred-expression-in-lens-and-is-essential-for-expression-of-clic5-and-normal-lens-suture-formation
#9
Jianguo Fan, Joshua Lerner, M Keith Wyatt, Phillip Cai, Katherine Peterson, Lijin Dong, Graeme Wistow
KLPH/lctl belongs to the Klotho family of proteins. Expressed sequence tag analyses unexpectedly revealed that KLPH is highly expressed in the eye lens while northern blots showed that expression is much higher in the eye than in other tissues. In situ hybridization in mouse localized mRNA to the lens, particularly in the equatorial epithelium. Immunofluorescence detected KLPH in lens epithelial cells with highest levels in the germinative/differentiation zone. The gene for KLPH in mouse was deleted by homologous recombination...
February 6, 2018: Experimental Eye Research
https://www.readbyqxmd.com/read/29421487/differentially-expressed-genes-in-response-to-cyadox-in-swine-liver-analyzed-by-ddrt-pcr
#10
Rui Yu, Yinfeng Zhang, Qirong Lu, Luqing Cui, Yulian Wang, Xu Wang, Guyue Cheng, Zhenli Liu, Menghong Dai, Zonghui Yuan
Cyadox is a good antimicrobial growth-promoter of quinoxalines. However, the molecular mechanism of action remains unclear. A growth performance study and mRNA differential display reverse transcription polymerase chain reaction (DDRT-PCR) in combination with Northern dot-blot and reverse Northern dot-blot analysis were conducted to determine the differentially expressed genes in liver tissues of piglets after treatment with cyadox. Transcription levels of the differentially expressed genes were quantificated by realtime RT-PCR in porcine primary hepotocytes...
January 25, 2018: Research in Veterinary Science
https://www.readbyqxmd.com/read/29416011/long-noncoding-rna-pandar-blocks-cdkn1a-gene-transcription-by-competitive-interaction-with-p53-protein-in-gastric-cancer
#11
Jun Liu, Qiwen Ben, Eryi Lu, Xiangyi He, Xiaoqun Yang, Jun Ma, Wen Zhang, Zhiming Wang, Tianshu Liu, Jianjun Zhang, Hongxia Wang
Emerging evidence indicates that lncRNAs play important roles in cancer tumourigenesis and could be used as potential diagnostic biomarkers or therapeutic targets. However, the clinical significance and molecular mechanism of lncRNAs in gastric cancer (GC) is still unclear. The aim of this study was to explore the expression and role of lncRNAs in GC. The relative expression level of lncRNAs in GC samples was examined by an lncRNA microarray analysis, northern blot analysis and qRT-PCR analysis. A Kaplan-Meier survival analysis and univariate and multivariate Cox proportional hazards models were performed to evaluate the clinical and prognostic significance of PANDAR (promoter of CDKN1A antisense DNA damage activated RNA) in GC patients...
February 7, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29415677/expression-profiling-and-intracellular-localization-studies-of-the-novel-proline-histidine-and-glycine-rich-protein-1-suggest-an-essential-role-in-gastro-intestinal-epithelium-and-a-potential-clinical-application-in-colorectal-cancer-diagnostics
#12
Satu Oltedal, Ivar Skaland, Jodi Maple-Grødem, Kjersti Tjensvoll, Emiel A M Janssen, Bjørnar Gilje, Rune Smaaland, Reino Heikkilä, Oddmund Nordgård
BACKGROUND: The primary function of the intestines is the absorption of water and nutrients. Although our knowledge about these processes on the cellular level is extensive, a number of important intracellular elements remain unknown. Here, we characterize the novel proline-, histidine-, glycine-rich 1 (PHGR1) mRNA and protein on the molecular level and propose a functional role of the PHGR1 protein in the intestinal and gastric epithelium. METHODS: PHGR1 mRNA and protein expression in human tissues and cell lines were characterized by quantitative RT-PCR, in situ hybridization, Northern blotting, Western blotting, and immunohistochemistry...
February 7, 2018: BMC Gastroenterology
https://www.readbyqxmd.com/read/29404037/preparation-of-monoclonal-antibody-against-human-kiaa0100-protein-and-northern-blot-analysis-of-human-kiaa0100-gene
#13
He Cui, Xi Lan, Shemin Lu, Fujun Zhang, Wanggang Zhang
Monoclonal antibodies (MAbs) are important tools for the study of proteins' function and structure. But there has been no report on the preparation of MAbs against human KIAA0100 protein up to date. Here, first, we generated the mouse MAb against human KIAA0100 protein using purified recombinant 6×Histidinc (6×His)-tagged human KIAA0100 protein segment (1557-2234) as an antigen; then, the mRNA expression of human KIAA0100 gene was detected in U937 cells using Northern blot analysis. The results showed that the mouse MAb against human KIAA0100 protein could sensitively recognize the human KIAA0100 protein using Western blot analysis and immunocytochemistry analysis...
June 2017: Journal of Pharmaceutical Analysis
https://www.readbyqxmd.com/read/29397416/overexpression-of-ghr-mir166b-generates-resistance-against-bemisia-tabaci-infestation-in-gossypium-hirsutum-plants
#14
Gazal Wamiq, Jawaid A Khan
In silico identified Gossypium hirsutum ghr-miR166b shows multi-compatible targets in mitochondrial ATP synthase of Bemisia tabaci. Its overexpression in planta has the potential to act as a biopesticide in reducing B. tabaci population, and consequently the spread of whitefly-transmitted plant viruses. Whiteflies (B. tabaci) are hemipterous insects that act as a vector to transmit plant viruses causing enormous losses to the plants. In the present study, G. hirsutum-encoded miRNAs targeting expressed sequence tags (ESTs) of B...
February 3, 2018: Planta
https://www.readbyqxmd.com/read/29393558/the-virome-of-the-arbuscular-mycorrhizal-fungus-gigaspora-margarita-reveals-the-first-report-of-dna-fragments-corresponding-to-replicating-non-retroviral-rna-viruses-in-fungi
#15
Massimo Turina, Stefano Ghignone, Nausicaa Astolfi, Alessandro Silvestri, Paola Bonfante, Luisa Lanfranco
Arbuscular Mycorrhizal Fungi (AMF) are key components of the plant microbiota. AMF genetic complexity is increased by the presence of endobacteria, which live inside many species. A further component of such complexity is the virome associated to AMF, whose knowledge is still very limited. Here, by exploiting transcriptomic data we describe the virome of Gigaspora margarita. A BLAST search for viral RNA-dependent RNA polymerases sequences allowed the identification of four mitoviruses, one Ourmia-like narnavirus, one Giardia-like virus, and two sequences related to Fusarium graminearum mycoviruses...
February 2, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29364282/phloem-sap-sampling-from-brassica-napus-for-3d-page-of-protein-and-ribonucleoprotein-complexes
#16
Steffen Pahlow, Anna Ostendorp, Lena Krüßel, Julia Kehr
Sampling the phloem of higher plants is often laborious and significantly dependent on the plant species. However, proteome studies under denaturing conditions could be achieved in different plant species. Native protein:protein and protein:nucleic acid complexes from phloem samples have as yet scarcely been analyzed, although they might play important roles in maintenance of this specialized compartment or in long-distance signaling. Large molecular assemblies can be isolated using a blue native gel electrophoresis (BN-PAGE)...
January 9, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29363793/signature-micrornas-of-nuclear-sm-complex-associated-with-breast-cancer-tumorigenesis
#17
Xinyi Zhang, Bo Shen, Yalei Cui
It is well known that Sm proteins, small nuclear ribonucleoproteins, act as core spliceosomal factors in alternative splicing of mRNA precursors. MicroRNAs (miRNAs) can function in alternative splicing by targeting mRNAs of splicing factors. However, the direct interaction between miRNAs and proteins of splicing complex in nucleus has not been explored. In this study, the mature miRNAs in nuclear Sm complex of breast cancer cells and normal breast epithelial cells were characterized. Small RNA sequencing of immunoprecipitated nuclear Sm complex with the SmD1-specific antibody identified 123 and 170 mature miRNAs in nuclear Sm complex of normal breast cells and breast cancer cells, respectively...
January 24, 2018: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29350358/streptomyces-ach-505-triggers-production-of-a-salicylic-acid-analogue-in-the-fungal-pathogen-heterobasidion-abietinum-that-enhances-infection-of-norway-spruce-seedlings
#18
Nadine Keilhofer, Jonny Nachtigall, Andreas Kulik, Margret Ecke, Rüdiger Hampp, Roderich D Süssmuth, Hans-Peter Fiedler, Silvia D Schrey
The necrotrophic fungus Heterobasidion spp. is the causal agent of 'annosum root rot' of Norway spruce. In the presence of the rhizosphere bacterium Streptomyces AcH 505, enhanced colonization of Norway spruce roots with Heterobasidion abietinum 331 has previously been observed. By analyzing dual cultures of H. abietinum 331 and Streptomyces AcH 505 with HPLC, a fungal metabolite was identified that was increased in the presence of Streptomyces AcH 505. Likewise, challenge of H. abietum 331 with common antifungals produced by soil streptomycetes rendered the same effect...
January 19, 2018: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29322447/characterization-of-circular-rna-concatemers
#19
Thomas B Hansen
Circular RNAs (circRNAs) constitute a novel subset in the fascinating world of noncoding RNA, and they are found in practically all eukaryotes. Most of them exhibit low expression levels but some are extremely abundant. Typically, circRNAs are studied by RT-PCR-based assays, but for certain types of analyses this technique is not suitable. Circular RNA with repetitive exons (circular concatemers) has been observed by us and others when transiently expressing circRNAs in cells, however techniques and assays to study these species have not been established...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29322446/nonradioactive-northern-blot-of-circrnas
#20
Xiaolin Wang, Ge Shan
Circular RNAs (circRNAs) are recognized as a special species of transcripts in metazoans with increasing studies, and northern blotting is a direct way to confirm the existence and to evaluate the size of individual circRNAs. Northern blotting probes can be radioactive isotope (32P) labeled, which is not environment-friendly and sometimes inconvenient to use. Here, we describe a nonradioactive northern blot protocol with digoxigenin-labeled probe to detect circRNA.
2018: Methods in Molecular Biology
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