scholarly journals A Protocol for Measurement of Noncoding RNA in Human Serum

2012 ◽  
Vol 2012 ◽  
pp. 1-4 ◽  
Author(s):  
Caroline J. Taylor ◽  
Sarang N. Satoor ◽  
Amaresh K. Ranjan ◽  
Maria V. Pereira e Cotta ◽  
Mugdha V. Joglekar
Keyword(s):  
Human Serum ◽  
Noncoding Rna ◽  
Noncoding Rnas ◽  
Cost Effective ◽  
Pcr Analysis ◽  
Messenger Rnas ◽  
Initial Report ◽  
Small Noncoding Rnas ◽  
Liquid Samples ◽  
Cost Effective Method

MicroRNAs (miRNAs) are small noncoding RNAs that act as regulators of gene expression by targeting mature messenger RNAs. Following the initial report of the presence of miRNAs in serum and plasma a number of studies have successfully demonstrated the use of these miRNAs as biomarkers of disease. Currently, there are many methods of isolating total RNA from liquid samples. Here, we describe a simple, cost effective method for extraction of RNA from human serum as well as subsequent real time PCR analysis of miRNA levels.

Direct electrochemical analysis in complex samples using ITO electrodes modified with permselective membranes consisting of vertically ordered silica mesochannels and micelles

2015 ◽  
Vol 51 (100) ◽  
pp. 17736-17739 ◽  
Author(s):  
Fei Yan ◽  
Wenjing Zheng ◽  
Lina Yao ◽  
Bin Su
Keyword(s):  
Human Serum ◽  
Electrochemical Detection ◽  
Cost Effective ◽  
Electrochemical Analysis ◽  
Complex Media ◽  
Complex Samples ◽  
Redox Active ◽  
Cost Effective Method ◽  
Pre Treatment ◽  
Organic Analytes

Herein we report a simple and cost-effective method for direct electrochemical detection of redox-active small organic analytes in complex media, such as soil dispersions, human serum and milk, without sample pre-treatment.

Long and small noncoding RNAs during oocyte-to-embryo transition in mammals

2017 ◽  
Vol 45 (5) ◽  
pp. 1117-1124 ◽  
Author(s):  
Petr Svoboda
Keyword(s):  
Noncoding Rna ◽  
Transcriptional Control ◽  
Noncoding Rnas ◽  
Rna Degradation ◽  
Early Embryo ◽  
Protein Coding ◽  
Small Noncoding Rnas ◽  
Major Genome ◽  
Silencing Pathways ◽  
And Function

Oocyte-to-embryo transition is a process during which an oocyte ovulates, is fertilized, and becomes a developing embryo. It involves the first major genome reprogramming event in life of an organism where gene expression, which gave rise to a differentiated oocyte, is remodeled in order to establish totipotency in blastomeres of an early embryo. This remodeling involves replacement of maternal RNAs with zygotic RNAs through maternal RNA degradation and zygotic genome activation. This review is focused on expression and function of long noncoding RNAs (lncRNAs) and small RNAs during oocyte-to-embryo transition in mammals. LncRNAs are an assorted rapidly evolving collection of RNAs, which have no apparent protein-coding capacity. Their biogenesis is similar to mRNAs including transcriptional control and post-transcriptional processing. Diverse molecular and biological roles were assigned to lncRNAs although most of them probably did not acquire a detectable biological role. Since some lncRNAs serve as precursors for small noncoding regulatory RNAs in RNA silencing pathways, both types of noncoding RNA are reviewed together.

scholarly journals Phylogenetic Placement of Isolates Within the Trans-Eurasian Clade A.Br.008/009 of Bacillus anthracis

2019 ◽  
Vol 7 (12) ◽  
pp. 689
Author(s):  
Markus Antwerpen ◽  
Wolfgang Beyer ◽  
Olga Bassy ◽  
María Victoria Ortega-García ◽  
Juan Carlos Cabria-Ramos ◽  
...  
Keyword(s):  
Bacillus Anthracis ◽  
Cost Effective ◽  
Variable Number ◽  
Pcr Analysis ◽  
Nucleotide Polymorphisms ◽  
Additional Information ◽  
Cost Effective Method ◽  
Amplification Assay ◽  
Human Infections ◽  
Chromosomal Sequences

The largest phylogenetic lineage known to date of the anthrax pathogen Bacillus anthracis is the wide-spread, so-called Trans-Eurasian clade systematically categorized as the A.Br.008/009 group sharing two defining canonical single-nucleotide polymorphisms (canSNP). In this study, we genome-sequenced a collection of 35 B. anthracis strains of this clade, derived from human infections, animal outbreaks or soil, mostly from European countries isolated between 1936 and 2008. The new data were subjected to comparative chromosomal analysis, together with 75 B. anthracis genomes available in public databases, and the relative placements of these isolates were determined within the global phylogeny of the A.Br.008/009 canSNP group. From this analysis, we have detected 3754 chromosomal SNPs, allowing the assignation of the new chromosomal sequences to established sub-clades, to define new sub-clades, such as two new Spanish, one Bulgarian or one German group(s), or to introduce orphan lineages. SNP-based results were compared with that of a multilocus variable number of tandem repeat analysis (MLVA). This analysis indicated that MLVA typing might provide additional information in cases when genomics yields identical genotypes or shows only minor differences. Introducing the delayed mismatch amplification assay (DMAA) PCR-analysis, we developed a cost-effective method to interrogate for a set of ten phylogenetically informative SNPs within genomes of A.Br.008/009 canSNP clade strains of B. anthracis. By this approach, additional 32 strains could be assigned to five of ten defined clades.

scholarly journals Of rodents and ruminants: a comparison of small noncoding RNA requirements in mouse and bovine reproduction

2021 ◽  
Vol 99 (3) ◽  
Author(s):  
Lauren G Chukrallah ◽  
Aditi Badrinath ◽  
Kelly Seltzer ◽  
Elizabeth M Snyder
Keyword(s):  
Germ Cell ◽  
Germ Cells ◽  
Noncoding Rna ◽  
Reproductive Potential ◽  
Noncoding Rnas ◽  
Model Organism ◽  
Cell Physiology ◽  
Male Germ Cells ◽  
Small Noncoding Rna ◽  
Small Noncoding Rnas

Abstract Ruminants are major producers of meat and milk, thus managing their reproductive potential is a key element in cost-effective, safe, and efficient food production. Of particular concern, defects in male germ cells and female germ cells may lead to significantly reduced live births relative to fertilization. However, the underlying molecular drivers of these defects are unclear. Small noncoding RNAs, such as piRNAs and miRNAs, are known to be important regulators of germ-cell physiology in mouse (the best-studied mammalian model organism) and emerging evidence suggests that this is also the case in a range of ruminant species, in particular bovine. Similarities exist between mouse and bovids, especially in the case of meiotic and postmeiotic male germ cells. However, fundamental differences in small RNA abundance and metabolism between these species have been observed in the female germ cell, differences that likely have profound impacts on their physiology. Further, parentally derived small noncoding RNAs are known to influence early embryos and significant species-specific differences in germ-cell born small noncoding RNAs have been observed. These findings demonstrate the mouse to be an imperfect model for understanding germ-cell small noncoding RNA biology in ruminants and highlight the need to increase research efforts in this underappreciated aspect of animal reproduction.

scholarly journals Reprogramming of Small Noncoding RNA Populations in Peripheral Blood Reveals Host Biomarkers for Latent and Active Mycobacterium tuberculosis Infection

mBio ◽  
2019 ◽  
Vol 10 (6) ◽  
Author(s):  
Leonardo Silva de Araujo ◽  
Marcelo Ribeiro-Alves ◽  
Thyago Leal-Calvo ◽  
Janaína Leung ◽  
Verónica Durán ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Peripheral Blood ◽  
Noncoding Rna ◽  
Mononuclear Cells ◽  
Human Peripheral Blood ◽  
Noncoding Rnas ◽  
Great Promise ◽  
Mycobacterium Tuberculosis Infection ◽  
Content Type ◽  
Small Noncoding Rnas

ABSTRACT In tuberculosis (TB), as in other infectious diseases, studies of small noncoding RNAs (sncRNA) in peripheral blood have focused on microRNAs (miRNAs) but have neglected the other major sncRNA classes in spite of their potential functions in host gene regulation. Using RNA sequencing of whole blood, we have therefore determined expression of miRNA, PIWI-interacting RNA (piRNA), small nucleolar RNA (snoRNA), and small nuclear RNA (snRNA) in patients with TB (n = 8), latent TB infection (LTBI; n = 21), and treated LTBI (LTBItt; n = 6) and in uninfected exposed controls (ExC; n = 14). As expected, sncRNA reprogramming was greater in TB than in LTBI, with the greatest changes seen in miRNA populations. However, substantial dynamics were also evident in piRNA and snoRNA populations. One miRNA and 2 piRNAs were identified as moderately accurate (area under the curve [AUC] = 0.70 to 0.74) biomarkers for LTBI, as were 1 miRNA, 1 piRNA, and 2 snoRNAs (AUC = 0.79 to 0.91) for accomplished LTBI treatment. Logistic regression identified the combination of 4 sncRNA (let-7a-5p, miR-589-5p, miR-196b-5p, and SNORD104) as a highly sensitive (100%) classifier to discriminate TB from all non-TB groups. Notably, it reclassified 8 presumed LTBI cases as TB cases, 5 of which turned out to have features of Mycobacterium tuberculosis infection on chest radiographs. SNORD104 expression decreased during M. tuberculosis infection of primary human peripheral blood mononuclear cells (PBMC) and M2-like (P = 0.03) but not M1-like (P = 0.31) macrophages, suggesting that its downregulation in peripheral blood in TB is biologically relevant. Taken together, the results demonstrate that snoRNA and piRNA should be considered in addition to miRNA as biomarkers and pathogenesis factors in the various stages of TB. IMPORTANCE Tuberculosis is the infectious disease with the worldwide largest disease burden and there remains a great need for better diagnostic biomarkers to detect latent and active M. tuberculosis infection. RNA molecules hold great promise in this regard, as their levels of expression may differ considerably between infected and uninfected subjects. We have measured expression changes in the four major classes of small noncoding RNAs in blood samples from patients with different stages of TB infection. We found that, in addition to miRNAs (which are known to be highly regulated in blood cells from TB patients), expression of piRNA and snoRNA is greatly altered in both latent and active TB, yielding promising biomarkers. Even though the functions of many sncRNA other than miRNA are still poorly understood, our results strongly suggest that at least piRNA and snoRNA populations may represent hitherto underappreciated players in the different stages of TB infection.

scholarly journals The Challenges and Opportunities in the Clinical Application of Noncoding RNAs: The Road Map for miRNAs and piRNAs in Cancer Diagnostics and Prognostics

2018 ◽  
Vol 2018 ◽  
pp. 1-18 ◽  
Author(s):  
Preethi Krishnan ◽  
Sambasivarao Damaraju
Keyword(s):  
Gene Expression ◽  
Noncoding Rna ◽  
Noncoding Rnas ◽  
Cancer Diagnostics ◽  
Master Regulators ◽  
The Road ◽  
Small Noncoding Rnas ◽  
Road Map ◽  
Challenges And Opportunities ◽  
Compare And Contrast

Discoveries on nonprotein-coding RNAs have induced a paradigm shift in our overall understanding of gene expression and regulation. We now understand that coding and noncoding RNA machinery work in concert to maintain overall homeostasis. Based on their length, noncoding RNAs are broadly classified into two groups—long (>200 nt) and small noncoding RNAs (<200 nt). These RNAs perform diverse functions—gene regulation, splicing, translation, and posttranscriptional modifications. MicroRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs) are two classes of small noncoding RNAs that are now classified as master regulators of gene expression. They have also demonstrated clinical significance as potential biomarkers and therapeutic targets for several diseases, including cancer. Despite these similarities, both these RNAs are generated through contrasting mechanisms, and one of the aims of this review is to cover the distance travelled since their discovery and compare and contrast the various facets of these RNAs. Although these RNAs show tremendous promise as biomarkers, translating the findings from bench to bedside is often met with roadblocks. The second aim of this review therefore is to highlight some of the challenges that hinder application of miRNA and piRNA as in guiding treatment decisions.

scholarly journals Dynamic expression of long noncoding RNAs reveals their potential roles in spermatogenesis and fertility†

2017 ◽  
Vol 97 (2) ◽  
pp. 313-323 ◽  
Author(s):  
Lauren Wichman ◽  
Saigopal Somasundaram ◽  
Christine Breindel ◽  
Dana M. Valerio ◽  
John R. McCarrey ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Noncoding Rna ◽  
Sex Chromosome ◽  
Sperm Count ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Small Noncoding Rnas ◽  
Meiotic Sex Chromosome Inactivation ◽  
Y Chromosomes ◽  
Dynamic Expression

Abstract Mammalian reproduction requires that males and females produce functional haploid germ cells through complex cellular differentiation processes known as spermatogenesis and oogenesis, respectively. While numerous studies have functionally characterized protein-coding genes and small noncoding RNAs (microRNAs and piRNAs) that are essential for gametogenesis, the roles of regulatory long noncoding RNAs (lncRNAs) are yet to be fully characterized. Previously, we and others have demonstrated that intergenic regions of the mammalian genome encode thousands of long noncoding RNAs, and many studies have now demonstrated their critical roles in key biological processes. Thus, we postulated that some lncRNAs may also impact mammalian spermatogenesis and fertility. In this study, we identified a dynamic expression pattern of lncRNAs during murine spermatogenesis. Importantly, we identified a subset of lncRNAs and very few mRNAs that appear to escape meiotic sex chromosome inactivation, an epigenetic process that leads to the silencing of the X- and Y-chromosomes at the pachytene stage of meiosis. Further, some of these lncRNAs and mRNAs show a strong testis expression pattern suggesting that they may play key roles in spermatogenesis. Lastly, we generated a mouse knockout of one X-linked lncRNA, Tslrn1 (testis-specific long noncoding RNA 1), and found that males carrying a Tslrn1 deletion displayed normal fertility but a significant reduction in spermatozoa. Our findings demonstrate that dysregulation of specific mammalian lncRNAs is a novel mechanism of low sperm count or infertility, thus potentially providing new biomarkers and therapeutic strategies.

scholarly journals Small Noncoding RNA CjNC110 Influences Motility, Autoagglutination, AI-2 Localization, Hydrogen Peroxide Sensitivity, and Chicken Colonization in Campylobacter jejuni

2020 ◽  
Vol 88 (7) ◽  
Author(s):  
Amanda J. Kreuder ◽  
Brandon Ruddell ◽  
Kathy Mou ◽  
Alan Hassall ◽  
Qijing Zhang ◽  
...  
Keyword(s):  
Hydrogen Peroxide ◽  
Quorum Sensing ◽  
Campylobacter Jejuni ◽  
Noncoding Rna ◽  
Noncoding Rnas ◽  
Wild Type ◽  
Content Type ◽  
Zoonotic Pathogen ◽  
Small Noncoding Rnas

ABSTRACT Small noncoding RNAs (ncRNAs) are involved in many important physiological functions in pathogenic microorganisms. Previous studies have identified the presence of noncoding RNAs in the major zoonotic pathogen Campylobacter jejuni; however, few have been functionally characterized to date. CjNC110 is a conserved ncRNA in C. jejuni, located downstream of the luxS gene, which is responsible for the production of the quorum sensing molecule autoinducer-2 (AI-2). In this study, we utilized strand specific high-throughput RNAseq to identify potential targets or interactive partners of CjNC110 in a sheep abortion clone of C. jejuni. These data were then utilized to focus further phenotypic evaluation of the role of CjNC110 in motility, autoagglutination, quorum sensing, hydrogen peroxide sensitivity, and chicken colonization in C. jejuni. Inactivation of the CjNC110 ncRNA led to a statistically significant decrease in autoagglutination ability as well as increased motility and hydrogen peroxide sensitivity compared to the wild-type. Extracellular AI-2 detection was decreased in ΔCjNC110; however, intracellular AI-2 accumulation was significantly increased, suggesting a key role of CjNC110 in modulating the transport of AI-2. Notably, ΔCjNC110 also showed a decreased ability to colonize chickens. Complementation of CjNC110 restored all phenotypic changes back to wild-type levels. The collective results of the phenotypic and transcriptomic changes observed in our data provide valuable insights into the pathobiology of C. jejuni sheep abortion clone and strongly suggest that CjNC110 plays an important role in the regulation of energy taxis, flagellar glycosylation, cellular communication via quorum sensing, oxidative stress tolerance, and chicken colonization in this important zoonotic pathogen.

scholarly journals Isolation of Small Noncoding RNAs from Human Serum

10.3791/51443 ◽  
2014 ◽  
Author(s):  
Samantha Khoury ◽  
Pamela Ajuyah ◽  
Nham Tran
Keyword(s):  
Human Serum ◽  
Noncoding Rnas ◽  
Small Noncoding Rnas
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