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https://www.readbyqxmd.com/read/28728902/role-of-mirnas-in-development-and-disease-lessons-learnt-from-small-organisms
#1
REVIEW
Swati Chandra, Divya Vimal, Divya Sharma, Vipin Rai, Subash Chandra Gupta, D Kar Chowdhuri
MicroRNAs (miRNAs) constitute a class of small (21-24 nucleotides) non-coding RNAs that regulate gene expression at the post-transcriptional level. Caenorhabditis elegans, Drosophila melanogaster, and many other small organisms have been instrumental in deciphering the biological functions of miRNAs. While some miRNAs from small organisms are highly conserved across the taxa, others are organism specific. The miRNAs are known to play a crucial role during development and in various cellular functions such as cell survival, cell proliferation, and differentiation...
July 17, 2017: Life Sciences
https://www.readbyqxmd.com/read/28723412/identification-of-a-viroid-like-rna-in-a-lychee-transcriptome-shotgun-assembly
#2
Jihong Jiang, Zhixiang Zhang, Bing Hu, Guibing Hu, Hongqing Wang, Chantal Faure, Armelle Marais, Thierry Candresse, Shifang Li
In the course of a systematic screen of plant transcriptomic data, the sequence of a novel viroid-like RNA was identified in four contigs in a recent Transcriptome Shotgun Assembly (TSA) from lychee in China. Portions of this sequence are closely related to the central conserved region (CCR) and terminal conserved region (TCR) present in members of the genus Apscaviroid, sequences that are important criteria for viroid classification. RT-PCR with two divergent adjacent primers amplified the full 304 nucleotide sequence of this viroid-like RNA which can be folded into the rod-like secondary structure that is a typical feature of viroids in the family Pospiviroidae...
July 16, 2017: Virus Research
https://www.readbyqxmd.com/read/28702464/a-cost-effective-rna-extraction-technique-from-animal-cells-and-tissue-using-silica-columns
#3
Mario D Escobar, Jason L Hunt
Ribonucleic acid (RNA) is widely used in molecular biology assays, and some of the most common assays include: northern blotting and RT-PCR gene expression analysis. RNA is generally extracted by two methods: phenol-chloroform or commercially available silica spin column kits. Phenol-chloroform extraction is generally more economical; however, it produces hazardous byproducts, and leftover chemicals in the sample that can inhibit downstream applications. Commercial kits usually have simple set ups and short preparation time; however, they can introduce a significant expense to laboratory budgets...
2017: Journal of Biological Methods
https://www.readbyqxmd.com/read/28701684/expression-of-aldo-keto-reductase-family-1-member-c14-during-ovulation-in-the-rat
#4
Phuong T M Dam, You-Jee Jang, Ja-Yeon Kim, Seul-Gee Choi, Jae-Il Park, Young-Woo Seo, Sang-Young Chun
The potent androgen 5α-dihydrotestosterone is metabolized to the weak androgen 5α-androstane-3α, 17β-diol (3α-diol) by the enzyme aldo-keto reductase family 1, member C14 (Akr1c14) in rodents. The purpose of the present study was to investigate the regulation of Akr1c14 expression during the ovulatory process in rat ovaries. Northern blot analysis revealed that treatment of immature rats with equine chorionic gonadotropin resulted in lowered Akr1c14 expression, whereas subsequent treatment with human chorionic gonadotropin (hCG) increased ovarian Akr1c14 expression within 3 h...
July 11, 2017: Endocrine Journal
https://www.readbyqxmd.com/read/28701405/propagation-of-astrovirus-va1-a-neurotropic-human-astrovirus-in-cell-culture
#5
Andrew B Janowski, Irma K Bauer, Lori R Holtz, David Wang
Astrovirus VA1/HMO-C (VA1; mamastrovirus 9) is a recently discovered astrovirus genotype that is divergent from the classic human astroviruses (mamastrovirus 1). The gastrointestinal tract is presumed to be the primary site of infection and pathogenicity for astroviruses. However, VA1 has been independently detected in brain tissue of five cases of human encephalitis. Studies of the pathogenicity of VA1 are currently impossible because there are no reported cell culture systems or in vivo models that support VA1 infection...
July 12, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28698239/enzymatic-production-of-single-molecule-fish-and-rna-capture-probes
#6
Imre Gaspar, Frank Wippich, Anne Ephrussi
Arrays of singly-labelled short oligonucleotides that hybridize to a specific target revolutionized RNA biology, enabling quantitative, single molecule microscopy analysis and high efficiency RNA/RNP capture. Here, we describe a simple and efficient method that allows flexible functionalization of inexpensive DNA oligonucleotides by different fluorescent dyes or biotin using terminal deoxynucleotidyl transferase and custom-made functional group conjugated dideoxy-UTP. We show that 1) all steps of the oligonucleotide labelling - including conjugation, enzymatic synthesis and product purification - can be performed in a standard biology laboratory, 2) the process yields >90 %, often >95 % labeled product with minimal carry-over of impurities and 3) the oligonucleotides can be labeled with different dyes or biotin, allowing single molecule FISH or RNA affinity purification, and northern-blot analysis to be performed...
July 11, 2017: RNA
https://www.readbyqxmd.com/read/28689921/the-novel-mef-c-mph-g-macrolide-resistance-genes-are-conveyed-in-the-environment-on-various-vectors
#7
Yuta Sugimoto, Satoru Suzuki, Lisa Nonaka, Chanchai Boonla, Nop Sukpanyatham, Hsin-Yiu Chou, Jer-Horng Wu
BACKGROUND: The novel tandem genes mef(C) and mph(G) have been reported in marine bacteria in Japan. This paper aimed to characterise the extent of environmental distribution of mef(C) and mph(G) as well as their dissemination and persistence in aquatic bacterial communities. METHODS: Erythromycin-resistant bacteria were isolated from Japan, Taiwan and Thailand aquaculture sites. The mef(C)-mph(G) genes were detected by PCR. The size of mobile genetic elements conveying mef(C) and mph(G) was examined by Southern blotting...
July 6, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28689267/the-novel-srna-s015-improves-nisin-yield-by-increasing-acid-tolerance-of-lactococcus-lactis-f44
#8
Jiakun Qi, Qinggele Caiyin, Hao Wu, Kairen Tian, Binbin Wang, Yanni Li, Jianjun Qiao
Nisin, a polycyclic antibacterial peptide produced by Lactococcus lactis, is stable at low pH. Improving the acid tolerance of L. lactis could thus enhance nisin yield. Small non-coding RNAs (sRNAs) play essential roles in acid tolerance by regulating their target mRNAs at the post-transcriptional level. In this study, a novel sRNA, s015, was identified in L. lactis F44 via the use of RNA sequencing, qRT-PCR analysis, and Northern blotting. s015 improved the acid tolerance of L. lactis and boosted nisin yield at low pH...
July 9, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28680061/a-comprehensive-ethnic-based-analysis-of-alpha-thalassaemia-allelle-frequency-in-northern-thailand
#9
Mattapong Kulaphisit, Jatupol Kampuansai, Kamonlak Leecharoenkiat, Methi Wathikthinnakon, Daoroong Kangwanpong, Thongperm Munkongdee, Saovaros Svasti, Suthat Fucharoen, Duncan R Smith, Pathrapol Lithanatudom
Alpha (α)-thalassaemia is one of the most prevalent hereditary blood disorders, commonly affecting Southeast Asian people, with the highest incidence (30-40%) being seen in northern Thailand. However, this high incidence was estimated without consideration of the variations between ethnic populations and the geographical location of the populations. To address this issue, a total of 688 samples from 13 different northern Thai ethnic groups (30 villages) categorized into three linguistic groups were genotyped for deletional alpha-thalassaemia (-α(3...
July 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28679533/a-hypertension-associated-mitochondrial-dna-mutation-alters-the-tertiary-interaction-and-function-of-trnaleu-uur
#10
Mi Zhou, Meng Wang, Ling Xue, Zhi Lin, Qiufen He, Wenwen Shi, Yaru Chen, Xiaofen Jin, Haiying Li, Pingping Jiang, Min-Xin Guan
Several mitochondrial tRNA mutations have been associated with hypertension, but their pathophysiology remains poorly understood. In this report, we identified a novel homoplasmic 3253T>C mutation in the mitochondrial tRNALeu(UUR) gene in a Han Chinese family with maternally inherited hypertension. The m.3253T>C mutation affected a highly conserved uridine at position 22 at the D-stem of tRNALeu(UUR), introducing a G-C base pairing (G13-C22) at the D-stem and a tertiary base pairing (C22-G46) between the D-stem and the variable loop...
July 5, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28679418/transitioning-from-antenatal-surveillance-surveys-to-routine-hiv-testing-a-turning-point-in-the-mother-to-child-transmission-prevention-programme-for-hiv-surveillance-in-brazil
#11
Gerson Fernando Mendes Pereira, Meritxell Sabidó, Alessandro Caruso, Adele Schwartz Benzaken
BACKGROUND: In Brazil, due to the rapid increase in programmes for the prevention of mother-to-child transmission (PMTCT), routine programme data are widely available. The objective of this study was to assess the utility of programmatic data to replace HIV surveillance based on the antenatal care (ANC) surveillance survey (SS). METHODS: We analysed ANC SS data from 219 maternity service clinics. PMTCT variables were extracted from the ANC SS data collection form, which allowed us to capture and compare the ANC SS data and PMTCT HIV test results for each pregnant woman who completed the ANC SS...
July 5, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28678443/mitochondrial-ribosome-mitoribosome-profiling-for-monitoring-mitochondrial-translation-in-vivo
#12
Mary T Couvillion, L Stirling Churchman
Translation in the mitochondria is regulated by mechanisms distinct from those acting in the cytosol and in bacteria, yet precise methods for investigating it have lagged behind. This unit describes an approach, mitochondrial ribosome (mitoribosome) profiling, to quantitatively monitor mitochondrial translation with high temporal and spatial resolution in Saccharomyces cerevisiae. Mitoribosomes are immunoprecipitated from whole-cell lysate and the protected mRNA fragments are isolated. These fragments are then converted to sequencing libraries or analyzed by northern blot hybridization to reveal the distribution of mitoribosomes across the mitochondrial transcriptome...
July 5, 2017: Current Protocols in Molecular Biology
https://www.readbyqxmd.com/read/28662365/a-compensatory-mutagenesis-study-of-a-conserved-hairpin-in-the-m-gene-segment-of-influenza-a-virus-shows-its-role-in-virus-replication
#13
M I Spronken, C E van de Sandt, E P de Jongh, O Vuong, S van der Vliet, T M Bestebroer, R C L Olsthoorn, G F Rimmelzwaan, R A M Fouchier, A P Gultyaev
RNA structures are increasingly recognized to be of importance during influenza A virus replication. Here, we investigated a predicted conserved hairpin in the M gene segment (nt 967-994) within the region of the vRNA 5' packaging signal. The existence of this RNA structure and its possible role in virus replication was investigated using a compensatory mutagenesis approach. Mutations were introduced in the hairpin stem, based on natural variation. Virus replication properties were studied for the mutant viruses with disrupted and restored RNA structures...
June 29, 2017: RNA Biology
https://www.readbyqxmd.com/read/28659539/progesterone-dose-dependently-modulates-hepatocyte-growth-factor-production-in-3t3-l1-mouse-preadipocytes
#14
Tomoki Ito, Daisuke Yamaji, Akihiro Kamikawa, Mabrouk Attia Abd Eldaim, Yuko Okamatsu-Ogura, Akira Terao, Masayuki Saito, Kazuhiro Kimura
It is well documented that estrogen is predominant inducer of hepatocyte growth factor (HGF) in a variety of cell types. However, the effect of progesterone (P) remains to be elusive. Thus, in the present study, we examined the effect of P and combined effect of P and 17β-estradiol (E2) on HGF expression and production in 3T3-L1 fibroblastic preadipocytes and mature adipocytes, as a model of stromal cells. Northern blot analysis showed that hgf mRNA expressed in preadipocytes was notably higher than that of mature adipocytes, and increased by treatment of preadipocytes with E2 or 10 nM P, but not with 1,000 nM P...
June 27, 2017: Endocrine Journal
https://www.readbyqxmd.com/read/28658256/a-noncoding-rna-containing-a-sine-b1-motif-associates-with-meiotic-metaphase-chromatin-and-has-an-indispensable-function-during-spermatogenesis
#15
Ryusuke Nakajima, Takuya Sato, Takehiko Ogawa, Hideyuki Okano, Toshiaki Noce
A search for early response genes that are activated following germ cell induction from mouse embryonic stem cells in vitro led us to the isolation of a long noncoding RNA that contains a SINE (short interspersed element)-B1F motif that was named R53. In situ hybridization and northern blot analyses revealed that the R53 subfragment RNA bears a B1F motif, is processed from the primary transcript, is expressed in adult testis and is predominantly localized in meiotic metaphase chromatin during spermatogenesis...
2017: PloS One
https://www.readbyqxmd.com/read/28651607/the-long-non-coding-rna-bc200-bcyrn1-is-critical-for-cancer-cell-survival-and-proliferation
#16
Evan P Booy, Ewan Ks McRae, Amit Koul, Francis Lin, Sean A McKenna
BACKGROUND: BC200 is a long non-coding RNA expressed at high levels in the brain and elevated in a variety of tumour types. BC200 has a hypothesized role in translational regulation; however, to date the functional role of BC200 in both normal and diseased states remains poorly characterized. METHODS: Detailed BC200 expression analyses were performed in tumor cell lines, primary and non-tumorigenic cultured breast and lung cells, and a panel of normal human tissues by quantitative real-time PCR and confirmed by northern blot...
June 26, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28647560/transcript-expression-bias-of-phosphatidylethanolamine-binding-protein-gene-in-bumblebee-bombus-lantschouensis-hymenoptera-apidae
#17
Jie Dong, Lei Han, Ye Wang, Jiaxing Huang, Jie Wu
The phosphatidylethanolamine-binding protein (PEBP) family is a highly conserved group of proteins found in a wide range of organism. It plays an important role in innate immunity of insects. Little is known on the expression characteristic and function of PEBP in bees. In the current study, we cloned the pebp gene and investigated its expression profiles at different developmental stages and reproductive status from bumblebee, Bombus lantschouensis (Vogt), which is one of the most abundant pollinators for wild plants and crops in Northern China...
June 21, 2017: Gene
https://www.readbyqxmd.com/read/28640671/regulation-of-a-muralytic-enzyme-encoding-gene-by-two-non-coding-rnas
#18
Renée J St-Onge, Marie A Elliot
Non-coding regulatory RNAs fine-tune gene expression post-transcriptionally. In the streptomycetes, rpfA - encoding a muralytic enzyme required for establishing and exiting dormancy - is flanked by non-coding regulatory RNA elements both upstream (riboswitch) and downstream [antisense small RNA (sRNA)]. In Streptomyces coelicolor, the upstream riboswitch decreases rpfA transcript abundance in response to the second messenger cyclic di-AMP, itself involved in cell wall metabolism and dormancy. There is, however, no obvious expression platform associated with this riboswitch and consequently, its mechanism of action is entirely unknown...
June 22, 2017: RNA Biology
https://www.readbyqxmd.com/read/28608345/nonradioactive-plant-small-rna-detection-using-biotin-labeled-probes
#19
Jun Hu, Yingguo Zhu
Small noncoding RNAs are essential for gene expression at transcriptional and posttranscriptional levels. Northern blot is the most used method for small RNA detection in tissues. Here we present an improved protocol for the Northern blot-based small RNA detection from plant tissues by using biotin-labeled probes. MicroRNAs and small interfering RNAs derived from Arabidopsis and Oryza sativa, respectively, have been detected with this methodology. Results suggest that this method is sensitive and efficient enough to detect small RNAs from plant tissues by using as low as 5 μg of total RNA...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28608344/nonradioactive-detection-of-small-rnas-using-digoxigenin-labeled-probes
#20
Ariel H Tomassi, Delfina Gagliardi, Damian A Cambiagno, Pablo A Manavella
Small RNAs have been traditionally detected and quantified using small RNA blots, a modified Northern blot technique. The small RNAs are size-fractionated from the rest of the cellular RNA molecules by polyacrylamide gel electrophoresis and transferred by blotting onto a positively charged membrane. A radiolabeled probe was then traditionally used to detect a specific small RNA in the cellular pool. Small RNA blotting is a relatively simple, inexpensive approach to visualize small RNAs without artifacts. However, the radioactive labeling of the probe is sometimes an impediment, especially due to the requirement of specialized facilities...
2017: Methods in Molecular Biology
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