1,205 research outputs found
Towards a universal “baseline” characterisation of air masses for high- and low-altitude observing stations using Radon-222
We demonstrate the ability of atmospheric radon concentrations to reliably and unambiguously identify local and
remote terrestrial influences on an air mass, and thereby the potential for alteration of trace gas composition by
anthropogenic and biogenic processes. Based on high accuracy (lower limit of detection 10–40 mBq m–3), high temporal
resolution (hourly) measurements of atmospheric radon concentration we describe, apply and evaluate a simple two-step
method for identifying and characterising constituent mole fractions in baseline air. The technique involves selecting a
radon-based threshold concentration to identify the “cleanest” (least terrestrially influenced) air masses, and then
performing an outlier removal step based on the distribution of constituent mole fractions in the identified clean air
masses. The efficacy of this baseline selection technique is tested at three contrasting WMO GAW stations: Cape Grim (a
coastal low-altitude site), Mauna Loa (a remote high-altitude island site), and Jungfraujoch (a continental high-altitude
site). At Cape Grim and Mauna Loa the two-step method is at least as effective as more complicated methods employed to
characterise baseline conditions, some involving up to nine steps. While it is demonstrated that Jungfraujoch air masses
rarely meet the baseline criteria of the more remote sites, a selection method based on a variable monthly radon threshold
is shown to produce credible “near baseline” characteristics. The seasonal peak-to-peak amplitude of recent monthly
baseline CO2 mole fraction deviations from the long-term trend at Cape Grim, Mauna Loa and Jungfraujoch are estimated
to be 1.1, 6.0 and 8.1 ppm, respectively
Widespread environmental contamination with Mycobacterium tuberculosis complex revealed by a molecular detection protocol
Environmental contamination with Mycobacterium tuberculosis complex (MTC) has been considered crucial for bovine tuberculosis persistence in multi-host-pathogen systems. However, MTC contamination has been difficult to detect due to methodological issues. In an attempt to overcome this limitation we developed an improved protocol for the detection of MTC DNA. MTC DNA concentration was estimated by the Most Probable Number (MPN) method. Making use of this protocol we showed that MTC contamination is widespread in different types of environmental samples from the Iberian Peninsula, which supports indirect transmission as a contributing mechanism for the maintenance of bovine tuberculosis in this multi-host-pathogen system. The proportion of MTC DNA positive samples was higher in the bovine tuberculosis-infected than in presumed negative area (0.32 and 0.18, respectively). Detection varied with the type of environmental sample and was more frequent in sediment from dams and less frequent in water also from dams (0.22 and 0.05, respectively). The proportion of MTC-positive samples was significantly higher in spring (p<0.001), but MTC DNA concentration per sample was higher in autumn and lower in summer. The average MTC DNA concentration in positive samples was 0.82 MPN/g (CI95 0.70-0.98 MPN/g). We were further able to amplify a DNA sequence specific of Mycobacterium bovis/caprae in 4 environmental samples from the bTB-infected area
Computational Analysis of mRNA Expression Profiles Identifies MicroRNA-29a/c as Predictor of Colorectal Cancer Early Recurrence
Colorectal cancer (CRC) is one of the leading malignant cancers with a rapid increase in incidence and mortality. The recurrences of CRC after curative resection are sometimes unavoidable and often take place within the first year after surgery. MicroRNAs may serve as biomarkers to predict early recurrence of CRC, but identifying them from over 1,400 known human microRNAs is challenging and costly. An alternative approach is to analyze existing expression data of messenger RNAs (mRNAs) because generally speaking the expression levels of microRNAs and their target mRNAs are inversely correlated. In this study, we extracted six mRNA expression data of CRC in four studies (GSE12032, GSE17538, GSE4526 and GSE17181) from the gene expression omnibus (GEO). We inferred microRNA expression profiles and performed computational analysis to identify microRNAs associated with CRC recurrence using the IMRE method based on the MicroCosm database that includes 568,071 microRNA-target connections between 711 microRNAs and 20,884 gene targets. Two microRNAs, miR-29a and miR-29c, were disclosed and further meta-analysis of the six mRNA expression datasets showed that these two microRNAs were highly significant based on the Fisher p-value combination (p = 9.14×10−9 for miR-29a and p = 1.14×10−6 for miR-29c). Furthermore, these two microRNAs were experimentally tested in 78 human CRC samples to validate their effect on early recurrence. Our empirical results showed that the two microRNAs were significantly down-regulated (p = 0.007 for miR-29a and p = 0.007 for miR-29c) in the early-recurrence patients. This study shows the feasibility of using mRNA profiles to indicate microRNAs. We also shows miR-29a/c could be potential biomarkers for CRC early recurrence
The Promoter of the pri-miR-375 Gene Directs Expression Selectively to the Endocrine Pancreas
microRNAs (miRNAs) are known to play an essential role in controlling a broad range of biological processes including animal development. Accordingly, many miRNAs are expressed preferentially in one or a small number of cell types. Yet the mechanisms responsible for this selectivity are not well understood. The aim of this study was to elucidate the molecular basis of cell-specific expression of the pri-miR-375 gene, which is selectively expressed in pancreatic islets, and has been implicated both in the development of islets, and the function of mature pancreatic beta cells. An evolutionarily conserved 768 bp region of DNA upstream of the pri-miR-375 gene was linked to GFP and luciferase reporter genes, and expression monitored in transgenic mice and transfected cultured cells. Deletion and targeted mutagenesis analysis was used to evaluate the functional significance of sequence blocks within the upstream fragment. 5′-RACE analysis was used for mapping the pri-miR-375 gene transcription start site. The conserved 768 bp region was able to direct preferential expression of a GFP reporter gene to pancreatic islets in transgenic mice. Deletion analysis using a luciferase reporter gene in transfected cultured cell lines confirmed the cell specificity of the putative promoter region, and identified several key cis-elements essential for optimal activity, including E-boxes and a TATA sequence. Consistent with this, 5′-RACE analysis identified a transcription start site within this DNA region, 24 bp downstream of the TATA sequence. These studies define the promoter of the pri-miR-375 gene, and show that islet-specific expression of the pri-miR-375 gene is controlled at the transcriptional level. Detailed analysis of the transcriptional mechanisms controlling expression of miRNA genes will be essential to permit a comprehensive understanding of the complex role of miRNAs such as miR-375 in developmental processes
Discovery of Novel Human Breast Cancer MicroRNAs from Deep Sequencing Data by Analysis of Pri-MicroRNA Secondary Structures
MicroRNAs (miRNAs) are key regulators of gene expression and contribute to a
variety of biological processes. Abnormal miRNA expression has been reported in
various diseases including pathophysiology of breast cancer, where they regulate
protumorigenic processes including vascular invasiveness, estrogen receptor
status, chemotherapy resistance, invasion and metastasis. The miRBase sequence
database, a public repository for newly discovered miRNAs, has grown rapidly
with approximately >10,000 entries to date. Despite this rapid growth, many
miRNAs have not yet been validated, and several others are yet to be identified.
A lack of a full complement of miRNAs has imposed limitations on recognizing
their important roles in cancer, including breast cancer. Using deep sequencing
technology, we have identified 189 candidate novel microRNAs in human breast
cancer cell lines with diverse tumorigenic potential. We further show that
analysis of 500-nucleotide pri-microRNA secondary structure constitutes a
reliable method to predict bona fide miRNAs as judged by experimental
validation. Candidate novel breast cancer miRNAs with stem lengths of greater
than 30 bp resulted in the generation of precursor and mature sequences
in vivo. On the other hand, candidates with stem length
less than 30 bp were less efficient in producing mature miRNA. This approach may
be used to predict which candidate novel miRNA would qualify as bona fide miRNAs
from deep sequencing data with approximately 90% accuracy
Comparative analysis of miRNAs and their targets across four plant species
BACKGROUND: MicroRNA (miRNA) mediated regulation of gene expression has been recognized as a major posttranscriptional regulatory mechanism also in plants. We performed a comparative analysis of miRNAs and their respective gene targets across four plant species: Arabidopsis thaliana (Ath), Medicago truncatula(Mtr), Brassica napus (Bna), and Chlamydomonas reinhardtii (Cre). RESULTS: miRNAs were obtained from mirBase with 218 miRNAs for Ath, 375 for Mtr, 46 for Bna, and 73 for Cre, annotated for each species respectively. miRNA targets were obtained from available database annotations, bioinformatic predictions using RNAhybrid as well as predicted from an analysis of mRNA degradation products (degradome sequencing) aimed at identifying miRNA cleavage products. On average, and considering both experimental and bioinformatic predictions together, every miRNA was associated with about 46 unique gene transcripts with considerably variation across species. We observed a positive and linear correlation between the number miRNAs and the total number of transcripts across different plant species suggesting that the repertoire of miRNAs correlates with the size of the transcriptome of an organism. Conserved miRNA-target pairs were found to be associated with developmental processes and transcriptional regulation, while species-specific (in particular, Ath) pairs are involved in signal transduction and response to stress processes. Conserved miRNAs have more targets and higher expression values than non-conserved miRNAs. We found evidence for a conservation of not only the sequence of miRNAs, but their expression levels as well. CONCLUSIONS: Our results support the notion of a high birth and death rate of miRNAs and that miRNAs serve many species specific functions, while conserved miRNA are related mainly to developmental processes and transcriptional regulation with conservation operating at both the sequence and expression level
Expression of Mir-21 and Mir-143 in Cervical Specimens Ranging from Histologically Normal through to Invasive Cervical Cancer
MicroRNA expression is severely disrupted in carcinogenesis, however limited evidence is available validating results from cell-line models in human clinical cancer specimens. MicroRNA-21 (mir-21) and microRNA-143 (mir-143) have previously been identified as significantly deregulated in a range of cancers including cervical cancer. Our goal was to investigate the expression patterns of several well-studied microRNA species in cervical samples and compare the results to cell line samples.We measured the expression of mir-21 and mir-143 in 142 formalin-fixed, paraffin embedded (FFPE) cervical biopsy tissue blocks, collected from Dantec Oncology Clinic, Dakar, Senegal. MicroRNA expression analysis was performed using Taqman-based real-time PCR assays. Protein immunohistochemical staining was also performed to investigate target protein expression on 72 samples. We found that mir-21 expression increased with worsening clinical diagnosis but that mir-143 was not correlated with histology. These observations were in stark contrast to previous reports involving cervical cancer cell lines in which mir-143 was consistently down-regulated but mir-21 largely unaffected. We also identified, for the first time, that cytoplasmic expression of Programmed Cell Death Protein 4 PDCD4; a known target of mir-21) was significantly lower in women with invasive cervical carcinoma (ICC) in comparison to those with cervical intraepithelial neoplasia (2-3) or carcinoma in situ (CIN2-3/CIS), although there was no significant correlation between mir-21 and PDCD4 expression, despite previous studies identifying PDCD4 transcript as a known mir-21 target.Whilst microRNA biomarkers have a number of promising features, more studies on expression levels in histologically defined clinical specimens are required to investigate clinical relevance of discovery-based studies. Mir-21 may be of some utility in predictive screening, given that we observed a significant correlation between mir-21 expression level and worsening histological diagnosis of cervical cancer
miR-Q: a novel quantitative RT-PCR approach for the expression profiling of small RNA molecules such as miRNAs in a complex sample
<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) are small endogenous non-coding interfering RNA molecules regarded as major regulators in eukaryotic gene expression. Different methods are employed for miRNA expression profiling. For a better understanding of their role in essential biological processes, convenient methods for differential miRNA expression analysis are required.</p> <p>Results</p> <p>Here, we present the miR-Q assay as a highly sensitive quantitative reverse transcription PCR (qRT-PCR) for expression analysis of small RNAs such as miRNA molecules. It shows a high dynamic range of 6 to 8 orders of magnitude comprising a sensitivity of up to 0.2 fM miRNA, which corresponds to single copies per cell. There is nearly no cross reaction among closely-related miRNA family members, which points to the high specificity of the assays. Using this approach, we quantified the expression of let-7b in different human cell lines as well as miR-145 and miR-21 expression in porcine intestinal samples.</p> <p>Conclusion</p> <p>miR-Q is a cost-effective and highly specific approach, which neither requires the use of fluorochromic probes, nor Locked Nucleic Acid (LNA)-modified oligonucleotides. Moreover, it provides a remarkable increase in specificity and simplified detection of small RNAs.</p
Stochastic Gravity: Theory and Applications
Whereas semiclassical gravity is based on the semiclassical Einstein equation
with sources given by the expectation value of the stress-energy tensor of
quantum fields, stochastic semiclassical gravity is based on the
Einstein-Langevin equation, which has in addition sources due to the noise
kernel.In the first part, we describe the fundamentals of this new theory via
two approaches: the axiomatic and the functional. In the second part, we
describe three applications of stochastic gravity theory. First, we consider
metric perturbations in a Minkowski spacetime: we compute the two-point
correlation functions for the linearized Einstein tensor and for the metric
perturbations. Second, we discuss structure formation from the stochastic
gravity viewpoint. Third, we discuss the backreaction of Hawking radiation in
the gravitational background of a quasi-static black hole.Comment: 75 pages, no figures, submitted to Living Reviews in Relativit
Self-management support interventions for stroke survivors: a systematic meta-review
There is considerable policy interest in promoting self-management in patients with long-term conditions, but it remains uncertain whether these interventions are effective in stroke patients.Systematic meta-review of the evidence for self-management support interventions with stroke survivors to inform provision of healthcare services.We searched MEDLINE, EMBASE, CINAHL, PsychINFO, AMED, BNI, Database of Abstracts of Reviews for Effectiveness, and Cochrane Database of Systematic Reviews for systematic reviews of self-management support interventions for stroke survivors. Quality was assessed using the R-AMSTAR tool, and data extracted using a customised data extraction form. We undertook a narrative synthesis of the reviews' findings.From 12,400 titles we selected 13 systematic reviews (published 2003-2012) representing 101 individual trials. Although the term 'self-management' was rarely used, key elements of self-management support such as goal setting, action planning, and problem solving were core components of therapy rehabilitation interventions. We found high quality evidence that supported self-management in the context of therapy rehabilitation delivered soon after the stroke event resulted in short-term (< 1 year) improvements in basic and extended activities of daily living, and a reduction in poor outcomes (dependence/death). There is some evidence that rehabilitation and problem solving interventions facilitated reintegration into the community.Self-management terminology is rarely used in the context of stroke. However, therapy rehabilitation currently successfully delivers elements of self-management support to stroke survivors and their caregivers with improved outcomes. Future research should focus on managing the emotional, medical and social tasks of long-term survivorship
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