WorldWideScience

Sample records for small matter micrornas

  1. Small Molecule, Big Prospects: MicroRNA in Pregnancy and Its Complications

    Directory of Open Access Journals (Sweden)

    Meng Cai

    2017-01-01

    Full Text Available MicroRNAs are small, noncoding RNA molecules that regulate target gene expression in the posttranscriptional level. Unlike siRNA, microRNAs are “fine-tuners” rather than “switches” in the regulation of gene expression; thus they play key roles in maintaining tissue homeostasis. The aberrant microRNA expression is implicated in the disease process. To date, numerous studies have demonstrated the regulatory roles of microRNAs in various pathophysiological conditions. In contrast, the study of microRNA in pregnancy and its associated complications, such as preeclampsia (PE, fetal growth restriction (FGR, and preterm labor, is a young field. Over the last decade, the knowledge of pregnancy-related microRNAs has increased and the molecular mechanisms by which microRNAs regulate pregnancy or its associated complications are emerging. In this review, we focus on the recent advances in the research of pregnancy-related microRNAs, especially their function in pregnancy-associated complications and the potential clinical applications. Here microRNAs that associate with pregnancy are classified as placenta-specific, placenta-associated, placenta-derived circulating, and uterine microRNA according to their localization and origin. MicroRNAs offer a great potential for developing diagnostic and therapeutic targets in pregnancy-related disorders.

  2. OP17MICRORNA PROFILING USING SMALL RNA-SEQ IN PAEDIATRIC LOW GRADE GLIOMAS

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    Jeyapalan, Jennie N.; Jones, Tania A.; Tatevossian, Ruth G.; Qaddoumi, Ibrahim; Ellison, David W.; Sheer, Denise

    2014-01-01

    INTRODUCTION: MicroRNAs regulate gene expression by targeting mRNAs for translational repression or degradation at the post-transcriptional level. In paediatric low-grade gliomas a few key genetic mutations have been identified, including BRAF fusions, FGFR1 duplications and MYB rearrangements. Our aim in the current study is to profile aberrant microRNA expression in paediatric low-grade gliomas and determine the role of epigenetic changes in the aetiology and behaviour of these tumours. METHOD: MicroRNA profiling of tumour samples (6 pilocytic, 2 diffuse, 2 pilomyxoid astrocytomas) and normal brain controls (4 adult normal brain samples and a primary glial progenitor cell-line) was performed using small RNA sequencing. Bioinformatic analysis included sequence alignment, analysis of the number of reads (CPM, counts per million) and differential expression. RESULTS: Sequence alignment identified 695 microRNAs, whose expression was compared in tumours v. normal brain. PCA and hierarchical clustering showed separate groups for tumours and normal brain. Computational analysis identified approximately 400 differentially expressed microRNAs in the tumours compared to matched location controls. Our findings will then be validated and integrated with extensive genetic and epigenetic information we have previously obtained for the full tumour cohort. CONCLUSION: We have identified microRNAs that are differentially expressed in paediatric low-grade gliomas. As microRNAs are known to target genes involved in the initiation and progression of cancer, they provide critical information on tumour pathogenesis and are an important class of biomarkers.

  3. Neuronal dark matter: The emerging role of microRNAs in neurodegeneration

    Directory of Open Access Journals (Sweden)

    Emily Frances Goodall

    2013-10-01

    Full Text Available MicroRNAs (miRNAs are small, abundant RNA molecules that constitute part of the cell’s non-coding RNA dark matter. In recent years, the discovery of miRNAs has revolutionised the traditional view of gene expression and our understanding of miRNA biogenesis and function has expanded. Altered expression of miRNAs is increasingly recognised as a feature of many disease states, including neurodegeneration. Here, we review the emerging role for miRNA dysfunction in Alzheimer’s disease, Parkinson’s disease, amyotrophic lateral sclerosis and Huntington’s disease pathogenesis. We emphasise the complex nature of gene regulatory networks and the need for systematic studies, with larger sample cohorts than have so far been reported, to reveal the most important miRNA regulators in disease. Finally, miRNA diversity and their potential to target multiple pathways, offers novel clinical applications for miRNAs as biomarkers and therapeutic agents in neurodegenerative diseases.

  4. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs

    DEFF Research Database (Denmark)

    Khan, Aly A; Betel, Doron; Miller, Martin L

    2009-01-01

    Transfection of small RNAs (such as small interfering RNAs (siRNAs) and microRNAs (miRNAs)) into cells typically lowers expression of many genes. Unexpectedly, increased expression of genes also occurs. We investigated whether this upregulation results from a saturation effect--that is, competiti...

  5. Small Molecule Modifiers of the microRNA and RNA Interference Pathway

    OpenAIRE

    Deiters, Alexander

    2009-01-01

    Recently, the RNA interference (RNAi) pathway has become the target of small molecule inhibitors and activators. RNAi has been well established as a research tool in the sequence-specific silencing of genes in eukaryotic cells and organisms by using exogenous, small, double-stranded RNA molecules of approximately 20 nucleotides. Moreover, a recently discovered post-transcriptional gene regulatory mechanism employs microRNAs (miRNAs), a class of endogenously expressed small RNA molecules, whic...

  6. Small but mighty: Dark matter substructures

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    Cyr-Racine, Francis-Yan; Keeton, Charles; Moustakas, Leonidas

    2018-01-01

    The fundamental properties of dark matter, such as its mass, self-interaction, and coupling to other particles, can have a major impact on the evolution of cosmological density fluctuations on small length scales. Strong gravitational lenses have long been recognized as powerful tools to study the dark matter distribution on these small subgalactic scales. In this talk, we discuss how gravitationally lensed quasars and extended lensed arcs could be used to probe non minimal dark matter models. We comment on the possibilities enabled by precise astrometry, deep imaging, and time delays to extract information about mass substructures inside lens galaxies. To this end, we introduce a new lensing statistics that allows for a robust diagnostic of the presence of perturbations caused by substructures. We determine which properties of mass substructures are most readily constrained by lensing data and forecast the constraining power of current and future observations.

  7. Small white matter lesion detection in cerebral small vessel disease

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    Ghafoorian, Mohsen; Karssemeijer, Nico; van Uden, Inge; de Leeuw, Frank E.; Heskes, Tom; Marchiori, Elena; Platel, Bram

    2015-03-01

    Cerebral small vessel disease (SVD) is a common finding on magnetic resonance images of elderly people. White matter lesions (WML) are important markers for not only the small vessel disease, but also neuro-degenerative diseases including multiple sclerosis, Alzheimer's disease and vascular dementia. Volumetric measurements such as the "total lesion load", have been studied and related to these diseases. With respect to SVD we conjecture that small lesions are important, as they have been observed to grow over time and they form the majority of lesions in number. To study these small lesions they need to be annotated, which is a complex and time-consuming task. Existing (semi) automatic methods have been aimed at volumetric measurements and large lesions, and are not suitable for the detection of small lesions. In this research we established a supervised voxel classification CAD system, optimized and trained to exclusively detect small WMLs. To achieve this, several preprocessing steps were taken, which included a robust standardization of subject intensities to reduce inter-subject intensity variability as much as possible. A number of features that were found to be well identifying small lesions were calculated including multimodal intensities, tissue probabilities, several features for accurate location description, a number of second order derivative features as well as multi-scale annular filter for blobness detection. Only small lesions were used to learn the target concept via Adaboost using random forests as its basic classifiers. Finally the results were evaluated using Free-response receiver operating characteristic.

  8. Cold dark matter: Controversies on small scales.

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    Weinberg, David H; Bullock, James S; Governato, Fabio; Kuzio de Naray, Rachel; Peter, Annika H G

    2015-10-06

    The cold dark matter (CDM) cosmological model has been remarkably successful in explaining cosmic structure over an enormous span of redshift, but it has faced persistent challenges from observations that probe the innermost regions of dark matter halos and the properties of the Milky Way's dwarf galaxy satellites. We review the current observational and theoretical status of these "small-scale controversies." Cosmological simulations that incorporate only gravity and collisionless CDM predict halos with abundant substructure and central densities that are too high to match constraints from galaxy dynamics. The solution could lie in baryonic physics: Recent numerical simulations and analytical models suggest that gravitational potential fluctuations tied to efficient supernova feedback can flatten the central cusps of halos in massive galaxies, and a combination of feedback and low star formation efficiency could explain why most of the dark matter subhalos orbiting the Milky Way do not host visible galaxies. However, it is not clear that this solution can work in the lowest mass galaxies, where discrepancies are observed. Alternatively, the small-scale conflicts could be evidence of more complex physics in the dark sector itself. For example, elastic scattering from strong dark matter self-interactions can alter predicted halo mass profiles, leading to good agreement with observations across a wide range of galaxy mass. Gravitational lensing and dynamical perturbations of tidal streams in the stellar halo provide evidence for an abundant population of low-mass subhalos in accord with CDM predictions. These observational approaches will get more powerful over the next few years.

  9. Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs.

    Directory of Open Access Journals (Sweden)

    Noah Fahlgren

    Full Text Available In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focused on plant and animal RNA silencing systems. Phytophthora species belong to a phylogenetically distinct group of economically important plant pathogens that cause billions of dollars in yield losses annually as well as ecologically devastating outbreaks. We analyzed the small RNA-generating components of the genomes of P. infestans, P. sojae and P. ramorum using bioinformatics, genetic, phylogenetic and high-throughput sequencing-based methods. Each species produces two distinct populations of small RNAs that are predominantly 21- or 25-nucleotides long. The 25-nucleotide small RNAs were primarily derived from loci encoding transposable elements and we propose that these small RNAs define a pathway of short-interfering RNAs that silence repetitive genetic elements. The 21-nucleotide small RNAs were primarily derived from inverted repeats, including a novel microRNA family that is conserved among the three species, and several gene families, including Crinkler effectors and type III fibronectins. The Phytophthora microRNA is predicted to target a family of amino acid/auxin permeases, and we propose that 21-nucleotide small RNAs function at the post-transcriptional level. The functional significance of microRNA-guided regulation of amino acid/auxin permeases and the association of 21-nucleotide small RNAs with Crinkler effectors remains unclear, but this work provides a framework for testing the role of small RNAs in Phytophthora biology and pathogenesis in future work.

  10. Phytophthora have distinct endogenous small RNA populations that include short interfering and microRNAs.

    Science.gov (United States)

    Fahlgren, Noah; Bollmann, Stephanie R; Kasschau, Kristin D; Cuperus, Josh T; Press, Caroline M; Sullivan, Christopher M; Chapman, Elisabeth J; Hoyer, J Steen; Gilbert, Kerrigan B; Grünwald, Niklaus J; Carrington, James C

    2013-01-01

    In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focused on plant and animal RNA silencing systems. Phytophthora species belong to a phylogenetically distinct group of economically important plant pathogens that cause billions of dollars in yield losses annually as well as ecologically devastating outbreaks. We analyzed the small RNA-generating components of the genomes of P. infestans, P. sojae and P. ramorum using bioinformatics, genetic, phylogenetic and high-throughput sequencing-based methods. Each species produces two distinct populations of small RNAs that are predominantly 21- or 25-nucleotides long. The 25-nucleotide small RNAs were primarily derived from loci encoding transposable elements and we propose that these small RNAs define a pathway of short-interfering RNAs that silence repetitive genetic elements. The 21-nucleotide small RNAs were primarily derived from inverted repeats, including a novel microRNA family that is conserved among the three species, and several gene families, including Crinkler effectors and type III fibronectins. The Phytophthora microRNA is predicted to target a family of amino acid/auxin permeases, and we propose that 21-nucleotide small RNAs function at the post-transcriptional level. The functional significance of microRNA-guided regulation of amino acid/auxin permeases and the association of 21-nucleotide small RNAs with Crinkler effectors remains unclear, but this work provides a framework for testing the role of small RNAs in Phytophthora biology and pathogenesis in future work.

  11. Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs

    Science.gov (United States)

    Fahlgren, Noah; Bollmann, Stephanie R.; Kasschau, Kristin D.; Cuperus, Josh T.; Press, Caroline M.; Sullivan, Christopher M.; Chapman, Elisabeth J.; Hoyer, J. Steen; Gilbert, Kerrigan B.; Grünwald, Niklaus J.; Carrington, James C.

    2013-01-01

    In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focused on plant and animal RNA silencing systems. Phytophthora species belong to a phylogenetically distinct group of economically important plant pathogens that cause billions of dollars in yield losses annually as well as ecologically devastating outbreaks. We analyzed the small RNA-generating components of the genomes of P. infestans, P. sojae and P. ramorum using bioinformatics, genetic, phylogenetic and high-throughput sequencing-based methods. Each species produces two distinct populations of small RNAs that are predominantly 21- or 25-nucleotides long. The 25-nucleotide small RNAs were primarily derived from loci encoding transposable elements and we propose that these small RNAs define a pathway of short-interfering RNAs that silence repetitive genetic elements. The 21-nucleotide small RNAs were primarily derived from inverted repeats, including a novel microRNA family that is conserved among the three species, and several gene families, including Crinkler effectors and type III fibronectins. The Phytophthora microRNA is predicted to target a family of amino acid/auxin permeases, and we propose that 21-nucleotide small RNAs function at the post-transcriptional level. The functional significance of microRNA-guided regulation of amino acid/auxin permeases and the association of 21-nucleotide small RNAs with Crinkler effectors remains unclear, but this work provides a framework for testing the role of small RNAs in Phytophthora biology and pathogenesis in future work. PMID:24204767

  12. Chimira: analysis of small RNA sequencing data and microRNA modifications.

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    Vitsios, Dimitrios M; Enright, Anton J

    2015-10-15

    Chimira is a web-based system for microRNA (miRNA) analysis from small RNA-Seq data. Sequences are automatically cleaned, trimmed, size selected and mapped directly to miRNA hairpin sequences. This generates count-based miRNA expression data for subsequent statistical analysis. Moreover, it is capable of identifying epi-transcriptomic modifications in the input sequences. Supported modification types include multiple types of 3'-modifications (e.g. uridylation, adenylation), 5'-modifications and also internal modifications or variation (ADAR editing or single nucleotide polymorphisms). Besides cleaning and mapping of input sequences to miRNAs, Chimira provides a simple and intuitive set of tools for the analysis and interpretation of the results (see also Supplementary Material). These allow the visual study of the differential expression between two specific samples or sets of samples, the identification of the most highly expressed miRNAs within sample pairs (or sets of samples) and also the projection of the modification profile for specific miRNAs across all samples. Other tools have already been published in the past for various types of small RNA-Seq analysis, such as UEA workbench, seqBuster, MAGI, OASIS and CAP-miRSeq, CPSS for modifications identification. A comprehensive comparison of Chimira with each of these tools is provided in the Supplementary Material. Chimira outperforms all of these tools in total execution speed and aims to facilitate simple, fast and reliable analysis of small RNA-Seq data allowing also, for the first time, identification of global microRNA modification profiles in a simple intuitive interface. Chimira has been developed as a web application and it is accessible here: http://www.ebi.ac.uk/research/enright/software/chimira. aje@ebi.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

  13. Undesired small RNAs originate from an artificial microRNA precursor in transgenic petunia (Petunia hybrida.

    Directory of Open Access Journals (Sweden)

    Yulong Guo

    Full Text Available Although artificial microRNA (amiRNA technology has been used frequently in gene silencing in plants, little research has been devoted to investigating the accuracy of amiRNA precursor processing. In this work, amiRNAchs1 (amiRchs1, based on the Arabidopsis miR319a precursor, was expressed in order to suppress the expression of CHS genes in petunia. The transgenic plants showed the CHS gene-silencing phenotype. A modified 5' RACE technique was used to map small-RNA-directed cleavage sites and to detect processing intermediates of the amiRchs1 precursor. The results showed that the target CHS mRNAs were cut at the expected sites and that the amiRchs1 precursor was processed from loop to base. The accumulation of small RNAs in amiRchs1 transgenic petunia petals was analyzed using the deep-sequencing technique. The results showed that, alongside the accumulation of the desired artificial microRNAs, additional small RNAs that originated from other regions of the amiRNA precursor were also accumulated at high frequency. Some of these had previously been found to be accumulated at low frequency in the products of ath-miR319a precursor processing and some of them were accompanied by 3'-tailing variant. Potential targets of the undesired small RNAs were discovered in petunia and other Solanaceae plants. The findings draw attention to the potential occurrence of undesired target silencing induced by such additional small RNAs when amiRNA technology is used. No appreciable production of secondary small RNAs occurred, despite the fact that amiRchs1 was designed to have perfect complementarity to its CHS-J target. This confirmed that perfect pairing between an amiRNA and its targets is not the trigger for secondary small RNA production. In conjunction with the observation that amiRNAs with perfect complementarity to their target genes show high efficiency and specificity in gene silencing, this finding has an important bearing on future applications of ami

  14. Undesired small RNAs originate from an artificial microRNA precursor in transgenic petunia (Petunia hybrida).

    Science.gov (United States)

    Guo, Yulong; Han, Yao; Ma, Jing; Wang, Huiping; Sang, Xianchun; Li, Mingyang

    2014-01-01

    Although artificial microRNA (amiRNA) technology has been used frequently in gene silencing in plants, little research has been devoted to investigating the accuracy of amiRNA precursor processing. In this work, amiRNAchs1 (amiRchs1), based on the Arabidopsis miR319a precursor, was expressed in order to suppress the expression of CHS genes in petunia. The transgenic plants showed the CHS gene-silencing phenotype. A modified 5' RACE technique was used to map small-RNA-directed cleavage sites and to detect processing intermediates of the amiRchs1 precursor. The results showed that the target CHS mRNAs were cut at the expected sites and that the amiRchs1 precursor was processed from loop to base. The accumulation of small RNAs in amiRchs1 transgenic petunia petals was analyzed using the deep-sequencing technique. The results showed that, alongside the accumulation of the desired artificial microRNAs, additional small RNAs that originated from other regions of the amiRNA precursor were also accumulated at high frequency. Some of these had previously been found to be accumulated at low frequency in the products of ath-miR319a precursor processing and some of them were accompanied by 3'-tailing variant. Potential targets of the undesired small RNAs were discovered in petunia and other Solanaceae plants. The findings draw attention to the potential occurrence of undesired target silencing induced by such additional small RNAs when amiRNA technology is used. No appreciable production of secondary small RNAs occurred, despite the fact that amiRchs1 was designed to have perfect complementarity to its CHS-J target. This confirmed that perfect pairing between an amiRNA and its targets is not the trigger for secondary small RNA production. In conjunction with the observation that amiRNAs with perfect complementarity to their target genes show high efficiency and specificity in gene silencing, this finding has an important bearing on future applications of amiRNAs in gene

  15. Small Engine, Big Power: MicroRNAs as Regulators of Cardiac Diseases and Regeneration

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    Darukeshwara Joladarashi

    2014-09-01

    Full Text Available Cardiac diseases are the predominant cause of human mortality in the United States and around the world. MicroRNAs (miRNAs are small non-coding RNAs that have been shown to modulate a wide range of biological functions under various pathophysiological conditions. miRNAs alter target expression by post-transcriptional regulation of gene expression. Numerous studies have implicated specific miRNAs in cardiovascular development, pathology, regeneration and repair. These observations suggest that miRNAs are potential therapeutic targets to prevent or treat cardiovascular diseases. This review focuses on the emerging role of miRNAs in cardiac development, pathogenesis of cardiovascular diseases, cardiac regeneration and stem cell-mediated cardiac repair. We also discuss the novel diagnostic and therapeutic potential of these miRNAs and their targets in patients with cardiac diseases.

  16. Small RNA sequencing reveals metastasis-related microRNAs in lung adenocarcinoma

    DEFF Research Database (Denmark)

    Daugaard, Iben; Venø, Morten T.; Yan, Yan

    2017-01-01

    The majority of lung cancer deaths are caused by metastatic disease. MicroRNAs (miRNAs) are posttranscriptional regulators of gene expression and miRNA dysregulation can contribute to metastatic progression. Here, small RNA sequencing was used to profile the miRNA and piwi-interacting RNA (piRNA......) transcriptomes in relation to lung cancer metastasis. RNA-seq was performed using RNA extracted from formalin-fixed paraffin embedded (FFPE) lung adenocarcinomas (LAC) and brain metastases from 8 patients, and LACs from 8 patients without detectable metastatic disease. Impact on miRNA and piRNA transcriptomes...... was subtle with 9 miRNAs and 8 piRNAs demonstrating differential expression between metastasizing and non-metastasizing LACs. For piRNAs, decreased expression of piR-57125 was the most significantly associated with distant metastasis. Validation by RT-qPCR in a LAC cohort comprising 52 patients confirmed...

  17. Concentrated dark matter: Enhanced small-scale structure from codecaying dark matter

    OpenAIRE

    Dror, Jeff A.; Kuflik, Eric; Melcher, Brandon; Watson, Scott

    2018-01-01

    We study the cosmological consequences of codecaying dark matter—a recently proposed mechanism for depleting the density of dark matter through the decay of nearly degenerate particles. A generic prediction of this framework is an early dark matter dominated phase in the history of the Universe, that results in the enhanced growth of dark matter perturbations on small scales. We compute the duration of the early matter dominated phase and show that the perturbations are robust against washout...

  18. Small Molecule Targeting of a MicroRNA Associated with Hepatocellular Carcinoma.

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    Childs-Disney, Jessica L; Disney, Matthew D

    2016-02-19

    Development of precision therapeutics is of immense interest, particularly as applied to the treatment of cancer. By analyzing the preferred cellular RNA targets of small molecules, we discovered that 5"-azido neomycin B binds the Drosha processing site in the microRNA (miR)-525 precursor. MiR-525 confers invasive properties to hepatocellular carcinoma (HCC) cells. Although HCC is one of the most common cancers, treatment options are limited, making the disease often fatal. Herein, we find that addition of 5"-azido neomycin B and its FDA-approved precursor, neomycin B, to an HCC cell line selectively inhibits production of the mature miRNA, boosts a downstream protein, and inhibits invasion. Interestingly, neomycin B is a second-line agent for hepatic encephalopathy (HE) and bacterial infections due to cirrhosis. Our results provocatively suggest that neomycin B, or second-generation derivatives, may be dual functioning molecules to treat both HE and HCC. Collectively, these studies show that rational design approaches can be tailored to disease-associated RNAs to afford potential lead therapeutics.

  19. Ambient particulate matter and microRNAs in extracellular vesicles: a pilot study of older individuals.

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    Rodosthenous, Rodosthenis S; Coull, Brent A; Lu, Quan; Vokonas, Pantel S; Schwartz, Joel D; Baccarelli, Andrea A

    2016-03-08

    Air pollution from particulate matter (PM) has been linked to cardiovascular morbidity and mortality; however the underlying biological mechanisms remain to be uncovered. Gene regulation by microRNAs (miRNAs) that are transferred between cells by extracellular vesicles (EVs) may play an important role in PM-induced cardiovascular risk. This study sought to determine if ambient PM2.5 levels are associated with expression of EV-encapsulated miRNAs (evmiRNAs), and to investigate the participation of such evmiRNAs in pathways related to cardiovascular disease (CVD). We estimated the short- (1-day), intermediate- (1-week and 1-month) and long-term (3-month, 6-month, and 1-year) moving averages of ambient PM2.5 levels at participants' addresses using a validated hybrid spatio-temporal land-use regression model. We collected 42 serum samples from 22 randomly selected participants in the Normative Aging Study cohort and screened for 800 miRNAs using the NanoString nCounter® platform. Mixed effects regression models, adjusted for potential confounders were used to assess the association between ambient PM2.5 levels and evmiRNAs. All p-values were adjusted for multiple comparisons. In-silico Ingenuity Pathway Analysis (IPA) was performed to identify biological pathways that are regulated by PM-associated evmiRNAs. We found a significant association between long-term ambient PM2.5 exposures and levels of multiple evmiRNAs circulating in serum. In the 6-month window, ambient PM2.5 exposures were associated with increased levels of miR-126-3p (0.74 ± 0.21; p = 0.02), miR-19b-3p (0.52 ± 0.15; p = 0.02), miR-93-5p (0.78 ± 0.22; p = 0.02), miR-223-3p (0.74 ± 0.22; p = 0.02), and miR-142-3p (0.81 ± 0.21; p = 0.03). Similarly, in the 1-year window, ambient PM2.5 levels were associated with increased levels of miR-23a-3p (0.83 ± 0.23; p = 0.02), miR-150-5p (0.90 ± 0.24; p = 0.02), miR-15a-5p (0.70 ± 0.21; p = 0

  20. MicroRNA-944 Affects Cell Growth by Targeting EPHA7 in Non-Small Cell Lung Cancer

    OpenAIRE

    Minxia Liu; Kecheng Zhou; Yi Cao

    2016-01-01

    MicroRNAs (miRNAs) have critical roles in lung tumorigenesis and development. To determine aberrantly expressed miRNAs involved in non-small cell lung cancer (NSCLC) and investigate pathophysiological functions and mechanisms, we firstly carried out small RNA deep sequencing in NSCLC cell lines (EPLC-32M1, A549 and 801D) and a human immortalized cell line 16HBE, we then studied miRNA function by cell proliferation and apoptosis. cDNA microarray, luciferase reporter assay and miRNA transfectio...

  1. Application of small RNA sequencing to identify microRNAs in acute kidney injury and fibrosis

    Energy Technology Data Exchange (ETDEWEB)

    Pellegrini, Kathryn L. [Department of Medicine, Renal Division, Brigham and Women' s Hospital, Harvard Medical School, Boston, MA (United States); Gerlach, Cory V. [Department of Medicine, Renal Division, Brigham and Women' s Hospital, Harvard Medical School, Boston, MA (United States); Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA (United States); Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Sciences, Harvard Medical School, Boston, MA (United States); Craciun, Florin L.; Ramachandran, Krithika [Department of Medicine, Renal Division, Brigham and Women' s Hospital, Harvard Medical School, Boston, MA (United States); Bijol, Vanesa [Department of Pathology, Brigham and Women' s Hospital, Harvard Medical School, Boston, MA (United States); Kissick, Haydn T. [Department of Surgery, Urology Division, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA (United States); Vaidya, Vishal S., E-mail: vvaidya@bwh.harvard.edu [Department of Medicine, Renal Division, Brigham and Women' s Hospital, Harvard Medical School, Boston, MA (United States); Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA (United States); Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Sciences, Harvard Medical School, Boston, MA (United States)

    2016-12-01

    Establishing a microRNA (miRNA) expression profile in affected tissues provides an important foundation for the discovery of miRNAs involved in the development or progression of pathologic conditions. We conducted small RNA sequencing to generate a temporal profile of miRNA expression in the kidneys using a mouse model of folic acid-induced (250 mg/kg i.p.) kidney injury and fibrosis. From the 103 miRNAs that were differentially expressed over the time course (> 2-fold, p < 0.05), we chose to further investigate miR-18a-5p, which is expressed during the acute stage of the injury; miR-132-3p, which is upregulated during transition between acute and fibrotic injury; and miR-146b-5p, which is highly expressed at the peak of fibrosis. Using qRT-PCR, we confirmed the increased expression of these candidate miRNAs in the folic acid model as well as in other established mouse models of acute injury (ischemia/reperfusion injury) and fibrosis (unilateral ureteral obstruction). In situ hybridization confirmed high expression of miR-18a-5p, miR-132-3p and miR-146b-5p throughout the kidney cortex in mice and humans with severe kidney injury or fibrosis. When primary human proximal tubular epithelial cells were treated with model nephrotoxicants such as cadmium chloride (CdCl{sub 2}), arsenic trioxide, aristolochic acid (AA), potassium dichromate (K{sub 2}Cr{sub 2}O{sub 7}) and cisplatin, miRNA-132-3p was upregulated 4.3-fold after AA treatment and 1.5-fold after K{sub 2}Cr{sub 2}O{sub 7} and CdCl{sub 2} treatment. These results demonstrate the application of temporal small RNA sequencing to identify miR-18a, miR-132 and miR-146b as differentially expressed miRNAs during distinct phases of kidney injury and fibrosis progression. - Highlights: • We used small RNA sequencing to identify differentially expressed miRNAs in kidney. • Distinct patterns were found for acute injury and fibrotic stages in the kidney. • Upregulation of miR-18a, -132 and -146b was confirmed in mice

  2. Isolation of Exosome-Like Nanoparticles and Analysis of MicroRNAs Derived from Coconut Water Based on Small RNA High-Throughput Sequencing.

    Science.gov (United States)

    Zhao, Zhehao; Yu, Siran; Li, Min; Gui, Xin; Li, Ping

    2018-03-21

    In this study, the presence of microRNAs in coconut water was identified by real-time polymerase chain reaction (PCR) based on the results of high-throughput small RNA sequencing. In addition, the differences in microRNA content between immature and mature coconut water were compared. A total of 47 known microRNAs belonging to 25 families and 14 new microRNAs were identified in coconut endosperm. Through analysis using a target gene prediction software, potential microRNA target genes were identified in the human genome. Real-time PCR showed that the level of most microRNAs was higher in mature coconut water than in immature coconut water. Then, exosome-like nanoparticles were isolated from coconut water. After ultracentrifugation, some particle structures were seen in coconut water samples using 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate fluorescence staining. Subsequent scanning electron microscopy observation and dynamic light scattering analysis also revealed some exosome-like nanoparticles in coconut water, and the mean diameters of the particles detected by the two methods were 13.16 and 59.72 nm, respectively. In conclusion, there are extracellular microRNAs in coconut water, and their levels are higher in mature coconut water than in immature coconut water. Some exosome-like nanoparticles were isolated from coconut water, and the diameter of these particles was smaller than that of animal-derived exosomes.

  3. Effective description of dark matter self-interactions in small dark matter haloes

    International Nuclear Information System (INIS)

    Kummer, Janis

    2017-07-01

    Self-interacting dark matter may have striking astrophysical signatures, such as observ- able offsets between galaxies and dark matter in merging galaxy clusters. Numerical N-body simulations used to predict such observables typically treat the galaxies as collisionless test particles, a questionable assumption given that each galaxy is embedded in its own dark matter halo. To enable a more accurate treatment we develop an effective description of small dark matter haloes taking into account the two major effects due to dark matter self-scatterings: deceleration and evaporation. We point out that self-scatterings can have a sizeable impact on the trajectories of galaxies, diminishing the separation between galaxies and dark matter in merging clusters. This effect depends sensitively on the underlying particle physics, in particular the angular dependence of the self-scattering cross section, and cannot be predicted from the momentum transfer cross section alone.

  4. MicroRNA-944 Affects Cell Growth by Targeting EPHA7 in Non-Small Cell Lung Cancer

    Directory of Open Access Journals (Sweden)

    Minxia Liu

    2016-09-01

    Full Text Available MicroRNAs (miRNAs have critical roles in lung tumorigenesis and development. To determine aberrantly expressed miRNAs involved in non-small cell lung cancer (NSCLC and investigate pathophysiological functions and mechanisms, we firstly carried out small RNA deep sequencing in NSCLC cell lines (EPLC-32M1, A549 and 801D and a human immortalized cell line 16HBE, we then studied miRNA function by cell proliferation and apoptosis. cDNA microarray, luciferase reporter assay and miRNA transfection were used to investigate interaction between the miRNA and target gene. miR-944 was significantly down-regulated in NSCLC and had many putative targets. Moreover, the forced expression of miR-944 significantly inhibited the proliferation of NSCLC cells in vitro. By integrating mRNA expression data and miR-944-target prediction, we disclosed that EPHA7 was a potential target of miR-944, which was further verified by luciferase reporter assay and microRNA transfection. Our data indicated that miR-944 targets EPHA7 in NSCLC and regulates NSCLC cell proliferation, which may offer a new mechanism underlying the development and progression of NSCLC.

  5. MicroRNA-944 Affects Cell Growth by Targeting EPHA7 in Non-Small Cell Lung Cancer.

    Science.gov (United States)

    Liu, Minxia; Zhou, Kecheng; Cao, Yi

    2016-09-26

    MicroRNAs (miRNAs) have critical roles in lung tumorigenesis and development. To determine aberrantly expressed miRNAs involved in non-small cell lung cancer (NSCLC) and investigate pathophysiological functions and mechanisms, we firstly carried out small RNA deep sequencing in NSCLC cell lines (EPLC-32M1, A549 and 801D) and a human immortalized cell line 16HBE, we then studied miRNA function by cell proliferation and apoptosis. cDNA microarray, luciferase reporter assay and miRNA transfection were used to investigate interaction between the miRNA and target gene. miR-944 was significantly down-regulated in NSCLC and had many putative targets. Moreover, the forced expression of miR-944 significantly inhibited the proliferation of NSCLC cells in vitro. By integrating mRNA expression data and miR-944-target prediction, we disclosed that EPHA7 was a potential target of miR-944, which was further verified by luciferase reporter assay and microRNA transfection. Our data indicated that miR-944 targets EPHA7 in NSCLC and regulates NSCLC cell proliferation, which may offer a new mechanism underlying the development and progression of NSCLC.

  6. High-throughput sequencing of small RNA transcriptome reveals salt stress regulated microRNAs in sugarcane.

    Directory of Open Access Journals (Sweden)

    Mariana Carnavale Bottino

    Full Text Available Salt stress is a primary cause of crop losses worldwide, and it has been the subject of intense investigation to unravel the complex mechanisms responsible for salinity tolerance. MicroRNA is implicated in many developmental processes and in responses to various abiotic stresses, playing pivotal roles in plant adaptation. Deep sequencing technology was chosen to determine the small RNA transcriptome of Saccharum sp cultivars grown on saline conditions. We constructed four small RNAs libraries prepared from plants grown on hydroponic culture submitted to 170 mM NaCl and harvested after 1 h, 6 hs and 24 hs. Each library was sequenced individually and together generated more than 50 million short reads. Ninety-eight conserved miRNAs and 33 miRNAs* were identified by bioinformatics. Several of the microRNA showed considerable differences of expression in the four libraries. To confirm the results of the bioinformatics-based analysis, we studied the expression of the 10 most abundant miRNAs and 1 miRNA* in plants treated with 170 mM NaCl and in plants with a severe treatment of 340 mM NaCl. The results showed that 11 selected miRNAs had higher expression in samples treated with severe salt treatment compared to the mild one. We also investigated the regulation of the same miRNAs in shoots of four cultivars grown on soil treated with 170 mM NaCl. Cultivars could be grouped according to miRNAs expression in response to salt stress. Furthermore, the majority of the predicted target genes had an inverse regulation with their correspondent microRNAs. The targets encode a wide range of proteins, including transcription factors, metabolic enzymes and genes involved in hormone signaling, probably assisting the plants to develop tolerance to salinity. Our work provides insights into the regulatory functions of miRNAs, thereby expanding our knowledge on potential salt-stressed regulated genes.

  7. High-throughput platform assay technology for the discovery of pre-microrna-selective small molecule probes.

    Science.gov (United States)

    Lorenz, Daniel A; Song, James M; Garner, Amanda L

    2015-01-21

    MicroRNAs (miRNA) play critical roles in human development and disease. As such, the targeting of miRNAs is considered attractive as a novel therapeutic strategy. A major bottleneck toward this goal, however, has been the identification of small molecule probes that are specific for select RNAs and methods that will facilitate such discovery efforts. Using pre-microRNAs as proof-of-concept, herein we report a conceptually new and innovative approach for assaying RNA-small molecule interactions. Through this platform assay technology, which we term catalytic enzyme-linked click chemistry assay or cat-ELCCA, we have designed a method that can be implemented in high throughput, is virtually free of false readouts, and is general for all nucleic acids. Through cat-ELCCA, we envision the discovery of selective small molecule ligands for disease-relevant miRNAs to promote the field of RNA-targeted drug discovery and further our understanding of the role of miRNAs in cellular biology.

  8. Epigenetic silencing of MicroRNA-503 regulates FANCA expression in non-small cell lung cancer cell.

    Science.gov (United States)

    Li, Ning; Zhang, Fangfang; Li, Suyun; Zhou, Suzhen

    2014-02-21

    It is reported that MicroRNA-503 (miR-503) regulates cell apoptosis, and thus modulates the resistance of non-small cell lung cancer cells (NSCLC) to cisplatin. However, the exact role of miR-503 in NSCLC remains unknown. In the present study, the level of miR-503 expression in NSCLC was evaluated using realtime PCR, and the DNA methylation status within miR-503 promoter was analyzed by Combined Bisulfite Restriction Analysis (COBRA) or bisulfite-treated DNA sequencing assays (BSP). We found that the expression of miR-503 was significantly decreased in NSCLC tissues compared to normal tissues. A statistically significant inverse association was found between miR-503 methylation status and expression of the miR-503 in tumor tissues (PFANCA) gene and represses its expression at the transcriptional level. Taken together, our results suggest that miR-503 regulates the resistance of non-small cell lung cancer cells to cisplatin at least in part by targeting FANCA. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. Isolation of microRNA targets using biotinylated synthetic microRNAs

    DEFF Research Database (Denmark)

    Ørom, Ulf Andersson; Lund, Anders H

    2007-01-01

    MicroRNAs are small regulatory RNAs found in multicellular organisms where they post-transcriptionally regulate gene expression. In animals, microRNAs bind mRNAs via incomplete base pairings making the identification of microRNA targets inherently difficult. Here, we present a detailed method...... for experimental identification of microRNA targets based on affinity purification of tagged microRNAs associated with their targets. Udgivelsesdato: 2007-Oct...

  10. Dark matter self-interactions and small scale structure

    Science.gov (United States)

    Tulin, Sean; Yu, Hai-Bo

    2018-02-01

    We review theories of dark matter (DM) beyond the collisionless paradigm, known as self-interacting dark matter (SIDM), and their observable implications for astrophysical structure in the Universe. Self-interactions are motivated, in part, due to the potential to explain long-standing (and more recent) small scale structure observations that are in tension with collisionless cold DM (CDM) predictions. Simple particle physics models for SIDM can provide a universal explanation for these observations across a wide range of mass scales spanning dwarf galaxies, low and high surface brightness spiral galaxies, and clusters of galaxies. At the same time, SIDM leaves intact the success of ΛCDM cosmology on large scales. This report covers the following topics: (1) small scale structure issues, including the core-cusp problem, the diversity problem for rotation curves, the missing satellites problem, and the too-big-to-fail problem, as well as recent progress in hydrodynamical simulations of galaxy formation; (2) N-body simulations for SIDM, including implications for density profiles, halo shapes, substructure, and the interplay between baryons and self-interactions; (3) semi-analytic Jeans-based methods that provide a complementary approach for connecting particle models with observations; (4) merging systems, such as cluster mergers (e.g., the Bullet Cluster) and minor infalls, along with recent simulation results for mergers; (5) particle physics models, including light mediator models and composite DM models; and (6) complementary probes for SIDM, including indirect and direct detection experiments, particle collider searches, and cosmological observations. We provide a summary and critical look for all current constraints on DM self-interactions and an outline for future directions.

  11. Identification and Characterization of MicroRNAs in Small Brown Planthopper (Laodephax striatellus) by Next-Generation Sequencing

    Science.gov (United States)

    Lou, Yonggen; Cheng, Jia'an; Zhang, Hengmu; Xu, Jian-Hong

    2014-01-01

    MicroRNAs (miRNAs) are endogenous non-coding small RNAs that regulate gene expression at the post-transcriptional level and are thought to play critical roles in many metabolic activities in eukaryotes. The small brown planthopper (Laodephax striatellus Fallén), one of the most destructive agricultural pests, causes great damage to crops including rice, wheat, and maize. However, information about the genome of L. striatellus is limited. In this study, a small RNA library was constructed from a mixed L. striatellus population and sequenced by Solexa sequencing technology. A total of 501 mature miRNAs were identified, including 227 conserved and 274 novel miRNAs belonging to 125 and 250 families, respectively. Sixty-nine conserved miRNAs that are included in 38 families are predicted to have an RNA secondary structure typically found in miRNAs. Many miRNAs were validated by stem-loop RT-PCR. Comparison with the miRNAs in 84 animal species from miRBase showed that the conserved miRNA families we identified are highly conserved in the Arthropoda phylum. Furthermore, miRanda predicted 2701 target genes for 378 miRNAs, which could be categorized into 52 functional groups annotated by gene ontology. The function of miRNA target genes was found to be very similar between conserved and novel miRNAs. This study of miRNAs in L. striatellus will provide new information and enhance the understanding of the role of miRNAs in the regulation of L. striatellus metabolism and development. PMID:25057821

  12. Identification and characterization of microRNAs in small brown planthopper (Laodephax striatellus by next-generation sequencing.

    Directory of Open Access Journals (Sweden)

    Guoyan Zhou

    Full Text Available MicroRNAs (miRNAs are endogenous non-coding small RNAs that regulate gene expression at the post-transcriptional level and are thought to play critical roles in many metabolic activities in eukaryotes. The small brown planthopper (Laodephax striatellus Fallén, one of the most destructive agricultural pests, causes great damage to crops including rice, wheat, and maize. However, information about the genome of L. striatellus is limited. In this study, a small RNA library was constructed from a mixed L. striatellus population and sequenced by Solexa sequencing technology. A total of 501 mature miRNAs were identified, including 227 conserved and 274 novel miRNAs belonging to 125 and 250 families, respectively. Sixty-nine conserved miRNAs that are included in 38 families are predicted to have an RNA secondary structure typically found in miRNAs. Many miRNAs were validated by stem-loop RT-PCR. Comparison with the miRNAs in 84 animal species from miRBase showed that the conserved miRNA families we identified are highly conserved in the Arthropoda phylum. Furthermore, miRanda predicted 2701 target genes for 378 miRNAs, which could be categorized into 52 functional groups annotated by gene ontology. The function of miRNA target genes was found to be very similar between conserved and novel miRNAs. This study of miRNAs in L. striatellus will provide new information and enhance the understanding of the role of miRNAs in the regulation of L. striatellus metabolism and development.

  13. Loss of white matter integrity is associated with gait disorders in cerebral small vessel disease

    NARCIS (Netherlands)

    Laat, K.F. de; Tuladhar, A.M.; Norden, A.G.W. van; Norris, D.G.; Zwiers, M.P.; Leeuw, F.E. de

    2011-01-01

    Gait disturbances are common in the elderly. Cerebral small vessel disease, including white matter lesions and lacunars infarcts, is thought to disrupt white matter tracts that connect important motor regions, hence resulting in gait disturbances. Pathological studies have demonstrated abnormalities

  14. Small RNA Deep Sequencing and the Effects of microRNA408 on Root Gravitropic Bending in Arabidopsis

    Science.gov (United States)

    Li, Huasheng; Lu, Jinying; Sun, Qiao; Chen, Yu; He, Dacheng; Liu, Min

    2015-11-01

    MicroRNA (miRNA) is a non-coding small RNA composed of 20 to 24 nucleotides that influences plant root development. This study analyzed the miRNA expression in Arabidopsis root tip cells using Illumina sequencing and real-time PCR before (sample 0) and 15 min after (sample 15) a 3-D clinostat rotational treatment was administered. After stimulation was performed, the expression levels of seven miRNA genes, including Arabidopsis miR160, miR161, miR394, miR402, miR403, miR408, and miR823, were significantly upregulated. Illumina sequencing results also revealed two novel miRNAsthat have not been previously reported, The target genes of these miRNAs included pentatricopeptide repeat-containing protein and diadenosine tetraphosphate hydrolase. An overexpression vector of Arabidopsis miR408 was constructed and transferred to Arabidopsis plant. The roots of plants over expressing miR408 exhibited a slower reorientation upon gravistimulation in comparison with those of wild-type. This result indicate that miR408 could play a role in root gravitropic response.

  15. Implications of MicroRNAs in the Treatment of Gefitinib-Resistant Non-Small Cell Lung Cancer

    Directory of Open Access Journals (Sweden)

    Thomas K. Sin

    2016-02-01

    Full Text Available Non-small cell lung cancer (NSCLC represents about 85% of the reported cases of lung cancer. Acquired resistance to targeted therapy with epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs, such as gefitinib, is not uncommon. It is thus vital to explore novel strategies to restore sensitivity to gefitinib. Provided that microRNAs (miRNAs negatively regulate their gene targets at the transcriptional level, it is speculated that miRNA mimetics may reduce the expression, activity and signal transduction of EGFR so that sensitization of tumour sites to gefitinib-induced cytotoxicity can be achieved. Indeed, a growing body of evidence has shown that the manipulation of endogenous levels of miRNA not only attenuates the EGFR/PI3K/Akt phosphorylation cascade, but also restores apoptotic cell death in in vitro models of experimentally-induced gefitinib resistance and provoked tumour regression/shrinkage in xenograft models. These data are in concordant with the clinical data showing that the differential expression profiles of miRNA in tumour tissues and blood associate strongly with drug response and overall survival. Furthermore, another line of studies indicate that the chemopreventive effects of a variety of natural compounds may involve miRNAs. The present review aims to discuss the therapeutic capacity of miRNAs in relation to recent discoveries on EGFR-TKI resistance, including chronic drug exposure and mutations.

  16. MicroRNA-133a suppresses multiple oncogenic membrane receptors and cell invasion in non-small cell lung carcinoma.

    Directory of Open Access Journals (Sweden)

    Lu-Kai Wang

    Full Text Available Non-small cell lung cancers (NSCLCs cause high mortality worldwide, and the cancer progression can be activated by several genetic events causing receptor dysregulation, including mutation or amplification. MicroRNAs are a group of small non-coding RNA molecules that function in gene silencing and have emerged as the fine-tuning regulators during cancer progression. MiR-133a is known as a key regulator in skeletal and cardiac myogenesis, and it acts as a tumor suppressor in various cancers. This study demonstrates that miR-133a expression negatively correlates with cell invasiveness in both transformed normal bronchial epithelial cells and lung cancer cell lines. The oncogenic receptors in lung cancer cells, including insulin-like growth factor 1 receptor (IGF-1R, TGF-beta receptor type-1 (TGFBR1, and epidermal growth factor receptor (EGFR, are direct targets of miR-133a. MiR-133a can inhibit cell invasiveness and cell growth through suppressing the expressions of IGF-1R, TGFBR1 and EGFR, which then influences the downstream signaling in lung cancer cell lines. The cell invasive ability is suppressed in IGF-1R- and TGFBR1-repressed cells and this phenomenon is mediated through AKT signaling in highly invasive cell lines. In addition, by using the in vivo animal model, we find that ectopically-expressing miR-133a dramatically suppresses the metastatic ability of lung cancer cells. Accordingly, patients with NSCLCs who have higher expression levels of miR-133a have longer survival rates compared with those who have lower miR-133a expression levels. In summary, we identified the tumor suppressor role of miR-133a in lung cancer outcome prognosis, and we demonstrated that it targets several membrane receptors, which generally produce an activating signaling network during the progression of lung cancer.

  17. miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy.

    Directory of Open Access Journals (Sweden)

    Alexander S Baras

    Full Text Available Small RNA RNA-seq for microRNAs (miRNAs is a rapidly developing field where opportunities still exist to create better bioinformatics tools to process these large datasets and generate new, useful analyses. We built miRge to be a fast, smart small RNA-seq solution to process samples in a highly multiplexed fashion. miRge employs a Bayesian alignment approach, whereby reads are sequentially aligned against customized mature miRNA, hairpin miRNA, noncoding RNA and mRNA sequence libraries. miRNAs are summarized at the level of raw reads in addition to reads per million (RPM. Reads for all other RNA species (tRNA, rRNA, snoRNA, mRNA are provided, which is useful for identifying potential contaminants and optimizing small RNA purification strategies. miRge was designed to optimally identify miRNA isomiRs and employs an entropy based statistical measurement to identify differential production of isomiRs. This allowed us to identify decreasing entropy in isomiRs as stem cells mature into retinal pigment epithelial cells. Conversely, we show that pancreatic tumor miRNAs have similar entropy to matched normal pancreatic tissues. In a head-to-head comparison with other miRNA analysis tools (miRExpress 2.0, sRNAbench, omiRAs, miRDeep2, Chimira, UEA small RNA Workbench, miRge was faster (4 to 32-fold and was among the top-two methods in maximally aligning miRNAs reads per sample. Moreover, miRge has no inherent limits to its multiplexing. miRge was capable of simultaneously analyzing 100 small RNA-Seq samples in 52 minutes, providing an integrated analysis of miRNA expression across all samples. As miRge was designed for analysis of single as well as multiple samples, miRge is an ideal tool for high and low-throughput users. miRge is freely available at http://atlas.pathology.jhu.edu/baras/miRge.html.

  18. QCD Axion Dark Matter with a Small Decay Constant.

    Science.gov (United States)

    Co, Raymond T; Hall, Lawrence J; Harigaya, Keisuke

    2018-05-25

    The QCD axion is a good dark matter candidate. The observed dark matter abundance can arise from misalignment or defect mechanisms, which generically require an axion decay constant f_{a}∼O(10^{11})  GeV (or higher). We introduce a new cosmological origin for axion dark matter, parametric resonance from oscillations of the Peccei-Quinn symmetry breaking field, that requires f_{a}∼(10^{8}-10^{11})  GeV. The axions may be warm enough to give deviations from cold dark matter in large scale structure.

  19. QCD Axion Dark Matter with a Small Decay Constant

    Science.gov (United States)

    Co, Raymond T.; Hall, Lawrence J.; Harigaya, Keisuke

    2018-05-01

    The QCD axion is a good dark matter candidate. The observed dark matter abundance can arise from misalignment or defect mechanisms, which generically require an axion decay constant fa˜O (1011) GeV (or higher). We introduce a new cosmological origin for axion dark matter, parametric resonance from oscillations of the Peccei-Quinn symmetry breaking field, that requires fa˜(108- 1011) GeV . The axions may be warm enough to give deviations from cold dark matter in large scale structure.

  20. Next-generation small RNA sequencing for microRNAs profiling in the honey bee Apis mellifera.

    Science.gov (United States)

    Chen, X; Yu, X; Cai, Y; Zheng, H; Yu, D; Liu, G; Zhou, Q; Hu, S; Hu, F

    2010-12-01

    MicroRNAs (miRNAs) are key regulators in various physiological and pathological processes via post-transcriptional regulation of gene expression. The honey bee (Apis mellifera) is a key model for highly social species, and its complex social behaviour can be interpreted theoretically as changes in gene regulation, in which miRNAs are thought to be involved. We used the SOLiD sequencing system to identify the repertoire of miRNAs in the honey bee by sequencing a mixed small RNA library from different developmental stages. We obtained a total of 36,796,459 raw sequences; of which 5,491,100 short sequences were fragments of mRNA and other noncoding RNAs (ncRNA), and 1,759,346 reads mapped to the known miRNAs. We predicted 267 novel honey bee miRNAs representing 380,182 short reads, including eight miRNAs of other insects in 14,107,583 genome-mapped sequences. We verified 50 of them using stem-loop reverse-transcription PCR (RT-PCR), in which 35 yielded PCR products. Cross-species analyses showed 81 novel miRNAs with homologues in other insects, suggesting that they were authentic miRNAs and have similar functions. The results of this study provide a basis for studies of the miRNA-modulating networks in development and some intriguing phenomena such as caste differentiation in A. mellifera. © 2010 The Authors. Insect Molecular Biology © 2010 The Royal Entomological Society.

  1. Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response

    Directory of Open Access Journals (Sweden)

    Chong Kang

    2009-09-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are endogenous small RNAs having large-scale regulatory effects on plant development and stress responses. Extensive studies of miRNAs have only been performed in a few model plants. Although miRNAs are proved to be involved in plant cold stress responses, little is known for winter-habit monocots. Brachypodium distachyon, with close evolutionary relationship to cool-season cereals, has recently emerged as a novel model plant. There are few reports of Brachypodium miRNAs. Results High-throughput sequencing and whole-genome-wide data mining led to the identification of 27 conserved miRNAs, as well as 129 predicted miRNAs in Brachypodium. For multiple-member conserved miRNA families, their sizes in Brachypodium were much smaller than those in rice and Populus. The genome organization of miR395 family in Brachypodium was quite different from that in rice. The expression of 3 conserved miRNAs and 25 predicted miRNAs showed significant changes in response to cold stress. Among these miRNAs, some were cold-induced and some were cold-suppressed, but all the conserved miRNAs were up-regulated under cold stress condition. Conclusion Our results suggest that Brachypodium miRNAs are composed of a set of conserved miRNAs and a large proportion of non-conserved miRNAs with low expression levels. Both kinds of miRNAs were involved in cold stress response, but all the conserved miRNAs were up-regulated, implying an important role for cold-induced miRNAs. The different size and genome organization of miRNA families in Brachypodium and rice suggest that the frequency of duplication events or the selection pressure on duplicated miRNAs are different between these two closely related plant species.

  2. MicroRNA Expression Profile in Penile Cancer Revealed by Next-Generation Small RNA Sequencing.

    Directory of Open Access Journals (Sweden)

    Li Zhang

    provides new insights into future investigations aimed to explore the in-depth mechanisms of miRNAs and other small RNAs including piRNAs in penile carcinogenesis regulation and effective target-specific theragnosis.

  3. P2X7 mRNA expression in non-small cell lung cancer: MicroRNA regulation and prognostic value

    OpenAIRE

    BOLDRINI, LAURA; GIORDANO, MIRELLA; ALÌ, GRETA; MELFI, FRANCA; ROMANO, GAETANO; LUCCHI, MARCO; FONTANINI, GABRIELLA

    2014-01-01

    The human P2X7 receptor is significant and exhibits several functions in neoplasia. At present, little is known with regard to its regulation. P2X7 expression may be regulated post-transcriptionally and putative microRNA (miRNA) binding sites are considered to be involved. The aim of this study was to determine whether miRNAs (miR-21, let-7 g and miR-205) regulate P2X7 mRNA stability. In addition, the impact of P2X7 expression in patients with non-small cell lung cancer (NSCLC) was investigat...

  4. MicroRNA-429 induces tumorigenesis of human non-small cell lung cancer cells and targets multiple tumor suppressor genes

    Energy Technology Data Exchange (ETDEWEB)

    Lang, Yaoguo; Xu, Shidong; Ma, Jianqun; Wu, Jun [Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, Heilongjiang 150081 (China); Jin, Shi; Cao, Shoubo [Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, Heilongjiang 150081 (China); Yu, Yan, E-mail: yuyan@hrbmu.edu.cn [Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, Heilongjiang 150081 (China)

    2014-07-18

    Highlights: • MiR-429 expression is upregulated in non-small cell lung cancer (NSCLC). • MiR-429 inhibits PTEN, RASSF8 and TIMP2 expression. • MiR-429 promotes metastasis and proliferation. • We report important regulatory mechanisms involved in NSCLC progression. • MiR-429 is a potential therapeutic target and diagnostic marker. - Abstract: Lung cancer is the major cause of cancer death globally. MicroRNAs are evolutionally conserved small noncoding RNAs that are critical for the regulation of gene expression. Aberrant expression of microRNA (miRNA) has been implicated in cancer initiation and progression. In this study, we demonstrated that the expression of miR-429 are often upregulated in non-small cell lung cancer (NSCLC) compared with normal lung tissues, and its expression level is also increased in NSCLC cell lines compared with normal lung cells. Overexpression of miR-429 in A549 NSCLC cells significantly promoted cell proliferation, migration and invasion, whereas inhibition of miR-429 inhibits these effects. Furthermore, we demonstrated that miR-429 down-regulates PTEN, RASSF8 and TIMP2 expression by directly targeting the 3′-untranslated region of these target genes. Taken together, our results suggest that miR-429 plays an important role in promoting the proliferation and metastasis of NSCLC cells and is a potential target for NSCLC therapy.

  5. MicroRNAs are associated with blood-pressure effects of exposure to particulate matter: Results from a mediated moderation analysis.

    Science.gov (United States)

    Motta, Valeria; Favero, Chiara; Dioni, Laura; Iodice, Simona; Battaglia, Cristina; Angelici, Laura; Vigna, Luisella; Pesatori, Angela Cecilia; Bollati, Valentina

    2016-04-01

    Exposure to particulate air pollution is associated with increased blood pressure (BP), a well-established risk factor for cardiovascular disease. To elucidate the mechanisms underlying this relationship, we investigated whether the effects of particulate matter of less than 10μm in aerodynamic diameter (PM10) on BP are mediated by microRNAs. We recruited 90 obese individuals and we assessed their PM10 exposure 24 and 48h before the recruitment day. We performed multivariate linear regression models to investigate the effects of PM10 on BP. Using the TaqMan® Low-Density Array, we experimentally evaluated and technically validated the expression levels of 377 human miRNAs in peripheral blood. We developed a mediated moderation analysis to estimate the proportion of PM10 effects on BP that was mediated by miRNA expression. PM10 exposure 24 and 48h before the recruitment day was associated with increased systolic BP (β=1.22mmHg, P=0.019; β=1.24mmHg, P=0.019, respectively) and diastolic BP (β=0.67mmHg, P=0.044; β=0.91mmHg, P=0.007, respectively). We identified nine miRNAs associated with PM10 levels 48h after exposure. A conditional indirect effect (CIE=-0.1431) of PM10 on diastolic BP, which was mediated by microRNA-101, was found in individuals with lower values of mean body mass index. Our data provide evidence that miRNAs are a molecular mechanism underlying the BP-related effects of air pollution exposure, and indicate miR-101 as epigenetic mechanism to be further investigated. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  6. MicroRNA pharmacogenomics

    DEFF Research Database (Denmark)

    Rukov, Jakob Lewin; Shomron, Noam

    2011-01-01

    polymorphisms, copy number variations or differences in gene expression levels of drug metabolizing or transporting genes and drug targets. In this review paper, we focus instead on microRNAs (miRNAs): small noncoding RNAs, prevalent in metazoans, that negatively regulate gene expression in many cellular...

  7. Combinatorial microRNA target predictions

    DEFF Research Database (Denmark)

    Krek, Azra; Grün, Dominic; Poy, Matthew N.

    2005-01-01

    MicroRNAs are small noncoding RNAs that recognize and bind to partially complementary sites in the 3' untranslated regions of target genes in animals and, by unknown mechanisms, regulate protein production of the target transcript1, 2, 3. Different combinations of microRNAs are expressed...... in different cell types and may coordinately regulate cell-specific target genes. Here, we present PicTar, a computational method for identifying common targets of microRNAs. Statistical tests using genome-wide alignments of eight vertebrate genomes, PicTar's ability to specifically recover published micro......RNA targets, and experimental validation of seven predicted targets suggest that PicTar has an excellent success rate in predicting targets for single microRNAs and for combinations of microRNAs. We find that vertebrate microRNAs target, on average, roughly 200 transcripts each. Furthermore, our results...

  8. MicroRNAs in Amoebozoa: deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs.

    Science.gov (United States)

    Avesson, Lotta; Reimegård, Johan; Wagner, E Gerhart H; Söderbom, Fredrik

    2012-10-01

    The RNA interference machinery has served as a guardian of eukaryotic genomes since the divergence from prokaryotes. Although the basic components have a shared origin, silencing pathways directed by small RNAs have evolved in diverse directions in different eukaryotic lineages. Micro (mi)RNAs regulate protein-coding genes and play vital roles in plants and animals, but less is known about their functions in other organisms. Here, we report, for the first time, deep sequencing of small RNAs from the social amoeba Dictyostelium discoideum. RNA from growing single-cell amoebae as well as from two multicellular developmental stages was sequenced. Computational analyses combined with experimental data reveal the expression of miRNAs, several of them exhibiting distinct expression patterns during development. To our knowledge, this is the first report of miRNAs in the Amoebozoa supergroup. We also show that overexpressed miRNA precursors generate miRNAs and, in most cases, miRNA* sequences, whose biogenesis is dependent on the Dicer-like protein DrnB, further supporting the presence of miRNAs in D. discoideum. In addition, we find miRNAs processed from hairpin structures originating from an intron as well as from a class of repetitive elements. We believe that these repetitive elements are sources for newly evolved miRNAs.

  9. Urban Structure Matters, Even in a Small Town

    DEFF Research Database (Denmark)

    Næss, Petter; Jensen, Ole B.

    2002-01-01

    A recent study in Frederikshavn, Denmark, shows that urban structural variables influence travel behavior also in a small town of around 30 000 inhabitants. As one might expect, socioeconomic and attitudinal factors play a role for the respondents? traveling patterns. But also when controlling...... are confirmed in qualitative interviews. The distance from the residence to the downtown area is a key factor influencing the accessibility to a number of facility types. These differences in accessibility result in corresponding differences in the actual traveling distances and modal split....

  10. DEWS (DEep White matter hyperintensity Segmentation framework): A fully automated pipeline for detecting small deep white matter hyperintensities in migraineurs.

    Science.gov (United States)

    Park, Bo-Yong; Lee, Mi Ji; Lee, Seung-Hak; Cha, Jihoon; Chung, Chin-Sang; Kim, Sung Tae; Park, Hyunjin

    2018-01-01

    Migraineurs show an increased load of white matter hyperintensities (WMHs) and more rapid deep WMH progression. Previous methods for WMH segmentation have limited efficacy to detect small deep WMHs. We developed a new fully automated detection pipeline, DEWS (DEep White matter hyperintensity Segmentation framework), for small and superficially-located deep WMHs. A total of 148 non-elderly subjects with migraine were included in this study. The pipeline consists of three components: 1) white matter (WM) extraction, 2) WMH detection, and 3) false positive reduction. In WM extraction, we adjusted the WM mask to re-assign misclassified WMHs back to WM using many sequential low-level image processing steps. In WMH detection, the potential WMH clusters were detected using an intensity based threshold and region growing approach. For false positive reduction, the detected WMH clusters were classified into final WMHs and non-WMHs using the random forest (RF) classifier. Size, texture, and multi-scale deep features were used to train the RF classifier. DEWS successfully detected small deep WMHs with a high positive predictive value (PPV) of 0.98 and true positive rate (TPR) of 0.70 in the training and test sets. Similar performance of PPV (0.96) and TPR (0.68) was attained in the validation set. DEWS showed a superior performance in comparison with other methods. Our proposed pipeline is freely available online to help the research community in quantifying deep WMHs in non-elderly adults.

  11. A new component of the interstellar matter - Small grains and large aromatic molecules

    International Nuclear Information System (INIS)

    Puget, J.L.

    1989-01-01

    Predictions from dust models constructed to account for the interstellar extinction curve are in conflict with emission data. This paper shows that the introduction of small grains and large aromatic molecules as a new component of the interstellar matter can resolve this conflict. Observational evidence for the existence of very small grains is also reviewed, along with the physics of IR emission by thermal fluctuations and its relation to very small particles. 99 refs

  12. Phytohormones and microRNAs as sensors and regulators of leaf senescence: assigning macro roles to small molecules.

    Science.gov (United States)

    Sarwat, Maryam; Naqvi, Afsar Raza; Ahmad, Parvaiz; Ashraf, Muhammad; Akram, Nudrat Aisha

    2013-12-01

    Ageing or senescence is an intricate and highly synchronized developmental phase in the life of plant parts including leaf. Senescence not only means death of a plant part, but during this process, different macromolecules undergo degradation and the resulting components are transported to other parts of the plant. During the period from when a leaf is young and green to the stage when it senesces, a multitude of factors such as hormones, environmental factors and senescence associated genes (SAGs) are involved. Plant hormones including salicylic acid, abscisic acid, jasmonic acid and ethylene advance leaf senescence, whereas others like cytokinins, gibberellins, and auxins delay this process. The environmental factors which generally affect plant development and growth, can hasten senescence, the examples being nutrient dearth, water stress, pathogen attack, radiations, high temperature and light intensity, waterlogging, and air, water or soil contamination. Other important influences include carbohydrate accumulation and high carbon/nitrogen level. To date, although several genes involved in this complex process have been identified, still not much information exists in the literature on the signalling mechanism of leaf senescence. Now, the Arabidopsis mutants have paved our way and opened new vistas to elucidate the signalling mechanism of leaf senescence for which various mutants are being utilized. Recent studies demonstrating the role of microRNAs in leaf senescence have reinforced our knowledge of this intricate process. This review provides a comprehensive and critical analysis of the information gained particularly on the roles of several plant growth regulators and microRNAs in regulation of leaf senescence. Copyright © 2013 Elsevier Inc. All rights reserved.

  13. Blood Pressure Control in Aging Predicts Cerebral Atrophy Related to Small-Vessel White Matter Lesions

    Directory of Open Access Journals (Sweden)

    Kyle C. Kern

    2017-05-01

    Full Text Available Cerebral small-vessel damage manifests as white matter hyperintensities and cerebral atrophy on brain MRI and is associated with aging, cognitive decline and dementia. We sought to examine the interrelationship of these imaging biomarkers and the influence of hypertension in older individuals. We used a multivariate spatial covariance neuroimaging technique to localize the effects of white matter lesion load on regional gray matter volume and assessed the role of blood pressure control, age and education on this relationship. Using a case-control design matching for age, gender, and educational attainment we selected 64 participants with normal blood pressure, controlled hypertension or uncontrolled hypertension from the Northern Manhattan Study cohort. We applied gray matter voxel-based morphometry with the scaled subprofile model to (1 identify regional covariance patterns of gray matter volume differences associated with white matter lesion load, (2 compare this relationship across blood pressure groups, and (3 relate it to cognitive performance. In this group of participants aged 60–86 years, we identified a pattern of reduced gray matter volume associated with white matter lesion load in bilateral temporal-parietal regions with relative preservation of volume in the basal forebrain, thalami and cingulate cortex. This pattern was expressed most in the uncontrolled hypertension group and least in the normotensives, but was also more evident in older and more educated individuals. Expression of this pattern was associated with worse performance in executive function and memory. In summary, white matter lesions from small-vessel disease are associated with a regional pattern of gray matter atrophy that is mitigated by blood pressure control, exacerbated by aging, and associated with cognitive performance.

  14. Endogenous MCM7 microRNA cluster as a novel platform to multiplex small interfering and nucleolar RNAs for combinational HIV-1 gene therapy.

    Science.gov (United States)

    Chung, Janet; Zhang, Jane; Li, Haitang; Ouellet, Dominique L; DiGiusto, David L; Rossi, John J

    2012-11-01

    Combinational therapy with small RNA inhibitory agents against multiple viral targets allows efficient inhibition of viral production by controlling gene expression at critical time points. Here we explore combinations of different classes of therapeutic anti-HIV-1 RNAs expressed from within the context of an intronic MCM7 (minichromosome maintenance complex component-7) platform that naturally harbors 3 microRNAs (miRNAs). We replaced the endogenous miRNAs with anti-HIV small RNAs, including small interfering RNAs (siRNAs) targeting HIV-1 tat and rev messages that function to induce post-transcriptional gene silencing by the RNA interference pathway, a nucleolar-localizing RNA ribozyme that targets the conserved U5 region of HIV-1 transcripts for degradation, and finally nucleolar trans-activation response (TAR) and Rev-binding element (RBE) RNA decoys designed to sequester HIV-1 Tat and Rev proteins inside the nucleolus. We demonstrate the versatility of the MCM7 platform in expressing and efficiently processing the siRNAs as miRNA mimics along with nucleolar small RNAs. Furthermore, three of the combinatorial constructs tested potently suppressed viral replication during a 1-month HIV challenge, with greater than 5-log inhibition compared with untransduced, HIV-1-infected CEM T lymphocytes. One of the most effective constructs contains an anti-HIV siRNA combined with a nucleolar-localizing U5 ribozyme and TAR decoy. This represents the first efficacious example of combining Drosha-processed siRNAs with small nucleolar ribonucleoprotein (snoRNP)-processed nucleolar RNA chimeras from a single intron platform for effective inhibition of viral replication. Moreover, we demonstrated enrichment/selection for cells expressing levels of the antiviral RNAs that provide optimal inhibition under the selective pressure of HIV. The combinations of si/snoRNAs represent a new paradigm for combinatorial RNA-based gene therapy applications.

  15. Descendit ad [in] inferna:'A matter of no small moment in bringing ...

    African Journals Online (AJOL)

    Descendit ad [in] inferna:'A matter of no small moment in bringing about redemption' ... and make one suspicious about certain ecclesiastical biases. Spatial terms in the Creed should therefore not be demythologised, but rather be transformed in accordance with the insights of the contemporary physics of time and space.

  16. Small RNA Transcriptome of Hibiscus Syriacus Provides Insights into the Potential Influence of microRNAs in Flower Development and Terpene Synthesis.

    Science.gov (United States)

    Kim, Taewook; Park, June Hyun; Lee, Sang-Gil; Kim, Soyoung; Kim, Jihyun; Lee, Jungho; Shin, Chanseok

    2017-08-01

    MicroRNAs (miRNAs) are essential small RNA molecules that regulate the expression of target mRNAs in plants and animals. Here, we aimed to identify miRNAs and their putative targets in Hibiscus syriacus , the national flower of South Korea. We employed high-throughput sequencing of small RNAs obtained from four different tissues ( i.e. , leaf, root, flower, and ovary) and identified 33 conserved and 30 novel miRNA families, many of which showed differential tissue-specific expressions. In addition, we computationally predicted novel targets of miRNAs and validated some of them using 5' rapid amplification of cDNA ends analysis. One of the validated novel targets of miR477 was a terpene synthase, the primary gene involved in the formation of disease-resistant terpene metabolites such as sterols and phytoalexins. In addition, a predicted target of conserved miRNAs, miR396, is SHORT VEGETATIVE PHASE , which is involved in flower initiation and is duplicated in H. syriacus . Collectively, this study provides the first reliable draft of the H. syriacus miRNA transcriptome that should constitute a basis for understanding the biological roles of miRNAs in H. syriacus.

  17. Global alteration of microRNAs and transposon-derived small RNAs in cotton (Gossypium hirsutum) during Cotton leafroll dwarf polerovirus (CLRDV) infection.

    Science.gov (United States)

    Romanel, Elisson; Silva, Tatiane F; Corrêa, Régis L; Farinelli, Laurent; Hawkins, Jennifer S; Schrago, Carlos E G; Vaslin, Maite F S

    2012-11-01

    Small RNAs (sRNAs) are a class of non-coding RNAs ranging from 20- to 40-nucleotides (nts) that are present in most eukaryotic organisms. In plants, sRNAs are involved in the regulation of development, the maintenance of genome stability and the antiviral response. Viruses, however, can interfere with and exploit the silencing-based regulatory networks, causing the deregulation of sRNAs, including small interfering RNAs (siRNAs) and microRNAs (miRNAs). To understand the impact of viral infection on the plant sRNA pathway, we deep sequenced the sRNAs in cotton leaves infected with Cotton leafroll dwarf virus (CLRDV), which is a member of the economically important virus family Luteoviridae. A total of 60 putative conserved cotton miRNAs were identified, including 19 new miRNA families that had not been previously described in cotton. Some of these miRNAs were clearly misregulated during viral infection, and their possible role in symptom development and disease progression is discussed. Furthermore, we found that the 24-nt heterochromatin-associated siRNAs were quantitatively and qualitatively altered in the infected plant, leading to the reactivation of at least one cotton transposable element. This is the first study to explore the global alterations of sRNAs in virus-infected cotton plants. Our results indicate that some CLRDV-induced symptoms may be correlated with the deregulation of miRNA and/or epigenetic networks.

  18. Solving the small-scale structure puzzles with dissipative dark matter

    Energy Technology Data Exchange (ETDEWEB)

    Foot, Robert [ARC Centre of Excellence for Particle Physics at the Terascale, School of Physics, University of Melbourne, Melbourne, Victoria 3010 (Australia); Vagnozzi, Sunny, E-mail: rfoot@unimelb.edu.au, E-mail: sunny.vagnozzi@fysik.su.se [The Oskar Klein Centre for Cosmoparticle Physics, Department of Physics, Stockholm University, AlbaNova University Center, Roslagstullbacken 21A, SE-106 91 Stockholm (Sweden)

    2016-07-01

    Small-scale structure is studied in the context of dissipative dark matter, arising for instance in models with a hidden unbroken Abelian sector, so that dark matter couples to a massless dark photon. The dark sector interacts with ordinary matter via gravity and photon-dark photon kinetic mixing. Mirror dark matter is a theoretically constrained special case where all parameters are fixed except for the kinetic mixing strength, ε. In these models, the dark matter halo around spiral and irregular galaxies takes the form of a dissipative plasma which evolves in response to various heating and cooling processes. It has been argued previously that such dynamics can account for the inferred cored density profiles of galaxies and other related structural features. Here we focus on the apparent deficit of nearby small galaxies (''missing satellite problem'), which these dissipative models have the potential to address through small-scale power suppression by acoustic and diffusion damping. Using a variant of the extended Press-Schechter formalism, we evaluate the halo mass function for the special case of mirror dark matter. Considering a simplified model where M {sub baryons} ∝ M {sub halo}, we relate the halo mass function to more directly observable quantities, and find that for ε ≈ 2 × 10{sup −10} such a simplified description is compatible with the measured galaxy luminosity and velocity functions. On scales M {sub halo} ∼< 10{sup 8} M {sub ⊙}, diffusion damping exponentially suppresses the halo mass function, suggesting a nonprimordial origin for dwarf spheroidal satellite galaxies, which we speculate were formed via a top-down fragmentation process as the result of nonlinear dissipative collapse of larger density perturbations. This could explain the planar orientation of satellite galaxies around Andromeda and the Milky Way.

  19. Solving the small-scale structure puzzles with dissipative dark matter

    Science.gov (United States)

    Foot, Robert; Vagnozzi, Sunny

    2016-07-01

    Small-scale structure is studied in the context of dissipative dark matter, arising for instance in models with a hidden unbroken Abelian sector, so that dark matter couples to a massless dark photon. The dark sector interacts with ordinary matter via gravity and photon-dark photon kinetic mixing. Mirror dark matter is a theoretically constrained special case where all parameters are fixed except for the kinetic mixing strength, epsilon. In these models, the dark matter halo around spiral and irregular galaxies takes the form of a dissipative plasma which evolves in response to various heating and cooling processes. It has been argued previously that such dynamics can account for the inferred cored density profiles of galaxies and other related structural features. Here we focus on the apparent deficit of nearby small galaxies (``missing satellite problem"), which these dissipative models have the potential to address through small-scale power suppression by acoustic and diffusion damping. Using a variant of the extended Press-Schechter formalism, we evaluate the halo mass function for the special case of mirror dark matter. Considering a simplified model where Mbaryons propto Mhalo, we relate the halo mass function to more directly observable quantities, and find that for epsilon ≈ 2 × 10-10 such a simplified description is compatible with the measured galaxy luminosity and velocity functions. On scales Mhalo lesssim 108 Msolar, diffusion damping exponentially suppresses the halo mass function, suggesting a nonprimordial origin for dwarf spheroidal satellite galaxies, which we speculate were formed via a top-down fragmentation process as the result of nonlinear dissipative collapse of larger density perturbations. This could explain the planar orientation of satellite galaxies around Andromeda and the Milky Way.

  20. Downregulation of six microRNAs is associated with advanced stage, lymph node metastasis and poor prognosis in small cell carcinoma of the cervix.

    Directory of Open Access Journals (Sweden)

    Long Huang

    Full Text Available BACKGROUND: Small cell carcinoma of the cervix (SCCC is very rare, and due to the long time period required to recruit sufficient numbers of patients, there is a paucity of information regarding the prognostic factors associated with survival. MicroRNAs (miRNAs have been used as cancer-related biomarkers in a variety of tumor types, and the objective of this study was to determine whether microRNA expression profiles can predict clinical outcome in SCCC. METHODOLOGY/PRINCIPAL FINDINGS: Forty-four patients with SCCC who underwent radical hysterectomy between January 2000 and October 2009 were enrolled. Using the GeneCopoeia All-in-One™ Customized Human qPCR Primer Array, the expression profiles of 30 miRNAs associated with tumor metastasis was obtained from the formalin-fixed paraffin embedded samples of all 44 patients. Seven miRNAs, has-let-7c, has-miR-10b, has-miR-100, has-miR-125b, has-miR-143, has-miR-145 and has-miR-199a-5p were significantly down-regulated in advanced stage SCCC patients (FIGO IB2-IV compared to early stage SCCC patients (FIGOIB1. Among, downregulation of six miRNAs, has-let-7c, has-miR-100, has-miR-125b, has-miR-143, has-miR-145 and has-miR-199a-5p were significantly associated with lymph node metastasis and reduced survival in SCCC. Kaplan-Meier survival analyses revealed that SCCC patients with low expression of has-miR-100 (P = 0.019 and has-miR-125b (P = 0.020 projected a significant tendency towards poorer prognosis. CONCLUSIONS/SIGNIFICANCE: This study demonstrates that downregulation of 7 miRNA associated with advanced stage, 6 miRNAs with metastasis and 2 with poor prognosis in SCCC. Functional analysis of these miRNAs may enhance our understanding of SCCC, as altered expression of specific miRNAs may regulate the metastatic pathway and provide novel targets for therapy.

  1. "Non-cold" dark matter at small scales: a general approach

    Science.gov (United States)

    Murgia, R.; Merle, A.; Viel, M.; Totzauer, M.; Schneider, A.

    2017-11-01

    Structure formation at small cosmological scales provides an important frontier for dark matter (DM) research. Scenarios with small DM particle masses, large momenta or hidden interactions tend to suppress the gravitational clustering at small scales. The details of this suppression depend on the DM particle nature, allowing for a direct link between DM models and astrophysical observations. However, most of the astrophysical constraints obtained so far refer to a very specific shape of the power suppression, corresponding to thermal warm dark matter (WDM), i.e., candidates with a Fermi-Dirac or Bose-Einstein momentum distribution. In this work we introduce a new analytical fitting formula for the power spectrum, which is simple yet flexible enough to reproduce the clustering signal of large classes of non-thermal DM models, which are not at all adequately described by the oversimplified notion of WDM . We show that the formula is able to fully cover the parameter space of sterile neutrinos (whether resonantly produced or from particle decay), mixed cold and warm models, fuzzy dark matter, as well as other models suggested by effective theory of structure formation (ETHOS). Based on this fitting formula, we perform a large suite of N-body simulations and we extract important nonlinear statistics, such as the matter power spectrum and the halo mass function. Finally, we present first preliminary astrophysical constraints, based on linear theory, from both the number of Milky Way satellites and the Lyman-α forest. This paper is a first step towards a general and comprehensive modeling of small-scale departures from the standard cold DM model.

  2. Neutrino masses, leptogenesis and dark matter from small lepton number violation?

    Energy Technology Data Exchange (ETDEWEB)

    Abada, Asmaa [CNRS, Univ. Paris-Sud, Univ. Paris-Saclay, Orsay (France). Lab. de Physique Theorique; Arcadi, Giorgio [Max Planck Institut fuer Kernphysik, Heidelberg (Germany); Domcke, Valerie [Paris Diderot Univ. (France). AstroParticule et Cosmologie (APC)/Paris Centre for Cosmological Physics (PCCP); Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Lucente, Michele [Univ. Catholique de Louvain, Louvain-la-Neuve (Belgium). Centre for Cosmology, Particle Physics and Phenomenology (CP3)

    2017-09-05

    We consider the possibility of simultaneously addressing the baryon asymmetry of the Universe, the dark matter problem and the neutrino mass generation in minimal extensions of the Standard Model via sterile fermions with (small) total lepton number violation. Within the framework of Inverse and Linear Seesaw models, the small lepton number violating parameters set the mass scale of the active neutrinos, the efficiency of leptogenesis through a small mass splitting between pairs of sterile fermions as well as the mass scale of a sterile neutrino dark matter candidate. We provide an improved parametrization of these seesaw models taking into account existing experimental constraints and derive a linearized system of Boltzmann equations to describe the leptogenesis process, which allows for an efficient investigation of the parameter space. This in particular enables us to perform a systematic study of the strong washout regime of leptogenesis. Our study reveals that one can have a successful leptogenesis at the temperature of the electroweak scale through oscillations between two sterile states with a natural origin of the (necessary) strong degeneracy in their mass spectrum. The minimal model however requires a non-standard cosmological history to account for the relic dark matter. Finally, we discuss the prospect for neutrinoless double beta decay and for testing, in future experiments, the values of mass and different active-sterile mixings required for successful leptogenesis.

  3. Neutrino masses, leptogenesis and dark matter from small lepton number violation?

    International Nuclear Information System (INIS)

    Abada, Asmaa; Domcke, Valerie; Lucente, Michele

    2017-01-01

    We consider the possibility of simultaneously addressing the baryon asymmetry of the Universe, the dark matter problem and the neutrino mass generation in minimal extensions of the Standard Model via sterile fermions with (small) total lepton number violation. Within the framework of Inverse and Linear Seesaw models, the small lepton number violating parameters set the mass scale of the active neutrinos, the efficiency of leptogenesis through a small mass splitting between pairs of sterile fermions as well as the mass scale of a sterile neutrino dark matter candidate. We provide an improved parametrization of these seesaw models taking into account existing experimental constraints and derive a linearized system of Boltzmann equations to describe the leptogenesis process, which allows for an efficient investigation of the parameter space. This in particular enables us to perform a systematic study of the strong washout regime of leptogenesis. Our study reveals that one can have a successful leptogenesis at the temperature of the electroweak scale through oscillations between two sterile states with a natural origin of the (necessary) strong degeneracy in their mass spectrum. The minimal model however requires a non-standard cosmological history to account for the relic dark matter. Finally, we discuss the prospect for neutrinoless double beta decay and for testing, in future experiments, the values of mass and different active-sterile mixings required for successful leptogenesis.

  4. Neutrino masses, leptogenesis and dark matter from small lepton number violation?

    Science.gov (United States)

    Abada, Asmaa; Arcadi, Giorgio; Domcke, Valerie; Lucente, Michele

    2017-12-01

    We consider the possibility of simultaneously addressing the baryon asymmetry of the Universe, the dark matter problem and the neutrino mass generation in minimal extensions of the Standard Model via sterile fermions with (small) total lepton number violation. Within the framework of Inverse and Linear Seesaw models, the small lepton number violating parameters set the mass scale of the active neutrinos, the efficiency of leptogenesis through a small mass splitting between pairs of sterile fermions as well as the mass scale of a sterile neutrino dark matter candidate. We provide an improved parametrization of these seesaw models taking into account existing experimental constraints and derive a linearized system of Boltzmann equations to describe the leptogenesis process, which allows for an efficient investigation of the parameter space. This in particular enables us to perform a systematic study of the strong washout regime of leptogenesis. Our study reveals that one can have a successful leptogenesis at the temperature of the electroweak scale through oscillations between two sterile states with a natural origin of the (necessary) strong degeneracy in their mass spectrum. The minimal model however requires a non-standard cosmological history to account for the relic dark matter. Finally, we discuss the prospect for neutrinoless double beta decay and for testing, in future experiments, the values of mass and different active-sterile mixings required for successful leptogenesis.

  5. Positive Bioluminescence Imaging of MicroRNA Expression in Small Animal Models Using an Engineered Genetic-Switch Expression System, RILES.

    Science.gov (United States)

    Baril, Patrick; Pichon, Chantal

    2016-01-01

    MicroRNAs (miRNAs) are a class of small, noncoding RNAs which regulate gene expression by directing their target mRNA for degradation or translational repression. Since their discovery in the early 1990s, miRNAs have emerged as key components in the posttranscriptional regulation of gene networks, shaping many biological processes from development, morphogenesis, differentiation, proliferation and apoptosis. Although understanding of the molecular basis of miRNA biology is improving, methods to monitor the dynamic and the spatiotemporal aspects of miRNA expression under physiopathological conditions are required. However, monitoring of miRNAs is difficult due to their small size, low abundance, high degree of sequence similarity, and their dynamic expression pattern which is subjected to tight transcriptional and post-transcriptional controls. Recently, we developed a miRNA monitoring system called RILES, standing for RNAi-inducible expression system, which relies on an engineered regulatable expression system, to switch on the expression of the luciferase gene when the targeted miRNA is expressed in cells. We demonstrated that RILES is a specific, sensitive, and robust method to determine the fine-tuning of miRNA expression during the development of an experimental pathological process in mice. Because RILES offers the possibility for longitudinal studies on individual subjects, sharper insights into miRNA regulation can be generated, with applications in physiology, pathophysiology and development of RNAi-based therapies. This chapter describes methods and protocols to monitor the expression of myomiR-206, -1, and -133 in the tibialis anterior muscle of mice. These protocols can be used and adapted to monitor the expression of other miRNAs in other biological processes.

  6. Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests.

    Science.gov (United States)

    Vitsios, Dimitrios M; Kentepozidou, Elissavet; Quintais, Leonor; Benito-Gutiérrez, Elia; van Dongen, Stijn; Davis, Matthew P; Enright, Anton J

    2017-12-01

    The discovery of microRNAs (miRNAs) remains an important problem, particularly given the growth of high-throughput sequencing, cell sorting and single cell biology. While a large number of miRNAs have already been annotated, there may well be large numbers of miRNAs that are expressed in very particular cell types and remain elusive. Sequencing allows us to quickly and accurately identify the expression of known miRNAs from small RNA-Seq data. The biogenesis of miRNAs leads to very specific characteristics observed in their sequences. In brief, miRNAs usually have a well-defined 5' end and a more flexible 3' end with the possibility of 3' tailing events, such as uridylation. Previous approaches to the prediction of novel miRNAs usually involve the analysis of structural features of miRNA precursor hairpin sequences obtained from genome sequence. We surmised that it may be possible to identify miRNAs by using these biogenesis features observed directly from sequenced reads, solely or in addition to structural analysis from genome data. To this end, we have developed mirnovo, a machine learning based algorithm, which is able to identify known and novel miRNAs in animals and plants directly from small RNA-Seq data, with or without a reference genome. This method performs comparably to existing tools, however is simpler to use with reduced run time. Its performance and accuracy has been tested on multiple datasets, including species with poorly assembled genomes, RNaseIII (Drosha and/or Dicer) deficient samples and single cells (at both embryonic and adult stage). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. High Throughput Sequencing of Small RNAs in the Two Cucurbita Germplasm with Different Sodium Accumulation Patterns Identifies Novel MicroRNAs Involved in Salt Stress Response.

    Science.gov (United States)

    Xie, Junjun; Lei, Bo; Niu, Mengliang; Huang, Yuan; Kong, Qiusheng; Bie, Zhilong

    2015-01-01

    MicroRNAs (miRNAs), a class of small non-coding RNAs, recognize their mRNA targets based on perfect sequence complementarity. MiRNAs lead to broader changes in gene expression after plants are exposed to stress. High-throughput sequencing is an effective method to identify and profile small RNA populations in non-model plants under salt stresses, significantly improving our knowledge regarding miRNA functions in salt tolerance. Cucurbits are sensitive to soil salinity, and the Cucurbita genus is used as the rootstock of other cucurbits to enhance salt tolerance. Several cucurbit crops have been used for miRNA sequencing but salt stress-related miRNAs in cucurbit species have not been reported. In this study, we subjected two Cucurbita germplasm, namely, N12 (Cucurbita. maxima Duch.) and N15 (Cucurbita. moschata Duch.), with different sodium accumulation patterns, to Illumina sequencing to determine small RNA populations in root tissues after 4 h of salt treatment and control. A total of 21,548,326 and 19,394,108 reads were generated from the control and salt-treated N12 root tissues, respectively. By contrast, 19,108,240 and 20,546,052 reads were obtained from the control and salt-treated N15 root tissues, respectively. Fifty-eight conserved miRNA families and 33 novel miRNAs were identified in the two Cucurbita germplasm. Seven miRNAs (six conserved miRNAs and one novel miRNAs) were up-regulated in salt-treated N12 and N15 samples. Most target genes of differentially expressed novel miRNAs were transcription factors and salt stress-responsive proteins, including dehydration-induced protein, cation/H+ antiporter 18, and CBL-interacting serine/threonine-protein kinase. The differential expression of miRNAs between the two Cucurbita germplasm under salt stress conditions and their target genes demonstrated that novel miRNAs play an important role in the response of the two Cucurbita germplasm to salt stress. The present study initially explored small RNAs in the

  8. High Throughput Sequencing of Small RNAs in the Two Cucurbita Germplasm with Different Sodium Accumulation Patterns Identifies Novel MicroRNAs Involved in Salt Stress Response.

    Directory of Open Access Journals (Sweden)

    Junjun Xie

    Full Text Available MicroRNAs (miRNAs, a class of small non-coding RNAs, recognize their mRNA targets based on perfect sequence complementarity. MiRNAs lead to broader changes in gene expression after plants are exposed to stress. High-throughput sequencing is an effective method to identify and profile small RNA populations in non-model plants under salt stresses, significantly improving our knowledge regarding miRNA functions in salt tolerance. Cucurbits are sensitive to soil salinity, and the Cucurbita genus is used as the rootstock of other cucurbits to enhance salt tolerance. Several cucurbit crops have been used for miRNA sequencing but salt stress-related miRNAs in cucurbit species have not been reported. In this study, we subjected two Cucurbita germplasm, namely, N12 (Cucurbita. maxima Duch. and N15 (Cucurbita. moschata Duch., with different sodium accumulation patterns, to Illumina sequencing to determine small RNA populations in root tissues after 4 h of salt treatment and control. A total of 21,548,326 and 19,394,108 reads were generated from the control and salt-treated N12 root tissues, respectively. By contrast, 19,108,240 and 20,546,052 reads were obtained from the control and salt-treated N15 root tissues, respectively. Fifty-eight conserved miRNA families and 33 novel miRNAs were identified in the two Cucurbita germplasm. Seven miRNAs (six conserved miRNAs and one novel miRNAs were up-regulated in salt-treated N12 and N15 samples. Most target genes of differentially expressed novel miRNAs were transcription factors and salt stress-responsive proteins, including dehydration-induced protein, cation/H+ antiporter 18, and CBL-interacting serine/threonine-protein kinase. The differential expression of miRNAs between the two Cucurbita germplasm under salt stress conditions and their target genes demonstrated that novel miRNAs play an important role in the response of the two Cucurbita germplasm to salt stress. The present study initially explored small

  9. Self-interacting inelastic dark matter: a viable solution to the small scale structure problems

    Energy Technology Data Exchange (ETDEWEB)

    Blennow, Mattias; Clementz, Stefan; Herrero-Garcia, Juan, E-mail: emb@kth.se, E-mail: scl@kth.se, E-mail: juan.herrero-garcia@adelaide.edu.au [Department of Physics, School of Engineering Sciences, KTH Royal Institute of Technology, AlbaNova University Center, 106 91 Stockholm (Sweden)

    2017-03-01

    Self-interacting dark matter has been proposed as a solution to the small-scale structure problems, such as the observed flat cores in dwarf and low surface brightness galaxies. If scattering takes place through light mediators, the scattering cross section relevant to solve these problems may fall into the non-perturbative regime leading to a non-trivial velocity dependence, which allows compatibility with limits stemming from cluster-size objects. However, these models are strongly constrained by different observations, in particular from the requirements that the decay of the light mediator is sufficiently rapid (before Big Bang Nucleosynthesis) and from direct detection. A natural solution to reconcile both requirements are inelastic endothermic interactions, such that scatterings in direct detection experiments are suppressed or even kinematically forbidden if the mass splitting between the two-states is sufficiently large. Using an exact solution when numerically solving the Schrödinger equation, we study such scenarios and find regions in the parameter space of dark matter and mediator masses, and the mass splitting of the states, where the small scale structure problems can be solved, the dark matter has the correct relic abundance and direct detection limits can be evaded.

  10. Supersymmetry with Small mu: Connections between Naturalness, DarkMatter, and (Possibly) Flavor

    Energy Technology Data Exchange (ETDEWEB)

    Kitano, Ryuichiro Kitano; Nomura, Yasunori

    2006-06-11

    Weak scale supersymmetric theories often suffer from several naturalness problems: the problems of reproducing the correct scale for electroweak symmetry breaking, the correct abundance for dark matter, and small rates for flavor violating processes. We argue that the first two problems point to particular regions of parameter space in models with weak scale supersymmetry: those with a small {mu} term. This has an interesting implication on direct dark matter detection experiments. We find that, if the signs of the three gaugino mass parameters are all equal, we can obtain a solid lower bound on the spin-independent neutralino-nucleon cross section, {sigma}{sub SI}. In the case that the gaugino masses satisfy the unified mass relations, we obtain {sigma}{sub SI} {approx}> 4 x 10{sup -46} cm{sup 2} (1 x 10{sup -46} cm{sup 2}) for fine-tuning in electroweak symmetry breaking no worse than 10% (5%). We also discuss a possibility that the three problems listed above are all connected to the hierarchy of fermion masses. This occurs if supersymmetry breaking and electroweak symmetry breaking (the Higgs fields) are coupled to matter fields with similar hierarchical structures. The discovery of {mu} {yields} e transition processes in near future experiments is predicted in such a framework.

  11. MicroRNA-106b-5p regulates cisplatin chemosensitivity by targeting polycystic kidney disease-2 in non-small-cell lung cancer.

    Science.gov (United States)

    Yu, Shaorong; Qin, Xiaobing; Chen, Tingting; Zhou, Leilei; Xu, Xiaoyue; Feng, Jifeng

    2017-09-01

    Systemic therapy with cytotoxic agents remains one of the main treatment methods for non-small-cell lung cancer (NSCLC). Cisplatin is a commonly used chemotherapeutic agent, that, when combined with other drugs, is an effective treatment for NSCLC. However, effective cancer therapy is hindered by a patient's resistance to cisplatin. Unfortunately, the potential mechanism underlying such resistance remains unclear. In this study, we explored the mechanism of microRNA-106b-5p (miR-106b-5p), which is involved in the resistance to cisplatin in the A549 cell line of NSCLC. Quantitative real-time PCR was used to test the expression of miR-106-5p in the A549 and the A549/DDP cell line of NSCLC. The cell counting kit-8 assay was used to detect cell viability. Flow cytometry was used to measure cell cycle and cell apoptosis. Luciferase reporter assays and western blot were performed to confirm whether polycystic kidney disease-2 (PKD2) is a direct target gene of miR-106b-5p. Immunohistochemistry was performed to examine the distribution of PKD2 expression in patients who are sensitive and resistant to cisplatin. The experiments indicated that the expression of miR-106b-5p was significantly decreased in A549/DDP compared with that in A549. MiR-106b-5p affected the tolerance of cells to cisplatin by negatively regulating PKD2. Upregulation of miR-106b-5p or downregulation of PKD2 expression can cause A549/DDP cells to become considerably more sensitive to cisplatin. The results showed that miR-106b-5p enhanced the sensitivity of A549/DDP cells to cisplatin by targeting the expression of PKD2. These findings suggest that the use of miR-106b-5p may be a promising clinical strategy in the treatment of NSCLC.

  12. A transcriptome-wide study on the microRNA- and the Argonaute 1-enriched small RNA-mediated regulatory networks involved in plant leaf senescence.

    Science.gov (United States)

    Qin, J; Ma, X; Yi, Z; Tang, Z; Meng, Y

    2016-03-01

    Leaf senescence is an important physiological process during the plant life cycle. However, systemic studies on the impact of microRNAs (miRNAs) on the expression of senescence-associated genes (SAGs) are lacking. Besides, whether other Argonaute 1 (AGO1)-enriched small RNAs (sRNAs) play regulatory roles in leaf senescence remains unclear. In this study, a total of 5,123 and 1,399 AGO1-enriched sRNAs, excluding miRNAs, were identified in Arabidopsis thaliana and rice (Oryza sativa), respectively. After retrieving SAGs from the Leaf Senescence Database, all of the AGO1-enriched sRNAs and the miRBase-registered miRNAs of these two plants were included for target identification. Supported by degradome signatures, 200 regulatory pairs involving 120 AGO1-enriched sRNAs and 40 SAGs, and 266 regulatory pairs involving 64 miRNAs and 42 SAGs were discovered in Arabidopsis. Moreover, 13 genes predicted to interact with some of the above-identified target genes at protein level were validated as regulated by 17 AGO1-enriched sRNAs and ten miRNAs in Arabidopsis. In rice, only one SAG was targeted by three AGO1-enriched sRNAs, and one SAG was targeted by miR395. However, five AGO1-enriched sRNAs were conserved between Arabidopsis and rice. Target genes conserved between the two plants were identified for three of the above five sRNAs, pointing to the conserved roles of these regulatory pairs in leaf senescence or other developmental procedures. Novel targets were discovered for three of the five AGO1-enriched sRNAs in rice, indicating species-specific functions of these sRNA-target pairs. These results could advance our understanding of the sRNA-involved molecular processes modulating leaf senescence. © 2015 German Botanical Society and The Royal Botanical Society of the Netherlands.

  13. Luteolin Inhibits Tumorigenesis and Induces Apoptosis of Non-Small Cell Lung Cancer Cells via Regulation of MicroRNA-34a-5p

    Directory of Open Access Journals (Sweden)

    Ze-Qun Jiang

    2018-02-01

    Full Text Available Luteolin (LTL exerts remarkable tumor suppressive activity on various types of cancers, including non-small cell lung cancer (NSCLC. However, it is not completely understood whether the mechanism of its action against NSCLC is related to microRNAs (miRNAs. In the present study, we investigated the anti-tumor effects of LTL on NSCLC in vitro and in vivo. The results revealed that LTL could inhibit cell proliferation and induce apoptosis in both A549 and H460 cells. In a H460 xenograft tumor model of nude mice, LTL significantly suppressed tumor growth, inhibited cell proliferation, and induced apoptosis. miRNA microarray and quantitative PCR (qPCR analysis indicated that miR-34a-5p was dramatically upregulated upon LTL treatment in tumor tissues. Furthermore, MDM4 was proved to be a direct target of miR-34a-5p by luciferase reporter gene assay. LTL treatment was associated with increased p53 and p21 protein expressions and decreased MDM4 protein expression in both NSCLC cells and tumor tissues. When miR-34a-5p was inhibited in vitro, the protein expressions of Bcl-2 and MDM4 were recovered, while that of p53, p21, and Bax were attenuated. Moreover, caspase-3 and caspase-9 activation induced by LHL treatment in vitro were also suppressed by miR-34a-5p inhibition. Overall, LTL could inhibit tumorigenesis and induce apoptosis of NSCLC cells by upregulation of miR-34a-5p via targeting MDM4. These findings provide novel insight into the molecular functions of LTL that suggest its potential as a therapeutic agent for human NSCLC.

  14. Linear scale bounds on dark matter--dark radiation interactions and connection with the small scale crisis of cold dark matter

    DEFF Research Database (Denmark)

    Hannestad, Steen; Archidiacono, Maria; Bohr, Sebastian

    2017-01-01

    One of the open questions in modern cosmology is the small scale crisis of the cold dark matter paradigm. Increasing attention has recently been devoted to self-interacting dark matter models as a possible answer. However, solving the so-called "missing satellites" problem requires in addition...... the presence of an extra relativistic particle (dubbed dark radiation) scattering with dark matter in the early universe. Here we investigate the impact of different theoretical models devising dark matter dark radiation interactions on large scale cosmological observables. We use cosmic microwave background...... data to put constraints on the dark radiation component and its coupling to dark matter. We find that the values of the coupling allowed by the data imply a cut-off scale of the halo mass function consistent with the one required to match the observations of satellites in the Milky Way....

  15. Deep sequencing of small RNA libraries from human prostate epithelial and stromal cells reveal distinct pattern of microRNAs primarily predicted to target growth factors.

    Science.gov (United States)

    Singh, Savita; Zheng, Yun; Jagadeeswaran, Guru; Ebron, Jey Sabith; Sikand, Kavleen; Gupta, Sanjay; Sunker, Ramanjulu; Shukla, Girish C

    2016-02-28

    Complex epithelial and stromal cell interactions are required during the development and progression of prostate cancer. Regulatory small non-coding microRNAs (miRNAs) participate in the spatiotemporal regulation of messenger RNA (mRNA) and regulation of translation affecting a large number of genes involved in prostate carcinogenesis. In this study, through deep-sequencing of size fractionated small RNA libraries we profiled the miRNAs of prostate epithelial (PrEC) and stromal (PrSC) cells. Over 50 million reads were obtained for PrEC in which 860,468 were unique sequences. Similarly, nearly 76 million reads for PrSC were obtained in which over 1 million were unique reads. Expression of many miRNAs of broadly conserved and poorly conserved miRNA families were identified. Sixteen highly expressed miRNAs with significant change in expression in PrSC than PrEC were further analyzed in silico. ConsensusPathDB showed the target genes of these miRNAs were significantly involved in adherence junction, cell adhesion, EGRF, TGF-β and androgen signaling. Let-7 family of tumor-suppressor miRNAs expression was highly pervasive in both, PrEC and PrSC cells. In addition, we have also identified several miRNAs that are unique to PrEC or PrSC cells and their predicted putative targets are a group of transcription factors. This study provides perspective on the miRNA expression in PrEC and PrSC, and reveals a global trend in miRNA interactome. We conclude that the most abundant miRNAs are potential regulators of development and differentiation of the prostate gland by targeting a set of growth factors. Additionally, high level expression of the most members of let-7 family miRNAs suggests their role in the fine tuning of the growth and proliferation of prostate epithelial and stromal cells. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  16. Prognostic value of the MicroRNA regulators dicer and drosha in non-small-cell lung cancer: co-expression of Drosha and miR-126 predicts poor survival

    OpenAIRE

    Lønvik, Kenneth; Sørbye, Sveinung Wergeland; Nilsen, Marit Nina; Paulssen, Ruth H

    2014-01-01

    Background Dicer and Drosha are important enzymes for processing microRNAs. Recent studies have exhibited possible links between expression of different miRNAs, levels of miRNA processing enzymes, and cancer prognosis. We have investigated the prognostic impact of Dicer and Drosha and their correlation with miR-126 expression in a large cohort of non-small cell lung cancer (NSCLC) patients. We aimed to find patient groups within the cohort that might have an advantage of receiving adjunctive ...

  17. Thermal evolution and small scale structure of Sommerfeld enhanced dark matter

    International Nuclear Information System (INIS)

    Aarssen, Laura Gusta van den

    2013-04-01

    Although the existence of Dark Matter (DM) has been confirmed by many independent observations on various scales, its nature still remains a mystery. Leading candidates for the cold, non-baryonic DM are Weakly Interacting Massive Particles (WIMPs), that are well motivated from particle physics and naturally explain the observed relic density by their thermal production mechanism. In this thesis we focus on a particular class of WIMP models in which the Sommerfeld effect has to be taken into account. This is a quantum mechanical phenomenon that can significantly enhance the annihilation cross section in the non-relativistic limit. To describe the non-perturbative effect, we use a non-relativistic effective field theory derived from the full quantum field theory. We include a detailed discussion of the calculation for the righthanded sneutrino, which is the superpartner of the neutrino and a viable DM candidate. The Sommerfeld enhancement can have a profound influence on the thermal evolution of the DM, which can no longer be described by the standard scenario. We introduce a framework to correctly take this effect into account and apply it to a simple leptophilic DM model. A new era of annihilations can decrease the DM density even after usual freeze-out, and in some cases where the Sommerfeld enhancement is especially large, even continue until after matter-radiation equality. The effect on the asymptotic WIMP temperature, which can be directly related to a small scale cutoff in the matter density fluctuations, causes the mass of the smallest gravitationally bound objects to be larger than expected from standard calculations. Furthermore we study the effect of velocity dependent DM self-scattering in relation to the small scale structure formation. Numerical simulations of ΛCDM have shown a remarkable agreement with the large scale structure of the Universe. However, the simulations are in tension with observed abundances, inner densities and velocity profiles of

  18. Using CMB spectral distortions to distinguish between dark matter solutions to the small-scale crisis

    Energy Technology Data Exchange (ETDEWEB)

    Diacoumis, James A.D.; Wong, Yvonne Y.Y., E-mail: j.diacoumis@unsw.edu.au, E-mail: yvonne.y.wong@unsw.edu.au [School of Physics, The University of New South Wales, Sydney NSW 2052 (Australia)

    2017-09-01

    The dissipation of small-scale perturbations in the early universe produces a distortion in the blackbody spectrum of cosmic microwave background photons. In this work, we propose to use these distortions as a probe of the microphysics of dark matter on scales 1 Mpc{sup -1}∼< k ∼< 10{sup 4} Mpc{sup -1}. We consider in particular models in which the dark matter is kinetically coupled to either neutrinos or photons until shortly before recombination, and compute the photon heating rate and the resultant μ-distortion in both cases. We show that the μ-parameter is generally enhanced relative to ΛCDM for interactions with neutrinos, and may be either enhanced or suppressed in the case of interactions with photons. The deviations from the ΛCDM signal are potentially within the sensitivity reach of a PRISM-like experiment if σ{sub DM-γ} ∼> 1.1 × 10{sup -30} (m{sub DM}/GeV) cm{sup 2} and σ{sub DM-ν} ∼> 4.8 × 10{sup -32} (m{sub DM}/GeV) cm{sup 2} for time-independent cross sections, and σ{sup 0}{sub DM-γ} ∼> 1.8 × 10{sup -40} (m{sub DM}/GeV) cm{sup 2} and σ{sup 0}{sub DM-ν} ∼> 2.5 × 10{sup -47} (m{sub DM}/GeV) cm{sup 2} for cross sections scaling as temperature squared, coinciding with the parameter regions in which late kinetic decoupling may serve as a solution to the small-scale crisis. Furthermore, these μ-distortion signals differ from those of warm dark matter (no deviation from ΛCDM) and a suppressed primordial power spectrum (a strongly suppressed or negative μ-parameter), demonstrating that CMB spectral distortion can potentially be used to distinguish between solutions to the small-scale crisis.

  19. Thermal evolution and small scale structure of Sommerfeld enhanced dark matter

    Energy Technology Data Exchange (ETDEWEB)

    Aarssen, Laura Gusta van den

    2013-04-15

    Although the existence of Dark Matter (DM) has been confirmed by many independent observations on various scales, its nature still remains a mystery. Leading candidates for the cold, non-baryonic DM are Weakly Interacting Massive Particles (WIMPs), that are well motivated from particle physics and naturally explain the observed relic density by their thermal production mechanism. In this thesis we focus on a particular class of WIMP models in which the Sommerfeld effect has to be taken into account. This is a quantum mechanical phenomenon that can significantly enhance the annihilation cross section in the non-relativistic limit. To describe the non-perturbative effect, we use a non-relativistic effective field theory derived from the full quantum field theory. We include a detailed discussion of the calculation for the righthanded sneutrino, which is the superpartner of the neutrino and a viable DM candidate. The Sommerfeld enhancement can have a profound influence on the thermal evolution of the DM, which can no longer be described by the standard scenario. We introduce a framework to correctly take this effect into account and apply it to a simple leptophilic DM model. A new era of annihilations can decrease the DM density even after usual freeze-out, and in some cases where the Sommerfeld enhancement is especially large, even continue until after matter-radiation equality. The effect on the asymptotic WIMP temperature, which can be directly related to a small scale cutoff in the matter density fluctuations, causes the mass of the smallest gravitationally bound objects to be larger than expected from standard calculations. Furthermore we study the effect of velocity dependent DM self-scattering in relation to the small scale structure formation. Numerical simulations of {Lambda}CDM have shown a remarkable agreement with the large scale structure of the Universe. However, the simulations are in tension with observed abundances, inner densities and velocity

  20. MicroRNA expression profiling of the porcine developing brain

    DEFF Research Database (Denmark)

    Podolska, Agnieszka; Kaczkowski, Bogumil; Busk, Peter Kamp

    2011-01-01

    MicroRNAs are small, non-coding RNA molecules that regulate gene expression at the post-transcriptional level and play an important role in the control of developmental and physiological processes. In particular, the developing brain contains an impressive diversity of microRNAs. Most micro...... and the growth curve when compared to humans. Considering these similarities, studies examining microRNA expression during porcine brain development could potentially be used to predict the expression profile and role of microRNAs in the human brain....

  1. Descendit ad [in] inferna: ‘A matter of no small moment in bringing about redemption’

    Directory of Open Access Journals (Sweden)

    Johan Buitendag

    2009-10-01

    Full Text Available This article endorses Calvin’s conviction that the ‘descendit ad inferna’ of the Apostles’ Creed is part of the ‘summary of doctrine‘ and a matter of ‘no small moment in bringing about redemption‘ (Calvin 1960:Inst. II, xvi, 8. The reason for this role, however, is not Calvin’s metaphorical interpretation of the clause. Instead, the author tries to argue that a scientific theological approach will maintain the clause because of its transcendence of finitude and the proclamation of Christ’s victory. The whole of creation is delivered from sin. Proper hermeneutics will take the original socio–historical environment into account and make one suspicious about certain ecclesiastical biases. Spatial terms in the Creed should therefore not be demythologised, but rather be transformed in accordance with the insights of the contemporary physics of time and space.

  2. Intronic microRNAs

    International Nuclear Information System (INIS)

    Ying, S.-Y.; Lin, S.-L.

    2005-01-01

    MicroRNAs (miRNAs), small single-stranded regulatory RNAs capable of interfering with intracellular mRNAs that contain partial complementarity, are useful for the design of new therapies against cancer polymorphism and viral mutation. MiRNA was originally discovered in the intergenic regions of the Caenorhabditis elegans genome as native RNA fragments that modulate a wide range of genetic regulatory pathways during animal development. However, neither RNA promoter nor polymerase responsible for miRNA biogenesis was determined. Recent findings of intron-derived miRNA in C. elegans, mouse, and human have inevitably led to an alternative pathway for miRNA biogenesis, which relies on the coupled interaction of Pol-II-mediated pre-mRNA transcription and intron excision, occurring in certain nuclear regions proximal to genomic perichromatin fibrils

  3. Assessment of background particulate matter concentrations in small cities and rural locations--Prince George, Canada.

    Science.gov (United States)

    Veira, Andreas; Jackson, Peter L; Ainslie, Bruce; Fudge, Dennis

    2013-07-01

    This study investigates the development and application of a simple method to calculate annual and seasonal PM2.5 and PM10 background concentrations in small cities and rural areas. The Low Pollution Sectors and Conditions (LPSC) method is based on existing measured long-term data sets and is designed for locations where particulate matter (PM) monitors are only influenced by local anthropogenic emission sources from particular wind sectors. The LPSC method combines the analysis of measured hourly meteorological data, PM concentrations, and geographical emission source distributions. PM background levels emerge from measured data for specific wind conditions, where air parcel trajectories measured at a monitoring station are assumed to have passed over geographic sectors with negligible local emissions. Seasonal and annual background levels were estimated for two monitoring stations in Prince George, Canada, and the method was also applied to four other small cities (Burns Lake, Houston, Quesnel, Smithers) in northern British Columbia. The analysis showed reasonable background concentrations for both monitoring stations in Prince George, whereas annual PM10 background concentrations at two of the other locations and PM2.5 background concentrations at one other location were implausibly high. For those locations where the LPSC method was successful, annual background levels ranged between 1.8 +/- 0.1 microg/m3 and 2.5 +/- 0.1 microg/m3 for PM2.5 and between 6.3 +/- 0.3 microg/m3 and 8.5 +/- 0.3 microg/m3 for PM10. Precipitation effects and patterns of seasonal variability in the estimated background concentrations were detectable for all locations where the method was successful. Overall the method was dependent on the configuration of local geography and sources with respect to the monitoring location, and may fail at some locations and under some conditions. Where applicable, the LPSC method can provide a fast and cost-efficient way to estimate background PM

  4. Small P Systems with Catalysts or Anti-Matter Simulating Generalized Register Machines and Generalized Counter Automata

    Directory of Open Access Journals (Sweden)

    Artiom Alhazov

    2015-11-01

    Full Text Available In this paper we focus on two weak forms of cooperation in P systems, namely, catalytic rules and matter/anti-matter annihilation rules. These variants of P systems both are computationally complete, while the corresponding rule complexity turns out to be of special interest. For establishing considerably small universal P systems in both cases, we found two suitable tools: generalized register machines and generalized counter automata. Depending on the features used in the different variants, we construct several small universal P systems.

  5. A small amount of mini-charged dark matter could cool the baryons in the early Universe.

    Science.gov (United States)

    Muñoz, Julian B; Loeb, Abraham

    2018-05-01

    The dynamics of our Universe is strongly influenced by pervasive-albeit elusive-dark matter, with a total mass about five times the mass of all the baryons 1,2 . Despite this, its origin and composition remain a mystery. All evidence for dark matter relies on its gravitational pull on baryons, and thus such evidence does not require any non-gravitational coupling between baryons and dark matter. Nonetheless, some small coupling would explain the comparable cosmic abundances of dark matter and baryons 3 , as well as solving structure-formation puzzles in the pure cold-dark-matter models 4 . A vast array of observations has been unable to find conclusive evidence for any non-gravitational interactions of baryons with dark matter 5-9 . Recent observations by the EDGES collaboration, however, suggest that during the cosmic dawn, roughly 200 million years after the Big Bang, the baryonic temperature was half of its expected value 10 . This observation is difficult to reconcile with the standard cosmological model but could be explained if baryons are cooled down by interactions with dark matter, as expected if their interaction rate grows steeply at low velocities 11 . Here we report that if a small fraction-less than one per cent-of the dark matter has a mini-charge, a million times smaller than the charge on the electron, and a mass in the range of 1-100 times the electron mass, then the data 10 from the EDGES experiment can be explained while remaining consistent with all other observations. We also show that the entirety of the dark matter cannot have a mini-charge.

  6. Role of microRNAs in sepsis.

    Science.gov (United States)

    Kingsley, S Manoj Kumar; Bhat, B Vishnu

    2017-07-01

    MicroRNAs have been found to be of high significance in the regulation of various genes and processes in the body. Sepsis is a serious clinical problem which arises due to the excessive host inflammatory response to infection. The non-specific clinical features and delayed diagnosis of sepsis has been a matter of concern for long time. MicroRNAs could enable better diagnosis of sepsis and help in the identification of the various stages of sepsis. Improved diagnosis may enable quicker and more effective treatment measures. The initial acute and transient phase of sepsis involves excessive secretion of pro-inflammatory cytokines which causes severe damage. MicroRNAs negatively regulate the toll-like receptor signaling pathway and regulate the production of inflammatory cytokines during sepsis. Likewise, microRNAs have shown to regulate the vascular barrier and endothelial function in sepsis. They are also involved in the regulation of the apoptosis, immunosuppression, and organ dysfunction in later stages of sepsis. Their importance at various levels of the pathophysiology of sepsis has been discussed along with the challenges and future perspectives. MicroRNAs could be key players in the diagnosis and staging of sepsis. Their regulation at various stages of sepsis suggests that they may have an important role in altering the outcome associated with sepsis.

  7. Altered small-world properties of gray matter networks in breast cancer

    Directory of Open Access Journals (Sweden)

    Hosseini S M

    2012-05-01

    Full Text Available Abstract Background Breast cancer survivors, particularly those treated with chemotherapy, are at significantly increased risk for long-term cognitive and neurobiologic impairments. These deficits tend to involve skills that are subserved by distributed brain networks. Additionally, neuroimaging studies have shown a diffuse pattern of brain structure changes in chemotherapy-treated breast cancer survivors that might impact large-scale brain networks. Methods We therefore applied graph theoretical analysis to compare the gray matter structural networks of female breast cancer survivors with a history of chemotherapy treatment and healthy age and education matched female controls. Results Results revealed reduced clustering coefficient and small-world index in the brain network of the breast cancer patients across a range of network densities. In addition, the network of the breast cancer group had less highly interactive nodes and reduced degree/centrality in the frontotemporal regions compared to controls, which may help explain the common impairments of memory and executive functioning among these patients. Conclusions These results suggest that breast cancer and chemotherapy may decrease regional connectivity as well as global network organization and integration, reducing efficiency of the network. To our knowledge, this is the first report of altered large-scale brain networks associated with breast cancer and chemotherapy.

  8. The effects of the small-scale behaviour of dark matter power spectrum on CMB spectral distortion

    Energy Technology Data Exchange (ETDEWEB)

    Sarkar, Abir; Sethi, Shiv K. [Raman Research Institute, CV Raman Ave Sadashivnagar, Bengaluru, Karnataka 560080 (India); Das, Subinoy, E-mail: abir@rri.res.in, E-mail: sethi@rri.res.in, E-mail: subinoy@iiap.res.in [Indian Institute of Astrophysics, 100 Feet Rd, Madiwala, 2nd Block, Koramangala, Bengaluru, Karnataka 560034 (India)

    2017-07-01

    After numerous astronomical and experimental searches, the precise particle nature of dark matter is still unknown. The standard Weakly Interacting Massive Particle(WIMP) dark matter, despite successfully explaining the large-scale features of the universe, has long-standing small-scale issues. The spectral distortion in the Cosmic Microwave Background(CMB) caused by Silk damping in the pre-recombination era allows one to access information on a range of small scales 0.3 Mpc < k < 10{sup 4} Mpc{sup −1}, whose dynamics can be precisely described using linear theory. In this paper, we investigate the possibility of using the Silk damping induced CMB spectral distortion as a probe of the small-scale power. We consider four suggested alternative dark matter candidates—Warm Dark Matter (WDM), Late Forming Dark Matter (LFDM), Ultra Light Axion (ULA) dark matter and Charged Decaying Dark Matter (CHDM); the matter power in all these models deviate significantly from the ΛCDM model at small scales. We compute the spectral distortion of CMB for these alternative models and compare our results with the ΛCDM model. We show that the main impact of alternative models is to alter the sub-horizon evolution of the Newtonian potential which affects the late-time behaviour of spectral distortion of CMB. The y -parameter diminishes by a few percent as compared to the ΛCDM model for a range of parameters of these models: LFDM for formation redshift z {sub f} = 10{sup 5} (7%); WDM for mass m {sub wdm} = 1 keV (2%); CHDM for decay redshift z {sub decay} = 10{sup 5} (5%); ULA for mass m {sub a} = 10{sup −24} eV (3%). This effect from the pre-recombination era can be masked by orders of magnitude higher y -distortions generated by late-time sources, e.g. the Epoch of Reionization and tSZ from the cluster of galaxies. We also briefly discuss the detectability of this deviation in light of the upcoming CMB experiment PIXIE, which might have the sensitivity to detect this signal from

  9. Targeting of microRNAs for therapeutics

    DEFF Research Database (Denmark)

    Stenvang, Jan; Lindow, Morten; Kauppinen, Sakari

    2008-01-01

    miRNAs (microRNAs) comprise a class of small endogenous non-coding RNAs that post-transcriptionally repress gene expression by base-pairing with their target mRNAs. Recent evidence has shown that miRNAs play important roles in a wide variety of human diseases, such as viral infections, cancer...

  10. MicroRNAs, Regulatory Networks, and Comorbidities

    DEFF Research Database (Denmark)

    Russo, Francesco; Belling, Kirstine; Jensen, Anders Boeck

    2017-01-01

    MicroRNAs (miRNAs) are small noncoding RNAs involved in the posttranscriptional regulation of messenger RNAs (mRNAs). Each miRNA targets a specific set of mRNAs. Upon binding the miRNA inhibits mRNA translation or facilitate mRNA degradation. miRNAs are frequently deregulated in several pathologies...

  11. Prognostic value of the MicroRNA regulators Dicer and Drosha in non-small-cell lung cancer: co-expression of Drosha and miR-126 predicts poor survival.

    Science.gov (United States)

    Lønvik, Kenneth; Sørbye, Sveinung W; Nilsen, Marit N; Paulssen, Ruth H

    2014-01-01

    Dicer and Drosha are important enzymes for processing microRNAs. Recent studies have exhibited possible links between expression of different miRNAs, levels of miRNA processing enzymes, and cancer prognosis. We have investigated the prognostic impact of Dicer and Drosha and their correlation with miR-126 expression in a large cohort of non-small cell lung cancer (NSCLC) patients. We aimed to find patient groups within the cohort that might have an advantage of receiving adjunctive therapies. Dicer expression in the cytoplasm and Drosha expression in the nucleus were evaluated by manual immunohistochemistry of tissue microarrays (TMAs), including tumor tissue samples from 335 patients with resected stages I to IIIA NSCLC. In addition, in situ hybridizations of TMAs for visualization of miR-126 were performed. Kaplan-Meier analysis was performed, and the log-rank test via SPSS v.22 was used for estimating significance levels. In patients with normal performance status (ECOG = 0, n = 197), high Dicer expression entailed a significantly better prognosis than low Dicer expression (P = 0.024). Dicer had no significant prognostic value in patients with reduced performance status (ECOG = 1-2, n = 138). High Drosha expression was significantly correlated with high levels of the microRNA 126 (miR-126) (P = 0.004). Drosha/miR-126 co-expression had a significant negative impact on the disease-specific survival (DSS) rate (P < 0.001). Multivariate analyses revealed that the interaction Dicer*Histology (P = 0.049) and Drosha/miR-126 co-expression (P = 0.033) were independent prognostic factors. In NSCLC patients with normal performance status, Dicer is a positive prognostic factor. The importance of Drosha as a prognostic factor in our material seems to be related to miR-126 and possibly other microRNAs.

  12. The effects of the small-scale behaviour of dark matter power spectrum on CMB spectral distortion

    Science.gov (United States)

    Sarkar, Abir; Sethi, Shiv. K.; Das, Subinoy

    2017-07-01

    After numerous astronomical and experimental searches, the precise particle nature of dark matter is still unknown. The standard Weakly Interacting Massive Particle(WIMP) dark matter, despite successfully explaining the large-scale features of the universe, has long-standing small-scale issues. The spectral distortion in the Cosmic Microwave Background(CMB) caused by Silk damping in the pre-recombination era allows one to access information on a range of small scales 0.3 Mpc Light Axion (ULA) dark matter and Charged Decaying Dark Matter (CHDM); the matter power in all these models deviate significantly from the ΛCDM model at small scales. We compute the spectral distortion of CMB for these alternative models and compare our results with the ΛCDM model. We show that the main impact of alternative models is to alter the sub-horizon evolution of the Newtonian potential which affects the late-time behaviour of spectral distortion of CMB. The y-parameter diminishes by a few percent as compared to the ΛCDM model for a range of parameters of these models: LFDM for formation redshift zf = 105 (7%); WDM for mass mwdm = 1 keV (2%); CHDM for decay redshift zdecay = 105 (5%); ULA for mass ma = 10-24 eV (3%). This effect from the pre-recombination era can be masked by orders of magnitude higher y-distortions generated by late-time sources, e.g. the Epoch of Reionization and tSZ from the cluster of galaxies. We also briefly discuss the detectability of this deviation in light of the upcoming CMB experiment PIXIE, which might have the sensitivity to detect this signal from the pre-recombination phase.

  13. Characterising the grey matter correlates of leukoaraiosis in cerebral small vessel disease

    Directory of Open Access Journals (Sweden)

    Christian Lambert

    2015-01-01

    We demonstrate that SVD severity is associated with regional cortical thinning. Furthermore a quantitative measure of SVD severity (WMH volume can be predicted from grey matter measures, supporting an association between white and grey matter damage. The pattern of cortical thinning and volumetric decline is distinctive for SVD severity compared to ageing. These results, taken together, suggest that there is a phenotypic pattern of atrophy associated with SVD severity.

  14. Systematic Prediction of the Impacts of Mutations in MicroRNA Seed Sequences

    Directory of Open Access Journals (Sweden)

    Bhattacharya Anindya

    2017-05-01

    Full Text Available MicroRNAs are a class of small non-coding RNAs that are involved in many important biological processes and the dysfunction of microRNA has been associated with many diseases. The seed region of a microRNA is of crucial importance to its target recognition. Mutations in microRNA seed regions may disrupt the binding of microRNAs to their original target genes and make them bind to new target genes. Here we use a knowledge-based computational method to systematically predict the functional effects of all the possible single nucleotide mutations in human microRNA seed regions. The result provides a comprehensive reference for the functional assessment of the impacts of possible natural and artificial single nucleotide mutations in microRNA seed regions.

  15. Small RNA Sequencing Reveals Dlk1-Dio3 Locus-Embedded MicroRNAs as Major Drivers of Ground-State Pluripotency.

    Science.gov (United States)

    Moradi, Sharif; Sharifi-Zarchi, Ali; Ahmadi, Amirhossein; Mollamohammadi, Sepideh; Stubenvoll, Alexander; Günther, Stefan; Salekdeh, Ghasem Hosseini; Asgari, Sassan; Braun, Thomas; Baharvand, Hossein

    2017-12-12

    Ground-state pluripotency is a cell state in which pluripotency is established and maintained through efficient repression of endogenous differentiation pathways. Self-renewal and pluripotency of embryonic stem cells (ESCs) are influenced by ESC-associated microRNAs (miRNAs). Here, we provide a comprehensive assessment of the "miRNome" of ESCs cultured under conditions favoring ground-state pluripotency. We found that ground-state ESCs express a distinct set of miRNAs compared with ESCs grown in serum. Interestingly, most "ground-state miRNAs" are encoded by an imprinted region on chromosome 12 within the Dlk1-Dio3 locus. Functional analysis revealed that ground-state miRNAs embedded in the Dlk1-Dio3 locus (miR-541-5p, miR-410-3p, and miR-381-3p) promoted pluripotency via inhibition of multi-lineage differentiation and stimulation of self-renewal. Overall, our results demonstrate that ground-state pluripotency is associated with a unique miRNA signature, which supports ground-state self-renewal by suppressing differentiation. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  16. New research progress of microRNAs in retinoblastoma

    Directory of Open Access Journals (Sweden)

    Jing Zeng

    2014-11-01

    Full Text Available Retinoblastoma(RBis the most common intraocular malignancy of children with extremely poor prognosis. MicroRNAs are small non-coding single-stranded RNAs in eukaryotic cells, which regulate the expression of gene by mRNA degradation or translation inhibition. MicroRNAs, acting as oncogenes or tumor suppressor genes, are associated with the occurrence and development of RB directly, which is vital for the early diagnosis and clinical targeted therapy of RB. This review summarized the expression of microRNAs in RB and the related mechanism.

  17. Compact stars with a small electric charge: the limiting radius to mass relation and the maximum mass for incompressible matter

    Energy Technology Data Exchange (ETDEWEB)

    Lemos, Jose P.S.; Lopes, Francisco J.; Quinta, Goncalo [Universidade de Lisboa, UL, Departamento de Fisica, Centro Multidisciplinar de Astrofisica, CENTRA, Instituto Superior Tecnico, IST, Lisbon (Portugal); Zanchin, Vilson T. [Universidade Federal do ABC, Centro de Ciencias Naturais e Humanas, Santo Andre, SP (Brazil)

    2015-02-01

    One of the stiffest equations of state for matter in a compact star is constant energy density and this generates the interior Schwarzschild radius to mass relation and the Misner maximum mass for relativistic compact stars. If dark matter populates the interior of stars, and this matter is supersymmetric or of some other type, some of it possessing a tiny electric charge, there is the possibility that highly compact stars can trap a small but non-negligible electric charge. In this case the radius to mass relation for such compact stars should get modifications. We use an analytical scheme to investigate the limiting radius to mass relation and the maximum mass of relativistic stars made of an incompressible fluid with a small electric charge. The investigation is carried out by using the hydrostatic equilibrium equation, i.e., the Tolman-Oppenheimer-Volkoff (TOV) equation, together with the other equations of structure, with the further hypothesis that the charge distribution is proportional to the energy density. The approach relies on Volkoff and Misner's method to solve the TOV equation. For zero charge one gets the interior Schwarzschild limit, and supposing incompressible boson or fermion matter with constituents with masses of the order of the neutron mass one finds that the maximum mass is the Misner mass. For a small electric charge, our analytical approximating scheme, valid in first order in the star's electric charge, shows that the maximum mass increases relatively to the uncharged case, whereas the minimum possible radius decreases, an expected effect since the new field is repulsive, aiding the pressure to sustain the star against gravitational collapse. (orig.)

  18. Small scale patches of suspended matter and phytoplankton in the Elbe river estuary, German Bight and tidal flats

    Energy Technology Data Exchange (ETDEWEB)

    Doerffer, R; Fischer, J; Stoessel, M; Brockmann, C [GKSS-Forschungszentrum Geesthacht GmbH, Geesthacht-Tesperhude (Germany, F.R.); Grassl, H [Max-Planck-Institut fuer Meteorologie, Hamburg (Germany, F.R.)

    1989-01-01

    Thematic mapper and ship data has been used to study small scale features in coastal waters of the North Sea. Three independent pieces of informations from all 7 TM channels were found with factor analysis: suspended matter concentration, atmospheric scattering and sea surface temperature. Near surface suspended matter concentrations may be detected within a factor of 2. For the required atmospheric correction the signal-to-noise ratio of the channels 5 and 7 has to be improved by averaging over 25 x 25 pixels. Thus TM allows to monitor aerosol optical depth and aerosol type over cloudfree water surfaces. Sea surface temperature is retrievable with an absolute accuracy of 1.0 K as long as radiosonde data are available for the correction of atmospheric effects, while relative temperature variations of 0.5 K are detectable. The patchiness of suspended matter and its relation to underwater topography was analysed with auto- and crosscorrelation: horizontal lengths, where the suspended matter concentration of single pixels are significantly correlated either with each another or with water depth, are < 800 m. (orig.).

  19. Research resources: comparative microRNA profiles in human corona radiata cells and cumulus oophorus cells detected by next-generation small RNA sequencing.

    Directory of Open Access Journals (Sweden)

    Xian-Hong Tong

    Full Text Available During folliculogenesis, cumulus cells surrounding the oocyte differentiate into corona radiata cells (CRCs and cumulus oophorus cells (COCs, which are involved in gonadal steroidogenesis and the development of germ cells. Several studies suggested that microRNAs (miRNAs play an important regulatory role at the post-transcriptional level in cumulus cells. However, comparative miRNA profiles and associated processes in human CRCs and COCs have not been reported before. In this study, miRNA profiles were obtained from CRCs and COCs using next generation sequencing in women undergoing controlled ovarian stimulation for IVF. A total of 785 and 799 annotated miRNAs were identified in CRCs and COCs, while high expression levels of six novel miRNAs were detected both in CRCs and in COCs. In addition, different expression patterns in CRCs and COCs were detected in 72 annotated miRNAs. To confirm the miRNA profile in COCs and CRCs, quantitative real-time PCR was used to validate the expression of annotated miRNAs, differentially expressed miRNAs, and novel miRNAs. The miRNAs in the let-7 family were found to be involved in the regulation of a broad range of biological processes in both cumulus cell populations, which was accompanied by a large amount of miRNA editing. Bioinformatics analysis showed that amino acid and energy metabolism were targeted significantly by miRNAs that were differentially expressed between CRCs and COCs. Our work extends the current knowledge of the regulatory role of miRNAs and their targeted pathways in folliculogenesis, and provides novel candidates for molecular biomarkers in the research of female infertility.

  20. Seasonal changes in photochemical properties of dissolved organic matter in small boreal streams

    Czech Academy of Sciences Publication Activity Database

    Porcal, Petr; Dillon, P. J.; Molot, L. A.

    2013-01-01

    Roč. 10, č. 8 (2013), s. 5533-5543 ISSN 1726-4170 R&D Projects: GA ČR(CZ) GAP503/12/0781 Institutional support: RVO:60077344 Keywords : photodegradation * dissolved organic matter * seasonal * stream Subject RIV: DA - Hydrology ; Limnology Impact factor: 3.753, year: 2013

  1. MicroRNAs associated with exercise and diet: a systematic review.

    Science.gov (United States)

    Flowers, Elena; Won, Gloria Y; Fukuoka, Yoshimi

    2015-01-01

    MicroRNAs are posttranscriptional regulators of gene expression. MicroRNAs reflect individual biologic adaptation to exposures in the environment. As such, measurement of circulating microRNAs presents an opportunity to evaluate biologic changes associated with behavioral interventions (i.e., exercise, diet) for weight loss. The aim of this study was to perform a systematic review of the literature to summarize what is known about circulating microRNAs associated with exercise, diet, and weight loss. We performed a systematic review of three scientific databases. We included studies reporting on circulating microRNAs associated with exercise, diet, and weight loss in humans. Of 1,219 studies identified in our comprehensive database search, 14 were selected for inclusion. Twelve reported on microRNAs associated with exercise, and two reported on microRNAs associated with diet and weight loss. The majority of studies used a quasiexperimental, cross-sectional design. There were numerous differences in the type and intensity of exercise and dietary interventions, the biologic source of microRNAs, and the methodological approaches used quantitate microRNAs. Data from several studies support an association between circulating microRNAs and exercise. The evidence for an association between circulating microRNAs and diet is weaker because of a small number of studies. Additional research is needed to validate previous observations using methodologically rigorous approaches to microRNA quantitation to determine the specific circulating microRNA signatures associated with behavioral approaches to weight loss. Future directions include longitudinal studies to determine if circulating microRNAs are predictive of response to behavioral interventions. Copyright © 2015 the American Physiological Society.

  2. Cerebral White Matter Hypoperfusion Increases with Small-Vessel Disease Burden. Data From the Third International Stroke Trial.

    Science.gov (United States)

    Arba, Francesco; Mair, Grant; Carpenter, Trevor; Sakka, Eleni; Sandercock, Peter A G; Lindley, Richard I; Inzitari, Domenico; Wardlaw, Joanna M

    2017-07-01

    Leukoaraiosis is associated with impaired cerebral perfusion, but the effect of individual and combined small-vessel disease (SVD) features on white matter perfusion is unclear. We studied patients recruited with perfusion imaging in the Third International Stroke Trial. We rated individual SVD features (leukoaraiosis, lacunes) and brain atrophy on baseline plain computed tomography or magnetic resonance imaging. Separately, we assessed white matter at the level of the lateral ventricles in the cerebral hemisphere contralateral to the stroke for visible areas of hypoperfusion (present or absent) on 4 time-based perfusion imaging parameters. We examined associations between SVD features (individually and summed) and presence of hypoperfusion using logistic regression adjusted for age, sex, baseline National Institutes of Health Stroke Scale, hypertension, and diabetes. A total of 115 patients with median (interquartile range) age of 81 (72-86) years, 78 (52%) of which were male, had complete perfusion data. Hypoperfusion was most frequent on mean transit time (MTT; 63 patients, 55%) and least frequent on time to maximum flow (19 patients, 17%). The SVD score showed stronger independent associations with hypoperfusion (e.g., MTT, odds ratio [OR] = 2.80; 95% confidence interval [CI] = 1.56-5.03) than individual SVD markers (e.g., white matter hypoattenuation score, MTT, OR = 1.49, 95% CI = 1.09-2.04). Baseline blood pressure did not differ by presence or absence of hypoperfusion or across strata of SVD score. Presence of white matter hypoperfusion increased with SVD summed score. The SVD summed score was associated with hypoperfusion more consistently than individual SVD features, providing validity to the SVD score concept. Increasing SVD burden indicates worse perfusion in the white matter. Copyright © 2017 National Stroke Association. Published by Elsevier Inc. All rights reserved.

  3. White matters - The influence of cerebral small-vessel disease on depression, cognition and functioning

    NARCIS (Netherlands)

    Grool, A.M.

    2012-01-01

    Depression and cognitive impairment are highly prevalent in later life, and frequently co-occur. One of the possible mechanisms that may underlie both conditions is the presence of cerebral small-vessel disease. The presence of cerebral small-vessel disease is strongly associated with common

  4. Epigenetic microRNA Regulation

    DEFF Research Database (Denmark)

    Wiklund, Erik Digman

    2011-01-01

    MicroRNAs (miRNAs) are small non-coding RNAs (ncRNAs) that negatively regulate gene expression post-transcriptionally by binding to complementary sequences in the 3’UTR of target mRNAs in the cytoplasm. However, recent evidence suggests that certain miRNAs are enriched in the nucleus, and their t......MicroRNAs (miRNAs) are small non-coding RNAs (ncRNAs) that negatively regulate gene expression post-transcriptionally by binding to complementary sequences in the 3’UTR of target mRNAs in the cytoplasm. However, recent evidence suggests that certain miRNAs are enriched in the nucleus...

  5. Tamarix microRNA Profiling Reveals New Insight into Salt Tolerance

    Directory of Open Access Journals (Sweden)

    Jianwen Wang

    2018-04-01

    Full Text Available The halophyte tamarisk (Tamarix is extremely salt tolerant, making it an ideal material for salt tolerance-related studies. Although many salt-responsive genes of Tamarix were identified in previous studies, there are no reports on the role of post-transcriptional regulation in its salt tolerance. We constructed six small RNA libraries of Tamarix chinensis roots with NaCl treatments. High-throughput sequencing of the six libraries was performed and microRNA expression profiles were constructed. We investigated salt-responsive microRNAs to uncover the microRNA-mediated genes regulation. From these analyses, 251 conserved and 18 novel microRNA were identified from all small RNAs. From 191 differentially expressed microRNAs, 74 co-expressed microRNAs were identified as salt-responsive candidate microRNAs. The most enriched GO (gene ontology terms for the 157 genes targeted by differentially expressed microRNAs suggested that transcriptions factors were highly active. Two hub microRNAs (miR414, miR5658, which connected by several target genes into an organic microRNA regulatory network, appeared to be the key regulators of post-transcriptional salt-stress responses. As the first survey on the tamarisk small RNAome, this study improves the understanding of tamarisk salt-tolerance mechanisms and will contribute to the molecular-assisted resistance breeding.

  6. Micro-RNAs

    DEFF Research Database (Denmark)

    Taipaleenmäki, H.; Hokland, L. B.; Chen, Li

    2012-01-01

    Osteoblast differentiation and bone formation (osteogenesis) are regulated by transcriptional and post-transcriptional mechanisms. Recently, a novel class of regulatory factors termed microRNAs has been identified as playing an important role in the regulation of many aspects of osteoblast biology...... including proliferation, differentiation, metabolism and apoptosis. Also, preliminary data from animal disease models suggest that targeting miRNAs in bone can be a novel approach to increase bone mass. This review highlights the current knowledge of microRNA biology and their role in bone formation...

  7. Theoretical analysis and experimental evaluation of small cyclone separator to remove fine particulate matter

    Energy Technology Data Exchange (ETDEWEB)

    Ko, Han Gyul; Kim, Hong Seok [Seoul Nat' l Univ., Seoul (Korea, Republic of)

    2013-01-15

    A cyclone separator has been widely used in various industrial processes for removing fine particulate matter because it is easy to fabricate, cost effective, and adaptable to extremely harsh conditions. However, owing to the complex flow field in cyclones, a complete understanding of the detailed mechanisms of particulate removal has not yet been gained. In this study, a theoretical analysis was performed for calculating the collection efficiency and cut off size in cyclones by taking into account the effects of geometrical and flow parameters. The collection efficiency and cut off size values predicted by the theoretical model showed good agreement with experimental measurements for particles with a diameter of 0.5-30{mu}m. It was also revealed that the surface friction, along with the flow and geometrical parameters, has a significant effect on the cyclone performance.

  8. Taking sputum samples from small children with cystic fibrosis: a matter of cooperation

    DEFF Research Database (Denmark)

    Pehn, Mette; Bregnballe, Vibeke

    2014-01-01

    Objectives: An important part of the disease control in Danish guidelines for care of patients with cystic fibrosis (CF) is a monthly sputum sample by tracheal suchtion. Coping to this unpleasant procedure in small children depends heavily on the support from parents and nurse. The objective...... of this study was to develop a tool to help parents and children to cope with tracheal suctioning. Methods: Three short videos showing how nurses perform tracheal suctioning to get a sputum sample from small children with cystic fibrosis were made. The videos were shown to and discussed with parents...... and children to help them identify their own challenges in coping with the procedure. The study was carried out in the outpatient clinic at the CF centre, Aarhus Univeristy Hospital. Results: The videos are a useful tool to convince the parents, nurses and children from the age of about four years...

  9. Estimating DSGE model parameters in a small open economy: Do real-time data matter?

    Directory of Open Access Journals (Sweden)

    Capek Jan

    2015-03-01

    Full Text Available This paper investigates the differences between parameters estimated using real-time and those estimated with revised data. The models used are New Keynesian DSGE models of the Czech, Polish, Hungarian, Swiss, and Swedish small open economies in interaction with the euro area. The paper also offers an analysis of data revisions of GDP growth and inflation and trend revisions of interest rates.

  10. Competencies matter: modeling effective entrepreneurship in northeast of Italy small firms

    OpenAIRE

    A. Camuffo; F. Gerli; P. Gubitta

    2012-01-01

    The purpose of this paper is to explore if and to what extent the competency portfolio of entrepreneurs affects firm's performance, controlling for a set of individual and organizational variables. Applying nonparametric statistical analysis on data from behavioral event interviews and survey questionnaires to a sample of 53 entrepreneurs (small firm owners), this study investigates: the type, scope and depth of the entrepreneurs' competence portfolio; and the relationship between the ent...

  11. [Spectral characteristics of dissolved organic matter released during the metabolic process of small medusa].

    Science.gov (United States)

    Guo, Dong-Hui; Yi, Yue-Yuan; Zhao, Lei; Guo, Wei-Dong

    2012-06-01

    The metabolic processes of jellyfish can produce dissolved organic matter (DOM) which will influence the functioning of the aquatic ecosystems, yet the optical properties of DOM released by jellyfish are unknown. Here we report the absorption and fluorescence properties of DOM released by a medusa species Black fordia virginica during a 24 h incubation experiment. Compared with the control group, an obvious increase in the concentrations of dissolved organic carbon (DOC), absorption coefficient (a280) and total dissolved nitrogen (TDN) was observed in incubation group. This clearly demonstrated the release of DOM, chromophoric DOM (CDOM) and dissolved nutrients by B. virginica which feed on enough of Artemia sp. before the experiment. The increase in spectral slope ratio (SR) and decrease in humification index (HIX) indicated that the released DOM was less-humified and had relatively lower molecular weight. Parallel factor analysis (PARAFAC) decomposed the fluorescence matrices of DOM into three humic-like components (C1-C3) and one protein-like component (C4). The Fmax of two components (C2: 400 nm showed little changes. Thus, we suggested a zooplankton index (ZIX) to trace and characterize the DOM excreted by metabolic activity of zooplankton, which is calculated as the ratio of the sum of Fmax of all fluorescence components with the emission wavelength 400 nm.

  12. Impacts of beaver ponds on dissolved organic matter cycling in small temperate streams.

    Science.gov (United States)

    Larsen, J.; Lambert, T.; Larsen, A.; Lane, S.

    2017-12-01

    Beavers are engineers that modify the structure of river reaches and their hydrological functioning. By building dams, they modify the travel time of running waters and can lead to the flooding of surrounding soils and terrestrial vegetation, with potentially significant impact on biogeochemical cycles. Contradictory effects of beaver ponds on dissolved organic matter (DOM) concentration and composition have however been reported, and the underlying reasons are still unclear. In this study, we aimed to investigate the role of the landscape morphology as an important driver determining how a beaver population can affect stream DOM cycling. Four streams localized in Switzerland and Germany were visited during different seasons (spring, summer, winter) and monitored at upstream and downstream locations of beaver ponds across a hydrological cycle. The sites differed in terms of river channel morphology, presence or absence of floodplain, and vegetation cover. DOM composition was investigated through absorbance and fluorescence measurements coupled with parallel factor analysis (PARAFAC) along with stream water quality (nutrients, pH, dissolved oxygen and water temperature). The results show that the effects of beaver dams were variable, and emphasizes the importance of the geomorphological context.

  13. Small Business Struggle in a Developing Economy:Does Organizational Culture Matter?

    Directory of Open Access Journals (Sweden)

    Michael STOICA

    2011-11-01

    Full Text Available The paper examines the relationship between two important variables that define small and medium-sized enterprises:organizational culture and responsiveness. Firms operating in Romania were selected for the study. The country offers a business context with many changes over the last two decades, a challenge and an opportunity for researchers. Results show that the combination of entrepreneurial characteristics and planning and goal oriented managerial styles suits best successful companies. The market-driven type of culture has the best coordination and is best positioned to deliver customer-centered versatility, while adhocracy helps businesses respond fast to changes in the market environment.

  14. Impact of Strategically Located White Matter Hyperintensities on Cognition in Memory Clinic Patients with Small Vessel Disease.

    Science.gov (United States)

    Biesbroek, J Matthijs; Weaver, Nick A; Hilal, Saima; Kuijf, Hugo J; Ikram, Mohammad Kamran; Xu, Xin; Tan, Boon Yeow; Venketasubramanian, Narayanaswamy; Postma, Albert; Biessels, Geert Jan; Chen, Christopher P L H

    2016-01-01

    Studies on the impact of small vessel disease (SVD) on cognition generally focus on white matter hyperintensity (WMH) volume. The extent to which WMH location relates to cognitive performance has received less attention, but is likely to be functionally important. We examined the relation between WMH location and cognition in a memory clinic cohort of patients with sporadic SVD. A total of 167 patients with SVD were recruited from memory clinics. Assumption-free region of interest-based analyses based on major white matter tracts and voxel-wise analyses were used to determine the association between WMH location and executive functioning, visuomotor speed and memory. Region of interest-based analyses showed that WMHs located particularly within the anterior thalamic radiation and forceps minor were inversely associated with both executive functioning and visuomotor speed, independent of total WMH volume. Memory was significantly associated with WMH volume in the forceps minor, independent of total WMH volume. An independent assumption-free voxel-wise analysis identified strategic voxels in these same tracts. Region of interest-based analyses showed that WMH volume within the anterior thalamic radiation explained 6.8% of variance in executive functioning, compared to 3.9% for total WMH volume; WMH volume within the forceps minor explained 4.6% of variance in visuomotor speed and 4.2% of variance in memory, compared to 1.8% and 1.3% respectively for total WMH volume. Our findings identify the anterior thalamic radiation and forceps minor as strategic white matter tracts in which WMHs are most strongly associated with cognitive impairment in memory clinic patients with SVD. WMH volumes in individual tracts explained more variance in cognition than total WMH burden, emphasizing the importance of lesion location when addressing the functional consequences of WMHs.

  15. Small scale variability of transport and composition of dissolved organic matter in the subsoil

    Science.gov (United States)

    Leinemann, T.; Mikutta, R.; Kalbitz, K.; Guggenberger, G.

    2016-12-01

    Dissolved organic matter (DOM) is the most mobile fraction of carbon in the soil and connects the carbon-rich topsoil with the subsoil where translocated OM may get stabilized. The water flux in soil is highly heterogeneous, both temporarily and spatially. We, therefore, hypothesize that at high flow velocities, DOM can bypass possible mineral binding sites and microorganisms, thus leading to less degraded DOM under high flow velocities. To address this question, we investigated water and DOM fluxes in situ using segmented suction plates (4 x 4 segments on 24 x 24 cm) installed into three soil observatories at three depths (10 cm, 50 cm, and 150 cm) in a Dystric Cambisol under Beech (Fagus sylvatica) near Hannover, Germany. To follow the transport of carbon from the litter layer through the soil, an in situ 13C-labelling experiment has been conducted in January 2015. Concentration of dissolved organic carbon (DOC) and DOM composition was analyzed using high temperature combustion and photometric methods. The amount of transported DOC decreased by ca. 80 % from 10 to 50 cm depth and by 40 % from 50 to 150 cm depth. Different flow patterns existed at the centimeter scale, which were stable over time for individual suction plate segments. The specific UV280 nm absorbance of DOM decreased with increasing soil depth. This indicates a selective loss of aromatic compounds. The influence of different flow regimes on the DOM quality became apparent in the subsoil samples (>50 cm depth) showing a correlation of increasing UV280 nm absorbance with increasing water flux. The 13C-labelling experiment showed that after 10 month just 0.3 % of the DOC in 150 cm depth was derived from fresh litter. The transport of leaf litter carbon seemed to be controlled by the flow regime as the DO13C ratio and the water flux correlated positively. This can be an indication for the importance of preferential flow on carbon transport to the subsoil.

  16. Identification and validation of human papillomavirus encoded microRNAs.

    Directory of Open Access Journals (Sweden)

    Kui Qian

    Full Text Available We report here identification and validation of the first papillomavirus encoded microRNAs expressed in human cervical lesions and cell lines. We established small RNA libraries from ten human papillomavirus associated cervical lesions including cancer and two human papillomavirus harboring cell lines. These libraries were sequenced using SOLiD 4 technology. We used the sequencing data to predict putative viral microRNAs and discovered nine putative papillomavirus encoded microRNAs. Validation was performed for five candidates, four of which were successfully validated by qPCR from cervical tissue samples and cell lines: two were encoded by HPV 16, one by HPV 38 and one by HPV 68. The expression of HPV 16 microRNAs was further confirmed by in situ hybridization, and colocalization with p16INK4A was established. Prediction of cellular target genes of HPV 16 encoded microRNAs suggests that they may play a role in cell cycle, immune functions, cell adhesion and migration, development, and cancer. Two putative viral target sites for the two validated HPV 16 miRNAs were mapped to the E5 gene, one in the E1 gene, two in the L1 gene and one in the LCR region. This is the first report to show that papillomaviruses encode their own microRNA species. Importantly, microRNAs were found in libraries established from human cervical disease and carcinoma cell lines, and their expression was confirmed in additional tissue samples. To our knowledge, this is also the first paper to use in situ hybridization to show the expression of a viral microRNA in human tissue.

  17. Birth weight and long-term metabolic outcomes: does the definition of smallness matter?

    Science.gov (United States)

    Verkauskiene, R; Figueras, F; Deghmoun, S; Chevenne, D; Gardosi, J; Levy-Marchal, M

    2008-01-01

    To establish the role of individual definition of smallness at birth in the association between birth weight and long-term metabolic outcomes. Lipid profile and oral glucose tolerance test were performed in young adults (22 years) born either small (SGA) or appropriate for gestational age (AGA). AGA/SGA were defined by both population-based and customized methods adjusting for individual maternal/pregnancy characteristics. 825 individuals were classified as AGA and 575 as SGA by both methods, 131 were SGA by the population-based method only (SGA(pop)) and 22 were SGA by the customized method only (SGA(cust)). SGA(cust) subjects had higher total cholesterol and triglyceride levels and lower high-density lipoprotein cholesterol concentrations than SGA(pop) and AGA subjects, however, insignificantly when adjusted for age, gender and body mass index. The homeostasis model assessment for insulin resistance (HOMA-IR) index was higher in the SGA(cust) (p = 0.05) and SGA(pop) (p = 0.02) versus the AGA group. Controlling for the HOMA-IR index, the insulinogenic index was significantly lower in the SGA(cust) versus SGA(pop) (p = 0.001) and AGA (p = 0.003) groups. In SGA(cust) individuals, the HOMA-IR index was clearly shifted to higher, while the insulinogenic index to lower tertiles of AGA distribution; SGA(pop) subjects had the HOMA-IR and insulinogenic index predominantly in the highest tertiles. Individualized birth weight standards allow to better identify subjects who failed to reach their genetic potential of intrauterine growth and are at higher risk of metabolic disturbances and impaired insulin secretion later in life. Copyright 2008 S. Karger AG, Basel.

  18. miRBase: annotating high confidence microRNAs using deep sequencing data.

    Science.gov (United States)

    Kozomara, Ana; Griffiths-Jones, Sam

    2014-01-01

    We describe an update of the miRBase database (http://www.mirbase.org/), the primary microRNA sequence repository. The latest miRBase release (v20, June 2013) contains 24 521 microRNA loci from 206 species, processed to produce 30 424 mature microRNA products. The rate of deposition of novel microRNAs and the number of researchers involved in their discovery continue to increase, driven largely by small RNA deep sequencing experiments. In the face of these increases, and a range of microRNA annotation methods and criteria, maintaining the quality of the microRNA sequence data set is a significant challenge. Here, we describe recent developments of the miRBase database to address this issue. In particular, we describe the collation and use of deep sequencing data sets to assign levels of confidence to miRBase entries. We now provide a high confidence subset of miRBase entries, based on the pattern of mapped reads. The high confidence microRNA data set is available alongside the complete microRNA collection at http://www.mirbase.org/. We also describe embedding microRNA-specific Wikipedia pages on the miRBase website to encourage the microRNA community to contribute and share textual and functional information.

  19. Immunosenescence and immunecheckpoint inhibitors in non-small cell lung cancer patients: Does age really matter?

    Science.gov (United States)

    Ferrara, Roberto; Mezquita, Laura; Auclin, Edouard; Chaput, Nathalie; Besse, Benjamin

    2017-11-01

    Immunotherapy has dramatically changed the therapeutic scenario in non-small cell lung cancer (NSCLC), extending overall survival, with a favorable safety profile. However, there is still a gap of knowledge about the efficacy of immune checkpoint inhibitors (ICIs) in elderly patients. Data from randomized clinical trials testing ICIs are conflicting and often lack adequate statistical power. Although two large meta-analyses suggested an absence of a significant survival benefit in patients older than 75years, expanded access programs and retrospective cohort studies of ICIs in the real-life setting, showed comparable survival outcomes and safety profiles between older and younger patients. In this complex scenario, a further unresolved issue is the potential correlation between older age and immunotherapy primary resistance, a phenomenon probably linked to the continuous and progressive remodeling of immune functions with ageing, known as immunosenescence. Defining the role of ICIs in elderly NSCLC patients and exploring the molecular mechanisms underlying a possible lack of benefit or even accelerated tumor growth during immunotherapy are two major challenges for future research in this field of cancer treatment. In this review, we describe the major hallmarks of immunosenescence and we summarize the existing clinical data of ICIs in elderly NSCLC patients. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  20. NAViGaTing the micronome--using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs.

    Directory of Open Access Journals (Sweden)

    Elize A Shirdel

    2011-02-01

    Full Text Available MicroRNAs are a class of small RNAs known to regulate gene expression at the transcript level, the protein level, or both. Since microRNA binding is sequence-based but possibly structure-specific, work in this area has resulted in multiple databases storing predicted microRNA:target relationships computed using diverse algorithms. We integrate prediction databases, compare predictions to in vitro data, and use cross-database predictions to model the microRNA:transcript interactome--referred to as the micronome--to study microRNA involvement in well-known signalling pathways as well as associations with disease. We make this data freely available with a flexible user interface as our microRNA Data Integration Portal--mirDIP (http://ophid.utoronto.ca/mirDIP.mirDIP integrates prediction databases to elucidate accurate microRNA:target relationships. Using NAViGaTOR to produce interaction networks implicating microRNAs in literature-based, KEGG-based and Reactome-based pathways, we find these signalling pathway networks have significantly more microRNA involvement compared to chance (p<0.05, suggesting microRNAs co-target many genes in a given pathway. Further examination of the micronome shows two distinct classes of microRNAs; universe microRNAs, which are involved in many signalling pathways; and intra-pathway microRNAs, which target multiple genes within one signalling pathway. We find universe microRNAs to have more targets (p<0.0001, to be more studied (p<0.0002, and to have higher degree in the KEGG cancer pathway (p<0.0001, compared to intra-pathway microRNAs.Our pathway-based analysis of mirDIP data suggests microRNAs are involved in intra-pathway signalling. We identify two distinct classes of microRNAs, suggesting a hierarchical organization of microRNAs co-targeting genes both within and between pathways, and implying differential involvement of universe and intra-pathway microRNAs at the disease level.

  1. Association of microRNA-33a Molecular Signature with Non-Small Cell Lung Cancer Diagnosis and Prognosis after Chemotherapy.

    Directory of Open Access Journals (Sweden)

    Li-Kun Hou

    Full Text Available This study aims to explore the expression pattern and prognostic significance of miR-33a in non-small cell lung cancer (NSCLC treated with adjuvant chemotherapy.MiR-33aexpression in NSCLC was analyzed in silico using the GEO database and was subsequently confirmed by quantitative RT-PCR in 147 NSCLC biopsies. Among these, 32 of these biopsies were paired with adjacent non-neoplastic tissues. The survival analysis of NSCLC by Kaplan-Meier estimates was stratified based on miR-33a expression. In addition, multivariate survival analysis in corresponding groups of NSCLC patients was conducted by Cox proportional hazards regression model.The in silico analysis of miR-33a expression in NSCLC resulted to its down-regulation in different tumor types. The expression level of miR-33a was lower in each grade of NSCLC tumor biopsies than in normal lung tissues. Univariate and multivariate survival analysis further established that low miR-33a expression was an important risk factor for overall survival and disease free survival in NSCLC patients.Our study implied that miR-33a expression levels may have an essential role in NSCLC progression, and could act as a specific and sensitive biomarker for NSCLC patients who have undergone adjuvant chemotherapy.

  2. Genetic variation in a microRNA-502 minding site in SET8 gene confers clinical outcome of non-small cell lung cancer in a Chinese population.

    Directory of Open Access Journals (Sweden)

    Jiali Xu

    Full Text Available BACKGROUND: Genetic variants may influence microRNA-target interaction through modulate their binding affinity, creating or destroying miRNA-binding sites. SET8, a member of the SET domain-containing methyltransferase, has been implicated in a variety array of biological processes. METHODS: Using Taqman assay, we genotyped a polymorphism rs16917496 T>C within the miR-502 binding site in the 3'-untranslated region of the SET8 gene in 576 non-small cell lung cancer (NSCLC patients. Functions of rs16917496 were investigated using luciferase activity assay and validated by immunostaining. RESULTS: Log-rank test and cox regression indicated that the CC genotype was associated with a longer survival and a reduced risk of death for NSCLC [58.0 vs. 41.0 months, P = 0.031; hazard ratio = 0.44, 95% confidential interval: 0.26-0.74]. Further stepwise regression analysis suggested rs16917496 was an independently favorable factor for prognosis and the protective effect more prominent in never smokers, patients without diabetes and patients who received chemotherapy. A significant interaction was observed between rs16917496 and smoking status in relation to NSCLC survival (PC located at miR-502 binding site contributes to NSCLC survival by altering SET8 expression through modulating miRNA-target interaction.

  3. BioM2MetDisease: a manually curated database for associations between microRNAs, metabolites, small molecules and metabolic diseases.

    Science.gov (United States)

    Xu, Yanjun; Yang, Haixiu; Wu, Tan; Dong, Qun; Sun, Zeguo; Shang, Desi; Li, Feng; Xu, Yingqi; Su, Fei; Liu, Siyao; Zhang, Yunpeng; Li, Xia

    2017-01-01

    BioM2MetDisease is a manually curated database that aims to provide a comprehensive and experimentally supported resource of associations between metabolic diseases and various biomolecules. Recently, metabolic diseases such as diabetes have become one of the leading threats to people’s health. Metabolic disease associated with alterations of multiple types of biomolecules such as miRNAs and metabolites. An integrated and high-quality data source that collection of metabolic disease associated biomolecules is essential for exploring the underlying molecular mechanisms and discovering novel therapeutics. Here, we developed the BioM2MetDisease database, which currently documents 2681 entries of relationships between 1147 biomolecules (miRNAs, metabolites and small molecules/drugs) and 78 metabolic diseases across 14 species. Each entry includes biomolecule category, species, biomolecule name, disease name, dysregulation pattern, experimental technique, a brief description of metabolic disease-biomolecule relationships, the reference, additional annotation information etc. BioM2MetDisease provides a user-friendly interface to explore and retrieve all data conveniently. A submission page was also offered for researchers to submit new associations between biomolecules and metabolic diseases. BioM2MetDisease provides a comprehensive resource for studying biology molecules act in metabolic diseases, and it is helpful for understanding the molecular mechanisms and developing novel therapeutics for metabolic diseases. http://www.bio-bigdata.com/BioM2MetDisease/. © The Author(s) 2017. Published by Oxford University Press.

  4. Synaptic vesicles contain small ribonucleic acids (sRNAs) including transfer RNA fragments (trfRNA) and microRNAs (miRNA).

    Science.gov (United States)

    Li, Huinan; Wu, Cheng; Aramayo, Rodolfo; Sachs, Matthew S; Harlow, Mark L

    2015-10-08

    Synaptic vesicles (SVs) are neuronal presynaptic organelles that load and release neurotransmitter at chemical synapses. In addition to classic neurotransmitters, we have found that synaptic vesicles isolated from the electric organ of Torpedo californica, a model cholinergic synapse, contain small ribonucleic acids (sRNAs), primarily the 5' ends of transfer RNAs (tRNAs) termed tRNA fragments (trfRNAs). To test the evolutionary conservation of SV sRNAs we examined isolated SVs from the mouse central nervous system (CNS). We found abundant levels of sRNAs in mouse SVs, including trfRNAs and micro RNAs (miRNAs) known to be involved in transcriptional and translational regulation. This discovery suggests that, in addition to inducing changes in local dendritic excitability through the release of neurotransmitters, SVs may, through the release of specific trfRNAs and miRNAs, directly regulate local protein synthesis. We believe these findings have broad implications for the study of chemical synaptic transmission.

  5. Small angle scattering from soft matter-application to complex mixed systems

    International Nuclear Information System (INIS)

    Boue, F.; Cousin, F.; Gummel, J.; Carrot, G.; El Harrak, A.; Oberdisse, J.

    2007-01-01

    The advantage of small angle neutron scattering associated with isotopic labelling through deuteration is illustrated in the case of mixed systems, created by associating already well-known systems of characteristic structures; this is also important for applications. Our first mixed system associates charged polymer chains, polyelectrolyte (here polystyrene sulfonate, PSS), with oppositely charged particles, proteins (here lysozyme). Different fractions of deuterated water (D 2 O) mixed with normal water are used to match the scattering length density of the protein or of the polymer in non-deuterated or deuterated version. First, this allows us to separate the protein and the polymer signal: we can then distinguish a case where the structures of each species alone in water are hardly modified by mixing, except for interconnections yielding a gel, and a case inducing complete change into a structure common to both species, made of aggregated globules. Secondly, using, for counter-ions of the poly-ions, deuterated Tetramethylammonium, together with matching both protein and polymer, we establish unambiguously the counter-ion release into the solvent. Thirdly, matching only a fraction of polymer chains, the other being deuterated, we extrapolate at zero deuterated fraction their form factor and describe the chain conformation inside the complexes. Fourthly, we illustrate the possibilities of modelling the signal on a second example of mixed system: a nano-composite made of silica particles surrounded by polymer dispersed into a deuterated polymer matrix. Chains are then visible in such reinforced polymer system, in particular when it is submitted to elongation: we discuss a possible model for an ideal system, introducing the scattering contribution from deformed chains. (authors)

  6. High-z objects and cold dark matter cosmogonies - Constraints on the primordial power spectrum on small scales

    Science.gov (United States)

    Kashlinsky, A.

    1993-01-01

    Modified cold dark matter (CDM) models were recently suggested to account for large-scale optical data, which fix the power spectrum on large scales, and the COBE results, which would then fix the bias parameter, b. We point out that all such models have deficit of small-scale power where density fluctuations are presently nonlinear, and should then lead to late epochs of collapse of scales M between 10 exp 9 - 10 exp 10 solar masses and (1-5) x 10 exp 14 solar masses. We compute the probabilities and comoving space densities of various scale objects at high redshifts according to the CDM models and compare these with observations of high-z QSOs, high-z galaxies and the protocluster-size object found recently by Uson et al. (1992) at z = 3.4. We show that the modified CDM models are inconsistent with the observational data on these objects. We thus suggest that in order to account for the high-z objects, as well as the large-scale and COBE data, one needs a power spectrum with more power on small scales than CDM models allow and an open universe.

  7. MicroRNA-100 is a potential molecular marker of non-small cell lung cancer and functions as a tumor suppressor by targeting polo-like kinase 1

    International Nuclear Information System (INIS)

    Liu, Jing; Lu, Kai-Hua; Liu, Zhi-Li; Sun, Ming; De, Wei; Wang, Zhao-Xia

    2012-01-01

    Polo-like kinase 1 (PLK1) is highly expressed in many human cancers and regulates critical steps in mitotic progression. Previously, we have reported that PLK1 was overexpressed in non-small cell lung cancer (NSCLC), but the underlying molecular mechanisms are not well understood. By using microRNA (miR) target prediction algorithms, we identified miR-100 that might potentially bind the 3’-untranslated region of PLK1 transcripts. The purpose of this study was to investigate the roles of miR-100 and its association with PLK1 in NSCLC development. Taqman real-time quantitative RT-PCR assay was performed to detect miR-100 expression 10 NSCLC tissues and corresponding nontumor tissues. Additionally, the expression of miR-100 in 110 NSCLC tissues and its correlation with clinicopathological factors or prognosis of patients was analyzed. Finally, the effects of miR-100 expression on growth, apoptosis and cell cycle of NSCLC cells by posttranscriptionally regulating PLK1 expression were determined. MiR-100 was significantly downregulated in NSCLC tissues, and low miR-100 expression was found to be closely correlated with higher clinical stage, advanced tumor classification and lymph node metastasis of patients. The overall survival of NSCLC patients with low miR-100 was significantly lower than that of those patients with high miR-100, and univariate and multivariate analyses indicated that low miR-100 expression might be a poor prognostic factor. Also, miR-100 mimics could lead to growth inhibition, G 2 /M cell cycle arrest and apoptosis enhancement in NSCLC cells. Meanwhile, miR-100 mimics could significantly inhibit PLK1 mRNA and protein expression and reduce the luciferase activity of a PLK1 3’ untranslated region-based reporter construct in A549 cells. Furthermore, small interfering RNA (siRNA)-mediated PLK1 downregulation could mimic the effects of miR-100 mimics while PLK1 overexpression could partially rescue the phenotypical changes of NSCLC cells induced by

  8. Integrated mRNA and microRNA analysis identifies genes and small miRNA molecules associated with transcriptional and post-transcriptional-level responses to both drought stress and re-watering treatment in tobacco.

    Science.gov (United States)

    Chen, Qiansi; Li, Meng; Zhang, Zhongchun; Tie, Weiwei; Chen, Xia; Jin, Lifeng; Zhai, Niu; Zheng, Qingxia; Zhang, Jianfeng; Wang, Ran; Xu, Guoyun; Zhang, Hui; Liu, Pingping; Zhou, Huina

    2017-01-10

    Drought stress is one of the most severe problem limited agricultural productivity worldwide. It has been reported that plants response to drought-stress by sophisticated mechanisms at both transcriptional and post-transcriptional levels. However, the precise molecular mechanisms governing the responses of tobacco leaves to drought stress and water status are not well understood. To identify genes and miRNAs involved in drought-stress responses in tobacco, we performed both mRNA and small RNA sequencing on tobacco leaf samples from the following three treatments: untreated-control (CL), drought stress (DL), and re-watering (WL). In total, we identified 798 differentially expressed genes (DEGs) between the DL and CL (DL vs. CL) treatments and identified 571 DEGs between the WL and DL (WL vs. DL) treatments. Further analysis revealed 443 overlapping DEGs between the DL vs. CL and WL vs. DL comparisons, and, strikingly, all of these genes exhibited opposing expression trends between these two comparisons, strongly suggesting that these overlapping DEGs are somehow involved in the responses of tobacco leaves to drought stress. Functional annotation analysis showed significant up-regulation of genes annotated to be involved in responses to stimulus and stress, (e.g., late embryogenesis abundant proteins and heat-shock proteins) antioxidant defense (e.g., peroxidases and glutathione S-transferases), down regulation of genes related to the cell cycle pathway, and photosynthesis processes. We also found 69 and 56 transcription factors (TFs) among the DEGs in, respectively, the DL vs. CL and the WL vs. DL comparisons. In addition, small RNA sequencing revealed 63 known microRNAs (miRNA) from 32 families and 368 novel miRNA candidates in tobacco. We also found that five known miRNA families (miR398, miR390, miR162, miR166, and miR168) showed differential regulation under drought conditions. Analysis to identify negative correlations between the differentially expressed mi

  9. A Regulatory MDM4 Genetic Variant Locating in the Binding Sequence of Multiple MicroRNAs Contributes to Susceptibility of Small Cell Lung Cancer.

    Directory of Open Access Journals (Sweden)

    Feng Gao

    Full Text Available A functional rs4245739 A>C single nucleotide polymorphism (SNP locating in the MDM43'-untranslated (3'-UTR region creates a miR-191-5p or miR-887-3p targeting sites. This change results in decreased expression of oncogene MDM4. Therefore, we examined the association between this SNP and small cell lung cancer (SCLC risk as well as its regulatory function in SCLC cells. Genotypes were determined in two independent case-control sets consisted of 520SCLC cases and 1040 controls from two regions of China. Odds ratios (ORs and 95% confidence intervals (CIs were estimated by logistic regression. The impact of the rs4245739 SNP on miR-191-5p/miR-887-3p mediated MDM4 expression regulation was investigated using luciferase reporter gene assays. We found that the MDM4 rs4245739AC and CC genotypes were significantly associated with decreased SCLC susceptibility compared with the AA genotype in both case-control sets (Shandong set: OR = 0.53, 95% CI = 0.32-0.89, P = 0.014; Jiangsu set: OR = 0.47, 95% CI = 0.26-0.879, P = 0.017. Stratified analyses indicated that there was a significantly multiplicative interaction between rs4245739 and smoking (Pinteractioin = 0.048. After co-tranfection of miRNAs and different allelic-MDM4 reporter constructs into SCLC cells, we found that the both miR-191-5p and miR-887-3p can lead to significantly decreased MDM4 expression activities in the construct with C-allelic 3'-UTR but not A-allelic 3'-UTR, suggesting a consistent genotype-phenotype correlation. Our data illuminate that the MDM4rs4245739SNP contributes to SCLC risk and support the notion that gene 3'-UTR genetic variants, impacting miRNA-binding, might modify SCLC susceptibility.

  10. Proton density differences in signal characteristics of multiple sclerosis plaques versus white matter lesions of small vessel disease and vasculitis on high-field strength MR images

    International Nuclear Information System (INIS)

    Peyster, R.G.; Siegal, T.L.

    1990-01-01

    This paper determines if variations in signal intensity characteristics on multi-spin-echo images obtained with a high-field-strength magnet can be useful in differentiating demyelinating plaques of multiple sclerosis from other pathologic white matter processes due to small vessel disease and vasculities. Using the first of two multi-spin-echo images obtained with a General Electric 1.5-T magnet, the investigators compared signal intensity characteristics in 30 patients with a firm clinical diagnosis of multiple sclerosis versus a control group of 30 patients with a known clinical history of small-vessel disease and vasculitis are isodense to gray matter on proton-density images

  11. Effect of microRNA-135a on Cell Proliferation, Migration, Invasion, Apoptosis and Tumor Angiogenesis Through the IGF-1/PI3K/Akt Signaling Pathway in Non-Small Cell Lung Cancer.

    Science.gov (United States)

    Zhou, Yufei; Li, Shaoxia; Li, Jiangtao; Wang, Dongfeng; Li, Quanxing

    2017-01-01

    This study explored the ability of microRNA-135a (miR-135a) to influence cell proliferation, migration, invasion, apoptosis and tumor angiogenesis through the IGF-1/PI3K/Akt signaling pathway in non-small cell lung cancer (NSCLC). NSCLC tissues and adjacent normal tissues were collected from 138 NSCLC patients. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the expression levels of miR-135a and IGF-1, PI3K, Akt, VEGF, bFGF and IL-8 mRNA; western blotting was used to determine the expression levels of IGF-1, PI3K and Akt protein; and enzyme-linked immunosorbent assay (ELISA) was used to analyze the expression levels of VEGF, bFGF and IL-8 protein. Human NSCLC cell lines (A549, H460, and H1299) and the human bronchial epithelial cell line (HBE) were selected. A549 cells were assigned to blank, negative control (NC), miR-135a mimics, miR-135a inhibitors, IGF-1 siRNA and miR-135a inhibitors + IGF-1 siRNA groups. The following were performed: an MTT assay to assess cell proliferation, a scratch test to detect cell migration, a Transwell assay to measure cell invasion, and a flow cytometry to analyze cell apoptosis. The expression level of miR-135a was lower while those of IGF-1, PI3K and Akt mRNA were higher in NSCLC tissues than in the adjacent normal tissues. Dual-luciferase reporter assay indicated IGF-1 as a target of miR-135a. The in vitro results showed that compared with the blank group, cell proliferation, migration and invasion were suppressed, mRNA and protein levels of IGF-1, PI3K, Akt, VEGF, bFGF and IL-8 were reduced, and cell apoptosis was enhanced in the miR-135a mimics and IGF-1 siRNA groups. Compared with the IGF-1 siRNA group, cells in the miR-135a inhibitors + IGF-1 siRNA group demonstrated increased cell proliferation, migration and invasion, elevated mRNA and protein levels of IGF-1, PI3K, Akt, VEGF, bFGF and IL-8 and reduced cell apoptosis. These findings indicated that miR-135a promotes cell apoptosis and inhibits

  12. Accurate microRNA target prediction correlates with protein repression levels

    Directory of Open Access Journals (Sweden)

    Simossis Victor A

    2009-09-01

    Full Text Available Abstract Background MicroRNAs are small endogenously expressed non-coding RNA molecules that regulate target gene expression through translation repression or messenger RNA degradation. MicroRNA regulation is performed through pairing of the microRNA to sites in the messenger RNA of protein coding genes. Since experimental identification of miRNA target genes poses difficulties, computational microRNA target prediction is one of the key means in deciphering the role of microRNAs in development and disease. Results DIANA-microT 3.0 is an algorithm for microRNA target prediction which is based on several parameters calculated individually for each microRNA and combines conserved and non-conserved microRNA recognition elements into a final prediction score, which correlates with protein production fold change. Specifically, for each predicted interaction the program reports a signal to noise ratio and a precision score which can be used as an indication of the false positive rate of the prediction. Conclusion Recently, several computational target prediction programs were benchmarked based on a set of microRNA target genes identified by the pSILAC method. In this assessment DIANA-microT 3.0 was found to achieve the highest precision among the most widely used microRNA target prediction programs reaching approximately 66%. The DIANA-microT 3.0 prediction results are available online in a user friendly web server at http://www.microrna.gr/microT

  13. Particulate matter pollution from aviation-related activity at a small airport of the Aegean Sea Insular Region.

    Science.gov (United States)

    Psanis, C; Triantafyllou, E; Giamarelou, M; Manousakas, M; Eleftheriadis, K; Biskos, G

    2017-10-15

    The unprecedented growth in aviation during the last years has resulted in a notable increase of local air pollution related to airports. The impacts of aviation on air quality can be extremely high particularly around airports serving remote insular regions with pristine atmospheric environments. Here we report measurements that show how the atmospheric aerosol is affected by the activity at a small airport in a remote region. More specifically, we provide measurements performed at the airport of Mytilene, Greece, a regional yet international airport that serves the entire island of Lesvos; the third largest island of the country. The measurements show that the activity during landing, taxiing and take-off of the aircrafts accounted for up to a 10-fold increase in particulate matter (PM) mass concentration in the vicinity of the airport. The number concentration of particles having diameters from 10 to 500nm also increased from ca. 4×10 2 to 8×10 5 particlescm -3 , while the mean particle diameter decreased to 20nm when aircrafts were present at the airport. Elemental analysis on particle samples collected simultaneously at the airport and at a remote site 3km away, showed that the former were significantly influenced by combustion sources, and specifically from the engines of the aircrafts. Our results show that despite their small size, local airports serving remote insular regions should be considered as important air pollution hotspots, raising concerns for the exposure of the people working and leaving in their vicinities to hazardous pollutants. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. MicroRNAs in Breastmilk and the Lactating Breast: Potential Immunoprotectors and Developmental Regulators for the Infant and the Mother

    Directory of Open Access Journals (Sweden)

    Mohammed Alsaweed

    2015-10-01

    Full Text Available Human milk (HM is the optimal source of nutrition, protection and developmental programming for infants. It is species-specific and consists of various bioactive components, including microRNAs, small non-coding RNAs regulating gene expression at the post-transcriptional level. microRNAs are both intra- and extra-cellular and are present in body fluids of humans and animals. Of these body fluids, HM appears to be one of the richest sources of microRNA, which are highly conserved in its different fractions, with milk cells containing more microRNAs than milk lipids, followed by skim milk. Potential effects of exogenous food-derived microRNAs on gene expression have been demonstrated, together with the stability of milk-derived microRNAs in the gastrointestinal tract. Taken together, these strongly support the notion that milk microRNAs enter the systemic circulation of the HM fed infant and exert tissue-specific immunoprotective and developmental functions. This has initiated intensive research on the origin, fate and functional significance of milk microRNAs. Importantly, recent studies have provided evidence of endogenous synthesis of HM microRNA within the human lactating mammary epithelium. These findings will now form the basis for investigations of the role of microRNA in the epigenetic control of normal and aberrant mammary development, and particularly lactation performance.

  15. Bioavailability of transgenic microRNAs in genetically modified plants

    Science.gov (United States)

    Transgenic expression of small RNAs is a prevalent approach in agrobiotechnology for the global enhancement of plant foods. Meanwhile, emerging studies have, on the one hand, emphasized the potential of transgenic microRNAs (miRNAs) as novel dietary therapeutics and, on the other, suggested potentia...

  16. Aberrant microRNA expression in multiple myeloma

    DEFF Research Database (Denmark)

    Dimopoulos, Konstantinos; Gimsing, Peter; Grønbæk, Kirsten

    2013-01-01

    Multiple myeloma (MM) is a devastating disease with a complex biology, and in spite of improved survivability by novel treatment strategies over the last decade, MM is still incurable by current therapy. MicroRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression at a post...

  17. Strategies to identify microRNA targets: New advances

    Science.gov (United States)

    MicroRNAs (miRNAs) are small regulatory RNA molecules functioning to modulate gene expression at the post-transcriptional level, and playing an important role in many developmental and physiological processes. Ten thousand miRNAs have been discovered in various organisms. Although considerable progr...

  18. The Potential of MicroRNAs as Prostate Cancer Biomarkers

    NARCIS (Netherlands)

    L. Fabris (Linda); Y. Ceder (Yvonne); A.M. Chinnaiyan (Arul); G.W. Jenster (Guido); K.D. Sorensen (Karina D.); S.A. Tomlins (Scott A); T. Visakorpi (Tapio); G.A. Calin (George)

    2016-01-01

    textabstractContext: Short noncoding RNAs known as microRNAs (miRNAs) control protein expression through the degradation of RNA or the inhibition of protein translation. The miRNAs influence a wide range of biologic processes and are often deregulated in cancer. This family of small RNAs constitutes

  19. Is dark matter with long-range interactions a solution to all small-scale problems of Λ cold dark matter cosmology?

    Science.gov (United States)

    van den Aarssen, Laura G; Bringmann, Torsten; Pfrommer, Christoph

    2012-12-07

    The cold dark matter paradigm describes the large-scale structure of the Universe remarkably well. However, there exists some tension with the observed abundances and internal density structures of both field dwarf galaxies and galactic satellites. Here, we demonstrate that a simple class of dark matter models may offer a viable solution to all of these problems simultaneously. Their key phenomenological properties are velocity-dependent self-interactions mediated by a light vector messenger and thermal production with much later kinetic decoupling than in the standard case.

  20. MicroRNA regulation of Autophagy

    DEFF Research Database (Denmark)

    Frankel, Lisa B; Lund, Anders H

    2012-01-01

    recently contributed to our understanding of the molecular mechanisms of the autophagy machinery, yet several gaps remain in our knowledge of this process. The discovery of microRNAs (miRNAs) established a new paradigm of post-transcriptional gene regulation and during the past decade these small non......RNAs to regulation of the autophagy pathway. This regulation occurs both through specific core pathway components as well as through less well-defined mechanisms. Although this field is still in its infancy, we are beginning to understand the potential implications of these initial findings, both from a pathological...

  1. Search for microRNAs expressed by intracellular bacterial pathogens in infected mammalian cells.

    Science.gov (United States)

    Furuse, Yuki; Finethy, Ryan; Saka, Hector A; Xet-Mull, Ana M; Sisk, Dana M; Smith, Kristen L Jurcic; Lee, Sunhee; Coers, Jörn; Valdivia, Raphael H; Tobin, David M; Cullen, Bryan R

    2014-01-01

    MicroRNAs are expressed by all multicellular organisms and play a critical role as post-transcriptional regulators of gene expression. Moreover, different microRNA species are known to influence the progression of a range of different diseases, including cancer and microbial infections. A number of different human viruses also encode microRNAs that can attenuate cellular innate immune responses and promote viral replication, and a fungal pathogen that infects plants has recently been shown to express microRNAs in infected cells that repress host cell immune responses and promote fungal pathogenesis. Here, we have used deep sequencing of total expressed small RNAs, as well as small RNAs associated with the cellular RNA-induced silencing complex RISC, to search for microRNAs that are potentially expressed by intracellular bacterial pathogens and translocated into infected animal cells. In the case of Legionella and Chlamydia and the two mycobacterial species M. smegmatis and M. tuberculosis, we failed to detect any bacterial small RNAs that had the characteristics expected for authentic microRNAs, although large numbers of small RNAs of bacterial origin could be recovered. However, a third mycobacterial species, M. marinum, did express an ∼ 23-nt small RNA that was bound by RISC and derived from an RNA stem-loop with the characteristics expected for a pre-microRNA. While intracellular expression of this candidate bacterial microRNA was too low to effectively repress target mRNA species in infected cultured cells in vitro, artificial overexpression of this potential bacterial pre-microRNA did result in the efficient repression of a target mRNA. This bacterial small RNA therefore represents the first candidate microRNA of bacterial origin.

  2. Search for microRNAs expressed by intracellular bacterial pathogens in infected mammalian cells.

    Directory of Open Access Journals (Sweden)

    Yuki Furuse

    Full Text Available MicroRNAs are expressed by all multicellular organisms and play a critical role as post-transcriptional regulators of gene expression. Moreover, different microRNA species are known to influence the progression of a range of different diseases, including cancer and microbial infections. A number of different human viruses also encode microRNAs that can attenuate cellular innate immune responses and promote viral replication, and a fungal pathogen that infects plants has recently been shown to express microRNAs in infected cells that repress host cell immune responses and promote fungal pathogenesis. Here, we have used deep sequencing of total expressed small RNAs, as well as small RNAs associated with the cellular RNA-induced silencing complex RISC, to search for microRNAs that are potentially expressed by intracellular bacterial pathogens and translocated into infected animal cells. In the case of Legionella and Chlamydia and the two mycobacterial species M. smegmatis and M. tuberculosis, we failed to detect any bacterial small RNAs that had the characteristics expected for authentic microRNAs, although large numbers of small RNAs of bacterial origin could be recovered. However, a third mycobacterial species, M. marinum, did express an ∼ 23-nt small RNA that was bound by RISC and derived from an RNA stem-loop with the characteristics expected for a pre-microRNA. While intracellular expression of this candidate bacterial microRNA was too low to effectively repress target mRNA species in infected cultured cells in vitro, artificial overexpression of this potential bacterial pre-microRNA did result in the efficient repression of a target mRNA. This bacterial small RNA therefore represents the first candidate microRNA of bacterial origin.

  3. Differentially expressed microRNA in multiple sclerosis: A window into pathogenesis?

    DEFF Research Database (Denmark)

    Martin, Nellie Anne; Illés, Zsolt

    2014-01-01

    MicroRNA are small non-coding RNA that mediate mRNA translation repression or mRNA degradation, and thereby refine protein expression levels. More than 30–60% of all genes are regulated by microRNA. Exploring disease-related microRNA signatures is an emerging tool in biomarker discovery, and sile......MicroRNA are small non-coding RNA that mediate mRNA translation repression or mRNA degradation, and thereby refine protein expression levels. More than 30–60% of all genes are regulated by microRNA. Exploring disease-related microRNA signatures is an emerging tool in biomarker discovery......RNA related to multiple sclerosis has increased significantly in recent years. Differentially expressed microRNA have been identified in the whole blood, serum, plasma, cerebrospinal fluid, peripheral blood mononuclear cells, blood-derived cell subsets and brain lesions of patients with multiple sclerosis....... Most studies applied a non-candidate approach of screening by microarray and validation by quantitative polymerase chain reaction or next generation sequencing; others used a candidate-driven approach. Despite a relatively high number of multiple sclerosis-associated microRNA, just a few could...

  4. MicroRNA expression in multiple myeloma is associated with genetic subtype, isotype and survival

    Directory of Open Access Journals (Sweden)

    Pezzella Francesco

    2011-05-01

    Full Text Available Abstract Background MicroRNAs are small RNA species that regulate gene expression post-transcriptionally and are aberrantly expressed in many cancers including hematological malignancies. However, the role of microRNAs in the pathogenesis of multiple myeloma (MM is only poorly understood. We therefore used microarray analysis to elucidate the complete miRNome (miRBase version 13.0 of purified tumor (CD138+ cells from 33 patients with MM, 5 patients with monoclonal gammopathy of undetermined significance (MGUS and 9 controls. Results Unsupervised cluster analysis revealed that MM and MGUS samples have a distinct microRNA expression profile from control CD138+ cells. The majority of microRNAs aberrantly expressed in MM (109/129 were up-regulated. A comparison of these microRNAs with those aberrantly expressed in other B-cell and T-cell malignancies revealed a surprising degree of similarity (~40% suggesting the existence of a common lymphoma microRNA signature. We identified 39 microRNAs associated with the pre-malignant condition MGUS. Twenty-three (59% of these were also aberrantly expressed in MM suggesting common microRNA expression events in MM progression. MM is characterized by multiple chromosomal abnormalities of varying prognostic significance. We identified specific microRNA signatures associated with the most common IgH translocations (t(4;14 and t(11;14 and del(13q. Expression levels of these microRNAs were distinct between the genetic subtypes (by cluster analysis and correctly predicted these abnormalities in > 85% of cases using the support vector machine algorithm. Additionally, we identified microRNAs associated with light chain only myeloma, as well as IgG and IgA-type MM. Finally, we identified 32 microRNAs associated with event-free survival (EFS in MM, ten of which were significant by univariate (logrank survival analysis. Conclusions In summary, this work has identified aberrantly expressed microRNAs associated with the

  5. MicroRNA expression in benign breast tissue and risk of subsequent invasive breast cancer.

    Science.gov (United States)

    Rohan, Thomas; Ye, Kenny; Wang, Yihong; Glass, Andrew G; Ginsberg, Mindy; Loudig, Olivier

    2018-01-01

    MicroRNAs are endogenous, small non-coding RNAs that control gene expression by directing their target mRNAs for degradation and/or posttranscriptional repression. Abnormal expression of microRNAs is thought to contribute to the development and progression of cancer. A history of benign breast disease (BBD) is associated with increased risk of subsequent breast cancer. However, no large-scale study has examined the association between microRNA expression in BBD tissue and risk of subsequent invasive breast cancer (IBC). We conducted discovery and validation case-control studies nested in a cohort of 15,395 women diagnosed with BBD in a large health plan between 1971 and 2006 and followed to mid-2015. Cases were women with BBD who developed subsequent IBC; controls were matched 1:1 to cases on age, age at diagnosis of BBD, and duration of plan membership. The discovery stage (316 case-control pairs) entailed use of the Illumina MicroRNA Expression Profiling Assay (in duplicate) to identify breast cancer-associated microRNAs. MicroRNAs identified at this stage were ranked by the strength of the correlation between Illumina array and quantitative PCR results for 15 case-control pairs. The top ranked 14 microRNAs entered the validation stage (165 case-control pairs) which was conducted using quantitative PCR (in triplicate). In both stages, linear regression was used to evaluate the association between the mean expression level of each microRNA (response variable) and case-control status (independent variable); paired t-tests were also used in the validation stage. None of the 14 validation stage microRNAs was associated with breast cancer risk. The results of this study suggest that microRNA expression in benign breast tissue does not influence the risk of subsequent IBC.

  6. Identification of differentially expressed microRNAs in human male breast cancer

    Directory of Open Access Journals (Sweden)

    Schipper Elisa

    2010-03-01

    Full Text Available Abstract Background The discovery of small non-coding RNAs and the subsequent analysis of microRNA expression patterns in human cancer specimens have provided completely new insights into cancer biology. Genetic and epigenetic data indicate oncogenic or tumor suppressor function of these pleiotropic regulators. Therefore, many studies analyzed the expression and function of microRNA in human breast cancer, the most frequent malignancy in females. However, nothing is known so far about microRNA expression in male breast cancer, accounting for approximately 1% of all breast cancer cases. Methods The expression of 319 microRNAs was analyzed in 9 primary human male breast tumors and in epithelial cells from 15 male gynecomastia specimens using fluorescence-labeled bead technology. For identification of differentially expressed microRNAs data were analyzed by cluster analysis and selected statistical methods. Expression levels were validated for the most up- or down-regulated microRNAs in this training cohort using real-time PCR methodology as well as in an independent test cohort comprising 12 cases of human male breast cancer. Results Unsupervised cluster analysis separated very well male breast cancer samples and control specimens according to their microRNA expression pattern indicating cancer-specific alterations of microRNA expression in human male breast cancer. miR-21, miR519d, miR-183, miR-197, and miR-493-5p were identified as most prominently up-regulated, miR-145 and miR-497 as most prominently down-regulated in male breast cancer. Conclusions Male breast cancer displays several differentially expressed microRNAs. Not all of them are shared with breast cancer biopsies from female patients indicating male breast cancer specific alterations of microRNA expression.

  7. MicroRNAs play big roles in modulating macrophages response toward mycobacteria infection.

    Science.gov (United States)

    Abdalla, Abualgasim Elgaili; Duan, Xiangke; Deng, Wanyan; Zeng, Jie; Xie, Jianping

    2016-11-01

    Macrophages are crucial player in the defense against multiple intracellular pathogens. Mycobacterium tuberculosis, the causative agent of tuberculosis which inflicted around one third of global population, can replicate and persist within macrophages. MicroRNAs, endogenous, small noncoding RNA, can regulate the expression of macrophages genes required for appropriate signaling. Mycobacteria can manipulate the expression of macrophages microRNAs to subvert cell response for its survival and persistence. This review summarized the progress of microRNAs in mycobacterial pathogenesis. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Micro-masters of glioblastoma biology and therapy: increasingly recognized roles for microRNAs.

    Science.gov (United States)

    Floyd, Desiree; Purow, Benjamin

    2014-05-01

    MicroRNAs are small noncoding RNAs encoded in eukaryotic genomes that have been found to play critical roles in most biological processes, including cancer. This is true for glioblastoma, the most common and lethal primary brain tumor, for which microRNAs have been shown to strongly influence cell viability, stem cell characteristics, invasiveness, angiogenesis, metabolism, and immune evasion. Developing microRNAs as prognostic markers or as therapeutic agents is showing increasing promise and has potential to reach the clinic in the next several years. This succinct review summarizes current progress and future directions in this exciting and steadily expanding field.

  9. MicroRNA expression profile in head and neck cancer: HOX-cluster embedded microRNA-196a and microRNA-10b dysregulation implicated in cell proliferation

    International Nuclear Information System (INIS)

    Severino, Patricia; Mathor, Monica Beatriz; Nunes, Fabio Daumas; Ragoussis, Jiannis; Tajara, Eloiza Helena; Brüggemann, Holger; Andreghetto, Flavia Maziero; Camps, Carme; Klingbeil, Maria de Fatima Garrido; Pereira, Welbert Oliveira de; Soares, Renata Machado; Moyses, Raquel; Wünsch-Filho, Victor

    2013-01-01

    Current evidence implicates aberrant microRNA expression patterns in human malignancies; measurement of microRNA expression may have diagnostic and prognostic applications. Roles for microRNAs in head and neck squamous cell carcinomas (HNSCC) are largely unknown. HNSCC, a smoking-related cancer, is one of the most common malignancies worldwide but reliable diagnostic and prognostic markers have not been discovered so far. Some studies have evaluated the potential use of microRNA as biomarkers with clinical application in HNSCC. MicroRNA expression profile of oral squamous cell carcinoma samples was determined by means of DNA microarrays. We also performed gain-of-function assays for two differentially expressed microRNA using two squamous cell carcinoma cell lines and normal oral keratinocytes. The effect of the over-expression of these molecules was evaluated by means of global gene expression profiling and cell proliferation assessment. Altered microRNA expression was detected for a total of 72 microRNAs. Among these we found well studied molecules, such as the miR-17-92 cluster, comprising potent oncogenic microRNA, and miR-34, recently found to interact with p53. HOX-cluster embedded miR-196a/b and miR-10b were up- and down-regulated, respectively, in tumor samples. Since validated HOX gene targets for these microRNAs are not consistently deregulated in HNSCC, we performed gain-of-function experiments, in an attempt to outline their possible role. Our results suggest that both molecules interfere in cell proliferation through distinct processes, possibly targeting a small set of genes involved in cell cycle progression. Functional data on miRNAs in HNSCC is still scarce. Our data corroborate current literature and brings new insights into the role of microRNAs in HNSCC. We also show that miR-196a and miR-10b, not previously associated with HNSCC, may play an oncogenic role in this disease through the deregulation of cell proliferation. The study of microRNA

  10. Suspended matter and nutrient gradients of a small-scale river plume in Sepetiba Bay, SE-Brazil

    Directory of Open Access Journals (Sweden)

    Raphael Paiva Rodrigues

    2009-04-01

    Full Text Available Coastal river plumes represent one of the final stages of material transport across the land-sea interface. Most studies, however have focused on the behavior of medium to large sized river plumes of coastal-shelf waters, whereas small sized river plumes acting within estuaries have been neglected. This study addressed the behavior of suspended particulate matter (SPM, dissolved inorganic nutrients (DIN, DIP and DSi and Chlorophyll a (Chl. a of a small sized river plume derived from the closely lain São Francisco and Guandú river channels, set in the Sepetiba Bay estuary, SE-Brazil. Two surface water sampling campaigns were conducted, one in January 2003 (humid summer conditions and the other in June 2003 (dry winter conditions. On both occasions, the plumes dispersed in a SE direction towards the inner portion of the bay. The "wet" event plume was more turbid, nutrient rich and dispersed beyond nearshore waters, whereas the "dry" event plume proliferated as a narrow, less turbid and more nutrient poor film alongshore. Both exhibited a marked degree of patchiness, induced by the differential input of materials from the river sources and resuspension processes from the shallow nearshore bottom. The São Francisco river channel was the main source of freshwater, SPM and nutrients, except for ammonia (NH4+-N derived from domestic effluents of the Guandú river. The mesohaline portion of the estuarine mixing zone of the plumes behaved as a slight source for SPM, DSi and DIP, due to bottom resuspension processes. N:P molar ratios ranged between 80:1 and 20:1 along the estuarine gradient, being higher in the summer than in the winter event, indicating that DIP was the potential nutrient limiting primary production. Chl. a concentrations increased at the outer premises of the plume, suggesting that the short residence times and turbidity of the plume waters, hampered primary production nearshore, particularly during the summer occasion. The small

  11. Large-scale identification of microRNA targets in murine Dgcr8-deficient embryonic stem cell lines.

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    Matthew P A Davis

    Full Text Available Small RNAs such as microRNAs play important roles in embryonic stem cell maintenance and differentiation. A broad range of microRNAs is expressed in embryonic stem cells while only a fraction of their targets have been identified. We have performed large-scale identification of embryonic stem cell microRNA targets using a murine embryonic stem cell line deficient in the expression of Dgcr8. These cells are heavily depleted for microRNAs, allowing us to reintroduce specific microRNA duplexes and identify refined target sets. We used deep sequencing of small RNAs, mRNA expression profiling and bioinformatics analysis of microRNA seed matches in 3' UTRs to identify target transcripts. Consequently, we have identified a network of microRNAs that converge on the regulation of several important cellular pathways. Additionally, our experiments have revealed a novel candidate for Dgcr8-independent microRNA genesis and highlighted the challenges currently facing miRNA annotation.

  12. White matter microstructural damage in small vessel disease is associated with Montreal cognitive assessment but not with mini mental state examination performances: vascular mild cognitive impairment Tuscany study.

    Science.gov (United States)

    Pasi, Marco; Salvadori, Emilia; Poggesi, Anna; Ciolli, Laura; Del Bene, Alessandra; Marini, Sandro; Nannucci, Serena; Pescini, Francesca; Valenti, Raffaella; Ginestroni, Andrea; Toschi, Nicola; Diciotti, Stefano; Mascalchi, Mario; Inzitari, Domenico; Pantoni, Leonardo

    2015-01-01

    Montreal Cognitive Assessment (MoCA) has been proposed as a screening tool in vascular cognitive impairment. Diffusion tensor imaging is sensitive to white matter microstructural damage. We investigated if diffusion tensor imaging-derived indices are more strongly associated with performances on MoCA or on the widely used mini mental state examination in patients with mild cognitive impairment and small vessel disease. Mild cognitive impairment patients with moderate/severe degrees of white matter hyperintensities on MRI were enrolled. Lacunar infarcts, cortical atrophy, medial temporal lobe atrophy and median values of mean diffusivity and fractional anisotropy of the cerebral white matter were studied and correlated with cognitive tests performances. Seventy-six patients (mean age 75.1±6.8 years, mean years of education 8.0±4.3) were assessed. In univariate analyses, a significant association of both MoCA and mini mental state examination scores with age, education, cortical atrophy, and medial temporal lobe atrophy was found, whereas mean diffusivity and fractional anisotropy were associated with MoCA. In partial correlation analyses, adjusting for all demographic and neuroimaging variables, both mean diffusivity and fractional anisotropy were associated only with MoCA (mean diffusivity: r= -0.275, P=0.023; fractional anisotropy: r=0.246, P=0.043). In patients with mild cognitive impairment and small vessel disease, diffusion tensor imaging-measured white matter microstructural damage is more related to MoCA than mini mental state examination performances. MoCA is suited for the cognitive screening of patients with small vessel disease. © 2014 American Heart Association, Inc.

  13. C. elegans microRNAs.

    Science.gov (United States)

    Vella, Monica C; Slack, Frank J

    2005-09-21

    MicroRNAs (miRNAs) are small, non-coding regulatory RNAs found in many phyla that control such diverse events as development, metabolism, cell fate and cell death. They have also been implicated in human cancers. The C. elegans genome encodes hundreds of miRNAs, including the founding members of the miRNA family lin-4 and let-7. Despite the abundance of C. elegans miRNAs, few miRNA targets are known and little is known about the mechanism by which they function. However, C. elegans research continues to push the boundaries of discovery in this area. lin-4 and let-7 are the best understood miRNAs. They control the timing of adult cell fate determination in hypodermal cells by binding to partially complementary sites in the mRNA of key developmental regulators to repress protein expression. For example, lin-4 is predicted to bind to seven sites in the lin-14 3' untranslated region (UTR) to repress LIN-14, while let-7 is predicted to bind two let-7 complementary sites in the lin-41 3' UTR to down-regulate LIN-41. Two other miRNAs, lsy-6 and mir-273, control left-right asymmetry in neural development, and also target key developmental regulators for repression. Approximately one third of the C. elegans miRNAs are differentially expressed during development indicating a major role for miRNAs in C. elegans development. Given the remarkable conservation of developmental mechanism across phylogeny, many of the principles of miRNAs discovered in C. elegans are likely to be applicable to higher animals.

  14. Study of white matter at the centrum semiovale level with magnetic resonance spectroscopy and diffusion tensor imaging in cerebral small vessel disease.

    Science.gov (United States)

    Huang, L A; Ling, X Y; Li, C; Zhang, S J; Chi, G B; Xu, A D

    2014-04-08

    White matter lesion (WML) in magnetic resonance imaging is commonly observed in patients with cerebral small vessel disease (SVD), but the pathological mechanism of WML in SVD is still unclear. We observed the metabolism and microscopic anatomy of white matter in SVD patients. Twelve subjects clinically diagnosed with SVD and 6 normal control subjects were examined with magnetic resonance spectroscopy (MRS) and diffusion tensor imaging (DTI). The white matter at the centrum semiovale level was selected as the region of interest (ROI). The ROI metabolism parameters, including N-acetyl-l-aspartic acid (NAA), creatine (Cr), and choline (Cho) were measured by MRS. Microscopic parameters such as mean diffusion (MD) and fractional anisotropy (FA) in ROI were obtained by DTI. Compared with the normal control group, bilateral MD values in the SVD group were significantly elevated, whereas bilateral FA values in SVD were decreased, but the difference was not statistically significant. Additionally, NAA/Cho, Cho/Cr, and NAA/Cr showed no significant statistical differences. Our study suggests that the mechanisms of the SVD cognitive impairment are related to damage of the white matter structures rather than to brain metabolism.

  15. MicroRNAs as potential biomarkers in adrenocortical cancer: progress and challenges

    Directory of Open Access Journals (Sweden)

    Nadia eCHERRADI

    2016-01-01

    Full Text Available Adrenocortical carcinoma is a rare malignancy with poor prognosis and limited therapeutic options. Over the last decade, pan-genomic analyses of genetic and epigenetic alterations and genome-wide expression profile studies allowed major advances in the understanding of the molecular genetics of adrenocortical carcinoma. Besides the well-known dysfunctional molecular pathways in adrenocortical tumors such as the IGF2 pathway, the Wnt pathway and TP53, high-throughput technologies enabled a more comprehensive genomic characterization of adrenocortical cancer. Integration of expression profile data with exome sequencing, SNP array analysis, methylation and microRNA profiling led to the identification of subgroups of malignant tumors with distinct molecular alterations and clinical outcomes. MicroRNAs post-transcriptionally silence their target gene expression either by degrading mRNA or by inhibiting translation. Although our knowledge of the contribution of deregulated microRNAs to the pathogenesis of adrenocortical carcinoma is still in its infancy, recent studies support their relevance in gene expression alterations in these tumors. Some microRNAs have been shown to carry potential diagnostic and prognostic values while others may be good candidates for therapeutic interventions. With the emergence of disease-specific blood-borne microRNAs signatures, analyses of small cohorts of patients with adrenocortical carcinoma suggest that circulating microRNAs represent promising non-invasive biomarkers of malignancy or recurrence. However, some technical challenges still remain, and most of the microRNAs reported in the literature have not yet been validated in sufficiently powered and longitudinal studies. In this review, we discuss the current knowledge regarding the deregulation of tumor-associated and circulating microRNAs in adrenocortical carcinoma patients, while emphasizing their potential significance in adrenocortical carcinoma pathogenic

  16. The Role of microRNAs in the Pathogenesis of Herpesvirus Infection.

    Science.gov (United States)

    Piedade, Diogo; Azevedo-Pereira, José Miguel

    2016-06-02

    MicroRNAs (miRNAs) are small non-coding RNAs important in gene regulation. They are able to regulate mRNA translation through base-pair complementarity. Cellular miRNAs have been involved in the regulation of nearly all cellular pathways, and their deregulation has been associated with several diseases such as cancer. Given the importance of microRNAs to cell homeostasis, it is no surprise that viruses have evolved to take advantage of this cellular pathway. Viruses have been reported to be able to encode and express functional viral microRNAs that target both viral and cellular transcripts. Moreover, viral inhibition of key proteins from the microRNA pathway and important changes in cellular microRNA pool have been reported upon viral infection. In addition, viruses have developed multiple mechanisms to avoid being targeted by cellular microRNAs. This complex interaction between host and viruses to control the microRNA pathway usually favors viral infection and persistence by either reducing immune detection, avoiding apoptosis, promoting cell growth, or promoting lytic or latent infection. One of the best examples of this virus-host-microRNA interplay emanates from members of the Herperviridae family, namely the herpes simplex virus type 1 and type 2 (HSV-1 and HSV-2), human cytomegalovirus (HCMV), human herpesvirus 8 (HHV-8), and the Epstein-Barr virus (EBV). In this review, we will focus on the general functions of microRNAs and the interactions between herpesviruses, human hosts, and microRNAs and will delve into the related mechanisms that contribute to infection and pathogenesis.

  17. microRNA Response to Listeria monocytogenes Infection in Epithelial Cells

    Science.gov (United States)

    Izar, Benjamin; Mannala, Gopala Krishna; Mraheil, Mobarak Abu; Chakraborty, Trinad; Hain, Torsten

    2012-01-01

    microRNAs represent a family of very small non-coding RNAs that control several physiologic and pathologic processes, including host immune response and cancer by antagonizing a number of target mRNAs. There is limited knowledge about cell expression and the regulatory role of microRNAs following bacterial infections. We investigated whether infection with a Gram-positive bacterium leads to altered expression of microRNAs involved in the host cell response in epithelial cells. Caco-2 cells were infected with Listeria monocytogenes EGD-e, a mutant strain (ΔinlAB or Δhly) or incubated with purified listeriolysin (LLO). Total RNA was isolated and microRNA and target gene expression was compared to the expression in non-infected cells using microRNA microarrays and qRT-PCR. We identified and validated five microRNAs (miR- 146b, miR-16, let-7a1, miR-145 and miR-155) that were significantly deregulated following listerial infection. We show that expression patterns of particular microRNAs strongly depend on pathogen localization and the presence of bacterial effector proteins. Strikingly, miR-155 which was shown to have an important role in inflammatory responses during infection was induced by wild-type bacteria, by LLO-deficient bacteria and following incubation with purified LLO. It was downregulated following ΔinlAB infection indicating a new potent role for internalins in listerial pathogenicity and miRNA regulation. Concurrently, we observed differences in target transcript expression of the investigated miRNAs. We provide first evidence that L. monocytogenes infection leads to deregulation of a set of microRNAs with important roles in host response. Distinct microRNA expression depends on both LLO and pathogen localization. PMID:22312311

  18. Elevated levels of circulating microRNA-200 family members correlate with serous epithelial ovarian cancer

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    Kan Casina WS

    2012-12-01

    Full Text Available Abstract Background There is a critical need for improved diagnostic markers for high grade serous epithelial ovarian cancer (SEOC. MicroRNAs are stable in the circulation and may have utility as biomarkers of malignancy. We investigated whether levels of serum microRNA could discriminate women with high-grade SEOC from age matched healthy volunteers. Methods To identify microRNA of interest, microRNA expression profiling was performed on 4 SEOC cell lines and normal human ovarian surface epithelial cells. Total RNA was extracted from 500 μL aliquots of serum collected from patients with SEOC (n = 28 and age-matched healthy donors (n = 28. Serum microRNA levels were assessed by quantitative RT-PCR following preamplification. Results microRNA (miR-182, miR-200a, miR-200b and miR-200c were highly overexpressed in the SEOC cell lines relative to normal human ovarian surface epithelial cells and were assessed in RNA extracted from serum as candidate biomarkers. miR-103, miR-92a and miR -638 had relatively invariant expression across all ovarian cell lines, and with small-nucleolar C/D box 48 (RNU48 were assessed in RNA extracted from serum as candidate endogenous normalizers. No correlation between serum levels and age were observed (age range 30-79 years for any of these microRNA or RNU48. Individually, miR-200a, miR-200b and miR-200c normalized to serum volume and miR-103 were significantly higher in serum of the SEOC cohort (P  Conclusions We identified serum microRNAs able to discriminate patients with high grade SEOC from age-matched healthy controls. The addition of these microRNAs to current testing regimes may improve diagnosis for women with SEOC.

  19. Evaluation of microRNA alignment techniques

    Science.gov (United States)

    Kaspi, Antony; El-Osta, Assam

    2016-01-01

    Genomic alignment of small RNA (smRNA) sequences such as microRNAs poses considerable challenges due to their short length (∼21 nucleotides [nt]) as well as the large size and complexity of plant and animal genomes. While several tools have been developed for high-throughput mapping of longer mRNA-seq reads (>30 nt), there are few that are specifically designed for mapping of smRNA reads including microRNAs. The accuracy of these mappers has not been systematically determined in the case of smRNA-seq. In addition, it is unknown whether these aligners accurately map smRNA reads containing sequence errors and polymorphisms. By using simulated read sets, we determine the alignment sensitivity and accuracy of 16 short-read mappers and quantify their robustness to mismatches, indels, and nontemplated nucleotide additions. These were explored in the context of a plant genome (Oryza sativa, ∼500 Mbp) and a mammalian genome (Homo sapiens, ∼3.1 Gbp). Analysis of simulated and real smRNA-seq data demonstrates that mapper selection impacts differential expression results and interpretation. These results will inform on best practice for smRNA mapping and enable more accurate smRNA detection and quantification of expression and RNA editing. PMID:27284164

  20. Immunomodulating microRNAs of mycobacterial infections.

    Science.gov (United States)

    Bettencourt, Paulo; Pires, David; Anes, Elsa

    2016-03-01

    MicroRNAs are a class of small non-coding RNAs that have emerged as key regulators of gene expression at the post-transcriptional level by sequence-specific binding to target mRNAs. Some microRNAs block translation, while others promote mRNA degradation, leading to a reduction in protein availability. A single miRNA can potentially regulate the expression of multiple genes and their encoded proteins. Therefore, miRNAs can influence molecular signalling pathways and regulate many biological processes in health and disease. Upon infection, host cells rapidly change their transcriptional programs, including miRNA expression, as a response against the invading microorganism. Not surprisingly, pathogens can also alter the host miRNA profile to their own benefit, which is of major importance to scientists addressing high morbidity and mortality infectious diseases such as tuberculosis. In this review, we present recent findings on the miRNAs regulation of the host response against mycobacterial infections, providing new insights into host-pathogen interactions. Understanding these findings and its implications could reveal new opportunities for designing better diagnostic tools, therapies and more effective vaccines. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Circulating MicroRNAs as Potential Molecular Biomarkers in Pathophysiological Evolution of Pregnancy

    Directory of Open Access Journals (Sweden)

    Dragos Cretoiu

    2016-01-01

    Full Text Available MicroRNAs represent nonprotein coding small RNA molecules that are very stable to degradation and responsible for gene silencing in most eukaryotic cells. Increased evidence has been accumulating over the years about their potential value as biomarkers for several diseases. MicroRNAs were predicted to be involved in nearly all biological processes from development to oncogenesis. In this review, we address the importance of circulating microRNAs in different conditions associated with pregnancy starting with the implantation period to preeclampsia and we shortly describe the correlation between placental circulating miRNAs and pregnancy status. We also discuss the importance of microRNAs in recurrent abortion and ectopic pregnancy.

  2. A conformation-induced fluorescence method for microRNA detection

    DEFF Research Database (Denmark)

    Aw, Sherry S; Tang, Melissa Xm; Teo, Yin Nah

    2016-01-01

    and quantify microRNAs may aid research into novel aspects of microRNA biology and contribute to the development of diagnostics. By introducing an additional stem loop into the fluorescent RNA Spinach and altering its 3' and 5' ends, we have generated a new RNA, Pandan, that functions as the basis for a micro......MicroRNAs play important roles in a large variety of biological systems and processes through their regulation of target mRNA expression, and show promise as clinical biomarkers. However, their small size presents challenges for tagging or direct detection. Innovation in techniques to sense......RNA sensor. Pandan contains two sequence-variable stem loops that encode complementary sequence for a target microRNA of interest. In its sensor form, it requires the binding of a target microRNA in order to reconstitute the RNA scaffold for fluorophore binding and fluorescence. Binding of the target micro...

  3. MicroRNA and cancer

    DEFF Research Database (Denmark)

    Jansson, Martin D; Lund, Anders H

    2012-01-01

    biological phenomena and pathologies. The best characterized non-coding RNA family consists in humans of about 1400 microRNAs for which abundant evidence have demonstrated fundamental importance in normal development, differentiation, growth control and in human diseases such as cancer. In this review, we...... summarize the current knowledge and concepts concerning the involvement of microRNAs in cancer, which have emerged from the study of cell culture and animal model systems, including the regulation of key cancer-related pathways, such as cell cycle control and the DNA damage response. Importantly, micro...

  4. Understanding alcoholism through microRNA signatures in brains of human alcoholics

    Directory of Open Access Journals (Sweden)

    R. Dayne eMayfield

    2012-04-01

    Full Text Available Advances in the fields of genomics and genetics in the last decade have identified a large number of genes that can potentially influence alcohol-drinking behavior in humans as well as animal models. Consequently, the task of identifying efficient molecular targets that could be used to develop effective therapeutics against the disease has become increasingly daunting. One of the reasons for this is the fact that each of the many alcohol-responsive genes only contributes a small effect to the overall mechanism and disease phenotype, as is characteristic of complex traits. Current research trends are hence shifting towards the analysis of gene networks rather than emphasizing individual genes. The discovery of microRNAs and their mechanisms of action on regulation of transcript level and protein translation have made evident the utility of these small non-coding RNA molecules that act as central coordinators of multiple cross-communicating cellular pathways. Cells exploit the fact that a single microRNA can target hundreds of mRNA transcripts and that a single mRNA transcript can be simultaneously targeted by distinct microRNAs, to ensure fine-tuned and/or redundant control over a large number of cellular functions. By the same token, we can use these properties of microRNAs to develop novel, targeted strategies to combat complex disorders. In this review, we will focus on recent discoveries of microRNA signatures in brain of human alcoholics supporting the hypothesis that changes in gene expression and regulation by microRNAs are responsible for long-term neuroadaptations occurring during development of alcoholism. We also discuss insights into the potential modulation of epigenetic regulators by a subset of microRNAs. Taken together, microRNA activity may be controlling many of the cellular mechanisms already known to be involved in the development of alcoholism, and suggests potential targets for the development of novel therapeutic

  5. MicroRNA's are novel biomarkers in sepsis

    DEFF Research Database (Denmark)

    Søndergaard, Edith Smed; Alamili, Mahdi; Coskun, Mehmet

    2015-01-01

    Purpose: Sepsis is one of the leading causes of death after admission to the intensive care unit (ICU). The discovery of small non-coding microRNAs (miRs) and their correlation to sepsis has gained increasing interest. Our aim was to systematically review the literature examining the association ...... searching the computational target prediction databases. Conclusion: Various miRs are associated with sepsis, but no corresponding predictor genes were found....

  6. Clinical applications of microRNAs [v3; ref status: indexed, http://f1000r.es/218

    Directory of Open Access Journals (Sweden)

    Per Hydbring

    2013-10-01

    Full Text Available MicroRNAs represent a class of small RNAs derived from polymerase II controlled transcriptional regions. The primary transcript forms one or several bulging double stranded hairpins which are processed by Drosha and Dicer into hetero-duplexes. The targeting microRNA strand of the duplex is incorporated into the RNA Induced Silencing Complex from where it silences up to hundreds of mRNA transcript by inducing mRNA degradation or blocking protein translation. Apart from involvement in a variety of biological processes, microRNAs were early recognized for their potential in disease diagnostics and therapeutics. Due to their stability, microRNAs could be used as biomarkers. Currently, there are microRNA panels helping physicians determining the origins of cancer in disseminated tumors. The development of microRNA therapeutics has proved more challenging mainly due to delivery issues. However, one drug is already in clinical trials and several more await entering clinical phases. This review summarizes what has been recognized pre-clinically and clinically on diagnostic microRNAs. In addition, it highlights individual microRNA drugs in running platforms driven by four leading microRNA-therapeutic companies.

  7. Clinical applications of microRNAs [v1; ref status: indexed, http://f1000r.es/14d

    Directory of Open Access Journals (Sweden)

    Per Hydbring

    2013-06-01

    Full Text Available MicroRNAs represent a class of small RNAs derived from polymerase II controlled transcriptional regions. The primary transcript forms one or several bulging double stranded hairpins which are processed by Drosha and Dicer into hetero-duplexes. The targeting microRNA strand of the duplex is incorporated into the RNA Induced Silencing Complex from where it silences up to hundreds of mRNA transcript by inducing mRNA degradation or blocking protein translation. Apart from involvement in a variety of biological processes, microRNAs were early recognized for their potential in disease diagnostics and therapeutics. Due to their stability, microRNAs could be used as biomarkers. Currently, there are microRNA panels helping physicians determining the origins of cancer in disseminated tumors. The development of microRNA therapeutics has proved more challenging mainly due to delivery issues. However, one drug is already in clinical trials and several more await entering clinical phases. This review summarizes what has been recognized pre-clinically and clinically on diagnostic microRNAs. In addition, it highlights individual microRNA drugs in running platforms driven by four leading microRNA-therapeutic companies.

  8. MicroRNA in Human Glioma

    Energy Technology Data Exchange (ETDEWEB)

    Li, Mengfeng, E-mail: limf@mail.sysu.edu.cn [Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Chinese Ministry of Education, Guangzhou 510080 (China); Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080 (China); Li, Jun [Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Chinese Ministry of Education, Guangzhou 510080 (China); Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080 (China); Liu, Lei; Li, Wei [Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Chinese Ministry of Education, Guangzhou 510080 (China); Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080 (China); Yang, Yi [Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Chinese Ministry of Education, Guangzhou 510080 (China); Department of Pharmacology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080 (China); Yuan, Jie [Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Chinese Ministry of Education, Guangzhou 510080 (China); Key Laboratory of Functional Molecules from Oceanic Microorganisms (Sun Yat-sen University), Department of Education of Guangdong Province, Guangzhou 510080 (China)

    2013-10-23

    Glioma represents a serious health problem worldwide. Despite advances in surgery, radiotherapy, chemotherapy, and targeting therapy, the disease remains one of the most lethal malignancies in humans, and new approaches to improvement of the efficacy of anti-glioma treatments are urgently needed. Thus, new therapeutic targets and tools should be developed based on a better understanding of the molecular pathogenesis of glioma. In this context, microRNAs (miRNAs), a class of small, non-coding RNAs, play a pivotal role in the development of the malignant phenotype of glioma cells, including cell survival, proliferation, differentiation, tumor angiogenesis, and stem cell generation. This review will discuss the biological functions of miRNAs in human glioma and their implications in improving clinical diagnosis, prediction of prognosis, and anti-glioma therapy.

  9. MicroRNA in Human Glioma

    International Nuclear Information System (INIS)

    Li, Mengfeng; Li, Jun; Liu, Lei; Li, Wei; Yang, Yi; Yuan, Jie

    2013-01-01

    Glioma represents a serious health problem worldwide. Despite advances in surgery, radiotherapy, chemotherapy, and targeting therapy, the disease remains one of the most lethal malignancies in humans, and new approaches to improvement of the efficacy of anti-glioma treatments are urgently needed. Thus, new therapeutic targets and tools should be developed based on a better understanding of the molecular pathogenesis of glioma. In this context, microRNAs (miRNAs), a class of small, non-coding RNAs, play a pivotal role in the development of the malignant phenotype of glioma cells, including cell survival, proliferation, differentiation, tumor angiogenesis, and stem cell generation. This review will discuss the biological functions of miRNAs in human glioma and their implications in improving clinical diagnosis, prediction of prognosis, and anti-glioma therapy

  10. MicroRNA Implication in Cancer

    Directory of Open Access Journals (Sweden)

    Iker BADIOLA

    2010-03-01

    Full Text Available MicroRNAs (miRNA are a new class of posttranscriptional regulators. These small non-coding RNAs regulate the expression of target mRNA transcripts and are linked to several human disease such as Alzheimer, cancer or heart disease. But it has been the cancer disease which has experimented the major number of studies of miRNA linked to the disease progression. In the last years it has been reported the deregulation pattern of the miRNAs in malignant cells which have disrupted the control of the proliferation, differentiation or apoptosis. The evidence of the presence of specific miRNA deregulated in concrete cancer types has become the miRNAs like possible biomarkers and therapeutic targets. The specific miRNA patterns deregulated in concrete cancer cell types open new opportunities to the diagnosis and therapy.

  11. Signatures of RNA binding proteins globally coupled to effective microRNA target sites

    DEFF Research Database (Denmark)

    Jacobsen, Anders; Wen, Jiayu; Marks, Debora S

    2010-01-01

    MicroRNAs (miRNAs) and small interfering RNAs (siRNAs), bound to Argonaute proteins (RISC), destabilize mRNAs through base-pairing with the mRNA. However, the gene expression changes after perturbations of these small RNAs are only partially explained by predicted miRNA/siRNA targeting. Targeting...

  12. The coupling of runoff and dissolved organic matter transport: Insights from in situ fluorescence measurements in small streams and large rivers

    Science.gov (United States)

    Pellerin, B. A.; Bergamaschi, B. A.; Downing, B. D.; Saraceno, J.; Shanley, J. B.; Aiken, G.; Murdoch, P. S.

    2011-12-01

    Understanding dissolved organic matter (DOM) dynamics in streams and rivers can help characterize mercury transport, assess causes of drinking water issues, and lead to improved understanding of watershed source areas and carbon loads to downstream ecosystems. However, traditional sampling approaches that collect discrete concentration data at weekly to monthly intervals often fail to adequately capture hydrological pulses ranging from early snowmelt periods to short-duration rainfall events. Continuous measurements of chromophoric dissolved organic matter fluorescence (FDOM) in rivers and streams now provide an opportunity to more accurately quantify DOM loads and processes in aquatic ecosystems at a range of scales. In this study, we used continuous FDOM data from in situ sensors along with discharge data to assess the coupling of FDOM transport and runoff in small streams and large rivers. Results from headwater catchments in New England and California show that FDOM is tightly coupled with runoff, supporting strong linkages between watershed flow paths and DOM concentrations in streams. Results also show that the magnitude of FDOM response relative to runoff varies seasonally, with highest concentrations during autumn rainfall events (after leaf fall) and lower concentrations during peak snowmelt for equivalent runoff. In large river basins, FDOM dynamics are also coupled with runoff and exhibit the same seasonal variability in the magnitude of FDOM response relative to discharge. However, the peaks in FDOM typically lag runoff by several days, reflecting the influence of a variety of factors such as water residence times, reservoir releases, and connectivity to organic matter-rich riparian floodplains and wetlands. Our results show that in situ FDOM data will be important for understanding the coupling of runoff and DOM across multiple scales and could serve a critical role in monitoring, assessment and decision-making in both small and large watersheds.

  13. MicroRNAs: From Female Fertility, Germ Cells, and Stem Cells to Cancer in Humans

    Directory of Open Access Journals (Sweden)

    Irma Virant-Klun

    2016-01-01

    Full Text Available MicroRNAs are a family of naturally occurring small noncoding RNA molecules that play an important regulatory role in gene expression. They are suggested to regulate a large proportion of protein encoding genes by mediating the translational suppression and posttranscriptional control of gene expression. Recent findings show that microRNAs are emerging as important regulators of cellular differentiation and dedifferentiation, and are deeply involved in developmental processes including human preimplantation development. They keep a balance between pluripotency and differentiation in the embryo and embryonic stem cells. Moreover, it became evident that dysregulation of microRNA expression may play a fundamental role in progression and dissemination of different cancers including ovarian cancer. The interest is still increased by the discovery of exosomes, that is, cell-derived vesicles, which can carry different proteins but also microRNAs between different cells and are involved in cell-to-cell communication. MicroRNAs, together with exosomes, have a great potential to be used for prognosis, therapy, and biomarkers of different diseases including infertility. The aim of this review paper is to summarize the existent knowledge on microRNAs related to female fertility and cancer: from primordial germ cells and ovarian function, germinal stem cells, oocytes, and embryos to embryonic stem cells.

  14. MicroRNAs in Heart Failure, Cardiac Transplantation, and Myocardial Recovery: Biomarkers with Therapeutic Potential.

    Science.gov (United States)

    Shah, Palak; Bristow, Michael R; Port, J David

    2017-12-01

    Heart failure is increasing in prevalence with a lack of recently developed therapies that produce major beneficial effects on its associated mortality. MicroRNAs are small non-coding RNA molecules that regulate gene expression, are differentially regulated in heart failure, and are found in the circulation serving as a biomarker of heart failure. Data suggests that microRNAs may be used to detect allograft rejection in cardiac transplantation and may predict the degree of myocardial recovery in patients with a left ventricular assist device or treated with beta-blocker therapy. Given their role in regulating cellular function, microRNAs are an intriguing target for oligonucleotide therapeutics, designed to mimic or antagonize (antagomir) their biological effects. We review the current state of microRNAs as biomarkers of heart failure and associated conditions, the mechanisms by which microRNAs control cellular function, and how specific microRNAs may be targeted with novel therapeutics designed to treat heart failure.

  15. Let-7 microRNAs are developmentally regulated in circulating human erythroid cells

    Directory of Open Access Journals (Sweden)

    Reed Christopher

    2009-11-01

    Full Text Available Abstract Background MicroRNAs are ~22nt-long small non-coding RNAs that negatively regulate protein expression through mRNA degradation or translational repression in eukaryotic cells. Based upon their importance in regulating development and terminal differentiation in model systems, erythrocyte microRNA profiles were examined at birth and in adults to determine if changes in their abundance coincide with the developmental phenomenon of hemoglobin switching. Methods Expression profiling of microRNA was performed using total RNA from four adult peripheral blood samples compared to four cord blood samples after depletion of plasma, platelets, and nucleated cells. Labeled RNAs were hybridized to custom spotted arrays containing 474 human microRNA species (miRBase release 9.1. Total RNA from Epstein-Barr virus (EBV-transformed lymphoblastoid cell lines provided a hybridization reference for all samples to generate microRNA abundance profile for each sample. Results Among 206 detected miRNAs, 79% of the microRNAs were present at equivalent levels in both cord and adult cells. By comparison, 37 microRNAs were up-regulated and 4 microRNAs were down-regulated in adult erythroid cells (fold change > 2; p let-7 miRNA family consistently demonstrated increased abundance in the adult samples by array-based analyses that were confirmed by quantitative PCR (4.5 to 18.4 fold increases in 6 of 8 let-7 miRNA. Profiling studies of messenger RNA (mRNA in these cells additionally demonstrated down-regulation of ten let-7 target genes in the adult cells. Conclusion These data suggest that a consistent pattern of up-regulation among let-7 miRNA in circulating erythroid cells occurs in association with hemoglobin switching during the fetal-to-adult developmental transition in humans.

  16. Does spatial proximity to small towns matter for rural livelihoods? : A propensity score matching analysis in Ethiopia

    NARCIS (Netherlands)

    Gebrekidan Abbay, A.; Rutten, R.P.J.H.

    2016-01-01

    The spatial dimension of rural–urban linkage has become a new subject of debate in regional development. In most empirical research the focus has usually been on the role of small urban centers in rural development. However, the effects of different particulars of the linkage such as spatial

  17. Size matters: pitch dimensions constrain inter-team distances and surface area difference in small-sided soccer games

    NARCIS (Netherlands)

    Frencken, Wouter; van der Plaats, Jorrit; Visscher, Chris; Lemmink, Koen

    2013-01-01

    Pitch size varies in official soccer matches and differently sized pitches are adopted for tactical purposes in small-sided training games. Since interactive team behaviour emerges under con- straints, the authors evaluate the effect of pitch size (task) manipulations on interactive team behaviour

  18. Posture does not matter! Paw usage and grasping paw preference in a small-bodied rooting quadrupedal mammal.

    Science.gov (United States)

    Joly, Marine; Scheumann, Marina; Zimmermann, Elke

    2012-01-01

    Recent results in birds, marsupials, rodents and nonhuman primates suggest that phylogeny and ecological factors such as body size, diet and postural habit of a species influence limb usage and the direction and strength of limb laterality. To examine to which extent these findings can be generalised to small-bodied rooting quadrupedal mammals, we studied trees shrews (Tupaia belangeri). We established a behavioural test battery for examining paw usage comparable to small-bodied primates and tested 36 Tupaia belangeri. We studied paw usage in a natural foraging situation (simple food grasping task) and measured the influence of varying postural demands (triped, biped, cling, sit) on paw preferences by applying a forced-food grasping task similar to other small-bodied primates. Our findings suggest that rooting tree shrews prefer mouth over paw usage to catch food in a natural foraging situation. Moreover, we demonstrated that despite differences in postural demand, tree shrews show a strong and consistent individual paw preference for grasping across different tasks, but no paw preference at a population level. Tree shrews showed less paw usage than small-bodied quadrupedal and arboreal primates, but the same paw preference. Our results confirm that individual paw preferences remain constant irrespective of postural demand in some small-bodied quadrupedal non primate and primate mammals which do not require fine motoric control for manipulating food items. Our findings suggest that the lack of paw/hand preference for grasping food at a population level is a universal pattern among those species and that the influence of postural demand on manual lateralisation in quadrupeds may have evolved in large-bodied species specialised in fine manipulations of food items.

  19. Posture does not matter! Paw usage and grasping paw preference in a small-bodied rooting quadrupedal mammal.

    Directory of Open Access Journals (Sweden)

    Marine Joly

    Full Text Available BACKGROUND: Recent results in birds, marsupials, rodents and nonhuman primates suggest that phylogeny and ecological factors such as body size, diet and postural habit of a species influence limb usage and the direction and strength of limb laterality. To examine to which extent these findings can be generalised to small-bodied rooting quadrupedal mammals, we studied trees shrews (Tupaia belangeri. METHODOLOGY/PRINCIPAL FINDINGS: We established a behavioural test battery for examining paw usage comparable to small-bodied primates and tested 36 Tupaia belangeri. We studied paw usage in a natural foraging situation (simple food grasping task and measured the influence of varying postural demands (triped, biped, cling, sit on paw preferences by applying a forced-food grasping task similar to other small-bodied primates. Our findings suggest that rooting tree shrews prefer mouth over paw usage to catch food in a natural foraging situation. Moreover, we demonstrated that despite differences in postural demand, tree shrews show a strong and consistent individual paw preference for grasping across different tasks, but no paw preference at a population level. CONCLUSIONS/SIGNIFICANCE: Tree shrews showed less paw usage than small-bodied quadrupedal and arboreal primates, but the same paw preference. Our results confirm that individual paw preferences remain constant irrespective of postural demand in some small-bodied quadrupedal non primate and primate mammals which do not require fine motoric control for manipulating food items. Our findings suggest that the lack of paw/hand preference for grasping food at a population level is a universal pattern among those species and that the influence of postural demand on manual lateralisation in quadrupeds may have evolved in large-bodied species specialised in fine manipulations of food items.

  20. Network-based ranking methods for prediction of novel disease associated microRNAs.

    Science.gov (United States)

    Le, Duc-Hau

    2015-10-01

    Many studies have shown roles of microRNAs on human disease and a number of computational methods have been proposed to predict such associations by ranking candidate microRNAs according to their relevance to a disease. Among them, machine learning-based methods usually have a limitation in specifying non-disease microRNAs as negative training samples. Meanwhile, network-based methods are becoming dominant since they well exploit a "disease module" principle in microRNA functional similarity networks. Of which, random walk with restart (RWR) algorithm-based method is currently state-of-the-art. The use of this algorithm was inspired from its success in predicting disease gene because the "disease module" principle also exists in protein interaction networks. Besides, many algorithms designed for webpage ranking have been successfully applied in ranking disease candidate genes because web networks share topological properties with protein interaction networks. However, these algorithms have not yet been utilized for disease microRNA prediction. We constructed microRNA functional similarity networks based on shared targets of microRNAs, and then we integrated them with a microRNA functional synergistic network, which was recently identified. After analyzing topological properties of these networks, in addition to RWR, we assessed the performance of (i) PRINCE (PRIoritizatioN and Complex Elucidation), which was proposed for disease gene prediction; (ii) PageRank with Priors (PRP) and K-Step Markov (KSM), which were used for studying web networks; and (iii) a neighborhood-based algorithm. Analyses on topological properties showed that all microRNA functional similarity networks are small-worldness and scale-free. The performance of each algorithm was assessed based on average AUC values on 35 disease phenotypes and average rankings of newly discovered disease microRNAs. As a result, the performance on the integrated network was better than that on individual ones. In

  1. Computational methods for ab initio detection of microRNAs

    Directory of Open Access Journals (Sweden)

    Malik eYousef

    2012-10-01

    Full Text Available MicroRNAs are small RNA sequences of 18-24 nucleotides in length, which serve as templates to drive post transcriptional gene silencing. The canonical microRNA pathway starts with transcription from DNA and is followed by processing via the Microprocessor complex, yielding a hairpin structure. Which is then exported into the cytosol where it is processed by Dicer and then incorporated into the RNA induced silencing complex. All of these biogenesis steps add to the overall specificity of miRNA production and effect. Unfortunately, their modes of action are just beginning to be elucidated and therefore computational prediction algorithms cannot model the process but are usually forced to employ machine learning approaches. This work focuses on ab initio prediction methods throughout; and therefore homology-based miRNA detection methods are not discussed. Current ab initio prediction algorithms, their ties to data mining, and their prediction accuracy are detailed.

  2. Role of Small RNAs in Trypanosomatid Infections

    Science.gov (United States)

    Linhares-Lacerda, Leandra; Morrot, Alexandre

    2016-01-01

    Trypanosomatid parasites survive and replicate in the host by using mechanisms that aim to establish a successful infection and ensure parasite survival. Evidence points to microRNAs as new players in the host-parasite interplay. MicroRNAs are small non-coding RNAs that control proteins levels via post-transcriptional gene down-regulation, either within the cells where they were produced or in other cells via intercellular transfer. These microRNAs can be modulated in host cells during infection and are among the growing group of small regulatory RNAs, for which many classes have been described, including the transfer RNA-derived small RNAs. Parasites can either manipulate microRNAs to evade host-driven damage and/or transfer small RNAs to host cells. In this mini-review, we present evidence for the involvement of small RNAs, such as microRNAs, in trypanosomatid infections which lack RNA interference. We highlight both microRNA profile alterations in host cells during those infections and the horizontal transfer of small RNAs and proteins from parasites to the host by membrane-derived extracellular vesicles in a cell communication mechanism. PMID:27065454

  3. In a world of big data, small effects can still matter: a reply to Boyce, Daly, Hounkpatin, and Wood (2017)

    OpenAIRE

    Matz, SC; Gladstone, JJ; Stillwell, David John

    2017-01-01

    We make three points in response to Boyce, Daly, Hounkpatin, and Wood (2017). First, we clarify a misunderstanding of the goal of our analyses, which was to investigate the links between life satisfaction and spending patterns, rather than spending volume. Second, we report a simulation study we ran to demonstrate that our results were not driven by the proposed statistical artifact. Finally, we discuss the broader issue of why, in a world of big data, small but reliable effect sizes can be v...

  4. Identifying Neutrino Mass Hierarchy at Extremely Small θ13 through Earth Matter Effects in a Supernova Signal

    International Nuclear Information System (INIS)

    Dasgupta, Basudeb; Dighe, Amol; Mirizzi, Alessandro

    2008-01-01

    Collective neutrino flavor transformations deep inside a supernova are sensitive to the neutrino mass hierarchy even at extremely small values of θ 13 . Exploiting this effect, we show that comparison of the antineutrino signals from a galactic supernova in two megaton class water Cherenkov detectors, one of which is shadowed by Earth, will enable us to distinguish between the hierarchies if sin 2 θ 13 -5 , where long baseline neutrino experiments would be ineffectual

  5. Does company size matter? Validation of an integrative model of safety behavior across small and large construction companies.

    Science.gov (United States)

    Guo, Brian H W; Yiu, Tak Wing; González, Vicente A

    2018-02-01

    Previous safety climate studies primarily focused on either large construction companies or the construction industry as a whole, while little is known about whether company size has significant effects on workers' understanding of safety climate measures and relationships between safety climate factors and safety behavior. Thus, this study aims to: (a) test the measurement equivalence (ME) of a safety climate measure across workers from small and large companies; (b) investigate if company size alters the causal structure of the integrative model developed by Guo, Yiu, and González (2016). Data were collected from 253 construction workers in New Zealand using a safety climate measure. This study used multi-group confirmatory factor analyses (MCFA) to test the measurement equivalence of the safety climate measure and structure invariance of the integrative model. Results indicate that workers from small and large companies understood the safety climate measure in a similar manner. In addition, it was suggested that company size does not change the causal structure and mediational processes of the integrative model. Both measurement equivalence of the safety climate measure and structural invariance of the integrative model were supported by this study. Practical applications: Findings of this study provided strong support for a meaningful use of the safety climate measure across construction companies in different sizes. Safety behavior promotion strategies designed based on the integrative model may be well suited for both large and small companies. Copyright © 2017 National Safety Council and Elsevier Ltd. All rights reserved.

  6. MicroRNAs and drug addiction

    Directory of Open Access Journals (Sweden)

    Paul J Kenny

    2013-05-01

    Full Text Available Drug addiction is considered a disorder of neuroplasticity in brain reward and cognition systems resulting from aberrant activation of gene expression programs in response to prolonged drug consumption. Noncoding RNAs are key regulators of almost all aspects of cellular physiology. MicroRNAs (miRNAs are small (~21–23 nucleotides noncoding RNA transcripts that regulate gene expression at the post-transcriptional level. Recently, microRNAs were shown to play key roles in the drug-induced remodeling of brain reward systems that likely drives the emergence of addiction. Here, we review evidence suggesting that one particular miRNA, miR-212, plays a particularly prominent role in vulnerability to cocaine addiction. We review evidence showing that miR-212 expression is increased in the dorsal striatum of rats that show compulsive-like cocaine-taking behaviors. Increases in miR-212 expression appear to protect against cocaine addiction, as virus-mediated striatal miR-212 over-expression decreases cocaine consumption in rats. Conversely, disruption of striatal miR-212 signaling using an antisense oligonucleotide increases cocaine intake. We also review data that identify two mechanisms by which miR-212 may regulate cocaine intake. First, miR-212 has been shown to amplify striatal CREB signaling through a mechanism involving activation of Raf1 kinase. Second, miR-212 was also shown to regulate cocaine intake by repressing striatal expression of methyl CpG binding protein 2 (MeCP2, consequently decreasing protein levels of brain-derived neurotrophic factor (BDNF. The concerted actions of miR-212 on striatal CREB and MeCP2/BDNF activity greatly attenuate the motivational effects of cocaine. These findings highlight the unique role for miRNAs in simultaneously controlling multiple signaling cascades implicated in addiction.

  7. Identification of Novel and Conserved microRNAs in Homalodisca vitripennis, the Glassy-Winged Sharpshooter by Expression Profiling.

    Directory of Open Access Journals (Sweden)

    Raja Sekhar Nandety

    Full Text Available The glassy-winged sharpshooter (GWSS Homalodisca vitripennis (Hemiptera: Cicadellidae, is a xylem-feeding leafhopper and an important vector of the bacterium Xylella fastidiosa; the causal agent of Pierce's disease of grapevines. MicroRNAs are a class of small RNAs that play an important role in the functional development of various organisms including insects. In H. vitripennis, we identified microRNAs using high-throughput deep sequencing of adults followed by computational and manual annotation. A total of 14 novel microRNAs that are not found in the miRBase were identified from adult H. vitripennis. Conserved microRNAs were also found in our datasets. By comparison to our previously determined transcriptome sequence of H. vitripennis, we identified the potential targets of the microRNAs in the transcriptome. This microRNA profile information not only provides a more nuanced understanding of the biological and physiological mechanisms that govern gene expression in H. vitripennis, but may also lead to the identification of novel mechanisms for biorationally designed management strategies through the use of microRNAs.

  8. MicroRNA involvement in glioblastoma pathogenesis

    International Nuclear Information System (INIS)

    Novakova, Jana; Slaby, Ondrej; Vyzula, Rostislav; Michalek, Jaroslav

    2009-01-01

    MicroRNAs are endogenously expressed regulatory noncoding RNAs. Altered expression levels of several microRNAs have been observed in glioblastomas. Functions and direct mRNA targets for these microRNAs have been relatively well studied over the last years. According to these data, it is now evident, that impairment of microRNA regulatory network is one of the key mechanisms in glioblastoma pathogenesis. MicroRNA deregulation is involved in processes such as cell proliferation, apoptosis, cell cycle regulation, invasion, glioma stem cell behavior, and angiogenesis. In this review, we summarize the current knowledge of miRNA functions in glioblastoma with an emphasis on its significance in glioblastoma oncogenic signaling and its potential to serve as a disease biomarker and a novel therapeutic target in oncology.

  9. MicroRNA function in Drosophila melanogaster.

    Science.gov (United States)

    Carthew, Richard W; Agbu, Pamela; Giri, Ritika

    2017-05-01

    Over the last decade, microRNAs have emerged as critical regulators in the expression and function of animal genomes. This review article discusses the relationship between microRNA-mediated regulation and the biology of the fruit fly Drosophila melanogaster. We focus on the roles that microRNAs play in tissue growth, germ cell development, hormone action, and the development and activity of the central nervous system. We also discuss the ways in which microRNAs affect robustness. Many gene regulatory networks are robust; they are relatively insensitive to the precise values of reaction constants and concentrations of molecules acting within the networks. MicroRNAs involved in robustness appear to be nonessential under uniform conditions used in conventional laboratory experiments. However, the robust functions of microRNAs can be revealed when environmental or genetic variation otherwise has an impact on developmental outcomes. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. microRNAs: Implications for air pollution research

    International Nuclear Information System (INIS)

    Jardim, Melanie J.

    2011-01-01

    The purpose of this review is to provide an update of the current understanding on the role of microRNAs in mediating genetic responses to air pollutants and to contemplate on how these responses ultimately control susceptibility to ambient air pollution. Morbidity and mortality attributable to air pollution continues to be a growing public health concern worldwide. Despite several studies on the health effects of ambient air pollution, underlying molecular mechanisms of susceptibility and disease remain elusive. In the last several years, special attention has been given to the role of epigenetics in mediating, not only genetic and physiological responses to certain environmental insults, but also in regulating underlying susceptibility to environmental stressors. Epigenetic mechanisms control the expression of gene products, both basally and as a response to a perturbation, without affecting the sequence of DNA itself. These mechanisms include structural regulation of the chromatin structure, such as DNA methylation and histone modifications, and post-transcriptional gene regulation, such as microRNA mediated repression of gene expression. microRNAs are small noncoding RNAs that have been quickly established as key regulators of gene expression. As such, miRNAs have been found to control several cellular processes including apoptosis, proliferation and differentiation. More recently, research has emerged suggesting that changes in the expression of some miRNAs may be critical for mediating biological, and ultimately physiological, responses to air pollutants. Although the study of microRNAs, and epigenetics as a whole, has come quite far in the field of cancer, the understanding of how these mechanisms regulate gene–environment interactions to environmental exposures in everyday life is unclear. This article does not necessarily reflect the views and policies of the US EPA.

  11. microRNAs: Implications for air pollution research

    Energy Technology Data Exchange (ETDEWEB)

    Jardim, Melanie J., E-mail: melaniejardim@gmail.com [Environmental Public Health Division, National Health and Environmental Effects Research Laboratory, United States Environmental Protection Agency, Chapel Hill, NC (United States)

    2011-12-01

    The purpose of this review is to provide an update of the current understanding on the role of microRNAs in mediating genetic responses to air pollutants and to contemplate on how these responses ultimately control susceptibility to ambient air pollution. Morbidity and mortality attributable to air pollution continues to be a growing public health concern worldwide. Despite several studies on the health effects of ambient air pollution, underlying molecular mechanisms of susceptibility and disease remain elusive. In the last several years, special attention has been given to the role of epigenetics in mediating, not only genetic and physiological responses to certain environmental insults, but also in regulating underlying susceptibility to environmental stressors. Epigenetic mechanisms control the expression of gene products, both basally and as a response to a perturbation, without affecting the sequence of DNA itself. These mechanisms include structural regulation of the chromatin structure, such as DNA methylation and histone modifications, and post-transcriptional gene regulation, such as microRNA mediated repression of gene expression. microRNAs are small noncoding RNAs that have been quickly established as key regulators of gene expression. As such, miRNAs have been found to control several cellular processes including apoptosis, proliferation and differentiation. More recently, research has emerged suggesting that changes in the expression of some miRNAs may be critical for mediating biological, and ultimately physiological, responses to air pollutants. Although the study of microRNAs, and epigenetics as a whole, has come quite far in the field of cancer, the understanding of how these mechanisms regulate gene-environment interactions to environmental exposures in everyday life is unclear. This article does not necessarily reflect the views and policies of the US EPA.

  12. Alien Mink Predation and Colonisation Processes of Rodent Prey on Small Islands of the Baltic Sea: Does Prey Naivete Matter?

    International Nuclear Information System (INIS)

    Fey, K.; Korpimaki, E.; Banks, P.B.

    2010-01-01

    Colonisation, an important part of meta-population dynamics of fragmented populations, depends on both the dispersal ability and the ability to establish in the new habitat. Predation can hinder successful establishment of prey, and where the predation pressure comes from an alien predator, the effects on colonisation might be devastating. We studied the establishment of field voles (Microtus agrestis) inhabiting small islands of the archipelago of the Baltic Sea, SW Finland, under presence and absence of the alien American mink (Mustela vison). We translocated experienced voles from islands with mink, and inexperienced voles from islands from which mink had been removed, to other islands where mink was present or absent. By radio-tracking we studied survival, space and micro habitat use of voles within four weeks after translocation. Survival of voles on mink islands was significantly lower than on mink-free islands, but experienced voles did not survive better than inexperienced voles. Experienced voles were more often located in juniper habitats than inexperienced voles, but they appeared not to gain any survival benefit from altered micro habitat use. This study provides novel evidence, that alien mink predation inhibits establishment of colonising field voles and may thus ultimately induce extinction of voles from the outer archipelago.

  13. Dose-responsiveness and persistence of microRNA expression alterations induced by cigarette smoke in mouse lung

    International Nuclear Information System (INIS)

    Izzotti, Alberto; Larghero, Patrizia; Longobardi, Mariagrazia; Cartiglia, Cristina; Camoirano, Anna; Steele, Vernon E.; De Flora, Silvio

    2011-01-01

    Our previous studies demonstrated that exposure to cigarette smoke (CS), either mainstream or environmental, results in a remarkable downregulation of microRNA expression in the lung of both mice and rats. The goals of the present study were to evaluate the dose responsiveness to CS and the persistence of microRNA alterations after smoking cessation. ICR (CD-1) neonatal mice were exposed whole-body to mainstream CS, at the doses of 119, 292, 438, and 631 mg/m 3 of total particulate matter. Exposure started within 12 h after birth and continued daily for 4 weeks. The levels of bulky DNA adducts and 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodGuo) were measured by 32 P postlabeling procedures, and the expression of 697 mouse microRNAs was analyzed by microarray. The highest CS dose was lethal. Exposure to CS caused a dose-dependent increase of DNA alterations. DNA adducts and, even more sharply, 8-oxodGuo were reverted 1 and 4 weeks after smoking cessation. Exposure to CS resulted in an evident dysregulation of microRNA expression profiles, mainly in the sense of downregulation. The two lowest doses were not particularly effective, while the highest nonlethal dose produced extensive microRNA alterations. The expression of most downregulated microRNAs, including among others 7 members of the let-7 family, was restored one week after smoking cessation. However, the recovery was incomplete for a limited array of microRNAs, including mir-34b, mir-345, mir-421, mir-450b, mir-466, and mir-469. Thus, it appears that microRNAs mainly behave as biomarkers of effect and that exposure to high-dose, lasting for an adequate period of time, is needed to trigger the CS-related carcinogenesis process in the experimental animal model used.

  14. Where You Live Matters: Localising Environmental Impacts on Health, Nutrition and Poverty in Cambodia Using Small Area Estimation Techniques

    Science.gov (United States)

    Nilsen, K.; van Soesbergen, A.; Matthews, Z.

    2016-12-01

    Socioeconomic development depends on local environments. However, the scientific evidence quantifying the impact of environmental factors on health, nutrition and poverty at subnational levels is limited. This is because socioeconomic indicators are derived from sample surveys representative only at aggregate levels compared to environmental variables mostly available in high-resolution grids. Cambodia was selected because of its commitment to development in the context of a rapidly deteriorating environment. Having made considerable progress since 2005, access to health services is limited, a quarter of the population is still poor and 40% rural children are malnourished. Cambodia is also facing considerable environmental challenges including high deforestation rates, land degradation and natural hazards. Addressing existing gaps in the knowledge of environmental impacts on health and livelihoods, this study applies small area estimation (SAE) to quantify health, nutritional and poverty outcomes in the context of local environments. SAE produces reliable subnational estimates of socioeconomic outcomes available only from sample surveys by combining them with information from auxiliary sources (census). A model is used to explain common trades across areas and a random effect structure is applied to explain the observed extra heterogeneity. SAE models predicting health, nutrition and poverty outcomes excluding and including contextual environmental variables on natural hazards vulnerability, forest cover, climate, and agricultural production are compared. Results are mapped at regional and district levels to spatially assess the impacts of environmental variation on the outcomes. Inter and intra-regional inequalities are also estimated to examine the efficacy of health/socioeconomic policy targeting based on geographic location. Preliminary results suggest that localised environmental factors have considerable impacts on the indicators estimated and should

  15. Being Small for Gestational Age: Does it Matter for the Neurodevelopment of Premature Infants? A Cohort Study.

    Directory of Open Access Journals (Sweden)

    Myriam Bickle Graz

    Full Text Available Whether being small for gestational age (SGA increases the risk of adverse neurodevelopmental outcome in premature infants remains controversial.to study the impact of SGA (birthweight < percentile 10 on cognition, behavior, neurodevelopmental impairment and use of therapy at 5 years old.This population-based prospective cohort included infants born before 32 weeks of gestation. Cognition was evaluated with the K-ABC, and behavior with the Strengths and Difficulties Questionnaire (SDQ. Primary outcomes were cognitive and behavioral scores, as well as neurodevelopmental impairment (cognitive score < 2SD, hearing loss, blindness, or cerebral palsy. The need of therapy, an indirect indicator of neurodevelopmental impairment, was a secondary outcome. Linear and logistic regression models were used to analyze the association of SGA with neurodevelopment.342/515 (76% premature infants were assessed. SGA was significantly associated with hyperactivity scores of the SDQ (coefficient 0.81, p < 0.04, but not with cognitive scores, neurodevelopmental impairment or the need of therapy. Gestational age, socio-economic status, and major brain lesions were associated with cognitive outcome in the univariate and multivariate model, whereas asphyxia, sepsis and bronchopulmonary dysplasia were associated in the univariate model only. Severe impairment was associated with fetal tobacco exposition, asphyxia, gestational age and major brain lesions. Different neonatal factors were associated with the use of single or multiple therapies: children with one therapy were more likely to have suffered birth asphyxia or necrotizing enterocolitis, whereas the need for several therapies was predicted by major brain lesions.In this large cohort of premature infants, assessed at 5 years old with a complete panel of tests, SGA was associated with hyperactive behavior, but not with cognition, neurodevelopmental impairment or use of therapy. Birthweight <10th percentile alone

  16. Chemical composition and speciation of particulate organic matter from modern residential small-scale wood combustion appliances.

    Science.gov (United States)

    Czech, Hendryk; Miersch, Toni; Orasche, Jürgen; Abbaszade, Gülcin; Sippula, Olli; Tissari, Jarkko; Michalke, Bernhard; Schnelle-Kreis, Jürgen; Streibel, Thorsten; Jokiniemi, Jorma; Zimmermann, Ralf

    2018-01-15

    Combustion technologies of small-scale wood combustion appliances are continuously developed decrease emissions of various pollutants and increase energy conversion. One strategy to reduce emissions is the implementation of air staging technology in secondary air supply, which became an established technique for modern wood combustion appliances. On that account, emissions from a modern masonry heater fuelled with three types of common logwood (beech, birch and spruce) and a modern pellet boiler fuelled with commercial softwood pellets were investigated, which refer to representative combustion appliances in northern Europe In particular, emphasis was put on the organic constituents of PM2.5, including polycyclic aromatic hydrocarbons (PAHs), oxygenated PAHs (OPAHs) and phenolic species, by targeted and non-targeted mass spectrometric analysis techniques. Compared to conventional wood stoves and pellet boilers, organic emissions from the modern appliances were reduced by at least one order of magnitude, but to a different extent for single species. Hence, characteristic ratios of emission constituents and emission profiles for wood combustion identification and speciation do not hold for this type of advanced combustion technology. Additionally, an overall substantial reduction of typical wood combustion markers, such as phenolic species and anhydrous sugars, were observed. Finally, it was found that slow ignition of log woods changes the distribution of characteristic resin acids and phytosterols as well as their thermal alteration products, which are used as markers for specific wood types. Our results should be considered for wood combustion identification in positive matrix factorisation or chemical mass balance in northern Europe. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Differential cross section study of fragment production, at small angle, in relativistic heavy ion collisions. Application at a calculation of heavy ion beam transport in the matter

    International Nuclear Information System (INIS)

    Morel, P.

    1992-02-01

    Relativistic heavy ion collisions present the opportunity of creating in laboratory small volumes of hot, dense nuclear matter. On the experimental point of view, the collision events are characterized by a great number of fragments, especially in the direction of the projectile. The first part is devoted to a survey of relativistic heavy ion physics. Then, we present two experimental set-ups which permit, in particular, the analyse of light fragment production at small angles. We present experimental results concerning light projectiles on Ca, Nb, Pb targets, with energies from 200 A.MeV up to 600 A.MeV. Different aspects of the collision are put in evidence. Momentum and charge differential cross section are extrapolated to other projectile/target systems; that is used in a transport calculation of Ne ions in a target of biological interest (water), with a collimator. We show that nuclear fragmentation produces a dispersion in the spatial and energy distributions, and that one light fragments have a range greater than the projectile range. That last point causes a distortion of the Bragg curve, and that distortion must be taken into account for the application of heavy ions to radiotherapy problems. 95 figs., 8 tabs

  18. Of Fish and Micrornas

    DEFF Research Database (Denmark)

    Bela-Ong, Dennis; Schyth, Brian Dall; Lorenzen, Niels

    Fish is an important small vertebrate multidisciplinary model for investigating various aspects of reproduction, development, disease (immunology, toxicology, carcinogenesis), and aging. It is also an important model for comparative and evolutionary studies because it represents the lower...... to the mechanisms of control of gene expression, impacting a broad range of biological processes. Thus far, >25, 000 miRNA sequences have been identified in 193 species, including fish. In fish, the interest on miRNAs started with the analysis of their expression and function during embryonic development. In our...... selection markers to identify disease-resistant fish....

  19. MicroRNA Expression during Viral Infection or PolyI:C Stimulation in a Fish Model

    DEFF Research Database (Denmark)

    Kristensen, Lasse Bøgelund Juel; Schyth, Brian Dall; Lorenzen, Niels

    Fish are important as small vertebrate models for studying various aspects of development and disease. MicroRNA regulation in fish has so far received attention especially in studies of their expression and function during embryonic development. In the studies carried out at the National Veterinary...... Institute in Århus we aim at using fish models for studying microRNA regulation during viral infection. In the studies presented here we make use of a qPCR method to detect miRNAs in fish cells. We present results regarding the expression of the immunologically relevant microRNAs, miR-155, miR-146a and mi......R-146b in fish cells during infection with the fish pathogenic virus viral hemorrhagic septicemia virus (VHSV) and during immune stimulation with double stranded RNA (polyI:C). We highlight the need of finding stable normalization genes for microRNA detection....

  20. microRNA involvement in developmental and functional aspects of the nervous system and in neurological diseases

    DEFF Research Database (Denmark)

    Christensen, Mette; Schratt, Gerhard M

    2009-01-01

    microRNAs, small non-coding RNAs that regulate gene expression at the post-transcriptional level, are emerging as important regulatory molecules involved in the fine-tuning of gene expression during neuronal development and function. microRNAs have roles during neuronal stem cell commitment...... and early differentiation as well as in later stages of neuronal development, such as dendritogenesis and synaptic plasticity. A link between microRNAs and neurological diseases, such as neurodegeneration or synaptic dysfunction, is becoming increasingly clear. This review summarizes the current knowledge...... of the function of microRNAs in the developing and adult nervous system and their potential contribution to the etiology of neurological diseases....

  1. Systematic validation of predicted microRNAs for cyclin D1

    International Nuclear Information System (INIS)

    Jiang, Qiong; Feng, Ming-Guang; Mo, Yin-Yuan

    2009-01-01

    MicroRNAs are the endogenous small non-coding RNA molecules capable of silencing protein coding genes at the posttranscriptional level. Based on computer-aided predictions, a single microRNA could have over a hundred of targets. On the other hand, a single protein-coding gene could be targeted by many potential microRNAs. However, only a relatively small number of these predicted microRNA/mRNA interactions are experimentally validated, and no systematic validation has been carried out using a reporter system. In this study, we used luciferease reporter assays to validate microRNAs that can silence cyclin D1 (CCND1) because CCND1 is a well known proto-oncogene implicated in a variety of types of cancers. We chose miRanda (http://www.microRNA.org) as a primary prediction method. We then cloned 51 of 58 predicted microRNA precursors into pCDH-CMV-MCS-EF1-copGFP and tested for their effect on the luciferase reporter carrying the 3'-untranslated region (UTR) of CCND1 gene. Real-time PCR revealed the 45 of 51 cloned microRNA precursors expressed a relatively high level of the exogenous microRNAs which were used in our validation experiments. By an arbitrary cutoff of 35% reduction, we identified 7 microRNAs that were able to suppress Luc-CCND1-UTR activity. Among them, 4 of them were previously validated targets and the rest 3 microRNAs were validated to be positive in this study. Of interest, we found that miR-503 not only suppressed the luciferase activity, but also suppressed the endogenous CCND1 both at protein and mRNA levels. Furthermore, we showed that miR-503 was able to reduce S phase cell populations and caused cell growth inhibition, suggesting that miR-503 may be a putative tumor suppressor. This study provides a more comprehensive picture of microRNA/CCND1 interactions and it further demonstrates the importance of experimental target validation

  2. MicroRNA Biomarkers in Neurodegenerative Diseases and Emerging Nano-Sensors Technology

    DEFF Research Database (Denmark)

    Shah, Pratik; Cho, Seok Keun; Thulstrup, Peter Waaben

    2017-01-01

    MicroRNAs (miRNAs) are essential small RNA molecules (20–24 nt) that negatively regulate the expression of target genes at the post-transcriptional level. Due to their roles in a variety of biological processes, the aberrant expression profiles of miRNAs have been identified as biomarkers for man...

  3. Microarray profiling of microRNAs expressed in testis tissues of developing primates

    DEFF Research Database (Denmark)

    Yan, Naihong; Lu, Yilu; Sun, Huaqin

    2009-01-01

    MicroRNAs (miRNAs) are small non-coding RNA molecules that have been identified as potent regulators of gene expression. Recent studies indicate that miRNAs are involved in mammalian spermatogenesis but the mechanism of regulation is largely unknown....

  4. Computational evidence for hundreds of non-conserved plant microRNAs

    DEFF Research Database (Denmark)

    Lindow, Morten; Krogh, Anders Stærmose

    2005-01-01

    Background MicroRNAs (miRNA) are small (20-25 nt) non-coding RNA molecules that regulate gene expression through interaction with mRNA in plants and metazoans. A few hundred miRNAs are known or predicted, and most of those are evolutionarily conserved. In general plant miRNA are different from...

  5. Gene function analysis by artificial microRNAs in Physcomitrella patens.

    KAUST Repository

    Khraiwesh, Basel; Fattash, Isam; Arif, Muhammad Asif; Frank, Wolfgang

    2011-01-01

    MicroRNAs (miRNAs) are ~21 nt long small RNAs transcribed from endogenous MIR genes which form precursor RNAs with a characteristic hairpin structure. miRNAs control the expression of cognate target genes by binding to reverse complementary

  6. Clinical applications of microRNAs [v2; ref status: indexed, http://f1000r.es/1o3

    Directory of Open Access Journals (Sweden)

    Per Hydbring

    2013-08-01

    Full Text Available MicroRNAs represent a class of small RNAs derived from polymerase II controlled transcriptional regions. The primary transcript forms one or several bulging double stranded hairpins which are processed by Drosha and Dicer into hetero-duplexes. The targeting microRNA strand of the duplex is incorporated into the RNA Induced Silencing Complex from where it silences up to hundreds of mRNA transcript by inducing mRNA degradation or blocking protein translation. Apart from involvement in a variety of biological processes, microRNAs were early recognized for their potential in disease diagnostics and therapeutics. Due to their stability, microRNAs could be used as biomarkers. Currently, there are microRNA panels helping physicians determining the origins of cancer in disseminated tumors. The development of microRNA therapeutics has proved more challenging mainly due to delivery issues. However, one drug is already in clinical trials and several more await entering clinical phases. This review summarizes what has been recognized pre-clinically and clinically on diagnostic microRNAs. In addition, it highlights individual microRNA drugs in running platforms driven by four leading microRNA-therapeutic companies.

  7. Identification of microRNAs in the coral Stylophora pistillata.

    KAUST Repository

    Liew, Yi Jin

    2014-03-21

    Coral reefs are major contributors to marine biodiversity. However, they are in rapid decline due to global environmental changes such as rising sea surface temperatures, ocean acidification, and pollution. Genomic and transcriptomic analyses have broadened our understanding of coral biology, but a study of the microRNA (miRNA) repertoire of corals is missing. miRNAs constitute a class of small non-coding RNAs of ∼22 nt in size that play crucial roles in development, metabolism, and stress response in plants and animals alike. In this study, we examined the coral Stylophora pistillata for the presence of miRNAs and the corresponding core protein machinery required for their processing and function. Based on small RNA sequencing, we present evidence for 31 bona fide microRNAs, 5 of which (miR-100, miR-2022, miR-2023, miR-2030, and miR-2036) are conserved in other metazoans. Homologues of Argonaute, Piwi, Dicer, Drosha, Pasha, and HEN1 were identified in the transcriptome of S. pistillata based on strong sequence conservation with known RNAi proteins, with additional support derived from phylogenetic trees. Examination of putative miRNA gene targets indicates potential roles in development, metabolism, immunity, and biomineralisation for several of the microRNAs. Here, we present first evidence of a functional RNAi machinery and five conserved miRNAs in S. pistillata, implying that miRNAs play a role in organismal biology of scleractinian corals. Analysis of predicted miRNA target genes in S. pistillata suggests potential roles of miRNAs in symbiosis and coral calcification. Given the importance of miRNAs in regulating gene expression in other metazoans, further expression analyses of small non-coding RNAs in transcriptional studies of corals should be informative about miRNA-affected processes and pathways.

  8. MicroRNAs as Biomarkers for Liver Disease and Hepatocellular Carcinoma

    Directory of Open Access Journals (Sweden)

    C. Nelson Hayes

    2016-02-01

    Full Text Available Serum levels of liver enzymes, such as alanine transaminase, aspartate transaminase, and α-fetoprotein, provide insight into liver function and are used during treatment of liver disease, but such information is limited. In the case of hepatocellular carcinoma (HCC, which is often not detected until an advanced stage, more sensitive biomarkers may help to achieve earlier detection. Serum also contains microRNAs, a class of small non-coding RNAs that play an important role in regulating gene expression. miR-122 is specific to the liver and correlates strongly with liver enzyme levels and necroinflammatory activity, and other microRNAs are correlated with the degree of fibrosis. miR-122 has also been found to be required for hepatitis C virus (HCV infection, whereas other microRNAs have been shown to play antiviral roles. miR-125a-5p and miR-1231 have been shown to directly target hepatitis B virus (HBV transcripts, and others are up- or down-regulated in infected individuals. MicroRNA profiles also differ in the case of HBV and HCV infection as well as between HBeAg-positive and negative patients, and in patients with occult versus active HBV infection. In such patients, monitoring of changes in microRNA profiles might provide earlier warning of neoplastic changes preceding HCC.

  9. Fluorescence In Situ Hybridization for MicroRNA Detection in Archived Oral Cancer Tissues

    Directory of Open Access Journals (Sweden)

    Zonggao Shi

    2012-01-01

    Full Text Available The noncoding RNA designated as microRNA (miRNA is a large group of small single-stranded regulatory RNA and has generated wide-spread interest in human disease studies. To facilitate delineating the role of microRNAs in cancer pathology, we sought to explore the feasibility of detecting microRNA expression in formalin-fixed paraffin-embedded (FFPE tissues. Using FFPE materials, we have compared fluorescent in situ hybridization (FISH procedures to detect miR-146a with (a different synthetic probes: regular custom DNA oligonucleotides versus locked nucleic acid (LNA incorporated DNA oligonucleotides; (b different reporters for the probes: biotin versus digoxigenin (DIG; (c different visualization: traditional versus tyramide signal amplification (TSA system; (d different blocking reagents for endogenous peroxidase. Finally, we performed miR-146a FISH on a commercially available oral cancer tissue microarray, which contains 40 cases of oral squamous cell carcinoma (OSCC and 10 cases of normal epithelia from the human oral cavity. A sample FISH protocol for detecting miR-146a is provided. In summary, we have established reliable in situ hybridization procedures for detecting the expression of microRNA in FFPE oral cancer tissues. This method is an important tool for studies on the involvement of microRNA in oral cancer pathology and may have potential prognostic or diagnostic value.

  10. The Role of microRNAs in the Biology of Rare Diseases

    Directory of Open Access Journals (Sweden)

    Domenica Taruscio

    2011-10-01

    Full Text Available Rare diseases (RD are characterized by low prevalence and affect not more than five individuals per 10,000 in the European population; they are a large and heterogeneous group of disorders including more than 7,000 conditions and often involve all organs and tissues, with several clinical subtypes within the same disease. Very often information concerning either diagnosis and/or prognosis on many RD is insufficient. microRNAs are a class of small non-coding RNAs that regulate gene expression at the posttranscriptional level by either degrading or blocking translation of messenger RNA targets. Recently, microRNA expression patterns of body fluids underscored their potential as noninvasive biomarkers for various diseases. The role of microRNAs as potential biomarkers has become particularly attractive. The identification of disease-related microRNAs is essential for understanding the pathogenesis of diseases at the molecular level, and is critical for designing specific molecular tools for diagnosis, treatment and prevention. Computational analysis of microRNA-disease associations is an important complementary means for prioritizing microRNAs for further experimental examination. In this article, we explored the added value of miRs as biomarkers in a selected panel of RD hitting different tissues/systems at different life stages, but sharing the need of better biomarkers for diagnostic and prognostic purposes.

  11. Circulating MicroRNAs as Biomarkers of Gestational Diabetes Mellitus: Updates and Perspectives

    Directory of Open Access Journals (Sweden)

    Elisa Guarino

    2018-01-01

    Full Text Available Gestational diabetes mellitus (GDM is defined as any degree of carbohydrate intolerance, with onset or first recognition during second or third trimester of gestation. It is estimated that approximately 7% of all pregnancies are complicated by GDM and that its prevalence is rising all over the world. Thus, the screening for abnormal glucose levels is generally recommended as a routine component of care for pregnant women. However, additional biomarkers are needed in order to predict the onset or accurately monitor the status of gestational diabetes. Recently, microRNAs, a class of small noncoding RNAs demonstrated to modulate gene expression, have been proven to be secreted by cells of origin and can be found in many biological fluids such as serum or plasma. Such feature renders microRNAs as optimal biomarkers and sensors of in situ tissue alterations. Furthermore, secretion of microRNAs via exosomes has been reported to contribute to tissue cross talk, thus potentially represents, if disrupted, a mechanistic cause of tissue/cell dysfunction in a specific disease. In this review, we summarized the recent findings on circulating microRNAs and gestational diabetes mellitus with particular focus on the potential use of microRNAs as putative biomarkers of disease as well as a potential cause of GDM complications and β cell dysfunction.

  12. MicroRNAs in CAG trinucleotide repeat expansion disorders: an integrated review of the literature.

    Science.gov (United States)

    Dumitrescu, Laura; Popescu, Bogdan O

    2015-01-01

    MicroRNAs are small RNAs involved in gene silencing. They play important roles in transcriptional regulation and are selectively and abundantly expressed in the central nervous system. A considerable amount of the human genome is comprised of tandem repeating nucleotide streams. Several diseases are caused by above-threshold expansion of certain trinucleotide repeats occurring in a protein-coding or non-coding region. Though monogenic, CAG trinucleotide repeat expansion disorders have a complex pathogenesis, various combinations of multiple coexisting pathways resulting in one common final consequence: selective neurodegeneration. Mutant protein and mutant transcript gain of toxic function are considered to be the core pathogenic mechanisms. The profile of microRNAs in CAG trinucleotide repeat disorders is scarcely described, however microRNA dysregulation has been identified in these diseases and microRNA-related intereference with gene expression is considered to be involved in their pathogenesis. Better understanding of microRNAs functions and means of manipulation promises to offer further insights into the pathogenic pathways of CAG repeat expansion disorders, to point out new potential targets for drug intervention and to provide some of the much needed etiopathogenic therapeutic agents. A number of disease-modifying microRNA silencing strategies are under development, but several implementation impediments still have to be resolved. CAG targeting seems feasible and efficient in animal models and is an appealing approach for clinical practice. Preliminary human trials are just beginning.

  13. Use of MicroRNA biomarkers to distinguish enchondroma from low-grade chondrosarcoma.

    Science.gov (United States)

    Zhang, Liang; Yang, Maozhou; Mayer, Theodore; Johnstone, Brian; Les, Clifford; Frisch, Nicholas; Parsons, Theodore; Mi, Qing-Sheng; Gibson, Gary

    2017-03-01

    Establishing a definitive diagnosis between benign enchondroma versus low-grade chondrosarcoma presents a potential challenge to both clinicians and pathologists. microRNAs (small non-coding RNAs) have proven to be effective biomarkers for the identification of tumors and tumor progression. We present analysis, both array and quantitative PCR, that shows consistently and substantially increased expression of two microRNAs, miRs-181a and -138, in low-grade chondrosarcomas compared with enchondromas. The data suggest these microRNAs would provide an analytical distinction between the chondrosarcoma and benign neoplasms that can be performed in formalin-fixed paraffin-embedded specimens. Together with recent publications, these data indicate that miRs-181a and -138 also play a role in tumor development and homeostasis and may provide new targets for the development of much needed therapeutic intervention.

  14. Bioinformatic analysis of microRNA biogenesis and function related proteins in eleven animal genomes.

    Science.gov (United States)

    Liu, Xiuying; Luo, GuanZheng; Bai, Xiujuan; Wang, Xiu-Jie

    2009-10-01

    MicroRNAs are approximately 22 nt long small non-coding RNAs that play important regulatory roles in eukaryotes. The biogenesis and functional processes of microRNAs require the participation of many proteins, of which, the well studied ones are Dicer, Drosha, Argonaute and Exportin 5. To systematically study these four protein families, we screened 11 animal genomes to search for genes encoding above mentioned proteins, and identified some new members for each family. Domain analysis results revealed that most proteins within the same family share identical or similar domains. Alternative spliced transcript variants were found for some proteins. We also examined the expression patterns of these proteins in different human tissues and identified other proteins that could potentially interact with these proteins. These findings provided systematic information on the four key proteins involved in microRNA biogenesis and functional pathways in animals, and will shed light on further functional studies of these proteins.

  15. How the RNA isolation method can affect microRNA microarray results

    DEFF Research Database (Denmark)

    Podolska, Agnieszka; Kaczkowski, Bogumil; Litman, Thomas

    2011-01-01

    RNA microarray analysis on porcine brain tissue. One method is a phenol-guanidine isothiocyanate-based procedure that permits isolation of total RNA. The second method, miRVana™ microRNA isolation, is column based and recovers the small RNA fraction alone. We found that microarray analyses give different results...... that depend on the RNA fraction used, in particular because some microRNAs appear very sensitive to the RNA isolation method. We conclude that precautions need to be taken when comparing microarray studies based on RNA isolated with different methods.......The quality of RNA is crucial in gene expression experiments. RNA degradation interferes in the measurement of gene expression, and in this context, microRNA quantification can lead to an incorrect estimation. In the present study, two different RNA isolation methods were used to perform micro...

  16. MicroRNAs: Potential Biomarkers and Therapeutic Targets for Alveolar Bone Loss in Periodontal Disease

    Directory of Open Access Journals (Sweden)

    Tadayoshi Kagiya

    2016-08-01

    Full Text Available Periodontal disease is an inflammatory disease caused by bacterial infection of tooth-supporting structures, which results in the destruction of alveolar bone. Osteoclasts play a central role in bone destruction. Osteoclasts are tartrate-resistant acid phosphatase (TRAP-positive multinucleated giant cells derived from hematopoietic stem cells. Recently, we and other researchers revealed that microRNAs are involved in osteoclast differentiation. MicroRNAs are novel, single-stranded, non-coding, small (20–22 nucleotides RNAs that act in a sequence-specific manner to regulate gene expression at the post-transcriptional level through cleavage or translational repression of their target mRNAs. They regulate various biological activities such as cellular differentiation, apoptosis, cancer development, and inflammatory responses. In this review, the roles of microRNAs in osteoclast differentiation and function during alveolar bone destruction in periodontal disease are described.

  17. In Situ Detection of MicroRNA Expression with RNAscope Probes.

    Science.gov (United States)

    Yin, Viravuth P

    2018-01-01

    Elucidating the spatial resolution of gene transcripts provides important insight into potential gene function. MicroRNAs are short, singled-stranded noncoding RNAs that control gene expression through base-pair complementarity with target mRNAs in the 3' untranslated region (UTR) and inhibiting protein expression. However, given their small size of ~22- to 24-nt and low expression levels, standard in situ hybridization detection methods are not amendable for microRNA spatial resolution. Here, I describe a technique that employs RNAscope probe design and propriety amplification technology that provides simultaneous single molecule detection of individual microRNA and its target gene. This method allows for rapid and sensitive detection of noncoding RNA transcripts in frozen tissue sections.

  18. Control of Metastatic Progression by microRNA Regulatory Networks

    Science.gov (United States)

    Pencheva, Nora; Tavazoie, Sohail F.

    2015-01-01

    Aberrant microRNA (miRNA) expression is a defining feature of human malignancy. Specific miRNAs have been identified as promoters or suppressors of metastatic progression. These miRNAs control metastasis through divergent or convergent regulation of metastatic gene pathways. Some miRNA regulatory networks govern cell-autonomous cancer phenotypes, while others modulate the cell-extrinsic composition of the metastatic microenvironment. The use of small RNAs as probes into the molecular and cellular underpinnings of metastasis holds promise for the identification of candidate genes for potential therapeutic intervention. PMID:23728460

  19. MicroRNA and Cancer: Tiny Molecules with Major Implications

    OpenAIRE

    VandenBoom II, Timothy G; Li, Yiwei; Philip, Philip A; Sarkar, Fazlul H

    2008-01-01

    Cancer is currently a major public health problem and, as such, emerging research is making significant progress in identifying major players in its biology. One recent topic of interest involves microRNAs (miRNAs) which are small, non-coding RNA molecules that inhibit gene expression post-transcriptionally. They accomplish this by binding to the 3? untranslated region (3?UTR) of target messengerRNA (mRNA), resulting in either their degradation or inhibition of translation, depending on the d...

  20. MicroRNAs in Prostate Cancer

    Science.gov (United States)

    2008-11-01

    lymphoma. Genes Chromosom. Cancer 39:167–69 131. O’Connell RM, Taganov KD, Boldin MP, Cheng G, Baltimore D. 2007. MicroRNA-155 is induced during the...carcinoma. J. Virol. 81:1033–36 155. Xi Y, Nakajima G, Gavin E, Morris CG, Kudo K, et al. 2007. Systematic analysis of microRNA expression of RNA extracted ...diversity. miRNAs were extracted from the unique sequences by searching against miRNA database (miRbase release 10.0; http://microrna.sanger.ac.uk

  1. MicroRNAs and Periodontal Homeostasis.

    Science.gov (United States)

    Luan, X; Zhou, X; Trombetta-eSilva, J; Francis, M; Gaharwar, A K; Atsawasuwan, P; Diekwisch, T G H

    2017-05-01

    MicroRNAs (miRNAs) are a group of small RNAs that control gene expression in all aspects of eukaryotic life, primarily through RNA silencing mechanisms. The purpose of the present review is to introduce key miRNAs involved in periodontal homeostasis, summarize the mechanisms by which they affect downstream genes and tissues, and provide an introduction into the therapeutic potential of periodontal miRNAs. In general, miRNAs function synergistically to fine-tune the regulation of biological processes and to remove expression noise rather than by causing drastic changes in expression levels. In the periodontium, miRNAs play key roles in development and periodontal homeostasis and during the loss of periodontal tissue integrity as a result of periodontal disease. As part of the anabolic phase of periodontal homeostasis and periodontal development, miRNAs direct periodontal fibroblasts toward alveolar bone lineage differentiation and new bone formation through WNT, bone morphogenetic protein, and Notch signaling pathways. miRNAs contribute equally to the catabolic aspect of periodontal homeostasis as they affect osteoclastogenesis and osteoclast function, either by directly promoting osteoclast activity or by inhibiting osteoclast signaling intermediaries or through negative feedback loops. Their small size and ability to target multiple regulatory networks of related sets of genes have predisposed miRNAs to become ideal candidates for drug delivery and tissue regeneration. To address the immense therapeutic potential of miRNAs and their antagomirs, an ever growing number of delivery approaches toward clinical applications have been developed, including nanoparticle carriers and secondary structure interference inhibitor systems. However, only a fraction of the miRNAs involved in periodontal health and disease are known today. It is anticipated that continued research will lead to a more comprehensive understanding of the periodontal miRNA world, and a systematic

  2. An Optimized Table-Top Small-Angle X-ray Scattering Set-up for the Nanoscale Structural Analysis of Soft Matter

    KAUST Repository

    Sibillano, T.; De Caro, L.; Altamura, D.; Siliqi, D.; Ramella, M.; Boccafoschi, F.; Ciasca, G.; Campi, G.; Tirinato, Luca; Di Fabrizio, Enzo M.; Giannini, C.

    2014-01-01

    The paper shows how a table top superbright microfocus laboratory X-ray source and an innovative restoring-data algorithm, used in combination, allow to analyze the super molecular structure of soft matter by means of Small Angle X-ray Scattering ex-situ experiments. The proposed theoretical approach is aimed to restore diffraction features from SAXS profiles collected from low scattering biomaterials or soft tissues, and therefore to deal with extremely noisy diffraction SAXS profiles/maps. As biological test cases we inspected: i) residues of exosomes' drops from healthy epithelial colon cell line and colorectal cancer cells; ii) collagen/human elastin artificial scaffolds developed for vascular tissue engineering applications; iii) apoferritin protein in solution. Our results show how this combination can provide morphological/structural nanoscale information to characterize new artificial biomaterials and/or to get insight into the transition between healthy and pathological tissues during the progression of a disease, or to morphologically characterize nanoscale proteins, based on SAXS data collected in a room-sized laboratory.

  3. An Optimized Table-Top Small-Angle X-ray Scattering Set-up for the Nanoscale Structural Analysis of Soft Matter

    KAUST Repository

    Sibillano, T.

    2014-11-10

    The paper shows how a table top superbright microfocus laboratory X-ray source and an innovative restoring-data algorithm, used in combination, allow to analyze the super molecular structure of soft matter by means of Small Angle X-ray Scattering ex-situ experiments. The proposed theoretical approach is aimed to restore diffraction features from SAXS profiles collected from low scattering biomaterials or soft tissues, and therefore to deal with extremely noisy diffraction SAXS profiles/maps. As biological test cases we inspected: i) residues of exosomes\\' drops from healthy epithelial colon cell line and colorectal cancer cells; ii) collagen/human elastin artificial scaffolds developed for vascular tissue engineering applications; iii) apoferritin protein in solution. Our results show how this combination can provide morphological/structural nanoscale information to characterize new artificial biomaterials and/or to get insight into the transition between healthy and pathological tissues during the progression of a disease, or to morphologically characterize nanoscale proteins, based on SAXS data collected in a room-sized laboratory.

  4. An Optimized Table-Top Small-Angle X-ray Scattering Set-up for the Nanoscale Structural Analysis of Soft Matter

    Science.gov (United States)

    Sibillano, T.; de Caro, L.; Altamura, D.; Siliqi, D.; Ramella, M.; Boccafoschi, F.; Ciasca, G.; Campi, G.; Tirinato, L.; di Fabrizio, E.; Giannini, C.

    2014-11-01

    The paper shows how a table top superbright microfocus laboratory X-ray source and an innovative restoring-data algorithm, used in combination, allow to analyze the super molecular structure of soft matter by means of Small Angle X-ray Scattering ex-situ experiments. The proposed theoretical approach is aimed to restore diffraction features from SAXS profiles collected from low scattering biomaterials or soft tissues, and therefore to deal with extremely noisy diffraction SAXS profiles/maps. As biological test cases we inspected: i) residues of exosomes' drops from healthy epithelial colon cell line and colorectal cancer cells; ii) collagen/human elastin artificial scaffolds developed for vascular tissue engineering applications; iii) apoferritin protein in solution. Our results show how this combination can provide morphological/structural nanoscale information to characterize new artificial biomaterials and/or to get insight into the transition between healthy and pathological tissues during the progression of a disease, or to morphologically characterize nanoscale proteins, based on SAXS data collected in a room-sized laboratory.

  5. Diffuse X-ray emission from the NGC 2300 group of galaxies - Implications for dark matter and galaxy evolution in small groups

    Science.gov (United States)

    Mulchaey, John S.; Davis, David S.; Mushotzky, Richard F.; Burstein, David

    1993-01-01

    The discovery of diffuse X-ray emission from the NGC 2300 group of galaxies using the ROSAT Position Sensitive Proportional Counter is reported. The gas distributions is roughly symmetric and extends to a radius of at least 0.2/h(50) Mpc. A Raymond-Smith hot plasma model provides an excellent fit the X-ray spectrum with a best-fit value temperature of 0.9 + -/15 or - 0.14 keV and abundance 0.06 + 0/.12 or - 0.05 solar. The assumption of gravitational confinement leads to a total mass of the group of 3.0 + 0.4 or - 0.5 x 10 exp 13 solar. Baryons can reasonably account for 4 percent of this mass, and errors could push this number not higher than 10-15 percent. This is one of the strongest pieces of evidence that dark matter dominates small groups such as this one. The intragroup medium in this system has the lowest metal abundance yet found in diffuse gas in a group or cluster.

  6. MicroRNAs regulate osteogenesis and chondrogenesis

    International Nuclear Information System (INIS)

    Dong, Shiwu; Yang, Bo; Guo, Hongfeng; Kang, Fei

    2012-01-01

    Highlights: ► To focus on the role of miRNAs in chondrogenesis and osteogenesis. ► Involved in the regulation of miRNAs in osteoarthritis. ► To speculate some therapeutic targets for bone diseases. -- Abstract: MicroRNAs (miRNAs) are a class of small molecules and non-coding single strand RNAs that regulate gene expression at the post-transcriptional level by binding to specific sequences within target genes. miRNAs have been recognized as important regulatory factors in organism development and disease expression. Some miRNAs regulate the proliferation and differentiation of osteoblasts, osteoclasts and chondrocytes, eventually influencing metabolism and bone formation. miRNAs are expected to provide potential gene therapy targets for the clinical treatment of metabolic bone diseases and bone injuries. Here, we review the recent research progress on the regulation of miRNAs in bone biology, with a particular focus on the miRNA-mediated control mechanisms of bone and cartilage formation.

  7. MicroRNAs horizon in retinoblastoma.

    Directory of Open Access Journals (Sweden)

    Mojgan Mirakholi

    2013-12-01

    Full Text Available In the retinoblastoma research, it is of great interest to identify molecular markers associated with the genetics of tumorigenesis. microRNAs (miRNAs are small non-coding RNA molecules that play a regulatory role in many crucial cellular pathways such as differentiation, cell cycle progression, and apoptosis. A body of evidences showed dysregulation of miRNAs in tumor biology and many diseases. They potentially play a significant role in tumorigenesis processes and have been the subject of research in many types of cancers including retinal tumorigenesis. miRNA expression profiling was found to be associated with tumor development, progression and treatment. These associations demonstrate the putative applications of miRNAs in monitoring of different aspect of tumors consisting diagnostic, prognostic and therapeutic. Herein, we review the current literature concerning to the study of miRNA target recognition, function to tumorigenesis and treatment in retinoblastoma. Identification the specific miRNA biomarkers associated with retinoblastoma cancer may help to establish new therapeutic approaches for salvage affected eyes in patients.

  8. Genomic Organization of Zebrafish microRNAs

    Directory of Open Access Journals (Sweden)

    Paydar Ima

    2008-05-01

    Full Text Available Abstract Background microRNAs (miRNAs are small (~22 nt non-coding RNAs that regulate cell movement, specification, and development. Expression of miRNAs is highly regulated, both spatially and temporally. Based on direct cloning, sequence conservation, and predicted secondary structures, a large number of miRNAs have been identified in higher eukaryotic genomes but whether these RNAs are simply a subset of a much larger number of noncoding RNA families is unknown. This is especially true in zebrafish where genome sequencing and annotation is not yet complete. Results We analyzed the zebrafish genome to identify the number and location of proven and predicted miRNAs resulting in the identification of 35 new miRNAs. We then grouped all 415 zebrafish miRNAs into families based on seed sequence identity as a means to identify possible functional redundancy. Based on genomic location and expression analysis, we also identified those miRNAs that are likely to be encoded as part of polycistronic transcripts. Lastly, as a resource, we compiled existing zebrafish miRNA expression data and, where possible, listed all experimentally proven mRNA targets. Conclusion Current analysis indicates the zebrafish genome encodes 415 miRNAs which can be grouped into 44 families. The largest of these families (the miR-430 family contains 72 members largely clustered in two main locations along chromosome 4. Thus far, most zebrafish miRNAs exhibit tissue specific patterns of expression.

  9. MicroRNAs regulate osteogenesis and chondrogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Dong, Shiwu, E-mail: shiwudong@gmail.com [Laboratory of Biomechanics, Department of Anatomy, The Third Military Medical University, Chongqing (China); Yang, Bo; Guo, Hongfeng; Kang, Fei [Laboratory of Biomechanics, Department of Anatomy, The Third Military Medical University, Chongqing (China)

    2012-02-24

    Highlights: Black-Right-Pointing-Pointer To focus on the role of miRNAs in chondrogenesis and osteogenesis. Black-Right-Pointing-Pointer Involved in the regulation of miRNAs in osteoarthritis. Black-Right-Pointing-Pointer To speculate some therapeutic targets for bone diseases. -- Abstract: MicroRNAs (miRNAs) are a class of small molecules and non-coding single strand RNAs that regulate gene expression at the post-transcriptional level by binding to specific sequences within target genes. miRNAs have been recognized as important regulatory factors in organism development and disease expression. Some miRNAs regulate the proliferation and differentiation of osteoblasts, osteoclasts and chondrocytes, eventually influencing metabolism and bone formation. miRNAs are expected to provide potential gene therapy targets for the clinical treatment of metabolic bone diseases and bone injuries. Here, we review the recent research progress on the regulation of miRNAs in bone biology, with a particular focus on the miRNA-mediated control mechanisms of bone and cartilage formation.

  10. Micronutrients: do small things matter?

    African Journals Online (AJOL)

    prevention of clinical deficiency syndromes, the fast developing field of immunonutrition has added yet another dimension to the importance of foods, nutrition and micronutrients in disease ... micronutrient requirements in the critically ill, a growing body of .... effects thereof.2 Intracellular glutathione and nonenzymatic ROS.

  11. MicroRNAs in Cardiometabolic Diseases

    Directory of Open Access Journals (Sweden)

    Anna Meiliana

    2013-08-01

    Full Text Available BACKGROUND: MicroRNAs (miRNAs are ~22-nucleotide noncoding RNAs with critical functions in multiple physiological and pathological processes. An explosion of reports on the discovery and characterization of different miRNA species and their involvement in almost every aspect of cardiac biology and diseases has established an exciting new dimension in gene regulation networks for cardiac development and pathogenesis. CONTENT: Alterations in the metabolic control of lipid and glucose homeostasis predispose an individual to develop cardiometabolic diseases, such as type 2 diabetes mellitus and atherosclerosis. Work over the last years has suggested that miRNAs play an important role in regulating these physiological processes. Besides a cell-specific transcription factor profile, cell-specific miRNA-regulated gene expression is integral to cell fate and activation decisions. Thus, the cell types involved in atherosclerosis, vascular disease, and its myocardial sequelae may be differentially regulated by distinct miRNAs, thereby controlling highly complex processes, for example, smooth muscle cell phenotype and inflammatory responses of endothelial cells or macrophages. The recent advancements in using miRNAs as circulating biomarkers or therapeutic modalities, will hopefully be able to provide a strong basis for future research to further expand our insights into miRNA function in cardiovascular biology. SUMMARY: MiRNAs are small, noncoding RNAs that function as post-transcriptional regulators of gene expression. They are potent modulators of diverse biological processes and pathologies. Recent findings demonstrated the importance of miRNAs in the vasculature and the orchestration of lipid metabolism and glucose homeostasis. MiRNA networks represent an additional layer of regulation for gene expression that absorbs perturbations and ensures the robustness of biological systems. A detailed understanding of the molecular and cellular mechanisms of mi

  12. Functions of MicroRNAs in Cardiovascular Biology and Disease

    Science.gov (United States)

    Hata, Akiko

    2015-01-01

    In 1993, lin-4 was discovered as a critical modulator of temporal development in Caenorhabditis elegans and, most notably, as the first in the class of small, single-stranded noncoding RNAs now defined as microRNAs (miRNAs). Another eight years elapsed before miRNA expression was detected in mammalian cells. Since then, explosive advancements in the field of miRNA biology have elucidated the basic mechanism of miRNA biogenesis, regulation, and gene-regulatory function. The discovery of this new class of small RNAs has augmented the complexity of gene-regulatory programs as well as the understanding of developmental and pathological processes in the cardiovascular system. Indeed, the contributions of miRNAs in cardiovascular development and function have been widely explored, revealing the extensive role of these small regulatory RNAs in cardiovascular physiology. PMID:23157557

  13. MicroRNAs in right ventricular remodelling.

    Science.gov (United States)

    Batkai, Sandor; Bär, Christian; Thum, Thomas

    2017-10-01

    Right ventricular (RV) remodelling is a lesser understood process of the chronic, progressive transformation of the RV structure leading to reduced functional capacity and subsequent failure. Besides conditions concerning whole hearts, some pathology selectively affects the RV, leading to a distinct RV-specific clinical phenotype. MicroRNAs have been identified as key regulators of biological processes that drive the progression of chronic diseases. The role of microRNAs in diseases affecting the left ventricle has been studied for many years, however there is still limited information on microRNAs specific to diseases in the right ventricle. Here, we review recently described details on the expression, regulation, and function of microRNAs in the pathological remodelling of the right heart. Recently identified strategies using microRNAs as pharmacological targets or biomarkers will be highlighted. Increasing knowledge of pathogenic microRNAs will finally help improve our understanding of underlying distinct mechanisms and help utilize novel targets or biomarkers to develop treatments for patients suffering from right heart diseases. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2017. For permissions, please email: journals.permissions@oup.com.

  14. Specific and Novel microRNAs Are Regulated as Response to Fungal Infection in Human Dendritic Cells

    Science.gov (United States)

    Dix, Andreas; Czakai, Kristin; Leonhardt, Ines; Schäferhoff, Karin; Bonin, Michael; Guthke, Reinhard; Einsele, Hermann; Kurzai, Oliver; Löffler, Jürgen; Linde, Jörg

    2017-01-01

    Within the last two decades, the incidence of invasive fungal infections has been significantly increased. They are characterized by high mortality rates and are often caused by Candida albicans and Aspergillus fumigatus. The increasing number of infections underlines the necessity for additional anti-fungal therapies, which require extended knowledge of gene regulations during fungal infection. MicroRNAs are regulators of important cellular processes, including the immune response. By analyzing their regulation and impact on target genes, novel therapeutic and diagnostic approaches may be developed. Here, we examine the role of microRNAs in human dendritic cells during fungal infection. Dendritic cells represent the bridge between the innate and the adaptive immune systems. Therefore, analysis of gene regulation of dendritic cells is of particular significance. By applying next-generation sequencing of small RNAs, we quantify microRNA expression in monocyte-derived dendritic cells after 6 and 12 h of infection with C. albicans and A. fumigatus as well as treatment with lipopolysaccharides (LPS). We identified 26 microRNAs that are differentially regulated after infection by the fungi or LPS. Three and five of them are specific for fungal infections after 6 and 12 h, respectively. We further validated interactions of miR-132-5p and miR-212-5p with immunological relevant target genes, such as FKBP1B, KLF4, and SPN, on both RNA and protein level. Our results indicate that these microRNAs fine-tune the expression of immune-related target genes during fungal infection. Beyond that, we identified previously undiscovered microRNAs. We validated three novel microRNAs via qRT-PCR. A comparison with known microRNAs revealed possible relations with the miR-378 family and miR-1260a/b for two of them, while the third one features a unique sequence with no resemblance to known microRNAs. In summary, this study analyzes the effect of known microRNAs in dendritic cells during

  15. MicroRNAs and Presbycusis.

    Science.gov (United States)

    Hu, Weiming; Wu, Junwu; Jiang, Wenjing; Tang, Jianguo

    2018-02-01

    Presbycusis (age-related hearing loss) is the most universal sensory degenerative disease in elderly people caused by the degeneration of cochlear cells. Non-coding microRNAs (miRNAs) play a fundamental role in gene regulation in almost every multicellular organism, and control the aging processes. It has been identified that various miRNAs are up- or down-regulated during mammalian aging processes in tissue-specific manners. Most miRNAs bind to specific sites on their target messenger-RNAs (mRNAs) and decrease their expression. Germline mutation may lead to dysregulation of potential miRNAs expression, causing progressive hair cell degeneration and age-related hearing loss. Therapeutic innovations could emerge from a better understanding of diverse function of miRNAs in presbycusis. This review summarizes the relationship between miRNAs and presbycusis, and presents novel miRNAs-targeted strategies against presbycusis.

  16. Dark matter detectors

    International Nuclear Information System (INIS)

    Forster, G.

    1995-01-01

    A fundamental question of astrophysics and cosmology is the nature of dark matter. Astrophysical observations show clearly the existence of some kind of dark matter, though they cannot yet reveal its nature. Dark matter can consist of baryonic particles, or of other (known or unknown) elementary particles. Baryonic dark matter probably exists in the form of dust, gas, or small stars. Other elementary particles constituting the dark matter can possibly be measured in terrestrial experiments. Possibilities for dark matter particles are neutrinos, axions and weakly interacting massive particles (WIMPs). While a direct detection of relic neutrinos seems at the moment impossible, there are experiments looking for baryonic dark matter in the form of Massive Compact Halo Objects, and for particle dark matter in the form of axions and WIMPS. (orig.)

  17. MicroRNAs as regulatory elements in psoriasis

    Directory of Open Access Journals (Sweden)

    Liu Yuan

    2016-01-01

    Full Text Available Psoriasis is a chronic, autoimmune, and complex genetic disorder that affects 23% of the European population. The symptoms of Psoriatic skin are inflammation, raised and scaly lesions. microRNA, which is short, nonprotein-coding, regulatory RNAs, plays critical roles in psoriasis. microRNA participates in nearly all biological processes, such as cell differentiation, development and metabolism. Recent researches reveal that multitudinous novel microRNAs have been identified in skin. Some of these substantial novel microRNAs play as a class of posttranscriptional gene regulator in skin disease, such as psoriasis. In order to insight into microRNAs biological functions and verify microRNAs biomarker, we review diverse references about characterization, profiling and subtype of microRNAs. Here we will share our opinions about how and which microRNAs are as regulatory in psoriasis.

  18. Isotope geochemistry and fluxes of carbon and organic matter in tropical small mountainous river systems and adjacent coastal waters of the Caribbean

    Science.gov (United States)

    Moyer, Ryan; Bauer, James; Grottoli, Andrea

    2012-01-01

    Recent studies have shown that small mountainous rivers (SMRs) may act as sources of aged and/or refractory carbon (C) to the coastal ocean, which may increase organic C burial at sea and subsidize coastal food webs and heterotrophy. However, the characteristics and spatial and temporal variability of C and organic matter (OM) exported from tropical SMR systems remain poorly constrained. To address this, the abundance and isotopic character (δ13C and Δ14C) of the three major C pools were measured in two Puerto Rico SMRs with catchments dominated by different land uses (agricultural vs. non-agricultural recovering forest). The abundance and character of C pools in associated estuaries and adjacent coastal waters were also examined. Riverine dissolved and particulate organic C (DOC and POC, respectively) concentrations were highly variable with respect to land use and sampling month, while dissolved inorganic C (DIC) was significantly higher at all times in the agricultural catchment. In both systems, riverine DOC and POC ranged from modern to highly aged (2,340 years before present), while DIC was always modern. The agricultural river and irrigation canals contained very old DOC (1,184 and 2,340 years before present, respectively), which is consistent with findings in temperate SMRs and indicates that these tropical SMRs provide a source of aged DOC to the ocean. During months of high river discharge, OM in estuarine and coastal waters had C isotope signatures reflective of direct terrestrial input, indicating that relatively unaltered OM is transported to the coastal ocean at these times. This is also consistent with findings in temperate SMRs and indicates that C transported to the coastal ocean by SMRs may differ from that of larger rivers because it is exported from smaller catchments that have steeper terrains and fewer land-use types.

  19. Detecting new microRNAs in human osteoarthritic chondrocytes identifies miR-3085 as a human, chondrocyte-selective, microRNA

    OpenAIRE

    Crowe, N.; Swingler, T.E.; Le, L.T.T.; Barter, M.J.; Wheeler, G.; Pais, H.; Donell, S.T.; Young, D.A.; Dalmay, T.; Clark, I.M.

    2016-01-01

    Summary Objective To use deep sequencing to identify novel microRNAs (miRNAs) in human osteoarthritic cartilage which have a functional role in chondrocyte phenotype or function. Design A small RNA library was prepared from human osteoarthritic primary chondrocytes using in-house adaptors and analysed by Illumina sequencing. Novel candidate miRNAs were validated by northern blot and qRT-PCR. Expression was measured in cartilage models. Targets of novel candidates were identified by microarray...

  20. Thematic mapper research in the earth sciences: Small scale patches of suspended matter and phytoplankton in the Elbe River Estuary, German Bight and Tidal Flats

    Science.gov (United States)

    Grassl, H.; Doerffer, R.; Fischer, J.; Brockmann, C.; Stoessel, M.

    1987-01-01

    A Thematic Mapper (TM) field experiment was followed by a data analysis to determine TM capabilities for analysis of suspended matter and phytoplankton. Factor analysis showed that suspended matter concentration, atmospheric scattering, and sea surface temperature can be retrieved as independent factors which determine the variation in the TM data over water areas. Spectral channels in the near infrared open the possibility of determining the Angstrom exponent better than for the coastal zone color scanner. The suspended matter distribution may then be calculated by the absolute radiance of channel 2 or 3 or the ratio of both. There is no indication of whether separation of chlorophyll is possible. The distribution of suspended matter and sea surface temperature can be observed with the expected fine structure. A good correlation between water depth and suspended matter distribution as found from ship data can now be analyzed for an entire area by the synoptic view of the TM scenes.

  1. Differential MicroRNA Expression in Human Macrophages with Mycobacterium tuberculosis Infection of Beijing/W and Non-Beijing/W Strain Types.

    Directory of Open Access Journals (Sweden)

    Lin Zheng

    Full Text Available The role of microRNAs in association with Mycobacterium tuberculosis (MTB infection and the immunology regulated by microRNAs upon MTB infection have not been fully unravelled. We examined the microRNA profiles of THP-1 macrophages upon the MTB infection of Beijing/W and non-Beijing/W clinical strains. We also studied the microRNA profiles of the host macrophages by microarray in a small cohort with active MTB disease, latent infection (LTBI, and from healthy controls.The results revealed that 14 microRNAs differentiated infections of Beijing/W from non-Beijing/W strains (P<0.05. A unique signature of 11 microRNAs in human macrophages was identified to differentiate active MTB disease from LTBI and healthy controls. Pathway analyses of these differentially expressed miRNAs suggest that the immune-regulatory interactions involving TGF-β signalling pathway take part in the dysregulation of critical TB processes in the macrophages, resulting in active expression of both cell communication and signalling transduction systems.We showed for the first time that the Beijing/W TB strains repressed a number of miRNAs expressions which may reflect their virulence characteristics in altering the host response. The unique signatures of 11 microRNAs may deserve further evaluation as candidates for biomarkers in the diagnosis of MTB and Beijing/W infections.

  2. MicroRNAs: role and therapeutic targets in viral hepatitis

    NARCIS (Netherlands)

    van der Ree, Meike H.; de Bruijne, Joep; Kootstra, Neeltje A.; Jansen, Peter Lm; Reesink, Hendrik W.

    2014-01-01

    MicroRNAs regulate gene expression by binding to the 3'-untranslated region (UTR) of target messenger RNAs (mRNAs). The importance of microRNAs has been shown for several liver diseases, for example, viral hepatitis. MicroRNA-122 is highly abundant in the liver and is involved in the regulation of

  3. miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments.

    Science.gov (United States)

    Hackenberg, Michael; Sturm, Martin; Langenberger, David; Falcón-Pérez, Juan Manuel; Aransay, Ana M

    2009-07-01

    Next-generation sequencing allows now the sequencing of small RNA molecules and the estimation of their expression levels. Consequently, there will be a high demand of bioinformatics tools to cope with the several gigabytes of sequence data generated in each single deep-sequencing experiment. Given this scene, we developed miRanalyzer, a web server tool for the analysis of deep-sequencing experiments for small RNAs. The web server tool requires a simple input file containing a list of unique reads and its copy numbers (expression levels). Using these data, miRanalyzer (i) detects all known microRNA sequences annotated in miRBase, (ii) finds all perfect matches against other libraries of transcribed sequences and (iii) predicts new microRNAs. The prediction of new microRNAs is an especially important point as there are many species with very few known microRNAs. Therefore, we implemented a highly accurate machine learning algorithm for the prediction of new microRNAs that reaches AUC values of 97.9% and recall values of up to 75% on unseen data. The web tool summarizes all the described steps in a single output page, which provides a comprehensive overview of the analysis, adding links to more detailed output pages for each analysis module. miRanalyzer is available at http://web.bioinformatics.cicbiogune.es/microRNA/.

  4. Application of serum microRNA-9-5p, 21-5p, and 223-3p combined with tumor markers in the diagnosis of non-small-cell lung cancer in Yunnan in southwestern China.

    Science.gov (United States)

    Yang, Yanlong; Chen, Kai; Zhou, Yongchun; Hu, Zaoxiu; Chen, Shuai; Huang, Yunchao

    2018-01-01

    Xuanwei City is located in late Permian coal-accumulating areas of the northeastern region of Yunnan Province. In China, morbidity and mortality from lung cancer are highest in Yunnan. Identifying useful circulating markers suitable for the diagnosis of lung cancer in this region is quite meaningful. In this study, we evaluated diagnostic roles of serum miR-9-5p, 21-5p, 223-3p, 135b-5p, 339-5p, and 501-5p in patients with non-small-cell lung cancer (NSCLC) in Yunnan. Moreover, we evaluated the diagnostic performance of several tumor markers, including carcinoembryonic antigen (CEA), cytokeratin 19 fragment 21-1 (CYFRA21-1), and squamous cell carcinoma-related antigen (SCC). Quantitative real-time polymerase chain reaction detected six miRNAs in the serum of 104 NSCLC patients and 50 cancer-free controls. Other markers, including CEA, CYFRA21-1, and SCC, in serum were also measured. The diagnostic ability of miRNAs and tumor markers was evaluated by receiver operating characteristic (ROC) curve analysis. The diagnostic performance of these serum markers was also evaluated in Xuanwei and non-Xuanwei subjects, because the etiological and the epidemiological characteristics of lung cancer in Xuanwei were quite different from those in other regions. Serum miR-9-5p, miR-21-5p, miR-223-3p, CEA, CYFRA21-1, and SCC were upregulated in NSCLC patients, compared with cancer-free controls. No significant difference was found in miR-135b-5p, miR-339-5p, and miR-501-5p expression. The area under ROC curves (AUCs) of miR-9-5p, miR-21-5p, miR-223-3p, CEA, CYFRA21-1, and SCC were 0.706, 0.765, 0.744, 0.749, 0.735, and 0.616, respectively. When combined, miRNAs and tumor markers yielded the highest diagnostic power, with AUC of 0.886, sensitivity of 82.69%, and specificity of 88.00%. In Xuanwei subjects, miR-223-3p and CEA may be suitable biomarkers to distinguish NSCLC from cancer-free states with AUCs of 0.752 and 0.791, respectively. The diagnostic power of the combination of mi

  5. Asymptotically Safe Dark Matter

    DEFF Research Database (Denmark)

    Sannino, Francesco; Shoemaker, Ian M.

    2015-01-01

    We introduce a new paradigm for dark matter (DM) interactions in which the interaction strength is asymptotically safe. In models of this type, the coupling strength is small at low energies but increases at higher energies, and asymptotically approaches a finite constant value. The resulting...... searches are the primary ways to constrain or discover asymptotically safe dark matter....

  6. MicroRNAs Change the Landscape of Cancer Resistance.

    Science.gov (United States)

    Zhu, Jun; Zhu, Wei; Wu, Wei

    2018-01-01

    One of the major challenges in the cancer treatment is the development of drug resistance. It represents a major obstacle to curing cancer with constrained efficacy of both conventional chemotherapy and targeted therapies, even recent immune checkpoint blockade therapy. Deciphering the mechanisms of resistance is critical to further understanding the multifactorial pathways involved, and developing more specific targeted treatments. To date, numerous studies have reported the potential role of microRNAs (miRNAs) in the resistance to various cancer treatments. MicroRNAs are a family of small noncoding RNAs that regulate gene expression by sequence-specific targeting of mRNAs causing translational repression or mRNA degradation. More than 1200 validated human miRNAs have been identified in human genome. While one miRNA can regulate hundreds of targets, a single target can also be affected by multiple miRNAs. Evidence suggests that dysregulation of specific miRNAs may be involved in the acquisition of resistance, thereby modulating the sensitivity of cancer cells to treatment. Therefore, manipulation of miRNAs may be an attractive strategy for more effective individualized therapies through reprograming resistant network in cancer cells.

  7. Identification and bioinformatics analysis of microRNAs from the sporophyte and gametophyte of Pyropia haitanensis

    Science.gov (United States)

    Huang, Aiyou; Wang, Guangce

    2016-05-01

    Pyropia haitanensis (T. J. Chang et B. F. Zheng) N. Kikuchi et M. Miyata ( Porphyra haitanensis) is an economically important genus that is cultured widely in China. P. haitanensis is cultured on a larger scale than Pyropia yezoensis, making up an important part of the total production of cultivated Pyropia in China. However, the majority of molecular mechanisms underlying the physiological processes of P. haitanensis remain unknown. P. haitanensis could utilize inorganic carbon and the sporophytes of P. haitanensis might possess a PCK-type C4-like carbon-fixation pathway. To identify microRNAs and their probable roles in sporophyte and gametophyte development, we constructed and sequenced small RNA libraries from sporophytes and gametophytes of P. haitanensis. Five microRNAs were identified that shared no sequence homology with known microRNAs. Our results indicated that P. haitanensis might posses a complex sRNA processing system in which the novel microRNAs act as important regulators of the development of different generations of P. haitanensis.

  8. Identification of novel and conserved microRNAs in Coffea canephora and Coffea arabica

    Directory of Open Access Journals (Sweden)

    Guilherme Loss-Morais

    2014-12-01

    Full Text Available As microRNAs (miRNAs are important regulators of many biological processes, a series of small RNAomes from plants have been produced in the last decade. However, miRNA data from several groups of plants are still lacking, including some economically important crops. Here microRNAs from Coffea canephora leaves were profiled and 58 unique sequences belonging to 33 families were found, including two novel microRNAs that have never been described before in plants. Some of the microRNA sequences were also identified in Coffea arabica that, together with C. canephora, correspond to the two major sources of coffee production in the world. The targets of almost all miRNAs were also predicted on coffee expressed sequences. This is the first report of novel miRNAs in the genus Coffea, and also the first in the plant order Gentianales. The data obtained establishes the basis for the understanding of the complex miRNA-target network on those two important crops.

  9. Blood cell mRNAs and microRNAs: optimized protocols for extraction and preservation.

    Science.gov (United States)

    Eikmans, Michael; Rekers, Niels V; Anholts, Jacqueline D H; Heidt, Sebastiaan; Claas, Frans H J

    2013-03-14

    Assessing messenger RNA (mRNA) and microRNA levels in peripheral blood cells may complement conventional parameters in clinical practice. Working with small, precious samples requires optimal RNA yields and minimal RNA degradation. Several procedures for RNA extraction and complementary DNA (cDNA) synthesis were compared for their efficiency. The effect on RNA quality of freeze-thawing peripheral blood cells and storage in preserving reagents was investigated. In terms of RNA yield and convenience, quality quantitative polymerase chain reaction signals per nanogram of total RNA and using NucleoSpin and mirVana columns is preferable. The SuperScript III protocol results in the highest cDNA yields. During conventional procedures of storing peripheral blood cells at -180°C and thawing them thereafter, RNA integrity is maintained. TRIzol preserves RNA in cells stored at -20°C. Detection of mRNA levels significantly decreases in degraded RNA samples, whereas microRNA molecules remain relatively stable. When standardized to reference targets, mRNA transcripts and microRNAs can be reliably quantified in moderately degraded (quality index 4-7) and severely degraded (quality index <4) RNA samples, respectively. We describe a strategy for obtaining high-quality and quantity RNA from fresh and stored cells from blood. The results serve as a guideline for sensitive mRNA and microRNA expression assessment in clinical material.

  10. MicroRNAs, epigenetics and disease

    DEFF Research Database (Denmark)

    Silahtaroglu, Asli; Stenvang, Jan

    2010-01-01

    Epigenetics is defined as the heritable chances that affect gene expression without changing the DNA sequence. Epigenetic regulation of gene expression can be through different mechanisms such as DNA methylation, histone modifications and nucleosome positioning. MicroRNAs are short RNA molecules...... which do not code for a protein but have a role in post-transcriptional silencing of multiple target genes by binding to their 3' UTRs (untranslated regions). Both epigenetic mechanisms, such as DNA methylation and histone modifications, and the microRNAs are crucial for normal differentiation...... diseases. In the present chapter we will mainly focus on microRNAs and methylation and their implications in human disease, mainly in cancer....

  11. Quantifying Matter

    CERN Document Server

    Angelo, Joseph A

    2011-01-01

    Quantifying Matter explains how scientists learned to measure matter and quantify some of its most fascinating and useful properties. It presents many of the most important intellectual achievements and technical developments that led to the scientific interpretation of substance. Complete with full-color photographs, this exciting new volume describes the basic characteristics and properties of matter. Chapters include:. -Exploring the Nature of Matter. -The Origin of Matter. -The Search for Substance. -Quantifying Matter During the Scientific Revolution. -Understanding Matter's Electromagnet

  12. microRNAs in mycobacterial disease: friend or foe?

    Directory of Open Access Journals (Sweden)

    Manali D Mehta

    2014-07-01

    Full Text Available As the role of microRNA in all aspects of biology continues to be unraveled, the interplay between microRNAs and human disease is becoming clearer. It should come of no surprise that microRNAs play a major part in the outcome of infectious diseases, since early work has implicated microRNAs as regulators of the immune response. Here, we provide a review on how microRNAs influence the course of mycobacterial infections, which cause two of humanity’s most ancient infectious diseases: tuberculosis and leprosy. Evidence derived from profiling and functional experiments suggests that regulation of specific microRNAs during infection can either enhance the immune response or facilitate pathogen immune evasion. Now, it remains to be seen if the manipulation of host cell microRNA profiles can be an opportunity for therapeutic intervention for these difficult-to-treat diseases.

  13. An improved method to quantitate mature plant microRNA in biological matrices using periodate treatment and internal control

    Science.gov (United States)

    MicroRNAs (miRNAs) ubiquitously exist in microorganisms, plants and animals, and appear to modulate a wide range of critical biological processes. However, no definitive conclusion has been reached regarding the uptake of exogenous dietary small RNAs into mammalian circulation and organs and cross-k...

  14. Genome-wide identification of microRNAs in pomegranate (Punica granatum L.) by high-throughput sequencing

    Science.gov (United States)

    Background: MicroRNAs (miRNAs), a class of small non-coding endogenous RNAs that regulate gene expression post-transcriptionally, play multiple key roles in plant growth and development and in biotic and abiotic stress response. Knowledge and roles of miRNAs in pomegranate fruit development have not...

  15. Two-dimensional combinatorial screening enables the bottom-up design of a microRNA-10b inhibitor.

    Science.gov (United States)

    Velagapudi, Sai Pradeep; Disney, Matthew D

    2014-03-21

    The RNA motifs that bind guanidinylated kanamycin A (G Kan A) and guanidinylated neomycin B (G Neo B) were identified via two-dimensional combinatorial screening (2DCS). The results of these studies enabled the "bottom-up" design of a small molecule inhibitor of oncogenic microRNA-10b.

  16. Impeded Dark Matter

    Energy Technology Data Exchange (ETDEWEB)

    Kopp, Joachim; Liu, Jia [PRISMA Cluster of Excellence & Mainz Institute for Theoretical Physics,Johannes Gutenberg University,Staudingerweg 7, 55099 Mainz (Germany); Slatyer, Tracy R. [Center for Theoretical Physics, Massachusetts Institute of Technology,Cambridge, MA 02139 (United States); Wang, Xiao-Ping [PRISMA Cluster of Excellence & Mainz Institute for Theoretical Physics,Johannes Gutenberg University,Staudingerweg 7, 55099 Mainz (Germany); Xue, Wei [Center for Theoretical Physics, Massachusetts Institute of Technology,Cambridge, MA 02139 (United States)

    2016-12-12

    We consider dark matter models in which the mass splitting between the dark matter particles and their annihilation products is tiny. Compared to the previously proposed Forbidden Dark Matter scenario, the mass splittings we consider are much smaller, and are allowed to be either positive or negative. To emphasize this modification, we dub our scenario “Impeded Dark Matter”. We demonstrate that Impeded Dark Matter can be easily realized without requiring tuning of model parameters. For negative mass splitting, we demonstrate that the annihilation cross-section for Impeded Dark Matter depends linearly on the dark matter velocity or may even be kinematically forbidden, making this scenario almost insensitive to constraints from the cosmic microwave background and from observations of dwarf galaxies. Accordingly, it may be possible for Impeded Dark Matter to yield observable signals in clusters or the Galactic center, with no corresponding signal in dwarfs. For positive mass splitting, we show that the annihilation cross-section is suppressed by the small mass splitting, which helps light dark matter to survive increasingly stringent constraints from indirect searches. As specific realizations for Impeded Dark Matter, we introduce a model of vector dark matter from a hidden SU(2) sector, and a composite dark matter scenario based on a QCD-like dark sector.

  17. Impeded Dark Matter

    International Nuclear Information System (INIS)

    Kopp, Joachim; Liu, Jia; Slatyer, Tracy R.; Wang, Xiao-Ping; Xue, Wei

    2016-01-01

    We consider dark matter models in which the mass splitting between the dark matter particles and their annihilation products is tiny. Compared to the previously proposed Forbidden Dark Matter scenario, the mass splittings we consider are much smaller, and are allowed to be either positive or negative. To emphasize this modification, we dub our scenario “Impeded Dark Matter”. We demonstrate that Impeded Dark Matter can be easily realized without requiring tuning of model parameters. For negative mass splitting, we demonstrate that the annihilation cross-section for Impeded Dark Matter depends linearly on the dark matter velocity or may even be kinematically forbidden, making this scenario almost insensitive to constraints from the cosmic microwave background and from observations of dwarf galaxies. Accordingly, it may be possible for Impeded Dark Matter to yield observable signals in clusters or the Galactic center, with no corresponding signal in dwarfs. For positive mass splitting, we show that the annihilation cross-section is suppressed by the small mass splitting, which helps light dark matter to survive increasingly stringent constraints from indirect searches. As specific realizations for Impeded Dark Matter, we introduce a model of vector dark matter from a hidden SU(2) sector, and a composite dark matter scenario based on a QCD-like dark sector.

  18. Shift of microRNA profile upon orthotopic xenografting of glioblastoma spheroid cultures

    DEFF Research Database (Denmark)

    Halle, Bo; Thomassen, Mads; Venkatesan, Ranga

    2016-01-01

    Glioblastomas always recur despite surgery, radiotherapy and chemotherapy. A key player in the therapeutic resistance may be immature tumor cells with stem-like properties (TSCs) escaping conventional treatment. A group of promising molecular targets are microRNAs (miRs). miRs are small non-codin...... therapeutic targets for anti-miRs to identify novel treatment options for GBM patients....

  19. Mapping posttranscriptional regulation of the human glycome uncovers microRNA defining the glycocode

    OpenAIRE

    Agrawal, Praveen; Kurcon, Tomasz; Pilobello, Kanoelani T.; Rakus, John F.; Koppolu, Sujeethraj; Liu, Zhongyin; Batista, Bianca S.; Eng, William S.; Hsu, Ku-Lung; Liang, Yaxuan; Mahal, Lara K.

    2014-01-01

    Carbohydrates (glycans) are complex cell surface molecules that control multiple aspects of cell biology, including cell–cell communication, cancer metastasis, and inflammation. Glycan biosynthesis requires the coordination of many enzymes, but how this is regulated is not well understood. Herein we show that microRNA (miRNA), small noncoding RNA, are a major regulator of cell surface glycosylation. We map miRNA expression onto carbohydrate signatures obtained by using lectin microarrays, a g...

  20. MicroRNA-223 controls susceptibility to tuberculosis by regulating lung neutrophil recruitment

    OpenAIRE

    Dorhoi, Anca; Iannaccone, Marco; Farinacci, Maura; Faé, Kellen C.; Schreiber, Jörg; Moura-Alves, Pedro; Nouailles, Geraldine; Mollenkopf, Hans-Joachim; Oberbeck-Müller, Dagmar; Jörg, Sabine; Heinemann, Ellen; Hahnke, Karin; Löwe, Delia; Del Nonno, Franca; Goletti, Delia

    2013-01-01

    The molecular mechanisms that control innate immune cell trafficking during chronic infection and inflammation, such as in tuberculosis (TB), are incompletely understood. During active TB, myeloid cells infiltrate the lung and sustain local inflammation. While the chemoattractants that orchestrate these processes are increasingly recognized, the posttranscriptional events that dictate their availability are unclear. We identified microRNA-223 (miR-223) as an upregulated small noncoding RNA in...

  1. Benign Metastasizing Leiomyoma of the Lung: Clinicopathologic, Immunohistochemical, and Micro-RNA Analyses

    OpenAIRE

    Nuovo, Gerard J.; Schmittgen, Thomas D.

    2008-01-01

    Benign metastasizing leiomyomas are rare tumors, which are typically found in the lungs and, thus, might be confused with leiomyosarcomas. Further, it is not clear whether the term “benign metastasizing leiomyoma” is a misnomer and whether these lesions actually represent low-grade malignant tumors that have a low proliferation index. Micro-RNAs (miRNAs) are small noncoding RNAs, which repress translation. The altered expression of miRNAs has been strongly correlated with the malignant phenot...

  2. Hidden charged dark matter

    International Nuclear Information System (INIS)

    Feng, Jonathan L.; Kaplinghat, Manoj; Tu, Huitzu; Yu, Hai-Bo

    2009-01-01

    Can dark matter be stabilized by charge conservation, just as the electron is in the standard model? We examine the possibility that dark matter is hidden, that is, neutral under all standard model gauge interactions, but charged under an exact (\\rm U)(1) gauge symmetry of the hidden sector. Such candidates are predicted in WIMPless models, supersymmetric models in which hidden dark matter has the desired thermal relic density for a wide range of masses. Hidden charged dark matter has many novel properties not shared by neutral dark matter: (1) bound state formation and Sommerfeld-enhanced annihilation after chemical freeze out may reduce its relic density, (2) similar effects greatly enhance dark matter annihilation in protohalos at redshifts of z ∼ 30, (3) Compton scattering off hidden photons delays kinetic decoupling, suppressing small scale structure, and (4) Rutherford scattering makes such dark matter self-interacting and collisional, potentially impacting properties of the Bullet Cluster and the observed morphology of galactic halos. We analyze all of these effects in a WIMPless model in which the hidden sector is a simplified version of the minimal supersymmetric standard model and the dark matter is a hidden sector stau. We find that charged hidden dark matter is viable and consistent with the correct relic density for reasonable model parameters and dark matter masses in the range 1 GeV ∼ X ∼< 10 TeV. At the same time, in the preferred range of parameters, this model predicts cores in the dark matter halos of small galaxies and other halo properties that may be within the reach of future observations. These models therefore provide a viable and well-motivated framework for collisional dark matter with Sommerfeld enhancement, with novel implications for astrophysics and dark matter searches

  3. Identification of rat lung-specific microRNAs by microRNA microarray: valuable discoveries for the facilitation of lung research

    OpenAIRE

    Chintagari Narendranath; Chen Zhongming; Gou Deming; Weng Tingting; Wang Yang; Liu Lin

    2007-01-01

    Abstract Background An important mechanism for gene regulation utilizes small non-coding RNAs called microRNAs (miRNAs). These small RNAs play important roles in tissue development, cell differentiation and proliferation, lipid and fat metabolism, stem cells, exocytosis, diseases and cancers. To date, relatively little is known about functions of miRNAs in the lung except lung cancer. Results In this study, we utilized a rat miRNA microarray containing 216 miRNA probes, printed in-house, to d...

  4. Isolation of Microarray-Grade Total RNA, MicroRNA, and DNA from a Single PAXgene Blood RNA Tube

    DEFF Research Database (Denmark)

    Kruhøffer, Mogens; Andersen, Lars Dyrskjøt; Voss, Thorsten

    2007-01-01

    We have developed a procedure for isolation of microRNA and genomic DNA in addition to total RNA from whole blood stabilized in PAXgene Blood RNA tubes. The procedure is based on automatic extraction on a BioRobot MDx and includes isolation of DNA from a fraction of the stabilized blood...... and recovery of small RNA species that are otherwise lost. The procedure presented here is suitable for large-scale experiments and is amenable to further automation. Procured total RNA and DNA was tested using Affymetrix Expression and single-nucleotide polymorphism GeneChips, respectively, and isolated micro......RNA was tested using spotted locked nucleic acid-based microarrays. We conclude that the yield and quality of total RNA, microRNA, and DNA from a single PAXgene blood RNA tube is sufficient for downstream microarray analysis....

  5. Expression of microRNA related to bone remodeling regulation in plasma in patients with acromegaly

    Directory of Open Access Journals (Sweden)

    Tatiana A. Grebennikova

    2017-11-01

    Full Text Available Backgraund. MiсroRNA are small regulatory factors that regulate gene expression by post-transcriptional regulation of mRNA, playing an important role in numerous cellular processes including organogenesis, apoptosis, cell proliferation and differentiation. Acromegaly causes bone fragility, but the pathogenetic mechanism is generally unknown. Aim. To evaluate levels of microRNA related to bone remodeling regulation in plasma samples from patients with acromegaly Materials and methods. Fasting plasma samples were taken and stored in aliquot at ≤ -80°C from consecutive subjects with clinically evident and biochemically confirmed active acromegaly and healthy volunteers matched by age, sex and body mass index (BMI. miRNeasy Serum/Plasma Kit, TaqMan Advanced miRNA cDNA Synthesis Kit, TaqMan Advanced miRNA Assays were used to assay plasma miRNA expression. Insulin-like growth factor 1 (IGF1 was measured by immunochemiluminescence assay (Liaison. Results. We enrolled 40 subjects 22 patients suffered from acromegaly and 18 matched healthy controls matched by sex, age and BMI. The median age of patients with acromegaly was 42 years (Q25;Q75 – 37;43 with no difference among the groups, p=0.205; BMI – 28 (24;32 kg/m2, p=0.253. The median IGF1 in subjects with acromegaly – 622 (514;1000 ng/ml was significantly higher as compared to the control group (p<0.001. Patients with acromegaly had significantly higher expression of microRNA-100-5р (p=0.051, microRNA-550а-5р (p=0.048, microRNA-7b-5р (p=0.005 and microRNA-96-5р (p=0.042 among 27 bone-specific microRNA tested in plasma Conclusions. This study reveals that several microRNAs, known to regulate bone remodeling can be detected in plasma samples of patients with acromegaly and may be suggested as biomarkers for skeletal involvement in patients with acromegaly.

  6. Using the Small Ruminant Nutrition System to develop and evaluate an alternative approach to estimating the dry matter intake of goats when accounting for ruminal fiber stratification.

    Science.gov (United States)

    Regadas Filho, J G L; Tedeschi, L O; Cannas, A; Vieira, R A M; Rodrigues, M T

    2014-11-01

    The first objective of this research was to assess the ability of the Small Ruminant Nutrition System (SRNS) mechanistic model to predict metabolizable energy intake (MEI) and milk yield (MY) when using a heterogeneous fiber pool scenario (GnG1), compared with a traditional, homogeneous scenario (G1). The second objective was to evaluate an alternative approach to estimating the dry matter intake (DMI) of goats to be used in the SRNS model. The GnG1 scenario considers an age-dependent fractional transference rate for fiber particles from the first ruminal fiber pool (raft) to an escapable pool (λr), and that this second ruminal fiber pool (i.e., escapable pool) follows an age-independent fractional escape rate for fiber particles (ke). Scenario G1 adopted only a single fractional passage rate (kp). All parameters were estimated individually by using equations published in the literature, except for 2 passage rate equations in the G1 scenario: 1 developed with sheep data (G1-S) and another developed with goat data (G1-G). The alternative approach to estimating DMI was based on an optimization process using a series of dietary constraints. The DMI, MEI, and MY estimated for the GnG1 and G1 scenarios were compared with the results of an independent dataset (n=327) that contained information regarding DMI, MEI, MY, and milk and dietary compositions. The evaluation of the scenarios was performed using the coefficient of determination (R(2)) between the observed and predicted values, mean bias (MB), bias correction factor (Cb), and concordance correlation coefficient. The MEI estimated by the GnG1 scenario yielded precise and accurate values (R(2) = 082; MB = 0.21 Mcal/d; Cb = 0.98) similar to those of the G1-S (R(2) = 0.85; MB = 0.10 Mcal/d; Cb=0.99) and G1-G (R(2) = 0.84; MB = 0.18 Mcal/d; Cb = 0.98) scenarios. The results were also similar for the MY, but a substantial MB was found as follows: GnG1 (R(2) = 0.74; MB = 0.70 kg/d; Cb = 0.79), G1-S (R(2) = 0.71; MB = 0

  7. MicroRNA mimicry blocks pulmonary fibrosis

    NARCIS (Netherlands)

    Montgomery, Rusty L; Yu, Guoying; Latimer, Paul A; Stack, Christianna; Robinson, Kathryn; Dalby, Christina M; Kaminski, Naftali; van Rooij, Eva

    2014-01-01

    Over the last decade, great enthusiasm has evolved for microRNA (miRNA) therapeutics. Part of the excitement stems from the fact that a miRNA often regulates numerous related mRNAs. As such, modulation of a single miRNA allows for parallel regulation of multiple genes involved in a particular

  8. MicroRNAs in skin tissue engineering.

    Science.gov (United States)

    Miller, Kyle J; Brown, David A; Ibrahim, Mohamed M; Ramchal, Talisha D; Levinson, Howard

    2015-07-01

    35.2 million annual cases in the U.S. require clinical intervention for major skin loss. To meet this demand, the field of skin tissue engineering has grown rapidly over the past 40 years. Traditionally, skin tissue engineering relies on the "cell-scaffold-signal" approach, whereby isolated cells are formulated into a three-dimensional substrate matrix, or scaffold, and exposed to the proper molecular, physical, and/or electrical signals to encourage growth and differentiation. However, clinically available bioengineered skin equivalents (BSEs) suffer from a number of drawbacks, including time required to generate autologous BSEs, poor allogeneic BSE survival, and physical limitations such as mass transfer issues. Additionally, different types of skin wounds require different BSE designs. MicroRNA has recently emerged as a new and exciting field of RNA interference that can overcome the barriers of BSE design. MicroRNA can regulate cellular behavior, change the bioactive milieu of the skin, and be delivered to skin tissue in a number of ways. While it is still in its infancy, the use of microRNAs in skin tissue engineering offers the opportunity to both enhance and expand a field for which there is still a vast unmet clinical need. Here we give a review of skin tissue engineering, focusing on the important cellular processes, bioactive mediators, and scaffolds. We further discuss potential microRNA targets for each individual component, and we conclude with possible future applications. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Diseases of white matter

    International Nuclear Information System (INIS)

    Holland, B.A.

    1987-01-01

    The diagnosis of white matter abnormalities was revolutionized by the advent of computed tomography (CT), which provided a noninvasive method of detection and assessment of progression of a variety of white matter processes. However, the inadequacies of CT were recognized early, including its relative insensitivity to small foci of abnormal myelin in the brain when correlated with autopsy findings and its inability to image directly white matter diseases of the spinal cord. Magnetic resonance imaging (MRI), on the other hand, sensitive to the slight difference in tissue composition of normal gray and white matter and to subtle increase in water content associated with myelin disorders, is uniquely suited for the examination of white matter pathology. Its clinical applications include the evaluation of the normal process of myelination in childhood and the various white matter diseases, including disorders of demyelination and dysmyelination

  10. MicroRNAs Expression Profiles in Cardiovascular Diseases

    Directory of Open Access Journals (Sweden)

    Elsa Bronze-da-Rocha

    2014-01-01

    Full Text Available The current search for new markers of cardiovascular diseases (CVDs is explained by the high morbidity and mortality still observed in developed and developing countries due to cardiovascular events. Recently, microRNAs (miRNAs or miRs have emerged as potential new biomarkers and are small sequences of RNAs that regulate gene expression at posttranscriptional level by inhibiting translation or inducing degradation of the target mRNAs. Circulating miRNAs are involved in the regulation of signaling pathways associated to aging and can be used as novel diagnostic markers for acute and chronic diseases such as cardiovascular pathologies. This review summarizes the biogenesis, maturation, and stability of miRNAs and their use as potential biomarkers for coronary artery disease (CAD, myocardial infarction (MI, and heart failure (HF.

  11. MicroRNAs Related to Polycystic Ovary Syndrome (PCOS)

    DEFF Research Database (Denmark)

    Sørensen, Anja Elaine; Wissing, Marie Louise Muff; Salö, Sofia

    2014-01-01

    Polycystic ovary syndrome (PCOS) is the most common, though heterogeneous, endocrine aberration in women of reproductive age, with high prevalence and socioeconomic costs. The syndrome is characterized by polycystic ovaries, chronic anovulation and hyperandrogenism, as well as being associated...... with infertility, insulin resistance, chronic low-grade inflammation and an increased life time risk of type 2 diabetes. MicroRNAs (miRNAs) are small, non-coding RNAs that are able to regulate gene expression at the post-transcriptional level. Altered miRNA levels have been associated with diabetes, insulin......RNAs with respect to PCOS will be summarized. Our understanding of miRNAs, particularly in relation to PCOS, is currently at a very early stage, and additional studies will yield important insight into the molecular mechanisms behind this complex and heterogenic syndrome...

  12. MicroRNAs: Processing, Maturation, Target Recognition and Regulatory Functions

    Science.gov (United States)

    Shukla, Girish C.; Singh, Jagjit; Barik, Sailen

    2012-01-01

    The remarkable discovery of small noncoding microRNAs (miRNAs) and their role in posttranscriptional gene regulation have revealed another fine-tuning step in the expression of genetic information. A large number of cellular pathways, which act in organismal development and are important in health and disease, appear to be modulated by miRNAs. At the molecular level, miRNAs restrain the production of proteins by affecting the stability of their target mRNA and/or by down-regulating their translation. This review attempts to offer a snapshot of aspects of miRNA coding, processing, target recognition and function in animals. Our goal here is to provide the readers with a thought-provoking and mechanistic introduction to the miRNA world rather than with a detailed encyclopedia. PMID:22468167

  13. MicroRNAs in prostate cancer: Functional role as biomarkers.

    Science.gov (United States)

    Kanwal, Rajnee; Plaga, Alexis R; Liu, Xiaoqi; Shukla, Girish C; Gupta, Sanjay

    2017-10-28

    MicroRNAs (miRNAs) are small endogenous non-coding molecules that alters gene expression through post-transcriptional regulation of messenger RNA. Compelling evidence suggest the role of miRNA in cancer biology having potential as diagnostic, prognostic and predictive biomarkers. This review summarizes the current knowledge on miRNA deregulated in prostate cancer and their role as oncogene, tumor suppressor and metastasis regulators. The emerging information elucidating the biological function of miRNA is promising and may lead to their potential usefulness as diagnostic/prognostic markers and development as effective therapeutic tools for management of prostate cancer. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. MicroRNAs in Experimental Models of Movement Disorders

    Directory of Open Access Journals (Sweden)

    Soon-Tae Lee

    2011-10-01

    Full Text Available MicroRNAs (miRNAs are small RNAs comprised of 20–25 nucleotides that regulates gene expression by inducing translational repression or degradation of target mRNA. The importance of miRNAs as a mediator of disease pathogenesis and therapeutic targets is rapidly emerging in neuroscience, as well as oncology, immunology, and cardiovascular diseases. In Parkinson’s disease and related disorders, multiple studies have identified the implications of specific miRNAs and the polymorphisms of miRNA target genes during the disease pathogenesis. With a focus on Parkinson’s disease, spinocerebellar ataxia, hereditary spastic paraplegia, and Huntington’s disease, this review summarizes and interprets the observations, and proposes future research topics in this field.

  15. Cellular Response to Ionizing Radiation: A MicroRNA Story

    Science.gov (United States)

    Halimi, Mohammad; Asghari, S. Mohsen; Sariri, Reyhaneh; Moslemi, Dariush; Parsian, Hadi

    2012-01-01

    MicroRNAs (miRNAs) represent a class of small non-coding RNA molecules that regulate gene expression at the post-transcriptional level. They play a crucial role in diverse cellular pathways. Ionizing radiation (IR) is one of the most important treatment protocols for patients that suffer from cancer and affects directly or indirectly cellular integration. Recently it has been discovered that microRNA-mediated gene regulation interferes with radio-related pathways in ionizing radiation. Here, we review the recent discoveries about miRNAs in cellular response to IR. Thoroughly understanding the mechanism of miRNAs in radiation response, it will be possible to design new strategies for improving radiotherapy efficiency and ultimately cancer treatment. PMID:24551775

  16. MicroRNAs in large herpesvirus DNA genomes: recent advances.

    Science.gov (United States)

    Sorel, Océane; Dewals, Benjamin G

    2016-08-01

    MicroRNAs (miRNAs) are small non-coding RNAs (ncRNAs) that regulate gene expression. They alter mRNA translation through base-pair complementarity, leading to regulation of genes during both physiological and pathological processes. Viruses have evolved mechanisms to take advantage of the host cells to multiply and/or persist over the lifetime of the host. Herpesviridae are a large family of double-stranded DNA viruses that are associated with a number of important diseases, including lymphoproliferative diseases. Herpesviruses establish lifelong latent infections through modulation of the interface between the virus and its host. A number of reports have identified miRNAs in a very large number of human and animal herpesviruses suggesting that these short non-coding transcripts could play essential roles in herpesvirus biology. This review will specifically focus on the recent advances on the functions of herpesvirus miRNAs in infection and pathogenesis.

  17. Prognostic value of circulating microRNAs on heart failure-related morbidity and mortality in two large diverse cohorts of general heart failure patients

    NARCIS (Netherlands)

    Bayés-Genis, Antoni; Lanfear, David E.; de Ronde, Maurice W. J.; Lupón, Josep; Leenders, Joost J.; Liu, Zhen; Zuithoff, Nicolaas P. A.; Eijkemans, Marinus J. C.; Zamora, Elisabet; de Antonio, Marta; Zwinderman, Aeilko H.; Pinto-Sietsma, Sara-Joan; Pinto, Yigal M.

    2018-01-01

    Aims Small studies suggested circulating microRNAs (miRNAs) as biomarkers for heart failure (HF). However, standardized approaches and quality assessment for measuring circulating miRNAs are not uniformly established, and most studies have been small, so that results are inconsistent. We used a

  18. Differentially expressed plasma microRNAs and the potential regulatory function of Let-7b in chronic thromboembolic pulmonary hypertension.

    Directory of Open Access Journals (Sweden)

    Lijuan Guo

    Full Text Available Chronic thromboembolic pulmonary hypertension (CTEPH is a progressive disease characterized by misguided thrombolysis and remodeling of pulmonary arteries. MicroRNAs are small non-coding RNAs involved in multiple cell processes and functions. During CTEPH, circulating microRNA profile endued with characteristics of diseased cells could be identified as a biomarker, and might help in recognition of pathogenesis. Thus, in this study, we compared the differentially expressed microRNAs in plasma of CTEPH patients and healthy controls and investigated their potential functions. Microarray was used to identify microRNA expression profile and qRT-PCR for validation. The targets of differentially expressed microRNAs were identified in silico, and the Gene Ontology database and Kyoto Encyclopedia of Genes and Genomes pathway database were used for functional investigation of target gene profile. Targets of let-7b were validated by fluorescence reporter assay. Protein expression of target genes was determined by ELISA or western blotting. Cell migration was evaluated by wound healing assay. The results showed that 1 thirty five microRNAs were differentially expressed in CTEPH patients, among which, a signature of 17 microRNAs, which was shown to be related to the disease pathogenesis by in silico analysis, gave diagnostic efficacy of both sensitivity and specificity >0.9. 2 Let-7b, one of the down-regulated anti-oncogenic microRNAs in the signature, was validated to decrease to about 0.25 fold in CTEPH patients. 3 ET-1 and TGFBR1 were direct targets of let-7b. Altering let-7b level influenced ET-1 and TGFBR1 expression in pulmonary arterial endothelial cells (PAECs as well as the migration of PAECs and pulmonary arterial smooth muscle cells (PASMCs. These results suggested that CTEPH patients had aberrant microRNA signature which might provide some clue for pathogenesis study and biomarker screening. Reduced let-7b might be involved in the pathogenesis of

  19. Differentially Expressed Plasma MicroRNAs and the Potential Regulatory Function of Let-7b in Chronic Thromboembolic Pulmonary Hypertension

    Science.gov (United States)

    Guo, Lijuan; Yang, Yuanhua; Liu, Jie; Wang, Lei; Li, Jifeng; Wang, Ying; Liu, Yan; Gu, Song; Gan, Huili; Cai, Jun; Yuan, Jason X.-J.; Wang, Jun; Wang, Chen

    2014-01-01

    Chronic thromboembolic pulmonary hypertension (CTEPH) is a progressive disease characterized by misguided thrombolysis and remodeling of pulmonary arteries. MicroRNAs are small non-coding RNAs involved in multiple cell processes and functions. During CTEPH, circulating microRNA profile endued with characteristics of diseased cells could be identified as a biomarker, and might help in recognition of pathogenesis. Thus, in this study, we compared the differentially expressed microRNAs in plasma of CTEPH patients and healthy controls and investigated their potential functions. Microarray was used to identify microRNA expression profile and qRT-PCR for validation. The targets of differentially expressed microRNAs were identified in silico, and the Gene Ontology database and Kyoto Encyclopedia of Genes and Genomes pathway database were used for functional investigation of target gene profile. Targets of let-7b were validated by fluorescence reporter assay. Protein expression of target genes was determined by ELISA or western blotting. Cell migration was evaluated by wound healing assay. The results showed that 1) thirty five microRNAs were differentially expressed in CTEPH patients, among which, a signature of 17 microRNAs, which was shown to be related to the disease pathogenesis by in silico analysis, gave diagnostic efficacy of both sensitivity and specificity >0.9. 2) Let-7b, one of the down-regulated anti-oncogenic microRNAs in the signature, was validated to decrease to about 0.25 fold in CTEPH patients. 3) ET-1 and TGFBR1 were direct targets of let-7b. Altering let-7b level influenced ET-1 and TGFBR1 expression in pulmonary arterial endothelial cells (PAECs) as well as the migration of PAECs and pulmonary arterial smooth muscle cells (PASMCs). These results suggested that CTEPH patients had aberrant microRNA signature which might provide some clue for pathogenesis study and biomarker screening. Reduced let-7b might be involved in the pathogenesis of CTEPH by

  20. MicroRNA signature of the human developing pancreas

    Directory of Open Access Journals (Sweden)

    Correa-Medina Mayrin

    2010-09-01

    Full Text Available Abstract Background MicroRNAs are non-coding RNAs that regulate gene expression including differentiation and development by either inhibiting translation or inducing target degradation. The aim of this study is to determine the microRNA expression signature during human pancreatic development and to identify potential microRNA gene targets calculating correlations between the signature microRNAs and their corresponding mRNA targets, predicted by bioinformatics, in genome-wide RNA microarray study. Results The microRNA signature of human fetal pancreatic samples 10-22 weeks of gestational age (wga, was obtained by PCR-based high throughput screening with Taqman Low Density Arrays. This method led to identification of 212 microRNAs. The microRNAs were classified in 3 groups: Group number I contains 4 microRNAs with the increasing profile; II, 35 microRNAs with decreasing profile and III with 173 microRNAs, which remain unchanged. We calculated Pearson correlations between the expression profile of microRNAs and target mRNAs, predicted by TargetScan 5.1 and miRBase altgorithms, using genome-wide mRNA expression data. Group I correlated with the decreasing expression of 142 target mRNAs and Group II with the increasing expression of 876 target mRNAs. Most microRNAs correlate with multiple targets, just as mRNAs are targeted by multiple microRNAs. Among the identified targets are the genes and transcription factors known to play an essential role in pancreatic development. Conclusions We have determined specific groups of microRNAs in human fetal pancreas that change the degree of their expression throughout the development. A negative correlative analysis suggests an intertwined network of microRNAs and mRNAs collaborating with each other. This study provides information leading to potential two-way level of combinatorial control regulating gene expression through microRNAs targeting multiple mRNAs and, conversely, target mRNAs regulated in

  1. Differential MicroRNA Expression in Human Macrophages with Mycobacterium tuberculosis Infection of Beijing/W and Non-Beijing/W Strain Types.

    Science.gov (United States)

    Zheng, Lin; Leung, Eric; Lee, Nelson; Lui, Grace; To, Ka-Fai; Chan, Raphael C Y; Ip, Margaret

    2015-01-01

    The role of microRNAs in association with Mycobacterium tuberculosis (MTB) infection and the immunology regulated by microRNAs upon MTB infection have not been fully unravelled. We examined the microRNA profiles of THP-1 macrophages upon the MTB infection of Beijing/W and non-Beijing/W clinical strains. We also studied the microRNA profiles of the host macrophages by microarray in a small cohort with active MTB disease, latent infection (LTBI), and from healthy controls. The results revealed that 14 microRNAs differentiated infections of Beijing/W from non-Beijing/W strains (PmicroRNAs in human macrophages was identified to differentiate active MTB disease from LTBI and healthy controls. Pathway analyses of these differentially expressed miRNAs suggest that the immune-regulatory interactions involving TGF-β signalling pathway take part in the dysregulation of critical TB processes in the macrophages, resulting in active expression of both cell communication and signalling transduction systems. We showed for the first time that the Beijing/W TB strains repressed a number of miRNAs expressions which may reflect their virulence characteristics in altering the host response. The unique signatures of 11 microRNAs may deserve further evaluation as candidates for biomarkers in the diagnosis of MTB and Beijing/W infections.

  2. MicroRNA-608 and microRNA-34a regulate chordoma malignancy by targeting EGFR, Bcl-xL and MET.

    Directory of Open Access Journals (Sweden)

    Ying Zhang

    Full Text Available Chordomas are rare malignant tumors that originate from the notochord remnants and occur in the skull base, spine and sacrum. Due to a very limited understanding of the molecular pathogenesis of chordoma, there are no adjuvant and molecular therapies besides surgical resection and radiation therapy. microRNAs (miRNAs are small noncoding regulatory RNA molecules with critical roles in cancer. The role of miRNAs in chordomas is mostly unknown. We uncover microRNA-608 (miR-608 and microRNA-34a (miR-34a as novel tumor suppressive microRNAs that regulate malignancy in chordoma. We find that miR-608 and miR-34a expressions are downregulated in human chordoma cell lines and primary cells at least partially via alteration of their genes' copy numbers. We identify the commonly deregulated oncogenes EGFR and Bcl-xL as direct targets of miR-608 and the receptor tyrosine kinase MET as direct target of miR-34a. We show that EGFR and MET activations promote chordoma cell proliferation and invasion and that pharmacological inhibition of EGFR and MET inhibits chordoma cell proliferation and survival. We demonstrate that restoration of miR-608 and miR-34a inhibits cell proliferation and invasion and induces apoptosis in chordoma cells. We find that miR-34a inversely correlates with MET expression and miR-608 inversely correlates with EGFR expression in chordoma cells. These findings demonstrate for the first time that miR-608 and miR-34a regulate chordoma malignancy by regulating EGFR, MET and Bcl-xL.

  3. Dark Matter

    Directory of Open Access Journals (Sweden)

    Einasto J.

    2011-06-01

    Full Text Available I give a review of the development of the concept of dark matter. The dark matter story passed through several stages from a minor observational puzzle to a major challenge for theory of elementary particles. Modern data suggest that dark matter is the dominant matter component in the Universe, and that it consists of some unknown non-baryonic particles. Dark matter is the dominant matter component in the Universe, thus properties of dark matter particles determine the structure of the cosmic web.

  4. High Throughput qPCR Expression Profiling of Circulating MicroRNAs Reveals Minimal Sex- and Sample Timing-Related Variation in Plasma of Healthy Volunteers.

    Directory of Open Access Journals (Sweden)

    Catherine Mooney

    Full Text Available MicroRNAs are a class of small non-coding RNA that regulate gene expression at a post-transcriptional level. MicroRNAs have been identified in various body fluids under normal conditions and their stability as well as their dysregulation in disease opens up a new field for biomarker study. However, diurnal and day-to-day variation in plasma microRNA levels, and differential regulation between males and females, may affect biomarker stability. A QuantStudio 12K Flex Real-Time PCR System was used to profile plasma microRNA levels using OpenArray in male and female healthy volunteers, in the morning and afternoon, and at four time points over a one month period. Using this system we were able to run four OpenArray plates in a single run, the equivalent of 32 traditional 384-well qPCR plates or 12,000 data points. Up to 754 microRNAs can be identified in a single plasma sample in under two hours. 108 individual microRNAs were identified in at least 80% of all our samples which compares favourably with other reports of microRNA profiles in serum or plasma in healthy adults. Many of these microRNAs, including miR-16-5p, miR-17-5p, miR-19a-3p, miR-24-3p, miR-30c-5p, miR-191-5p, miR-223-3p and miR-451a are highly expressed and consistent with previous studies using other platforms. Overall, microRNA levels were very consistent between individuals, males and females, and time points and we did not detect significant differences in levels of microRNAs. These results suggest the suitability of this platform for microRNA profiling and biomarker discovery and suggest minimal confounding influence of sex or sample timing. However, the platform has not been subjected to rigorous validation which must be demonstrated in future biomarker studies where large differences may exist between disease and control samples.

  5. MicroRNAs in Coronary Heart Disease: Ready to Enter the Clinical Arena?

    Directory of Open Access Journals (Sweden)

    Elena Cavarretta

    2016-01-01

    Full Text Available Coronary artery disease (CAD and its complication remain the leading cause of mortality in industrialized countries despite great advances in terms of diagnosis, prognosis, and treatment options. MicroRNAs (miRNAs, small noncoding RNAs, act as posttranscriptional gene expression modulators and have been implicated as key regulators in several physiological and pathological processes linked to CAD. Circulating miRNAs have been evaluated as promising novel biomarkers of CAD, acute coronary syndromes, and acute myocardial infarction, with prognostic implications. Several challenges related to technical aspects, miRNAs normalization, drugs interaction, and quality reporting of statistical multivariable analysis of the miRNAs observational studies remain unresolved. MicroRNA-based therapies in cardiovascular diseases are not ready yet for human trials but definitely appealing. Through this review we will provide clinicians with a concise overview of the pros and cons of microRNAs.

  6. Molecular mechanisms of peripheral nerve regeneration: Emerging roles of microRNAs

    Directory of Open Access Journals (Sweden)

    Di eWu

    2013-04-01

    Full Text Available microRNAs are small non-coding RNAs that suppress gene expression through target mRNA degradation or translation repression. Recent studies suggest that miRNA plays an important role in multiple physiological and pathological processes in the nervous system. In this review article, we described what is currently known about the mechanisms in peripheral nerve regeneration on the cellular and molecular levels. Recently, changes in microRNA expression profiles have been detected in different injury models, and emerging evidence strongly indicates that these changes promote neurons to survive and shift their physiology from maintaining a structure and supporting synaptic transmission toward a regenerative phenotype. We reviewed the putative mechanisms involved in miRNA mediated post-transcriptional regulation and pointed out several areas where future research is necessary to advance our understanding of how targeting miRNA machinery can be used as a therapeutic approach for treating nerve injuries.

  7. Research advances in microRNAs in regulating hepatitis C virus replication and antiviral therapy

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    CUI Xianghua

    2015-05-01

    Full Text Available Hepatitis C virus (HCV infection is one of the most common causes of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. MicroRNAs (miRNAs, a class of small, non-coding RNA, are involved in a variety of physiological and pathological processes in human bodies. The mechanism by which miRNAs regulate HCV replication is described, and the effects of liver-specific microRNA-122 antagonists on hepatitis C antiviral therapy are discussed. Our study indicates that miRNAs play an important regulatory role in HCV expression. Targeting miRNAs may be a potential therapeutic approach for treating HCV infection, but further studies are still in need.

  8. MicroRNA expression in nodal and extranodal Diffuse Large B-cell Lymphoma

    DEFF Research Database (Denmark)

    Mandrup, Charlotte; Petersen, Anders; Højfeldt, Anne Dirks

    MicroRNA expression in nodal and extranodal Diffuse Large B-cell Lymphoma   C. Mandrup1, A. Petersen1, A. D. Hoejfeldt1, H. F. Thomsen1, J. Madsen1, J. Dahlgaard1, P. Johansen2, A. Bukh1, K. Dybkaer1 and H. E Johnsen1. 1Department of Hematology, 2Pathological Institute, Aalborg Hospital, Aarhus...... University Hospital, Aalborg, Denmark Introduction: The aim of this project was to analyse microRNA (miRNA) expression in nodal and extranodal diffuse large B-cell lymphoma (DLBCL). Manifestation at diagnosis may be nodal and/or extranodal. At present, there are no known determinants for none...... of the manifestations, and no way to predict the potential progression from nodal to extranodal disease. miRNA are small regulatory RNA molecules with core function to repress/cleave sequence complementary mRNA targets. Abnormalities in miRNA genetics and expression are known to affect initiation and development...

  9. Micro-RNAs and Their Roles in Breast Cancer Pathogenesis; An Updated Review Article

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    Mohammad Hossein Bakhshi Aliabad

    2016-11-01

    Full Text Available Micro-RNAs (miRNAs are small molecules that modulate the translation of target mRNA through binding to these molecules. In cancer, the expression of oncogenes and suppressors are increased and decreased, respectively. MiRNAs are one of the causing factors in the formation of cancer. To collect data, research articles in PubMed and Google Scholar were searched under keywords including breast cancer and micro-RNA. The data obtained from articles published in prestigious journals showed that some miRNAs are involved in the suppression and some in the induction of cancer cell growth in breast cancer tissue. Some of them are also involved in the aggression and metastasis. According to the obtained results, it seems that assessing miRNAs in breast cancer tissue can be considered as a potential candidate for prognosis and may be used in pre-diagnosis of the disease in near future.

  10. The functional role of exosome microRNAs in lung cancer

    Directory of Open Access Journals (Sweden)

    Li Jia

    2017-09-01

    Full Text Available Lung cancer causes the highest incidence and mortality rates of cancer disease worldwide. Despite obvious advances in lung cancer research, a better understanding of the disease is urgently needed to improve early detection and correct diagnoses. Exosomes are released from cancer cells and modulate cell-cell communication. Exosomes transfer a wide variety of molecules including microRNAs. MicroRNAs (miRNAs are single-stranded, small noncoding RNAs that regulate gene expression. Accumulating evidence indicates that miRNA expression patterns represent the status of physiology and disease. The focus of this review is to provide an update on the progress of miRNAs of cancer-derived exosome as potential biomarkers for lung cancer.

  11. Identification of conserved microRNAs and their targets in chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Hu, Jihong; Sun, Lulu; Ding, Yi

    2013-04-01

    The microRNAs (miRNAs) are a new class of non-protein coding small RNAs that regulate gene expression at the post-transcriptional level in plants. Although thousands of miRNAs have been identified in many plant species, little studies have been reported about chickpea microRNAs. In this study, 28 potential miRNA candidates belonging to 20 families were identified from 16 ESTs and 12 GSSs in chickpea using a comparative genome-based computational analysis. A total of 664 miRNA targets were predicted and some of them encoded transcription factors as well as genes that function in stress response, signal transduction, methylation and a variety of other metabolic processes. These findings lay the foundation for further understanding of miRNA function in the development of chickpea.

  12. MicroRNA from tuberculosis RNA: A bioinformatics study

    OpenAIRE

    Wiwanitkit, Somsri; Wiwanitkit, Viroj

    2012-01-01

    The role of microRNA in the pathogenesis of pulmonary tuberculosis is the interesting topic in chest medicine at present. Recently, it was proposed that the microRNA can be a useful biomarker for monitoring of pulmonary tuberculosis and might be the important part in pathogenesis of disease. Here, the authors perform a bioinformatics study to assess the microRNA within known tuberculosis RNA. The microRNA part can be detected and this can be important key information in further study of the p...

  13. Hypomethylation of miR-142 promoter and upregulation of microRNAs that target the oxytocin receptor gene in the autism prefrontal cortex.

    Science.gov (United States)

    Mor, Michal; Nardone, Stefano; Sams, Dev Sharan; Elliott, Evan

    2015-01-01

    MicroRNAs are small RNA molecules that regulate the translation of protein from gene transcripts and are a powerful mechanism to regulate gene networks. Next-generation sequencing technologies have produced important insights into gene transcription changes that occur in the brain of individuals diagnosed with autism spectrum disorder (asd). However, these technologies have not yet been employed to uncover changes in microRNAs in the brain of individuals diagnosed with asd. Small RNA next-generation sequencing was performed on RNA extracted from 12 human autism brain samples and 12 controls. Real-time PCR was used to validate a sample of the differentially expressed microRNAs, and bioinformatic analysis determined common pathways of gene targets. MicroRNA expression data was correlated to genome-wide DNA methylation data to determine if there is epigenetic regulation of dysregulated microRNAs in the autism brain. Luciferase assays, real-time PCR, and Western blot analysis were used to determine how dysregulated microRNAs may regulate the expression and translation of an autism-related gene transcript. We determined that miR-142-5p, miR-142-3p, miR-451a, miR-144-3p, and miR-21-5p are overexpressed in the asd brain. Furthermore, the promoter region of the miR-142 gene is hypomethylated in the same brain samples, suggesting that epigenetics plays a role in dysregulation of microRNAs in the brain. Bioinformatic analysis revealed that these microRNAs target genes that are involved in synaptic function. Further bioinformatic analysis, coupled with in vitro luciferase assays, determined that miR-451a and miR-21-5p can target the oxytocin receptor (OXTR) gene. OXTR gene expression is increased in these same brain samples, and there is a positive correlation between miR-21-5p and OXTR expression. However, miR-21-5p expression negatively correlates to production of OXTR protein from the OXTR transcript. Therefore, we suggest that miR-21-5p may attenuate OXTR expression in

  14. LNA-FISH for detection of microRNAs in frozen sections

    DEFF Research Database (Denmark)

    Silahtaroglu, Asli N

    2010-01-01

    MicroRNAs (miRNAs) are small ( approximately 22 nt) noncoding RNA molecules that regulate the expression of protein coding genes either by cleavage or translational repression. miRNAs comprise one of the most abundant classes of gene regulatory molecules in multicellular organisms. Yet, the funct......MicroRNAs (miRNAs) are small ( approximately 22 nt) noncoding RNA molecules that regulate the expression of protein coding genes either by cleavage or translational repression. miRNAs comprise one of the most abundant classes of gene regulatory molecules in multicellular organisms. Yet...

  15. DARK MATTER: Optical shears

    International Nuclear Information System (INIS)

    Anon.

    1994-01-01

    Evidence for dark matter continues to build up. Last year (December 1993, page 4) excitement rose when the French EROS (Experience de Recherche d'Objets Sombres) and the US/Australia MACHO collaborations reported hints that small inert 'brown dwarf stars could provide some of the Universe's missing matter. In the 1930s, astronomers first began to suspect that there is a lot more to the Universe than meets the eye

  16. MicroRNA transcriptome profiles during swine skeletal muscle development

    Directory of Open Access Journals (Sweden)

    Sonstegard Tad S

    2009-02-01

    Full Text Available Abstract Background MicroRNA (miR are a class of small RNAs that regulate gene expression by inhibiting translation of protein encoding transcripts. To evaluate the role of miR in skeletal muscle of swine, global microRNA abundance was measured at specific developmental stages including proliferating satellite cells, three stages of fetal growth, day-old neonate, and the adult. Results Twelve potential novel miR were detected that did not match previously reported sequences. In addition, a number of miR previously reported to be expressed in mammalian muscle were detected, having a variety of abundance patterns through muscle development. Muscle-specific miR-206 was nearly absent in proliferating satellite cells in culture, but was the highest abundant miR at other time points evaluated. In addition, miR-1 was moderately abundant throughout developmental stages with highest abundance in the adult. In contrast, miR-133 was moderately abundant in adult muscle and either not detectable or lowly abundant throughout fetal and neonate development. Changes in abundance of ubiquitously expressed miR were also observed. MiR-432 abundance was highest at the earliest stage of fetal development tested (60 day-old fetus and decreased throughout development to the adult. Conversely, miR-24 and miR-27 exhibited greatest abundance in proliferating satellite cells and the adult, while abundance of miR-368, miR-376, and miR-423-5p was greatest in the neonate. Conclusion These data present a complete set of transcriptome profiles to evaluate miR abundance at specific stages of skeletal muscle growth in swine. Identification of these miR provides an initial group of miR that may play a vital role in muscle development and growth.

  17. Solid Matter

    CERN Document Server

    Angelo, Joseph A

    2011-01-01

    Supported by a generous quantity of full-color illustrations and interesting sidebars, Solid Matter introduces the basic characteristics and properties of solid matter. It briefly describes the cosmic connection of the elements, leading readers through several key events in human pre-history that resulted in more advanced uses of matter in the solid state. Chapters include:. -Solid Matter: An Initial Perspective. -Physical Behavior of Matter. -The Gravity of Matter. -Fundamentals of Materials Science. -Rocks and Minerals. -Metals. -Building Materials. -Carbon Earth's Most Versatile Element. -S

  18. Laser capture microdissection followed by next-generation sequencing identifies disease-related microRNAs in psoriatic skin that reflect systemic microRNA changes in psoriasis

    DEFF Research Database (Denmark)

    Løvendorf, Marianne B; Mitsui, Hiroshi; Zibert, John R

    2015-01-01

    Psoriasis is a systemic disease with cutaneous manifestations. MicroRNAs (miRNAs) are small non-coding RNA molecules that are differentially expressed in psoriatic skin; however, only few cell- and region-specific miRNAs have been identified in psoriatic lesions. We used laser capture...... microdissection (LCM) and next-generation sequencing (NGS) to study the specific miRNA expression profiles in the epidermis (Epi) and dermal inflammatory infiltrates (RD) of psoriatic skin (N = 6). We identified 24 deregulated miRNAs in the Epi and 37 deregulated miRNAs in the RD of psoriatic plaque compared...... with normal psoriatic skin (FCH > 2, FDR

  19. Dynamical modeling of microRNA action on the protein translation process.

    Science.gov (United States)

    Zinovyev, Andrei; Morozova, Nadya; Nonne, Nora; Barillot, Emmanuel; Harel-Bellan, Annick; Gorban, Alexander N

    2010-02-24

    Protein translation is a multistep process which can be represented as a cascade of biochemical reactions (initiation, ribosome assembly, elongation, etc.), the rate of which can be regulated by small non-coding microRNAs through multiple mechanisms. It remains unclear what mechanisms of microRNA action are the most dominant: moreover, many experimental reports deliver controversial messages on what is the concrete mechanism actually observed in the experiment. Nissan and Parker have recently demonstrated that it might be impossible to distinguish alternative biological hypotheses using the steady state data on the rate of protein synthesis. For their analysis they used two simple kinetic models of protein translation. In contrary to the study by Nissan and Parker, we show that dynamical data allow discriminating some of the mechanisms of microRNA action. We demonstrate this using the same models as developed by Nissan and Parker for the sake of comparison but the methods developed (asymptotology of biochemical networks) can be used for other models. We formulate a hypothesis that the effect of microRNA action is measurable and observable only if it affects the dominant system (generalization of the limiting step notion for complex networks) of the protein translation machinery. The dominant system can vary in different experimental conditions that can partially explain the existing controversy of some of the experimental data. Our analysis of the transient protein translation dynamics shows that it gives enough information to verify or reject a hypothesis about a particular molecular mechanism of microRNA action on protein translation. For multiscale systems only that action of microRNA is distinguishable which affects the parameters of dominant system (critical parameters), or changes the dominant system itself. Dominant systems generalize and further develop the old and very popular idea of limiting step. Algorithms for identifying dominant systems in multiscale

  20. Dynamical modeling of microRNA action on the protein translation process

    Directory of Open Access Journals (Sweden)

    Barillot Emmanuel

    2010-02-01

    Full Text Available Abstract Background Protein translation is a multistep process which can be represented as a cascade of biochemical reactions (initiation, ribosome assembly, elongation, etc., the rate of which can be regulated by small non-coding microRNAs through multiple mechanisms. It remains unclear what mechanisms of microRNA action are the most dominant: moreover, many experimental reports deliver controversial messages on what is the concrete mechanism actually observed in the experiment. Nissan and Parker have recently demonstrated that it might be impossible to distinguish alternative biological hypotheses using the steady state data on the rate of protein synthesis. For their analysis they used two simple kinetic models of protein translation. Results In contrary to the study by Nissan and Parker, we show that dynamical data allow discriminating some of the mechanisms of microRNA action. We demonstrate this using the same models as developed by Nissan and Parker for the sake of comparison but the methods developed (asymptotology of biochemical networks can be used for other models. We formulate a hypothesis that the effect of microRNA action is measurable and observable only if it affects the dominant system (generalization of the limiting step notion for complex networks of the protein translation machinery. The dominant system can vary in different experimental conditions that can partially explain the existing controversy of some of the experimental data. Conclusions Our analysis of the transient protein translation dynamics shows that it gives enough information to verify or reject a hypothesis about a particular molecular mechanism of microRNA action on protein translation. For multiscale systems only that action of microRNA is distinguishable which affects the parameters of dominant system (critical parameters, or changes the dominant system itself. Dominant systems generalize and further develop the old and very popular idea of limiting step

  1. Speech Matters

    DEFF Research Database (Denmark)

    Hasse Jørgensen, Stina

    2011-01-01

    About Speech Matters - Katarina Gregos, the Greek curator's exhibition at the Danish Pavillion, the Venice Biannual 2011.......About Speech Matters - Katarina Gregos, the Greek curator's exhibition at the Danish Pavillion, the Venice Biannual 2011....

  2. Memory Matters

    Science.gov (United States)

    ... Staying Safe Videos for Educators Search English Español Memory Matters KidsHealth / For Kids / Memory Matters What's in ... of your complex and multitalented brain. What Is Memory? When an event happens, when you learn something, ...

  3. Does Actor Perspective Matter? A Case Study of Designing Intervention for Small-Scale Palm Oil Production Enterprises in Kwaebibirem District of Ghana

    NARCIS (Netherlands)

    Osei-Amponsah, C.; Visser, Leontine

    2016-01-01

    Despite the fact that the government of Ghana imports the bulk of its industrial palm oil needs, it still fails to give assistance to about 80 percent of small-scale producers to enhance development in the industry. To design interventions that will be sustainable for and beneficial to these

  4. Interacting dark matter disguised as warm dark matter

    International Nuclear Information System (INIS)

    Boehm, Celine; Riazuelo, Alain; Hansen, Steen H.; Schaeffer, Richard

    2002-01-01

    We explore some of the consequences of dark-matter-photon interactions on structure formation, focusing on the evolution of cosmological perturbations and performing both an analytical and a numerical study. We compute the cosmic microwave background anisotropies and matter power spectrum in this class of models. We find, as the main result, that when dark matter and photons are coupled, dark matter perturbations can experience a new damping regime in addition to the usual collisional Silk damping effect. Such dark matter particles (having quite large photon interactions) behave like cold dark matter or warm dark matter as far as the cosmic microwave background anisotropies or matter power spectrum are concerned, respectively. These dark-matter-photon interactions leave specific imprints at sufficiently small scales on both of these two spectra, which may allow us to put new constraints on the acceptable photon-dark-matter interactions. Under the conservative assumption that the abundance of 10 12 M · galaxies is correctly given by the cold dark matter, and without any knowledge of the abundance of smaller objects, we obtain the limit on the ratio of the dark-matter-photon cross section to the dark matter mass σ γ-DM /m DM -6 σ Th /(100 GeV)≅6x10 -33 cm 2 GeV -1

  5. Dark Matter

    Indian Academy of Sciences (India)

    What You See Ain't What. You Got, Resonance, Vol.4,. No.9,1999. Dark Matter. 2. Dark Matter in the Universe. Bikram Phookun and Biman Nath. In Part 11 of this article we learnt that there are compelling evidences from dynamics of spiral galaxies, like our own, that there must be non-luminous matter in them. In this.

  6. MicroRNA and gene signature of severe cutaneous drug ...

    African Journals Online (AJOL)

    Purpose: To build a microRNA and gene signature of severe cutaneous adverse drug reactions (SCAR), including Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN). Methods: MicroRNA expression profiles were downloaded from miRNA expression profile of patients' skin suffering from TEN using an ...

  7. Diet-responsive microRNAs are likely exogenous

    Science.gov (United States)

    In a recent report Title "et al". fostered miRNA-375 and miR-200c knock-out pups to wild-type dams and arrived at the conclusion that milk microRNAs are bioavailable in trace amounts at best and that postprandial concentrations of microRNAs are too low to elicit biological effects. Their take home m...

  8. MicroRNA and gene signature of severe cutaneous drug ...

    African Journals Online (AJOL)

    greater than 30 % of the same patients [5]. Nevertheless, the mechanisms of SJS and TEN are not fully elucidated. MicroRNAs or miRs are single stranded RNAs that are capable of posttranscriptional gene regulation via targeting their Mrna [6]. MicroRNAs are very important regulators in many human diseases, for instance,.

  9. RNAi therapeutics and applications of microRNAs in cancer treatment.

    Science.gov (United States)

    Uchino, Keita; Ochiya, Takahiro; Takeshita, Fumitaka

    2013-06-01

    RNA interference-based therapies are proving to be powerful tools for combating various diseases, including cancer. Scientists are researching the development of safe and efficient systems for the delivery of small RNA molecules, which are extremely fragile in serum, to target organs and cells in the human body. A dozen pre-clinical and clinical trials have been under way over the past few years involving biodegradable nanoparticles, lipids, chemical modification and conjugation. On the other hand, microRNAs, which control the balance of cellular biological processes, have been studied as attractive therapeutic targets in cancer treatment. In this review, we provide an overview of RNA interference-based therapeutics in clinical trials and discuss the latest technology for the systemic delivery of nucleic acid drugs. Furthermore, we focus on dysregulated microRNAs in human cancer, which have progressed in pre-clinical trials as therapeutic targets, and describe a wide range of strategies to control the expression levels of endogenous microRNAs. Further development of RNA interference technologies and progression of clinical trials will contribute to the achievement of practical applications of nucleic acid drugs.

  10. MicroRNAs: A Puzzling Tool in Cancer Diagnostics and Therapy.

    Science.gov (United States)

    D'Angelo, Barbara; Benedetti, Elisabetta; Cimini, Annamaria; Giordano, Antonio

    2016-11-01

    MicroRNAs (miRNAs) constitute a dominating class of small RNAs that regulate diverse cellular functions. Due the pivotal role of miRNAs in biological processes, a deregulated miRNA expression is likely involved in human cancers. MicroRNAs possess tumor suppressor capability, as well as display oncogenic characteristics. Interestingly, miRNAs exist in various biological fluids as circulating entities. Changes in the profile of circulating miRNAs are indicative of pathophysiological conditions in human cancer. This concept has led to consider circulating miRNAs valid biomarkers in cancer diagnostics. Furthermore, current research promotes the use of miRNAs as a target in cancer therapy. However, miRNAs are an evolving research field. Although miRNAs have been demonstrated to be potentially valuable tools both in cancer diagnosis and treatment, a greater effort should be made to improve our understanding of miRNAs biology. This review describes the biology of microRNAs, emphasizing on the use of miRNAs in cancer diagnostics and therapy. Copyright© 2016 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

  11. Utility of MicroRNAs and siRNAs in Cervical Carcinogenesis

    Directory of Open Access Journals (Sweden)

    Sacnite del Mar Díaz-González

    2015-01-01

    Full Text Available MicroRNAs and siRNAs belong to a family of small noncoding RNAs which bind through partial sequence complementarity to 3′-UTR regions of mRNA from target genes, resulting in the regulation of gene expression. MicroRNAs have become an attractive target for genetic and pharmacological modulation due to the critical function of their target proteins in several signaling pathways, and their expression profiles have been found to be altered in various cancers. A promising technology platform for selective silencing of cell and/or viral gene expression using siRNAs is currently in development. Cervical cancer is the most common cancer in women in the developing world and sexually transmitted infection with HPV is the cause of this malignancy. Therefore, a cascade of abnormal events is induced during cervical carcinogenesis, including the induction of genomic instability, reprogramming of cellular metabolic pathways, deregulation of cell proliferation, inhibition of apoptotic mechanisms, disruption of cell cycle control mechanisms, and alteration of gene expression. Thus, in the present review article, we highlight new research on microRNA expression profiles which may be utilized as biomarkers for cervical cancer. Furthermore, we discuss selective silencing of HPV E6 and E7 with siRNAs which represents a potential gene therapy strategy against cervical cancer.

  12. The MicroRNA Repertoire of Symbiodinium, the Dinoflagellate Symbiont of Reef-Building Corals

    KAUST Repository

    Baumgarten, Sebastian

    2013-07-01

    Animal and plant genomes produce numerous small RNAs (smRNAs) that regulate gene expression post-transcriptionally affecting metabolism, development, and epigenetic inheritance. In order to characterize the repertoire of endogenous microRNAs and potential gene targets, we conducted smRNA and mRNA expression profiling over nine experimental treatments of cultures from the dinoflagellate Symbiodinium sp. A1, a photosynthetic symbiont of scleractinian corals. We identified a total of 75 novel smRNAs in Symbiodinum sp. A1 that share stringent key features with functional microRNAs from other model organisms. A subset of 38 smRNAs was predicted independently over all nine treatments and their putative gene targets were identified. We found 3,187 animal-like target sites in the 3’UTRs of 12,858 mRNAs and 53 plantlike target sites in 51,917 genes. Furthermore, we identified the core RNAi protein machinery in Symbiodinium. Integration of smRNA and mRNA expression profiling identified a variety of processes that could be under microRNA control, e.g. regulation of translation, DNA modification, and chromatin silencing. Given that Symbiodinium seems to have a paucity of transcription factors and differentially expressed genes, identification and characterization of its smRNA repertoire establishes the possibility of a range of gene regulatory mechanisms in dinoflagellates acting post-transcriptionally.

  13. MicroRNAs are suitable for assessment as biomarkers from formalin-fixed paraffin-embedded tissue, and miR-24 represents an appropriate reference microRNA for diffuse large B-cell lymphoma studies.

    Science.gov (United States)

    Culpin, Rachel Emily; Sieniawski, Michal; Proctor, Stephen John; Menon, Geetha; Mainou-Fowler, Tryfonia

    2013-03-01

    Tissue biopsy specimens in the form of formalin-fixed paraffin-embedded tissue (FFPET) represent a valuable resource for biomarker identification and validation. However, to date, they remain an underused asset due to uncertainty regarding RNA extraction and the reliability of downstream techniques, including quantitative RT-PCR. Recently, much interest has emerged in the study of microRNAs; small single-stranded RNAs with a role in transcriptional regulation, that are thought to be well preserved in FFPET. In this study, we show that microRNA expression is comparable between FFPET and matched fresh-frozen samples (miR-17-5p: p=0.01, miR-92: p=0.003), and demonstrate that no significant deterioration in expression occurs over prolonged FFPET storage (p=0.06). Furthermore, microRNA expression is equivalent dependant on RNA extraction method (p<0.001) or DNAse treatment of total RNA (p<0.001). Finally, we validate miR-24 as a suitable reference microRNA for diffuse large B-cell lymphoma (DLBCL) FFPET studies.

  14. A rheo-optical apparatus for real time kinetic studies on shear-induced alignment of self-assembled soft matter with small sample volumes

    Science.gov (United States)

    Laiho, Ari; Ikkala, Olli

    2007-01-01

    In soft materials, self-assembled nanoscale structures can allow new functionalities but a general problem is to align such local structures aiming at monodomain overall order. In order to achieve shear alignment in a controlled manner, a novel type of rheo-optical apparatus has here been developed that allows small sample volumes and in situ monitoring of the alignment process during the shear. Both the amplitude and orientation angles of low level linear birefringence and dichroism are measured while the sample is subjected to large amplitude oscillatory shear flow. The apparatus is based on a commercial rheometer where we have constructed a flow cell that consists of two quartz teeth. The lower tooth can be set in oscillatory motion whereas the upper one is connected to the force transducers of the rheometer. A custom made cylindrical oven allows the operation of the flow cell at elevated temperatures up to 200 °C. Only a small sample volume is needed (from 9 to 25 mm3), which makes the apparatus suitable especially for studying new materials which are usually obtainable only in small quantities. Using this apparatus the flow alignment kinetics of a lamellar polystyrene-b-polyisoprene diblock copolymer is studied during shear under two different conditions which lead to parallel and perpendicular alignment of the lamellae. The open device geometry allows even combined optical/x-ray in situ characterization of the alignment process by combining small-angle x-ray scattering using concepts shown by Polushkin et al. [Macromolecules 36, 1421 (2003)].

  15. Selected microRNAs define cell fate determination of murine central memory CD8 T cells.

    Directory of Open Access Journals (Sweden)

    Gonzalo Almanza

    2010-06-01

    Full Text Available During an immune response T cells enter memory fate determination, a program that divides them into two main populations: effector memory and central memory T cells. Since in many systems protection appears to be preferentially mediated by T cells of the central memory it is important to understand when and how fate determination takes place. To date, cell intrinsic molecular events that determine their differentiation remains unclear. MicroRNAs are a class of small, evolutionarily conserved RNA molecules that negatively regulate gene expression, causing translational repression and/or messenger RNA degradation. Here, using an in vitro system where activated CD8 T cells driven by IL-2 or IL-15 become either effector memory or central memory cells, we assessed the role of microRNAs in memory T cell fate determination. We found that fate determination to central memory T cells is under the balancing effects of a discrete number of microRNAs including miR-150, miR-155 and the let-7 family. Based on miR-150 a new target, KChIP.1 (K (+ channel interacting protein 1, was uncovered, which is specifically upregulated in developing central memory CD8 T cells. Our studies indicate that cell fate determination such as surface phenotype and self-renewal may be decided at the pre-effector stage on the basis of the balancing effects of a discrete number of microRNAs. These results may have implications for the development of T cell vaccines and T cell-based adoptive therapies.

  16. Use of care management practices in small- and medium-sized physician groups: do public reporting of physician quality and financial incentives matter?

    Science.gov (United States)

    Alexander, Jeffrey A; Maeng, Daniel; Casalino, Lawrence P; Rittenhouse, Diane

    2013-04-01

    To examine the effect of public reporting (PR) and financial incentives tied to quality performance on the use of care management practices (CMPs) among small- and medium-sized physician groups. Survey data from The National Study of Small and Medium-sized Physician Practices were used. Primary data collection was also conducted to assess community-level PR activities. The final sample included 643 practices engaged in quality reporting; about half of these practices were subject to PR. We used a treatment effects model. The instrumental variables were the community-level variables that capture the level of PR activity in each community in which the practices operate. (1) PR is associated with increased use of CMPs, but the estimate is not statistically significant; (2) financial incentives are associated with greater use of CMPs; (3) practices' awareness/sensitivity to quality reports is positively related to their use of CMPs; and (4) combined PR and financial incentives jointly affect CMP use to a greater degree than either of these factors alone. Small- to medium-sized practices appear to respond to PR and financial incentives by greater use of CMPs. Future research needs to investigate the appropriate mix and type of incentive arrangements and quality reporting. © Health Research and Educational Trust.

  17. MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Hafidh Said

    2009-12-01

    Full Text Available Abstract Background New generation sequencing technology has allowed investigation of the small RNA populations of flowering plants at great depth. However, little is known about small RNAs in their reproductive cells, especially in post-meiotic cells of the gametophyte generation. Pollen - the male gametophyte - is the specialised haploid structure that generates and delivers the sperm cells to the female gametes at fertilisation. Whether development and differentiation of the male gametophyte depends on the action of microRNAs and trans-acting siRNAs guiding changes in gene expression is largely unknown. Here we have used 454 sequencing to survey the various small RNA populations present in mature pollen of Arabidopsis thaliana. Results In this study we detected the presence of 33 different microRNA families in mature pollen and validated the expression levels of 17 selected miRNAs by Q-RT-PCR. The majority of the selected miRNAs showed pollen-enriched expression compared with leaves. Furthermore, we report for the first time the presence of trans-acting siRNAs in pollen. In addition to describing new patterns of expression for known small RNAs in each of these classes, we identified 7 putative novel microRNAs. One of these, ath-MIR2939, targets a pollen-specific F-box transcript and we demonstrate cleavage of its target mRNA in mature pollen. Conclusions Despite the apparent simplicity of the male gametophyte, comprising just two different cell types, pollen not only utilises many miRNAs and trans-acting siRNAs expressed in the somatic tissues but also expresses novel miRNAs.

  18. Rapid Generation of MicroRNA Sponges for MicroRNA Inhibition

    NARCIS (Netherlands)

    Kluiver, Joost; Gibcus, Johan H.; Hettinga, Chris; Adema, Annelies; Richter, Mareike K. S.; Halsema, Nancy; Slezak-Prochazka, Izabella; Ding, Ye; Kroesen, Bart-Jan; van den Berg, Anke

    2012-01-01

    MicroRNA (miRNA) sponges are transcripts with repeated miRNA antisense sequences that can sequester miRNAs from endogenous targets. MiRNA sponges are valuable tools for miRNA loss-of-function studies both in vitro and in vivo. We developed a fast and flexible method to generate miRNA sponges and

  19. Regulation of cardiac microRNAs by serum response factor

    Directory of Open Access Journals (Sweden)

    Wei Jeanne Y

    2011-02-01

    Full Text Available Abstract Serum response factor (SRF regulates certain microRNAs that play a role in cardiac and skeletal muscle development. However, the role of SRF in the regulation of microRNA expression and microRNA biogenesis in cardiac hypertrophy has not been well established. In this report, we employed two distinct transgenic mouse models to study the impact of SRF on cardiac microRNA expression and microRNA biogenesis. Cardiac-specific overexpression of SRF (SRF-Tg led to altered expression of a number of microRNAs. Interestingly, downregulation of miR-1, miR-133a and upregulation of miR-21 occurred by 7 days of age in these mice, long before the onset of cardiac hypertrophy, suggesting that SRF overexpression impacted the expression of microRNAs which contribute to cardiac hypertrophy. Reducing cardiac SRF level using the antisense-SRF transgenic approach (Anti-SRF-Tg resulted in the expression of miR-1, miR-133a and miR-21 in the opposite direction. Furthermore, we observed that SRF regulates microRNA biogenesis, specifically the transcription of pri-microRNA, thereby affecting the mature microRNA level. The mir-21 promoter sequence is conserved among mouse, rat and human; one SRF binding site was found to be in the mir-21 proximal promoter region of all three species. The mir-21 gene is regulated by SRF and its cofactors, including myocardin and p49/Strap. Our study demonstrates that the downregulation of miR-1, miR-133a, and upregulation of miR-21 can be reversed by one single upstream regulator, SRF. These results may help to develop novel therapeutic interventions targeting microRNA biogenesis.

  20. Emerging roles of microRNAs as molecular switches in the integrated circuit of the cancer cell

    Science.gov (United States)

    Sotiropoulou, Georgia; Pampalakis, Georgios; Lianidou, Evi; Mourelatos, Zissimos

    2009-01-01

    Transformation of normal cells into malignant tumors requires the acquisition of six hallmark traits, e.g., self-sufficiency in growth signals, insensitivity to antigrowth signals and self-renewal, evasion of apoptosis, limitless replication potential, angiogenesis, invasion, and metastasis, which are common to all cancers (Hanahan and Weinberg 2000). These new cellular traits evolve from defects in major regulatory microcircuits that are fundamental for normal homeostasis. The discovery of microRNAs (miRNAs) as a new class of small non-protein-coding RNAs that control gene expression post-transcriptionally by binding to various mRNA targets suggests that these tiny RNA molecules likely act as molecular switches in the extensive regulatory web that involves thousands of transcripts. Most importantly, accumulating evidence suggests that numerous microRNAs are aberrantly expressed in human cancers. In this review, we discuss the emergent roles of microRNAs as switches that function to turn on/off known cellular microcircuits. We outline recent compelling evidence that deregulated microRNA-mediated control of cellular microcircuits cooperates with other well-established regulatory mechanisms to confer the hallmark traits of the cancer cell. Furthermore, these exciting insights into aberrant microRNA control in cancer-associated circuits may be exploited for cancer therapies that will target deregulated miRNA switches. PMID:19561119

  1. Small silencing RNAs: an expanding universe.

    Science.gov (United States)

    Ghildiyal, Megha; Zamore, Phillip D

    2009-02-01

    Since the discovery in 1993 of the first small silencing RNA, a dizzying number of small RNA classes have been identified, including microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). These classes differ in their biogenesis, their modes of target regulation and in the biological pathways they regulate. There is a growing realization that, despite their differences, these distinct small RNA pathways are interconnected, and that small RNA pathways compete and collaborate as they regulate genes and protect the genome from external and internal threats.

  2. The Roles of MicroRNAs in Breast Cancer

    International Nuclear Information System (INIS)

    Takahashi, Ryou-u; Miyazaki, Hiroaki; Ochiya, Takahiro

    2015-01-01

    MicroRNAs (miRNAs) constitute a large family of small, approximately 20–22 nucleotide, non-coding RNAs that regulate the expression of target genes, mainly at the post-transcriptional level. Accumulating lines of evidence have indicated that miRNAs play important roles in the maintenance of biological homeostasis and that aberrant expression levels of miRNAs are associated with the onset of many diseases, including cancer. In various cancers, miRNAs play important roles in tumor initiation, drug resistance and metastasis. Recent studies reported that miRNAs could also be secreted via small endosome-derived vesicles called exosomes, which are derived from multiple cell types, including dendritic cells, lymphocytes, and tumor cells. Exosomal miRNAs play an important role in cell-to-cell communication and have been investigated as prognostic and diagnostic biomarkers. In this review, we summarize the major findings related to the functions of miRNAs in breast cancer, which is the most frequent cancer in women, and discuss the potential clinical uses of miRNAs, including their roles as therapeutic targets and diagnostic markers

  3. The Roles of MicroRNAs in Breast Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Takahashi, Ryou-u [Division of Molecular and Cellular Medicine, National Cancer Center Research Institute 1-1, Tsukiji 5-chome, Chuo-ku, Tokyo 104-0045 (Japan); Miyazaki, Hiroaki [Division of Molecular and Cellular Medicine, National Cancer Center Research Institute 1-1, Tsukiji 5-chome, Chuo-ku, Tokyo 104-0045 (Japan); Department of Oral and Maxillofacial Surgery, Showa University School of Dentistry, 1-5-8 Hatanodai Shinagawa-ku, Tokyo 142-8555 (Japan); Ochiya, Takahiro, E-mail: tochiya@ncc.go.jp [Division of Molecular and Cellular Medicine, National Cancer Center Research Institute 1-1, Tsukiji 5-chome, Chuo-ku, Tokyo 104-0045 (Japan)

    2015-04-09

    MicroRNAs (miRNAs) constitute a large family of small, approximately 20–22 nucleotide, non-coding RNAs that regulate the expression of target genes, mainly at the post-transcriptional level. Accumulating lines of evidence have indicated that miRNAs play important roles in the maintenance of biological homeostasis and that aberrant expression levels of miRNAs are associated with the onset of many diseases, including cancer. In various cancers, miRNAs play important roles in tumor initiation, drug resistance and metastasis. Recent studies reported that miRNAs could also be secreted via small endosome-derived vesicles called exosomes, which are derived from multiple cell types, including dendritic cells, lymphocytes, and tumor cells. Exosomal miRNAs play an important role in cell-to-cell communication and have been investigated as prognostic and diagnostic biomarkers. In this review, we summarize the major findings related to the functions of miRNAs in breast cancer, which is the most frequent cancer in women, and discuss the potential clinical uses of miRNAs, including their roles as therapeutic targets and diagnostic markers.

  4. Inflatable Dark Matter.

    Science.gov (United States)

    Davoudiasl, Hooman; Hooper, Dan; McDermott, Samuel D

    2016-01-22

    We describe a general scenario, dubbed "inflatable dark matter," in which the density of dark matter particles can be reduced through a short period of late-time inflation in the early Universe. The overproduction of dark matter that is predicted within many, otherwise, well-motivated models of new physics can be elegantly remedied within this context. Thermal relics that would, otherwise, be disfavored can easily be accommodated within this class of scenarios, including dark matter candidates that are very heavy or very light. Furthermore, the nonthermal abundance of grand unified theory or Planck scale axions can be brought to acceptable levels without invoking anthropic tuning of initial conditions. A period of late-time inflation could have occurred over a wide range of scales from ∼MeV to the weak scale or above, and could have been triggered by physics within a hidden sector, with small but not necessarily negligible couplings to the standard model.

  5. Phase transitions in nuclear matter

    International Nuclear Information System (INIS)

    Glendenning, N.K.

    1984-11-01

    The rather general circumstances under which a phase transition in hadronic matter at finite temperature to an abnormal phase in which baryon effective masses become small and in which copious baryon-antibaryon pairs appear is emphasized. A preview is also given of a soliton model of dense matter, in which at a density of about seven times nuclear density, matter ceases to be a color insulator and becomes increasingly color conducting. 22 references

  6. MicroRNAs in mantle cell lymphoma

    DEFF Research Database (Denmark)

    Husby, Simon; Geisler, Christian; Grønbæk, Kirsten

    2013-01-01

    Mantle cell lymphoma (MCL) is a rare and aggressive subtype of non-Hodgkin lymphoma. New treatment modalities, including intensive induction regimens with immunochemotherapy and autologous stem cell transplant, have improved survival. However, many patients still relapse, and there is a need...... for novel therapeutic strategies. Recent progress has been made in the understanding of the role of microRNAs (miRNAs) in MCL. Comparisons of tumor samples from patients with MCL with their normal counterparts (naive B-cells) have identified differentially expressed miRNAs with roles in cellular growth...

  7. MicroRNA Delivery for Regenerative Medicine

    OpenAIRE

    Peng, Bo; Chen, Yongming; Leong, Kam W.

    2015-01-01

    MicroRNA (miRNA) directs post-transcriptional regulation of a network of genes by targeting mRNA. Although relatively recent in development, many miRNAs direct differentiation of various stem cells including induced pluripotent stem cells (iPSCs), a major player in regenerative medicine. An effective and safe delivery of miRNA holds the key to translating miRNA technologies. Both viral and nonviral delivery systems have seen success in miRNA delivery, and each approach possesses advantages an...

  8. D matter

    International Nuclear Information System (INIS)

    Shiu, Gary; Wang Liantao

    2004-01-01

    We study the properties and phenomenology of particlelike states originating from D branes whose spatial dimensions are all compactified. They are nonperturbative states in string theory and we refer to them as D matter. In contrast to other nonperturbative objects such as 't Hooft-Polyakov monopoles, D-matter states could have perturbative couplings among themselves and with ordinary matter. The lightest D particle (LDP) could be stable because it is the lightest state carrying certain (integer or discrete) quantum numbers. Depending on the string scale, they could be cold dark matter candidates with properties similar to that of WIMPs or wimpzillas. The spectrum of excited states of D matter exhibits an interesting pattern which could be distinguished from that of Kaluza-Klein modes, winding states, and string resonances. We speculate about possible signatures of D matter from ultrahigh energy cosmic rays and colliders

  9. Context matters: volunteer bias, small sample size, and the value of comparison groups in the assessment of research-based undergraduate introductory biology lab courses.

    Science.gov (United States)

    Brownell, Sara E; Kloser, Matthew J; Fukami, Tadashi; Shavelson, Richard J

    2013-01-01

    The shift from cookbook to authentic research-based lab courses in undergraduate biology necessitates the need for evaluation and assessment of these novel courses. Although the biology education community has made progress in this area, it is important that we interpret the effectiveness of these courses with caution and remain mindful of inherent limitations to our study designs that may impact internal and external validity. The specific context of a research study can have a dramatic impact on the conclusions. We present a case study of our own three-year investigation of the impact of a research-based introductory lab course, highlighting how volunteer students, a lack of a comparison group, and small sample sizes can be limitations of a study design that can affect the interpretation of the effectiveness of a course.

  10. Phosphorus mass balance in a highly eutrophic semi-enclosed inlet near a big metropolis: a small inlet can contribute towards particulate organic matter production.

    Science.gov (United States)

    Asaoka, Satoshi; Yamamoto, Tamiji

    2011-01-01

    Terrigenous loading into enclosed water bodies has been blamed for eutrophic conditions marked by massive algal growth and subsequent hypoxia due to decomposition of dead algal cells. This study aims to describe the eutrophication and hypoxia processes in a semi-enclosed water body lying near a big metropolis. Phosphorus mass balance in a small inlet, Ohko Inlet, located at the head of Hiroshima Bay, Japan, was quantified using a numerical model. Dissolved inorganic phosphorous inflow from Kaita Bay next to the inlet was five times higher than that from terrigenous load, which may cause an enhancement of primary production. Therefore, it was concluded that not only the reduction of material load from the land and the suppression of benthic flux are needed, but also reducing the inflow of high phosphorus and oxygen depleted water from Kaita Bay will form a collective alternative measure to remediate the environmental condition of the inlet. Copyright © 2011 Elsevier Ltd. All rights reserved.

  11. Context Matters: Volunteer Bias, Small Sample Size, and the Value of Comparison Groups in the Assessment of Research-Based Undergraduate Introductory Biology Lab Courses

    Directory of Open Access Journals (Sweden)

    Sara E. Brownell

    2013-08-01

    Full Text Available The shift from cookbook to authentic research-based lab courses in undergraduate biology necessitates the need for evaluation and assessment of these novel courses. Although the biology education community has made progress in this area, it is important that we interpret the effectiveness of these courses with caution and remain mindful of inherent limitations to our study designs that may impact internal and external validity. The specific context of a research study can have a dramatic impact on the conclusions. We present a case study of our own three-year investigation of the impact of a research-based introductory lab course, highlighting how volunteer students, a lack of a comparison group, and small sample sizes can be limitations of a study design that can affect the interpretation of the effectiveness of a course.

  12. Identification and Functional Analysis of microRNAs Involved in the Anther Development in Cotton Genic Male Sterile Line Yu98-8A

    Directory of Open Access Journals (Sweden)

    Xiaojie Yang

    2016-10-01

    Full Text Available Hybrid vigor contributes in a large way to the yield and quality of cotton (Gossypium hirsutum fiber. Although microRNAs play essential regulatory roles in flower induction and development, it is still unclear if microRNAs are involved in male sterility, as the regulatory molecular mechanisms of male sterility in cotton need to be better defined. In this study, two independent small RNA libraries were constructed and sequenced from the young buds collected from the sporogenous cell formation to the meiosis stage of the male sterile line Yu98-8A and the near-isogenic line. Sequencing revealed 1588 and 1536 known microRNAs and 347 and 351 novel miRNAs from male sterile and male fertile libraries, respectively. MicroRNA expression profiles revealed that 49 conserved and 51 novel miRNAs were differentially expressed. Bioinformatic and degradome analysis indicated the regulatory complexity of microRNAs during flower induction and development. Further RT-qPCR and physiological analysis indicated that, among the different Kyoto Encyclopedia Gene and Genomes pathways, indole-3-acetic acid and gibberellic acid signaling transduction pathways may play pivotal regulatory functions in male sterility.

  13. Expression of coding (mRNA) and non-coding (microRNA) RNA in lung tissue and blood isolated from pigs suffering from bacterial pleuropneumonia

    DEFF Research Database (Denmark)

    Skovgaard, Kerstin; Schou, Kirstine Klitgaard; Wendt, Karin Tarp

    2010-01-01

    MicroRNAs are small non-coding RNA molecules (18-23 nt), that regulate the activity of other genes at the post-transcriptional level. Recently it has become evident that microRNA plays an important role in modulating and fine tuning innate and adaptive immune responses. Still, little is known about...... the impact of microRNAs in the development and pathogenesis of lung infections. Expression of microRNA known to be induced by bacterial (i.e., LPS) ligands and thus supposed to play a role in the regulation of antimicrobial defence, were studied in lung tissue and in blood from pigs experimentally infected...... with Actinobacillus pleuropneumoniae (AP). Expression differences of mRNA and microRNA were quantified at different time points (6h, 12h, 24h, 48h PI) using reverse transcription quantitative real-time PCR (Rotor-Gene and Fluidigm). Expression profiles of miRNA in blood of seven animals were further studied using mi...

  14. MicroRNAs in sensorineural diseases of the ear

    Directory of Open Access Journals (Sweden)

    Kathy eUshakov

    2013-12-01

    Full Text Available Non-coding microRNAs have a fundamental role in gene regulation and expression in almost every multicellular organism. Only discovered in the last decade, microRNAs are already known to play a leading role in many aspects of disease. In the vertebrate inner ear, microRNAs are essential for controlling development and survival of hair cells. Moreover, dysregulation of microRNAs has been implicated in sensorineural hearing impairment, as well as in other ear diseases such as cholesteatomas, vestibular schwannomas and otitis media. Due to the inaccessibility of the ear in humans, animal models have provided the optimal tools to study microRNA expression and function, in particular mice and zebrafish. A major focus of current research has been to discover the targets of the microRNAs expressed in the inner ear, in order to determine the regulatory pathways of the auditory and vestibular systems. The potential for microRNA manipulation in development of therapeutic tools for hearing impairment is as yet unexplored, paving the way for future work in the field.

  15. Carbon stable isotope composition of charophyte organic matter in a small and shallow Spanish water body as a baseline for future trophic studies

    Directory of Open Access Journals (Sweden)

    María Antonia Rodrigo

    2015-12-01

    Full Text Available Quantitative descriptions of foodweb structure based on isotope niche space require knowledge of producers’ isotopic signatures. In freshwater ecosystems charophytes are one of the main components of submerged vegetation and the feeding base for many herbivorous consumers, but knowledge about their organic carbon isotopic signatures is sparse. In this study, the δ13C organic values (and organic %C and %N of the four species of submerged macrophytes (three charophytes - Chara hispida, Nitella hyalina and Tolypella glomerata - and one angiosperm, Myriophyllum spicatum growing in a newly created shallow pond were measured monthly over a period of one year, to discern if i all charophyte species susceptible to being food for consumers and growing in the same waterbody have the same C isotopic composition; ii the δ13C values of a charophyte species change on a seasonal and spatial scale; iii the different parts (apical nodes, internodes, rhizoids, reproductive organs, oospores of a charophyte species have the same isotopic composition. The δ13C, %C and %N values of organic matter in the sediments where the plants were rooted were also measured as well as several limnological variables. The δ13C values for the angiosperm (-13.7±0.7‰ indicated 13C-enrichment, whereas the N. hyalina δ13C values were the most negative (-22.4±0.7‰. The mean δ13C value for C. hispida was -19.0±1.0‰ and -20.7±0.8‰ for T. glomerata. C. hispida δ13C values had a significant seasonal variation with 13C-poor values in the cold season, and slight spatial differences. Statistically significant differences were found between charophyte rhizoids (13C-enriched and the other parts of the thalli. The δ13C values in the sediments varied throughout time (-13‰ to -26‰. The C content was lower in the charophytes than in the angiosperm and there were no large differences among the charophytes. Charophyte fructifications were enriched in organic C compared to the

  16. Dark Matter

    International Nuclear Information System (INIS)

    Holt, S. S.; Bennett, C. L.

    1995-01-01

    These proceedings represent papers presented at the Astrophysics conference in Maryland, organized by NASA Goddard Space Flight Center and the University of Maryland. The topics covered included low mass stars as dark matter, dark matter in galaxies and clusters, cosmic microwave background anisotropy, cold and hot dark matter, and the large scale distribution and motions of galaxies. There were eighty five papers presented. Out of these, 10 have been abstracted for the Energy Science and Technology database

  17. Dark Matter

    International Nuclear Information System (INIS)

    Bashir, A.; Cotti, U.; De Leon, C. L.; Raya, A; Villasenor, L.

    2008-01-01

    One of the biggest scientific mysteries of our time resides in the identification of the particles that constitute a large fraction of the mass of our Universe, generically known as dark matter. We review the observations and the experimental data that imply the existence of dark matter. We briefly discuss the properties of the two best dark-matter candidate particles and the experimental techniques presently used to try to discover them. Finally, we mention a proposed project that has recently emerged within the Mexican community to look for dark matter

  18. MicroRNAs in inflammation and response to injuries induced by environmental pollution

    International Nuclear Information System (INIS)

    Sonkoly, Enikö; Pivarcsi, Andor

    2011-01-01

    MicroRNAs (miRNAs) are small noncoding RNAs that regulate basic biological processes by posttranscriptional suppression of their target genes. Altered miRNA expression may lead to widespread gene expression changes and has been implicated in pathophysiological processes such as cancer and inflammation. In this review, we summarize the present knowledge about the role of miRNAs in inflammation and in the response to environmental agents and pollutants, such as cigarette smoke, ethanol, carcinogenic chemicals such as benzo(a)pyrene (BaP) and dioxin, and UV radiation.

  19. MicroRNAs in inflammation and response to injuries induced by environmental pollution

    Energy Technology Data Exchange (ETDEWEB)

    Sonkoly, Enikoe [Molecular Dermatology Research Group, Unit of Dermatology and Venerology, Department of Medicine, Karolinska Institute, Stockholm (Sweden); Department of Dermatology and Allergology, University of Szeged, Szeged (Hungary); Pivarcsi, Andor, E-mail: andor.pivarcsi@ki.se [Molecular Dermatology Research Group, Unit of Dermatology and Venerology, Department of Medicine, Karolinska Institute, Stockholm (Sweden); Department of Dermatology and Allergology, University of Szeged, Szeged (Hungary)

    2011-12-01

    MicroRNAs (miRNAs) are small noncoding RNAs that regulate basic biological processes by posttranscriptional suppression of their target genes. Altered miRNA expression may lead to widespread gene expression changes and has been implicated in pathophysiological processes such as cancer and inflammation. In this review, we summarize the present knowledge about the role of miRNAs in inflammation and in the response to environmental agents and pollutants, such as cigarette smoke, ethanol, carcinogenic chemicals such as benzo(a)pyrene (BaP) and dioxin, and UV radiation.

  20. Angiotensin II Regulates microRNA-132/-212 in Hypertensive Rats and Humans

    DEFF Research Database (Denmark)

    Eskildsen, Tilde V; Jeppesen, Pia L; Schneider, Mikael

    2013-01-01

    MicroRNAs (miRNAs), a group of small non-coding RNAs that fine tune translation of multiple target mRNAs, are emerging as key regulators in cardiovascular development and disease. MiRNAs are involved in cardiac hypertrophy, heart failure and remodeling following cardiac infarction; however, mi...... no effect. Taken together, these data suggest that miR-132 and miR-212 are involved in AngII induced hypertension, providing a new perspective in hypertensive disease mechanisms....

  1. MicroRNAs - A New Generation Molecular Targets for Treating Cellular Diseases

    OpenAIRE

    Paulmurugan, Ramasamy

    2013-01-01

    MicroRNAs (miRNAs) are a unique class of non-coding, small RNAs, similar to mRNAs, transcribed by cells, but for entirely different reasons. While mRNAs are transcribed to code for proteins, miRNAs are produced to regulate the production of proteins from mRNAs. miRNAs are central components that tightly and temporally regulating gene expression in cells. Dysregulation of miRNAs expressions in cellular pathogenesis, including cancer, has been reported, and it clearly supports the importance of...

  2. MicroRNA silencing in primates: towards development of novel therapeutics

    DEFF Research Database (Denmark)

    Petri, Andreas; Lindow, Morten; Kauppinen, Sakari

    2009-01-01

    MicroRNAs (miRNA) comprise an abundant class of small noncoding RNAs that act as important posttranscriptional regulators of gene expression. Accumulating evidence showing that aberrantly expressed miRNAs play important roles in human cancers underscores them as potential targets for therapeutic ...... intervention. Recent reports on efficient miRNA silencing in rodents and nonhuman primates using high-affinity targeting by chemically modified antisense oligonucleotides highlight the utility of such compounds in the development of miRNA-based cancer therapeutics....

  3. Progress in research on ionizing radiation-induced microRNA

    International Nuclear Information System (INIS)

    Hu Zheng; Tie Yi; Sun Zhixian; Zheng Xiaofei

    2011-01-01

    MicroRNAs (miRNAs) are small single-stranded noncoding RNAs consisting of 21-23 nucleotides that play important gene-regulatory roles in eukaryotes by pairing to the mRNAs of protein-coding genes to direct their posttranscriptional repression. A growing body of evidence indicates that alterations in miRNA expression may occur following exposure to several oxidative stress including ionizing radiation. So miRNAs may serve as potential new targets for co-therapies aiming to improve the effects of radiation disease therapy in cancer patients. The progress in research on ionizing radiation-induced miRNAs is reviewed in this paper. (authors)

  4. Customization of Artificial MicroRNA Design.

    Science.gov (United States)

    Van Vu, Tien; Do, Vinh Nang

    2017-01-01

    RNAi approaches, including microRNA (miRNA) regulatory pathway, offer great tools for functional characterization of unknown genes. Moreover, the applications of artificial microRNA (amiRNA) in the field of plant transgenesis have also been advanced to engineer pathogen-resistant or trait-improved transgenic plants. Until now, despite the high potency of amiRNA approach, no commercial plant cultivar expressing amiRNAs with improved traits has been released yet. Beside the issues of biosafety policies, the specificity and efficacy of amiRNAs are of major concerns. Sufficient cares should be taken for the specificity and efficacy of amiRNAs due to their potential off-target effects and other issues relating to in vivo expression of pre-amiRNAs. For these reasons, the proper design of amiRNAs with the lowest off-target possibility is very important for successful applications of the approach in plant. Therefore, there are many studies with the aim to improve the amiRNA design and amiRNA expressing backbones for obtaining better specificity and efficacy. However, the requirement for an efficient reference for the design is still needed. In the present chapter, we attempt to summarize and discuss all the major concerns relating to amiRNA design with the hope to provide a significant guideline for this approach.

  5. GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda

    Science.gov (United States)

    2014-01-01

    Background Non-coding sequences such as microRNAs have important roles in disease processes. Computational microRNA target identification (CMTI) is becoming increasingly important since traditional experimental methods for target identification pose many difficulties. These methods are time-consuming, costly, and often need guidance from computational methods to narrow down candidate genes anyway. However, most CMTI methods are computationally demanding, since they need to handle not only several million query microRNA and reference RNA pairs, but also several million nucleotide comparisons within each given pair. Thus, the need to perform microRNA identification at such large scale has increased the demand for parallel computing. Methods Although most CMTI programs (e.g., the miRanda algorithm) are based on a modified Smith-Waterman (SW) algorithm, the existing parallel SW implementations (e.g., CUDASW++ 2.0/3.0, SWIPE) are unable to meet this demand in CMTI tasks. We present CUDA-miRanda, a fast microRNA target identification algorithm that takes advantage of massively parallel computing on Graphics Processing Units (GPU) using NVIDIA's Compute Unified Device Architecture (CUDA). CUDA-miRanda specifically focuses on the local alignment of short (i.e., ≤ 32 nucleotides) sequences against longer reference sequences (e.g., 20K nucleotides). Moreover, the proposed algorithm is able to report multiple alignments (up to 191 top scores) and the corresponding traceback sequences for any given (query sequence, reference sequence) pair. Results Speeds over 5.36 Giga Cell Updates Per Second (GCUPs) are achieved on a server with 4 NVIDIA Tesla M2090 GPUs. Compared to the original miRanda algorithm, which is evaluated on an Intel Xeon E5620@2.4 GHz CPU, the experimental results show up to 166 times performance gains in terms of execution time. In addition, we have verified that the exact same targets were predicted in both CUDA-miRanda and the original mi

  6. Small angle scattering from soft matter-application to complex mixed systems; Diffusion de neutrons aux petits angles par la matiere molle-application aux systemes mixtes

    Energy Technology Data Exchange (ETDEWEB)

    Boue, F.; Cousin, F.; Gummel, J.; Carrot, G.; El Harrak, A. [CEA Saclay, Lab. Leon Brillouin, CNRS, 91 - Gif-sur-Yvette (France); Oberdisse, J. [Montpellier-2 Univ., Lab. des Colloides, Verres et Nanomateriaux, UMR 5587, 34 (France)

    2007-09-15

    The advantage of small angle neutron scattering associated with isotopic labelling through deuteration is illustrated in the case of mixed systems, created by associating already well-known systems of characteristic structures; this is also important for applications. Our first mixed system associates charged polymer chains, polyelectrolyte (here polystyrene sulfonate, PSS), with oppositely charged particles, proteins (here lysozyme). Different fractions of deuterated water (D{sub 2}O) mixed with normal water are used to match the scattering length density of the protein or of the polymer in non-deuterated or deuterated version. First, this allows us to separate the protein and the polymer signal: we can then distinguish a case where the structures of each species alone in water are hardly modified by mixing, except for interconnections yielding a gel, and a case inducing complete change into a structure common to both species, made of aggregated globules. Secondly, using, for counter-ions of the poly-ions, deuterated Tetramethylammonium, together with matching both protein and polymer, we establish unambiguously the counter-ion release into the solvent. Thirdly, matching only a fraction of polymer chains, the other being deuterated, we extrapolate at zero deuterated fraction their form factor and describe the chain conformation inside the complexes. Fourthly, we illustrate the possibilities of modelling the signal on a second example of mixed system: a nano-composite made of silica particles surrounded by polymer dispersed into a deuterated polymer matrix. Chains are then visible in such reinforced polymer system, in particular when it is submitted to elongation: we discuss a possible model for an ideal system, introducing the scattering contribution from deformed chains. (authors)

  7. Identification of Conserved and Novel MicroRNAs in Blueberry

    Directory of Open Access Journals (Sweden)

    Junyang Yue

    2017-06-01

    Full Text Available MicroRNAs (miRNAs are a class of small endogenous RNAs that play important regulatory roles in cells by negatively affecting gene expression at both transcriptional and post-transcriptional levels. There have been extensive studies aiming to identify miRNAs and to elucidate their functions in various plant species. In the present study, we employed the high-throughput sequencing technology to profile miRNAs in blueberry fruits. A total of 9,992,446 small RNA tags with sizes ranged from 18 to 30 nt were obtained, indicating that blueberry fruits have a large and diverse small RNA population. Bioinformatic analysis identified 412 conserved miRNAs belonging to 29 families, and 35 predicted novel miRNAs that are likely to be unique to blueberries. Among them, expression profiles of five conserved miRNAs were validated by stem loop qRT-PCR. Furthermore, the potential target genes of conserved and novel miRNAs were predicted and subjected to Gene Ontology (GO annotation. Enrichment analysis of the GO-represented biological processes and molecular functions revealed that these target genes were potentially involved in a wide range of metabolic pathways and developmental processes. Particularly, anthocyanin biosynthesis has been predicted to be directly or indirectly regulated by diverse miRNA families. This study is the first report on genome-wide miRNA profile analysis in blueberry and it provides a useful resource for further elucidation of the functional roles of miRNAs during fruit development and ripening.

  8. Convergent microRNA actions coordinate neocortical development.

    Science.gov (United States)

    Barca-Mayo, Olga; De Pietri Tonelli, Davide

    2014-08-01

    Neocortical development is a complex process that, at the cellular level, involves tight control of self-renewal, cell fate commitment, survival, differentiation and delamination/migration. These processes require, at the molecular level, the precise regulation of intrinsic signaling pathways and extrinsic factors with coordinated action in a spatially and temporally specific manner. Transcriptional regulation plays an important role during corticogenesis; however, microRNAs (miRNAs) are emerging as important post-transcriptional regulators of various aspects of central nervous system development. miRNAs are a class of small, single-stranded noncoding RNA molecules that control the expression of the majority of protein coding genes (i.e., targets). How do different miRNAs achieve precise control of gene networks during neocortical development? Here, we critically review all the miRNA-target interactions validated in vivo, with relevance to the generation and migration of pyramidal-projection glutamatergic neurons, and for the initial formation of cortical layers in the embryonic development of rodent neocortex. In particular, we focus on convergent miRNA actions, which are still a poorly understood layer of complexity in miRNA signaling, but potentially one of the keys to disclosing how miRNAs achieve the precise coordination of complex biological processes such as neocortical development.

  9. Identifying MicroRNAs and Transcript Targets in Jatropha Seeds

    Science.gov (United States)

    Galli, Vanessa; Guzman, Frank; de Oliveira, Luiz F. V.; Loss-Morais, Guilherme; Körbes, Ana P.; Silva, Sérgio D. A.; Margis-Pinheiro, Márcia M. A. N.; Margis, Rogério

    2014-01-01

    MicroRNAs, or miRNAs, are endogenously encoded small RNAs that play a key role in diverse plant biological processes. Jatropha curcas L. has received significant attention as a potential oilseed crop for the production of renewable oil. Here, a sRNA library of mature seeds and three mRNA libraries from three different seed development stages were generated by deep sequencing to identify and characterize the miRNAs and pre-miRNAs of J. curcas. Computational analysis was used for the identification of 180 conserved miRNAs and 41 precursors (pre-miRNAs) as well as 16 novel pre-miRNAs. The predicted miRNA target genes are involved in a broad range of physiological functions, including cellular structure, nuclear function, translation, transport, hormone synthesis, defense, and lipid metabolism. Some pre-miRNA and miRNA targets vary in abundance between the three stages of seed development. A search for sequences that produce siRNA was performed, and the results indicated that J. curcas siRNAs play a role in nuclear functions, transport, catalytic processes and disease resistance. This study presents the first large scale identification of J. curcas miRNAs and their targets in mature seeds based on deep sequencing, and it contributes to a functional understanding of these miRNAs. PMID:24551031

  10. [Use of microRNAs in heart failure management].

    Science.gov (United States)

    Arias Sosa, Luis Alejandro

    Heart failure (HF) is a high impact disease that affects all human populations, demanding the development of new strategies and methods to manage this pathology. That's why microRNAs, small noncoding RNAs that regulate gene expression, appear as an important option in the diagnosis, prognosis and treatment of this disease. MiRNAs seems to have a future on HF handling, because can be isolated from body fluids such as blood, and changes in its levels can be associated with the presence, stage and specific disease features, which makes them an interesting option as biomarkers. Also, due to the important role of these molecules on regulation of gene expression and cell homeostasis, it has been explored its potential use as a therapeutic method to prevent or treat HF. That is why this review seeks to show the importance of biomedical research involving the use of miRNAs as a method to approach the HF, showing the impact of disease in the world, aspects of miRNAs biology, and their use as biomarkers and as important therapeutic targets. Copyright © 2017 Instituto Nacional de Cardiología Ignacio Chávez. Publicado por Masson Doyma México S.A. All rights reserved.

  11. MicroRNAs: an epigenetic tool to study celiac disease

    Directory of Open Access Journals (Sweden)

    Karla A. Bascuñán-Gamboa

    2014-05-01

    Full Text Available This article summarizes recent findings on the role of microRNAs (miRNAs in biological processes associated with the regulation of chronic inflammation and autoimmunity. miRNAs are small non-coding RNA molecules that have been recently emerged as a new class of modulators of gene expression at the post-transcriptional level. MiRNAs bind to complementary sequences of specific targets of messengers RNA, which can interfere with protein synthesis. We reviewed studies that evaluated the expression patterns of miRNAs in different autoimmune diseases, especially in celiac disease (CD. CD is a chronic enteropathy triggered by gluten proteins, characterized by altered immune responses in genetically susceptible individuals that results in damage to the bowel mucosa. CD has a high prevalence and an effective treatment by a specific diet ("gluten free diet". Genetic factors confer susceptibility but do not explain the whole disease, suggesting that environmental factors do play a relevant role in the development of the condition. The evaluation of the potential role of miRNA is of particular interest in CD given that these epigenetic mechanisms in the pathogenesis of autoimmune and inflammatory diseases have been recently described. Improving our understanding of miRNAs in CD will contribute to clarify the role of altered epigenetic regulation in the development and course of this disease.

  12. MicroRNAs Related to Polycystic Ovary Syndrome (PCOS)

    Science.gov (United States)

    Sørensen, Anja Elaine; Wissing, Marie Louise; Salö, Sofia; Englund, Anne Lis Mikkelsen; Dalgaard, Louise Torp

    2014-01-01

    Polycystic ovary syndrome (PCOS) is the most common, though heterogeneous, endocrine aberration in women of reproductive age, with high prevalence and socioeconomic costs. The syndrome is characterized by polycystic ovaries, chronic anovulation and hyperandrogenism, as well as being associated with infertility, insulin resistance, chronic low-grade inflammation and an increased life time risk of type 2 diabetes. MicroRNAs (miRNAs) are small, non-coding RNAs that are able to regulate gene expression at the post-transcriptional level. Altered miRNA levels have been associated with diabetes, insulin resistance, inflammation and various cancers. Studies have shown that circulating miRNAs are present in whole blood, serum, plasma and the follicular fluid of PCOS patients and that they might serve as potential biomarkers and a new approach for the diagnosis of PCOS. In this review, recent work on miRNAs with respect to PCOS will be summarized. Our understanding of miRNAs, particularly in relation to PCOS, is currently at a very early stage, and additional studies will yield important insight into the molecular mechanisms behind this complex and heterogenic syndrome. PMID:25158044

  13. Clinical implications of microRNAs in human glioblastoma

    Directory of Open Access Journals (Sweden)

    Masahiro eMizoguchi

    2013-02-01

    Full Text Available Glioblastoma (GBM is one of the most common and dismal brain tumors in adults. Further elucidation of the molecular pathogenesis of GBM is mandatory to improve the overall survival of patients. A novel small non-coding RNA molecule, microRNA (miRNA, appears to represent one of the most attractive target molecules contributing to the pathogenesis of various types of tumors. Recent global analyses have revealed that several miRNAs are clinically implicated in GBM, with some reports indicating the association of miRNA dysregulation with acquired temozolomide (TMZ resistance. More recent studies have revealed that miRNAs could play a role in cancer stem cell (CSC properties, contributing to treatment resistance. In addition, greater impact might be expected from miRNA-targeted therapies based on tumor-derived exosomes that contain numerous functional miRNAs, which could be transferred between tumor cells and surrounding structures. Tumor-derived miRNAs are now considered to be a novel molecular mechanism promoting the progression of GBM. Establishment of miRNA-targeted therapies based on miRNA dysregulation of CSCs could provide effective therapeutic strategies for TMZ-resistant GBM. Recent progress has revealed that miRNAs are not only putative biological markers for diagnosis, but also one of the most promising targets for GBM treatment. Herein, we summarize the translational aspects of miRNAs in the diagnosis and treatment of GBM.

  14. The Destiny of Glucose from a MicroRNA Perspective.

    Science.gov (United States)

    Mirra, Paola; Nigro, Cecilia; Prevenzano, Immacolata; Leone, Alessia; Raciti, Gregory Alexander; Formisano, Pietro; Beguinot, Francesco; Miele, Claudia

    2018-01-01

    Glucose serves as a primary, and for some tissues the unique, fuel source in order to generate and maintain the biological functions. Hyperglycemia is a hallmark of type 2 diabetes and is the direct consequence of perturbations in the glucose homeostasis. Insulin resistance, referred to as a reduced response of target tissues to the hormone, contributes to the development of hyperglycemia. The molecular mechanisms responsible for the altered glucose homeostasis are numerous and not completely understood. MicroRNAs (miRNAs) are now recognized as regulators of the lipid and glucose metabolism and are involved in the onset of metabolic diseases. Indeed, these small non-coding RNA molecules operate in the RNA silencing and posttranscriptional regulation of gene expression and may modulate the levels of kinases and enzymes in the glucose metabolism. Therefore, a better characterization of the function of miRNAs and a deeper understanding of their role in disease may represent a fundamental step toward innovative treatments addressing the causes, not only the symptoms, of hyperglycemia, using approaches aimed at restoring either miRNAs or their specific targets. In this review, we outline the current understanding regarding the impact of miRNAs in the glucose metabolism and highlight the need for further research focused on altered key kinases and enzymes in metabolic diseases.

  15. Circulating microRNAs as Potential Biomarkers of Infectious Disease

    Science.gov (United States)

    Correia, Carolina N.; Nalpas, Nicolas C.; McLoughlin, Kirsten E.; Browne, John A.; Gordon, Stephen V.; MacHugh, David E.; Shaughnessy, Ronan G.

    2017-01-01

    microRNAs (miRNAs) are a class of small non-coding endogenous RNA molecules that regulate a wide range of biological processes by post-transcriptionally regulating gene expression. Thousands of these molecules have been discovered to date, and multiple miRNAs have been shown to coordinately fine-tune cellular processes key to organismal development, homeostasis, neurobiology, immunobiology, and control of infection. The fundamental regulatory role of miRNAs in a variety of biological processes suggests that differential expression of these transcripts may be exploited as a novel source of molecular biomarkers for many different disease pathologies or abnormalities. This has been emphasized by the recent discovery of remarkably stable miRNAs in mammalian biofluids, which may originate from intracellular processes elsewhere in the body. The potential of circulating miRNAs as biomarkers of disease has mainly been demonstrated for various types of cancer. More recently, however, attention has focused on the use of circulating miRNAs as diagnostic/prognostic biomarkers of infectious disease; for example, human tuberculosis caused by infection with Mycobacterium tuberculosis, sepsis caused by multiple infectious agents, and viral hepatitis. Here, we review these developments and discuss prospects and challenges for translating circulating miRNA into novel diagnostics for infectious disease. PMID:28261201

  16. Cerebellar neurodegeneration in the absence of microRNAs

    Science.gov (United States)

    Schaefer, Anne; O'Carroll, Dónal; Tan, Chan Lek; Hillman, Dean; Sugimori, Mutsuyuki; Llinas, Rodolfo; Greengard, Paul

    2007-01-01

    Genome-encoded microRNAs (miRNAs) are potent regulators of gene expression. The significance of miRNAs in various biological processes has been suggested by studies showing an important role of these small RNAs in regulation of cell differentiation. However, the role of miRNAs in regulation of differentiated cell physiology is not well established. Mature neurons express a large number of distinct miRNAs, but the role of miRNAs in postmitotic neurons has not been examined. Here, we provide evidence for an essential role of miRNAs in survival of differentiated neurons. We show that conditional Purkinje cell–specific ablation of the key miRNA-generating enzyme Dicer leads to Purkinje cell death. Deficiency in Dicer is associated with progressive loss of miRNAs, followed by cerebellar degeneration and development of ataxia. The progressive neurodegeneration in the absence of Dicer raises the possibility of an involvement of miRNAs in neurodegenerative disorders. PMID:17606634

  17. MicroRNAs in Human Placental Development and Pregnancy Complications

    Directory of Open Access Journals (Sweden)

    Chun Peng

    2013-03-01

    Full Text Available MicroRNAs (miRNAs are small non-coding RNAs, which function as critical posttranscriptional regulators of gene expression by promoting mRNA degradation and translational inhibition. Placenta expresses many ubiquitous as well as specific miRNAs. These miRNAs regulate trophoblast cell differentiation, proliferation, apoptosis, invasion/migration, and angiogenesis, suggesting that miRNAs play important roles during placental development. Aberrant miRNAs expression has been linked to pregnancy complications, such as preeclampsia. Recent research of placental miRNAs focuses on identifying placental miRNA species, examining differential expression of miRNAs between placentas from normal and compromised pregnancies, and uncovering the function of miRNAs in the placenta. More studies are required to further understand the functional significance of miRNAs in placental development and to explore the possibility of using miRNAs as biomarkers and therapeutic targets for pregnancy-related disorders. In this paper, we reviewed the current knowledge about the expression and function of miRNAs in placental development, and propose future directions for miRNA studies.

  18. Regulation of IGF-1 signaling by microRNAs

    Directory of Open Access Journals (Sweden)

    Hwa Jin eJung

    2015-01-01

    Full Text Available The insulin-like growth factor 1 (IGF-1 signaling pathway regulates critical biological processes including development, homeostasis, and aging. Dysregulation of this pathway has been implicated in a myriad of diseases such as cancers, neurodegenerative diseases, and metabolic disorders, making the IGF-1 signaling pathway a prime target to develop therapeutic and intervention strategies. Recently, small non-coding RNA molecules in ~22 nucleotide length, microRNAs (miRNAs, have emerged as a new regulator of biological processes in virtually all organ systems and increasing studies are linking altered miRNA function to disease mechanisms. A miRNA binds to 3’UTRs of multiple target genes and coordinately down-regulates their expression, thereby exerting a profound influence on gene regulatory networks. Here we review the components of the IGF-1 signaling pathway that are known targets of miRNA regulation, and highlight recent studies that suggest therapeutic potential of these miRNAs against various diseases.

  19. Cell Cycle Regulation of Stem Cells by MicroRNAs.

    Science.gov (United States)

    Mens, Michelle M J; Ghanbari, Mohsen

    2018-06-01

    MicroRNAs (miRNAs) are a class of small non-coding RNA molecules involved in the regulation of gene expression. They are involved in the fine-tuning of fundamental biological processes such as proliferation, differentiation, survival and apoptosis in many cell types. Emerging evidence suggests that miRNAs regulate critical pathways involved in stem cell function. Several miRNAs have been suggested to target transcripts that directly or indirectly coordinate the cell cycle progression of stem cells. Moreover, previous studies have shown that altered expression levels of miRNAs can contribute to pathological conditions, such as cancer, due to the loss of cell cycle regulation. However, the precise mechanism underlying miRNA-mediated regulation of cell cycle in stem cells is still incompletely understood. In this review, we discuss current knowledge of miRNAs regulatory role in cell cycle progression of stem cells. We describe how specific miRNAs may control cell cycle associated molecules and checkpoints in embryonic, somatic and cancer stem cells. We further outline how these miRNAs could be regulated to influence cell cycle progression in stem cells as a potential clinical application.

  20. Circulating MicroRNAs as Potential Biomarkers of Exercise Response

    Directory of Open Access Journals (Sweden)

    Mája Polakovičová

    2016-10-01

    Full Text Available Systematic physical activity increases physical fitness and exercise capacity that lead to the improvement of health status and athletic performance. Considerable effort is devoted to identifying new biomarkers capable of evaluating exercise performance capacity and progress in training, early detection of overtraining, and monitoring health-related adaptation changes. Recent advances in OMICS technologies have opened new opportunities in the detection of genetic, epigenetic and transcriptomic biomarkers. Very promising are mainly small non-coding microRNAs (miRNAs. miRNAs post-transcriptionally regulate gene expression by binding to mRNA and causing its degradation or inhibiting translation. A growing body of evidence suggests that miRNAs affect many processes and play a crucial role not only in cell differentiation, proliferation and apoptosis, but also affect extracellular matrix composition and maintaining processes of homeostasis. A number of studies have shown changes in distribution profiles of circulating miRNAs (c-miRNAs associated with various diseases and disorders as well as in samples taken under physiological conditions such as pregnancy or physical exercise. This overview aims to summarize the current knowledge related to the response of blood c-miRNAs profiles to different modes of exercise and to highlight their potential application as a novel class of biomarkers of physical performance capacity and training adaptation.

  1. MicroRNAs Related to Polycystic Ovary Syndrome (PCOS

    Directory of Open Access Journals (Sweden)

    Anja Elaine Sørensen

    2014-08-01

    Full Text Available Polycystic ovary syndrome (PCOS is the most common, though heterogeneous, endocrine aberration in women of reproductive age, with high prevalence and socioeconomic costs. The syndrome is characterized by polycystic ovaries, chronic anovulation and hyperandrogenism, as well as being associated with infertility, insulin resistance, chronic low-grade inflammation and an increased life time risk of type 2 diabetes. MicroRNAs (miRNAs are small, non-coding RNAs that are able to regulate gene expression at the post-transcriptional level. Altered miRNA levels have been associated with diabetes, insulin resistance, inflammation and various cancers. Studies have shown that circulating miRNAs are present in whole blood, serum, plasma and the follicular fluid of PCOS patients and that they might serve as potential biomarkers and a new approach for the diagnosis of PCOS. In this review, recent work on miRNAs with respect to PCOS will be summarized. Our understanding of miRNAs, particularly in relation to PCOS, is currently at a very early stage, and additional studies will yield important insight into the molecular mechanisms behind this complex and heterogenic syndrome.

  2. Control of the gut microbiome by fecal microRNA

    Directory of Open Access Journals (Sweden)

    Shirong Liu

    2016-03-01

    Full Text Available Since their discovery in the early 90s, microRNAs (miRNAs, small non-coding RNAs, have mainly been associated with posttranscriptional regulation of gene expression on a cell-autonomous level. Recent evidence has extended this role by adding inter-species communication to the manifold functional range. In our latest study [Liu S, et al., 2016, Cell Host & Microbe], we identified miRNAs in gut lumen and feces of both mice and humans. We found that intestinal epithelial cells (IEC and Hopx+ cells were the two main sources of fecal miRNA. Deficiency of IEC-miRNA resulted in gut dysbiosis and WT fecal miRNA transplantation restored the gut microbiota. We investigated potential mechanisms for this effect and found that miRNAs were able to regulate the gut microbiome. By culturing bacteria with miRNAs, we found that host miRNAs were able to enter bacteria, specifically regulate bacterial gene transcripts and affect bacterial growth. Oral administration of synthetic miRNA mimics affected specific bacteria in the gut. Our findings describe a previously unknown pathway by which the gut microbiome is regulated by the host and raises the possibility that miRNAs may be used therapeutically to manipulate the microbiome for the treatment of disease.

  3. Roles of microRNA-15 family in normal and pathological late lung development

    OpenAIRE

    Sakkas, Elpidoforos

    2016-01-01

    MicroRNAs are key regulators of organogenesis and during the last years many studies focused on microRNA expression during embryonic development. To date, there is no study to report possible roles of microRNAs in late lung development and especially during the alveolarization process. The objective of this study was to identify microRNAs that are deregulated under hyperoxic conditions and to assess whether microRNA expression can be modulated in vivo. Lung microRNA expression screening wa...

  4. The Role of MicroRNAs in Pancreatitis

    Science.gov (United States)

    2015-10-01

    AD______________ AWARD NUMBER: W81XWH-14-1-0469 TITLE: The Role of microRNAs in Pancreatitis PRINCIPAL INVESTIGATOR: Li, Yong RECIPIENT...The Role of MicroRNAs in Pancreatitis 5b. GRANT NUMBER W81XWH-14-1-0469 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER Li, Yong 5e...AVAILABILITY STATEMENT Approved for Public Release; Distribution Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Pancreatitis (inflammation of the

  5. The miR-10 microRNA precursor family

    DEFF Research Database (Denmark)

    Tehler, Disa; Høyland-Kroghsbo, Nina Molin; Lund, Anders H

    2011-01-01

    The miR-10 microRNA precursor family encodes a group of short non-coding RNAs involved in gene regulation. The miR-10 family is highly conserved and has sparked the interest of many research groups because of the genomic localization in the vicinity of, coexpression with and regulation of the Hox...... gene developmental regulators. Here, we review the current knowledge of the evolution, physiological function and involvement in cancer of this family of microRNAs....

  6. Common features of microRNA target prediction tools

    Directory of Open Access Journals (Sweden)

    Sarah M. Peterson

    2014-02-01

    Full Text Available The human genome encodes for over 1800 microRNAs, which are short noncoding RNA molecules that function to regulate gene expression post-transcriptionally. Due to the potential for one microRNA to target multiple gene transcripts, microRNAs are recognized as a major mechanism to regulate gene expression and mRNA translation. Computational prediction of microRNA targets is a critical initial step in identifying microRNA:mRNA target interactions for experimental validation. The available tools for microRNA target prediction encompass a range of different computational approaches, from the modeling of physical interactions to the incorporation of machine learning. This review provides an overview of the major computational approaches to microRNA target prediction. Our discussion highlights three tools for their ease of use, reliance on relatively updated versions of miRBase, and range of capabilities, and these are DIANA-microT-CDS, miRanda-mirSVR, and TargetScan. In comparison across all microRNA target prediction tools, four main aspects of the microRNA:mRNA target interaction emerge as common features on which most target prediction is based: seed match, conservation, free energy, and site accessibility. This review explains these features and identifies how they are incorporated into currently available target prediction tools. MicroRNA target prediction is a dynamic field with increasing attention on development of new analysis tools. This review attempts to provide a comprehensive assessment of these tools in a manner that is accessible across disciplines. Understanding the basis of these prediction methodologies will aid in user selection of the appropriate tools and interpretation of the tool output.

  7. Regulation of Corticosteroidogenic Genes by MicroRNAs

    Directory of Open Access Journals (Sweden)

    Stacy Robertson

    2017-01-01

    Full Text Available The loss of normal regulation of corticosteroid secretion is important in the development of cardiovascular disease. We previously showed that microRNAs regulate the terminal stages of corticosteroid biosynthesis. Here, we assess microRNA regulation across the whole corticosteroid pathway. Knockdown of microRNA using Dicer1 siRNA in H295R adrenocortical cells increased levels of CYP11A1, CYP21A1, and CYP17A1 mRNA and the secretion of cortisol, corticosterone, 11-deoxycorticosterone, 18-hydroxycorticosterone, and aldosterone. Bioinformatic analysis of genes involved in corticosteroid biosynthesis or metabolism identified many putative microRNA-binding sites, and some were selected for further study. Manipulation of individual microRNA levels demonstrated a direct effect of miR-125a-5p and miR-125b-5p on CYP11B2 and of miR-320a-3p levels on CYP11A1 and CYP17A1 mRNA. Finally, comparison of microRNA expression profiles from human aldosterone-producing adenoma and normal adrenal tissue showed levels of various microRNAs, including miR-125a-5p to be significantly different. This study demonstrates that corticosteroidogenesis is regulated at multiple points by several microRNAs and that certain of these microRNAs are differentially expressed in tumorous adrenal tissue, which may contribute to dysregulation of corticosteroid secretion. These findings provide new insights into the regulation of corticosteroid production and have implications for understanding the pathology of disease states where abnormal hormone secretion is a feature.

  8. Gaseous Matter

    CERN Document Server

    Angelo, Joseph A

    2011-01-01

    aseous Matter focuses on the many important discoveries that led to the scientific interpretation of matter in the gaseous state. This new, full-color resource describes the basic characteristics and properties of several important gases, including air, hydrogen, helium, oxygen, and nitrogen. The nature and scope of the science of fluids is discussed in great detail, highlighting the most important scientific principles upon which the field is based. Chapters include:. Gaseous Matter An Initial Perspective. Physical Characteristics of Gases. The Rise of the Science of Gases. Kinetic Theory of

  9. MicroRNA profiling reveals dysregulated microRNAs and their target gene regulatory networks in cemento-ossifying fibroma.

    Science.gov (United States)

    Pereira, Thaís Dos Santos Fontes; Brito, João Artur Ricieri; Guimarães, André Luiz Sena; Gomes, Carolina Cavaliéri; de Lacerda, Júlio Cesar Tanos; de Castro, Wagner Henriques; Coimbra, Roney Santos; Diniz, Marina Gonçalves; Gomez, Ricardo Santiago

    2018-01-01

    Cemento-ossifying fibroma (COF) is a benign fibro-osseous neoplasm of uncertain pathogenesis, and its treatment results in morbidity. MicroRNAs (miRNA) are small non-coding RNAs that regulate gene expression and may represent therapeutic targets. The purpose of the study was to generate a comprehensive miRNA profile of COF compared to normal bone. Additionally, the most relevant pathways and target genes of differentially expressed miRNA were investigated by in silico analysis. Nine COF and ten normal bone samples were included in the study. miRNA profiling was carried out by using TaqMan® OpenArray® Human microRNA panel containing 754 validated human miRNAs. We identified the most relevant miRNAs target genes through the leader gene approach, using STRING and Cytoscape software. Pathways enrichment analysis was performed using DIANA-miRPath. Eleven miRNAs were downregulated (hsa-miR-95-3p, hsa-miR-141-3p, hsa-miR-205-5p, hsa-miR-223-3p, hsa-miR-31-5p, hsa-miR-944, hsa-miR-200b-3p, hsa-miR-135b-5p, hsa-miR-31-3p, hsa-miR-223-5p and hsa-miR-200c-3p), and five were upregulated (hsa-miR-181a-5p, hsa-miR-181c-5p, hsa-miR-149-5p, hsa-miR-138-5p and hsa-miR-199a-3p) in COF compared to normal bone. Eighteen common target genes were predicted, and the leader genes approach identified the following genes involved in human COF: EZH2, XIAP, MET and TGFBR1. According to the biology of bone and COF, the most relevant KEGG pathways revealed by enrichment analysis were proteoglycans in cancer, miRNAs in cancer, pathways in cancer, p53-, PI3K-Akt-, FoxO- and TGF-beta signalling pathways, which were previously found to be differentially regulated in bone neoplasms, odontogenic tumours and osteogenesis. miRNA dysregulation occurs in COF, and EZH2, XIAP, MET and TGFBR1 are potential targets for functional analysis validation. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  10. MicroRNA expression characterizes oligometastasis(es).

    Science.gov (United States)

    Lussier, Yves A; Xing, H Rosie; Salama, Joseph K; Khodarev, Nikolai N; Huang, Yong; Zhang, Qingbei; Khan, Sajid A; Yang, Xinan; Hasselle, Michael D; Darga, Thomas E; Malik, Renuka; Fan, Hanli; Perakis, Samantha; Filippo, Matthew; Corbin, Kimberly; Lee, Younghee; Posner, Mitchell C; Chmura, Steven J; Hellman, Samuel; Weichselbaum, Ralph R

    2011-01-01

    Cancer staging and treatment presumes a division into localized or metastatic disease. We proposed an intermediate state defined by ≤ 5 cumulative metastasis(es), termed oligometastases. In contrast to widespread polymetastases, oligometastatic patients may benefit from metastasis-directed local treatments. However, many patients who initially present with oligometastases progress to polymetastases. Predictors of progression could improve patient selection for metastasis-directed therapy. Here, we identified patterns of microRNA expression of tumor samples from oligometastatic patients treated with high-dose radiotherapy. Patients who failed to develop polymetastases are characterized by unique prioritized features of a microRNA classifier that includes the microRNA-200 family. We created an oligometastatic-polymetastatic xenograft model in which the patient-derived microRNAs discriminated between the two metastatic outcomes. MicroRNA-200c enhancement in an oligometastatic cell line resulted in polymetastatic progression. These results demonstrate a biological basis for oligometastases and a potential for using microRNA expression to identify patients most likely to remain oligometastatic after metastasis-directed treatment.

  11. MicroRNA expression characterizes oligometastasis(es.

    Directory of Open Access Journals (Sweden)

    Yves A Lussier

    Full Text Available Cancer staging and treatment presumes a division into localized or metastatic disease. We proposed an intermediate state defined by ≤ 5 cumulative metastasis(es, termed oligometastases. In contrast to widespread polymetastases, oligometastatic patients may benefit from metastasis-directed local treatments. However, many patients who initially present with oligometastases progress to polymetastases. Predictors of progression could improve patient selection for metastasis-directed therapy.Here, we identified patterns of microRNA expression of tumor samples from oligometastatic patients treated with high-dose radiotherapy.Patients who failed to develop polymetastases are characterized by unique prioritized features of a microRNA classifier that includes the microRNA-200 family. We created an oligometastatic-polymetastatic xenograft model in which the patient-derived microRNAs discriminated between the two metastatic outcomes. MicroRNA-200c enhancement in an oligometastatic cell line resulted in polymetastatic progression.These results demonstrate a biological basis for oligometastases and a potential for using microRNA expression to identify patients most likely to remain oligometastatic after metastasis-directed treatment.

  12. Conditional Knockdown of Endogenous MicroRNAs in CHO Cells Using TET-ON-SanDI Sponge Vectors.

    Science.gov (United States)

    Costello, Alan; Lao, Nga; Clynes, Martin; Barron, Niall

    2017-01-01

    MicroRNAs (miRNAs) are small, noncoding RNAs of about 22 nucleotides in length and have proven to be useful targets for genetic modifications for desirable phenotype in the biotech industry. The use of constitutively expressed "miRNA sponge" vectors in which multiple, tandem miRNA binding sites containing transcripts are transcriptionally regulated by a constitutive promoter for down regulating the levels of endogenous microRNAs in Chinese hamster ovary (CHO) cells has shown to be more advantageous than using synthetic antisense oligonucleotides. The application of miRNA sponges in biotechnological processes, however, could be more effective, if expression of miRNA sponges could be tuned. In this chapter, we present a method for the generation of stable CHO cell lines expressing a TET-ON-SanDI-miRNA-sponge that is in theory expressed only in the presence of an inducer.

  13. MicroRNAs in the Hypothalamus

    DEFF Research Database (Denmark)

    Meister, Björn; Herzer, Silke; Silahtaroglu, Asli

    2013-01-01

    MicroRNAs (miRNAs) are short (∼22 nucleotides) non-coding ribonucleic acid (RNA) molecules that negatively regulate the expression of protein-coding genes. Posttranscriptional silencing of target genes by miRNA is initiated by binding to the 3'-untranslated regions of target mRNAs, resulting...... of the hypothalamus and miRNAs have recently been shown to be important regulators of hypothalamic control functions. The aim of this review is to summarize some of the current knowledge regarding the expression and role of miRNAs in the hypothalamus.......RNA molecules are abundantly expressed in tissue-specific and regional patterns and have been suggested as potential biomarkers, disease modulators and drug targets. The central nervous system is a prominent site of miRNA expression. Within the brain, several miRNAs are expressed and/or enriched in the region...

  14. Dark matters

    International Nuclear Information System (INIS)

    Silk, Joseph

    2010-01-01

    One of the greatest mysteries in the cosmos is that it is mostly dark. That is, not only is the night sky dark, but also most of the matter and the energy in the universe is dark. For every atom visible in planets, stars and galaxies today there exists at least five or six times as much 'Dark Matter' in the universe. Astronomers and particle physicists today are seeking to unravel the nature of this mysterious but pervasive dark matter, which has profoundly influenced the formation of structure in the universe. Dark energy remains even more elusive, as we lack candidate fields that emerge from well established physics. I will describe various attempts to measure dark matter by direct and indirect means, and discuss the prospects for progress in unravelling dark energy.

  15. Dirac matter

    CERN Document Server

    Rivasseau, Vincent; Fuchs, Jean-Nöel

    2017-01-01

    This fifteenth volume of the Poincare Seminar Series, Dirac Matter, describes the surprising resurgence, as a low-energy effective theory of conducting electrons in many condensed matter systems, including graphene and topological insulators, of the famous equation originally invented by P.A.M. Dirac for relativistic quantum mechanics. In five highly pedagogical articles, as befits their origin in lectures to a broad scientific audience, this book explains why Dirac matters. Highlights include the detailed "Graphene and Relativistic Quantum Physics", written by the experimental pioneer, Philip Kim, and devoted to graphene, a form of carbon crystallized in a two-dimensional hexagonal lattice, from its discovery in 2004-2005 by the future Nobel prize winners Kostya Novoselov and Andre Geim to the so-called relativistic quantum Hall effect; the review entitled "Dirac Fermions in Condensed Matter and Beyond", written by two prominent theoreticians, Mark Goerbig and Gilles Montambaux, who consider many other mater...

  16. microRNAs and lipid metabolism

    Science.gov (United States)

    Aryal, Binod; Singh, Abhishek K.; Rotllan, Noemi; Price, Nathan; Fernández-Hernando, Carlos

    2017-01-01

    Purpose of review Work over the last decade has identified the important role of microRNAs (miRNAS) in regulating lipoprotein metabolism and associated disorders including metabolic syndrome, obesity and atherosclerosis. This review summarizes the most recent findings in the field, highlighting the contribution of miRNAs in controlling low-density lipoprotein (LDL) and high-density lipoprotein (HDL) metabolism. Recent findings A number of miRNAs have emerged as important regulators of lipid metabolism, including miR-122 and miR-33. Work over the last two years has identified additional functions of miR-33 including the regulation of macrophage activation and mitochondrial metabolism. Moreover, it has recently been shown that miR-33 regulates vascular homeostasis and cardiac adaptation in response to pressure overload. In addition to miR-33 and miR-122, recent GWAS have identified single nucleotide polymorphisms (SNP) in the proximity of miRNAs genes associated with abnormal levels of circulating lipids in humans. Several of these miRNA, such as miR-148a and miR-128-1, target important proteins that regulate cellular cholesterol metabolism, including the low-density lipoprotein receptor (LDLR) and the ATP-binding cassette A1 (ABCA1). Summary microRNAs have emerged as critical regulators of cholesterol metabolism and promising therapeutic targets for treating cardiometabolic disorders including atherosclerosis. Here, we discuss the recent findings in the field highlighting the novel mechanisms by which miR-33 controls lipid metabolism and atherogenesis and the identification of novel miRNAs that regulate LDL metabolism. Finally, we summarize the recent findings that identified miR-33 as an important non-coding RNA that controls cardiovascular homeostasis independent of its role in regulating lipid metabolism. PMID:28333713

  17. Resonant SIMP dark matter

    Directory of Open Access Journals (Sweden)

    Soo-Min Choi

    2016-07-01

    Full Text Available We consider a resonant SIMP dark matter in models with two singlet complex scalar fields charged under a local dark U(1D. After the U(1D is broken down to a Z5 discrete subgroup, the lighter scalar field becomes a SIMP dark matter which has the enhanced 3→2 annihilation cross section near the resonance of the heavier scalar field. Bounds on the SIMP self-scattering cross section and the relic density can be fulfilled at the same time for perturbative couplings of SIMP. A small gauge kinetic mixing between the SM hypercharge and dark gauge bosons can be used to make SIMP dark matter in kinetic equilibrium with the SM during freeze-out.

  18. Cloning, characterization and expression analysis of porcine microRNAs

    Directory of Open Access Journals (Sweden)

    Desilva Udaya

    2009-02-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are small ~22-nt regulatory RNAs that can silence target genes, by blocking their protein production or degrading the mRNAs. Pig is an important animal in the agriculture industry because of its utility in the meat production. Besides, pig has tremendous biomedical importance as a model organism because of its closer proximity to humans than the mouse model. Several hundreds of miRNAs have been identified from mammals, humans, mice and rats, but little is known about the miRNA component in the pig genome. Here, we adopted an experimental approach to identify conserved and unique miRNAs and characterize their expression patterns in diverse tissues of pig. Results By sequencing a small RNA library generated using pooled RNA from the pig heart, liver and thymus; we identified a total of 120 conserved miRNA homologs in pig. Expression analysis of conserved miRNAs in 14 different tissue types revealed heart-specific expression of miR-499 and miR-208 and liver-specific expression of miR-122. Additionally, miR-1 and miR-133 in the heart, miR-181a and miR-142-3p in the thymus, miR-194 in the liver, and miR-143 in the stomach showed the highest levels of expression. miR-22, miR-26b, miR-29c and miR-30c showed ubiquitous expression in diverse tissues. The expression patterns of pig-specific miRNAs also varied among the tissues examined. Conclusion Identification of 120 miRNAs and determination of the spatial expression patterns of a sub-set of these in the pig is a valuable resource for molecular biologists, breeders, and biomedical investigators interested in post-transcriptional gene regulation in pig and in related mammals, including humans.

  19. Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa.

    Science.gov (United States)

    Morin, Ryan D; Aksay, Gozde; Dolgosheina, Elena; Ebhardt, H Alexander; Magrini, Vincent; Mardis, Elaine R; Sahinalp, S Cenk; Unrau, Peter J

    2008-04-01

    The diversity of microRNAs and small-interfering RNAs has been extensively explored within angiosperms by focusing on a few key organisms such as Oryza sativa and Arabidopsis thaliana. A deeper division of the plants is defined by the radiation of the angiosperms and gymnosperms, with the latter comprising the commercially important conifers. The conifers are expected to provide important information regarding the evolution of highly conserved small regulatory RNAs. Deep sequencing provides the means to characterize and quantitatively profile small RNAs in understudied organisms such as these. Pyrosequencing of small RNAs from O. sativa revealed, as expected, approximately 21- and approximately 24-nt RNAs. The former contained known microRNAs, and the latter largely comprised intergenic-derived sequences likely representing heterochromatin siRNAs. In contrast, sequences from Pinus contorta were dominated by 21-nt small RNAs. Using a novel sequence-based clustering algorithm, we identified sequences belonging to 18 highly conserved microRNA families in P. contorta as well as numerous clusters of conserved small RNAs of unknown function. Using multiple methods, including expressed sequence folding and machine learning algorithms, we found a further 53 candidate novel microRNA families, 51 appearing specific to the P. contorta library. In addition, alignment of small RNA sequences to the O. sativa genome revealed six perfectly conserved classes of small RNA that included chloroplast transcripts and specific types of genomic repeats. The conservation of microRNAs and other small RNAs between the conifers and the angiosperms indicates that important RNA silencing processes were highly developed in the earliest spermatophytes. Genomic mapping of all sequences to the O. sativa genome can be viewed at http://microrna.bcgsc.ca/cgi-bin/gbrowse/rice_build_3/.

  20. Imperfect Dark Matter

    Energy Technology Data Exchange (ETDEWEB)

    Mirzagholi, Leila; Vikman, Alexander, E-mail: l.mirzagholi@physik.uni-muenchen.de, E-mail: alexander.vikman@lmu.de [Arnold Sommerfeld Center for Theoretical Physics, Ludwig Maximilian University Munich, Theresienstr. 37, Munich, D-80333 Germany (Germany)

    2015-06-01

    We consider cosmology of the recently introduced mimetic matter with higher derivatives (HD). Without HD this system describes irrotational dust—Dark Matter (DM) as we see it on cosmologically large scales. DM particles correspond to the shift-charges—Noether charges of the shifts in the field space. Higher derivative corrections usually describe a deviation from the thermodynamical equilibrium in the relativistic hydrodynamics. Thus we show that mimetic matter with HD corresponds to an imperfect DM which: i) renormalises the Newton's constant in the Friedmann equations, ii) has zero pressure when there is no extra matter in the universe, iii) survives the inflationary expansion which puts the system on a dynamical attractor with a vanishing shift-charge, iv) perfectly tracks any external matter on this attractor, v) can become the main (and possibly the only) source of DM, provided the shift-symmetry in the HD terms is broken during some small time interval in the radiation domination époque. In the second part of the paper we present a hydrodynamical description of general anisotropic and inhomogeneous configurations of the system. This imperfect mimetic fluid has an energy flow in the field's rest frame. We find that in the Eckart and in the Landau-Lifshitz frames the mimetic fluid possesses nonvanishing vorticity appearing already at the first order in the HD. Thus, the structure formation and gravitational collapse should proceed in a rather different fashion from the simple irrotational DM models.

  1. Imperfect Dark Matter

    International Nuclear Information System (INIS)

    Mirzagholi, Leila; Vikman, Alexander

    2015-01-01

    We consider cosmology of the recently introduced mimetic matter with higher derivatives (HD). Without HD this system describes irrotational dust—Dark Matter (DM) as we see it on cosmologically large scales. DM particles correspond to the shift-charges—Noether charges of the shifts in the field space. Higher derivative corrections usually describe a deviation from the thermodynamical equilibrium in the relativistic hydrodynamics. Thus we show that mimetic matter with HD corresponds to an imperfect DM which: i) renormalises the Newton's constant in the Friedmann equations, ii) has zero pressure when there is no extra matter in the universe, iii) survives the inflationary expansion which puts the system on a dynamical attractor with a vanishing shift-charge, iv) perfectly tracks any external matter on this attractor, v) can become the main (and possibly the only) source of DM, provided the shift-symmetry in the HD terms is broken during some small time interval in the radiation domination époque. In the second part of the paper we present a hydrodynamical description of general anisotropic and inhomogeneous configurations of the system. This imperfect mimetic fluid has an energy flow in the field's rest frame. We find that in the Eckart and in the Landau-Lifshitz frames the mimetic fluid possesses nonvanishing vorticity appearing already at the first order in the HD. Thus, the structure formation and gravitational collapse should proceed in a rather different fashion from the simple irrotational DM models

  2. Imperfect Dark Matter

    Science.gov (United States)

    Mirzagholi, Leila; Vikman, Alexander

    2015-06-01

    We consider cosmology of the recently introduced mimetic matter with higher derivatives (HD). Without HD this system describes irrotational dust—Dark Matter (DM) as we see it on cosmologically large scales. DM particles correspond to the shift-charges—Noether charges of the shifts in the field space. Higher derivative corrections usually describe a deviation from the thermodynamical equilibrium in the relativistic hydrodynamics. Thus we show that mimetic matter with HD corresponds to an imperfect DM which: i) renormalises the Newton's constant in the Friedmann equations, ii) has zero pressure when there is no extra matter in the universe, iii) survives the inflationary expansion which puts the system on a dynamical attractor with a vanishing shift-charge, iv) perfectly tracks any external matter on this attractor, v) can become the main (and possibly the only) source of DM, provided the shift-symmetry in the HD terms is broken during some small time interval in the radiation domination époque. In the second part of the paper we present a hydrodynamical description of general anisotropic and inhomogeneous configurations of the system. This imperfect mimetic fluid has an energy flow in the field's rest frame. We find that in the Eckart and in the Landau-Lifshitz frames the mimetic fluid possesses nonvanishing vorticity appearing already at the first order in the HD. Thus, the structure formation and gravitational collapse should proceed in a rather different fashion from the simple irrotational DM models.

  3. Z2 SIMP dark matter

    International Nuclear Information System (INIS)

    Bernal, Nicolás; Chu, Xiaoyong

    2016-01-01

    Dark matter with strong self-interactions provides a compelling solution to several small-scale structure puzzles. Under the assumption that the coupling between dark matter and the Standard Model particles is suppressed, such strongly interacting massive particles (SIMPs) allow for a successful thermal freeze-out through N-to-N' processes, where N dark matter particles annihilate to N' of them. In the most common scenarios, where dark matter stability is guaranteed by a Z 2 symmetry, the seemingly leading annihilating channel, i.e. 3-to-2 process, is forbidden, so the 4-to-2 one dominate the production of the dark matter relic density. Moreover, cosmological observations require that the dark matter sector is colder than the thermal bath of Standard Model particles, a condition that can be dynamically generated via a small portal between dark matter and Standard Model particles, à la freeze-in. This scenario is exemplified in the context of the Singlet Scalar dark matter model

  4. Application of organic matter to enhance phytoremediation of mercury contaminated soils using local plant species: a case study on small-scale gold mining locations in Banyuwangi of East Java

    Directory of Open Access Journals (Sweden)

    N. Muddarisna

    2014-10-01

    Full Text Available The discharge of small-scale gold mine tailing to agricultural lands at Pesanggaran village of Banyuwangi Regency caused soil degradation as indicated by reduced crop production. This soil degradation is mainly due to the toxicity of mercury contained in the tailing. The purpose of this study was to explore the potential of three local plant species, i.e. Lindernia crustacea, Digitaria radicosa, and Cyperus kyllingia for phytoremediation of agricultural land contaminated gold mine waste containing mercury, and its influence on the growth of maize. Six treatments (three plant species, and two levels of organic matter application were arranged in a randomized block design with three replicates. Maize was grown on soil after phytoremediation for 8 weeks. The results showed that among the three plant species tested, Cyperus kyllingia was the potential candidate plant species for phytoremediation of soil contaminated with gold mine tailing containing mercury because of its ability to accumulate mercury from 32.06 to 73.90 mg / kg of soil in 60 days. Phytoremediation of mercury contaminated soil using Cyperus kyllingia using increased maize yield by 126% compared to that the biomass yield of maize grown on soil without phytoremediation. Induce phytoremediation needs to be carried out to accelerate the process of remediation of mercury contaminated soils

  5. Identification and Characterization of Liver MicroRNAs of the Chinese Tree Shrew via Deep Sequencing.

    Science.gov (United States)

    Feng, Yue; Feng, Yue-Mei; Feng, Yang; Lu, Caixia; Liu, Li; Sun, Xiaomei; Dai, Jiejie; Xia, Xueshan

    2015-10-01

    Chinese tree shrew (Tupaia belangeri chinensis) is a small animal that possess many features, which are valuable in biomedical research, as experimental models. Currently, there are numerous attempts to utilize tree shrews as models for hepatitis C virus (HCV) infection. This study aimed to construct a liver microRNA (miRNA) data of the tree shrew. Three second filial generation tree shrews were used in this study. Total RNA was extracted from each liver of the tree shrew and equal quality mixed, then reverse-transcribed to complementary DNA (cDNA). The cDNAs were amplified by polymerase chain reaction and subjected to high-throughput sequencing. A total of 2060 conserved miRNAs were identified through alignment with the mature miRNAs in miRBase 20.0 database. The gene ontology and Kyoto encyclopedia of genes and genomes analyses of the target genes of the miRNAs revealed several candidate miRNAs, genes and pathways that may involve in the process of HCV infection. The abundance of miR-122 and Let-7 families and their other characteristics provided us more evidences for the utilization of this animal, as a potential model for HCV infection and other related biomedical research. Moreover, 80 novel microRNAs were predicted using the software Mireap. The top 3 abundant miRNAs were validated in other tree samples, based on stem-loop quantitative reverse transcription-polymerase chain reaction. According to the liver microRNA data of Chinese tree shrew, characteristics of the miR-122 and Let-7 families further highlight the suitability of tree shrew as the animal model in HCV research.

  6. MicroRNA-133a Inhibits Osteosarcoma Cells Proliferation and Invasion via Targeting IGF-1R

    Directory of Open Access Journals (Sweden)

    Guangnan Chen

    2016-02-01

    Full Text Available Background/Aims: MicroRNAs (miRNAs are a class of small noncoding RNAs that regulate gene expression by repressing translation or cleaving RNA transcripts in a sequence-specific manner. Downregulated microRNAs and their roles in cancer development have attracted much attention. A growing body of evidence showed that microRNA-133a (miR-133a has inhibitory effects on cell proliferation, migration, invasion, and metastasis of osteosarcoma. Methods: MiR-133a expression in human osteosarcoma cell lines and human normal osteoblastic cell line hFOB was investigated by real-time PCR (RT-PCR. The role of miR-133a in human osteosarcoma growth and invasion was assessed in cell lines in vitro and in vivo. Then, luciferase reporter assay validated IGF-1R as a downstream and functional target of miR-133a, and functional studies revealed that the anti-tumor effect of miR-133a was probably due to targeting and repressing of IGF-1R expression. Results: MiR-133a was lower expressed in human osteosarcoma cell lines than human normal osteoblastic cell line hFOB and its effect on inhibiting proliferation, invasion and metastasis is mediated by its direct interaction with the IGF-1R. Furthermore, the tumour-suppressive function of miR-133a probably contributed to inhibiting the activation AKT and ERK signaling pathway. Conclusion: MiR-133a suppresses osteosarcoma progression and metastasis by targeting IGF-1R in human osteosarcoma cells, providing a novel candidate prognostic factor and a potential anti-metastasis therapeutic target in osteosarcoma.

  7. Regulation of Plant Microprocessor Function in Shaping microRNA Landscape

    Directory of Open Access Journals (Sweden)

    Jakub Dolata

    2018-06-01

    Full Text Available MicroRNAs are small molecules (∼21 nucleotides long that are key regulators of gene expression. They originate from long stem–loop RNAs as a product of cleavage by a protein complex called Microprocessor. The core components of the plant Microprocessor are the RNase type III enzyme Dicer-Like 1 (DCL1, the zinc finger protein Serrate (SE, and the double-stranded RNA binding protein Hyponastic Leaves 1 (HYL1. Microprocessor assembly and its processing of microRNA precursors have been reported to occur in discrete nuclear bodies called Dicing bodies. The accessibility of and modifications to Microprocessor components affect microRNA levels and may have dramatic consequences in plant development. Currently, numerous lines of evidence indicate that plant Microprocessor activity is tightly regulated. The cellular localization of HYL1 is dependent on a specific KETCH1 importin, and the E3 ubiquitin ligase COP1 indirectly protects HYL1 from degradation in a light-dependent manner. Furthermore, proper localization of HYL1 in Dicing bodies is regulated by MOS2. On the other hand, the Dicing body localization of DCL1 is regulated by NOT2b, which also interacts with SE in the nucleus. Post-translational modifications are substantial factors that contribute to protein functional diversity and provide a fine-tuning system for the regulation of protein activity. The phosphorylation status of HYL1 is crucial for its activity/stability and is a result of the interplay between kinases (MPK3 and SnRK2 and phosphatases (CPL1 and PP4. Additionally, MPK3 and SnRK2 are known to phosphorylate SE. Several other proteins (e.g., TGH, CDF2, SIC, and RCF3 that interact with Microprocessor have been found to influence its RNA-binding and processing activities. In this minireview, recent findings on the various modes of Microprocessor activity regulation are discussed.

  8. Regulation of neutrophil senescence by microRNAs.

    Directory of Open Access Journals (Sweden)

    Jon R Ward

    2011-01-01

    Full Text Available Neutrophils are rapidly recruited to sites of tissue injury or infection, where they protect against invading pathogens. Neutrophil functions are limited by a process of neutrophil senescence, which renders the cells unable to respond to chemoattractants, carry out respiratory burst, or degranulate. In parallel, aged neutrophils also undergo spontaneous apoptosis, which can be delayed by factors such as GMCSF. This is then followed by their subsequent removal by phagocytic cells such as macrophages, thereby preventing unwanted inflammation and tissue damage. Neutrophils translate mRNA to make new proteins that are important in maintaining functional longevity. We therefore hypothesised that neutrophil functions and lifespan might be regulated by microRNAs expressed within human neutrophils. Total RNA from highly purified neutrophils was prepared and subjected to microarray analysis using the Agilent human miRNA microarray V3. We found human neutrophils expressed a selected repertoire of 148 microRNAs and that 6 of these were significantly upregulated after a period of 4 hours in culture, at a time when the contribution of apoptosis is negligible. A list of predicted targets for these 6 microRNAs was generated from http://mirecords.biolead.org and compared to mRNA species downregulated over time, revealing 83 genes targeted by at least 2 out of the 6 regulated microRNAs. Pathway analysis of genes containing binding sites for these microRNAs identified the following pathways: chemokine and cytokine signalling, Ras pathway, and regulation of the actin cytoskeleton. Our data suggest that microRNAs may play a role in the regulation of neutrophil senescence and further suggest that manipulation of microRNAs might represent an area of future therapeutic interest for the treatment of inflammatory disease.

  9. MicroRNAs expression profile in solid and unicystic ameloblastomas

    Science.gov (United States)

    Setién-Olarra, A.; Bediaga, N. G.; Aguirre-Echebarria, P.; Aguirre-Urizar, J. M.; Mosqueda-Taylor, A.

    2017-01-01

    Objectives Odontogenic tumors (OT) represent a specific pathological category that includes some lesions with unpredictable biological behavior. Although most of these lesions are benign, some, such as the ameloblastoma, exhibit local aggressiveness and high recurrence rates. The most common types of ameloblastoma are the solid/multicystic (SA) and the unicystic ameloblastoma (UA); the latter considered a much less aggressive entity as compared to the SA. The microRNA system regulates the expression of many human genes while its deregulation has been associated with neoplastic development. The aim of the current study was to determine the expression profiles of microRNAs present in the two most common types of ameloblastomas. Material & methods MicroRNA expression profiles were assessed using TaqMan® Low Density Arrays (TLDAs) in 24 samples (8 SA, 8 UA and 8 control samples). The findings were validated using quantitative RTqPCR in an independent cohort of 19 SA, 8 UA and 19 dentigerous cysts as controls. Results We identified 40 microRNAs differentially regulated in ameloblastomas, which are related to neoplastic development and differentiation, and with the osteogenic process. Further validation of the top ranked microRNAs revealed significant differences in the expression of 6 of them in relation to UA, 7 in relation to SA and 1 (miR-489) that was related to both types. Conclusion We identified a new microRNA signature for the ameloblastoma and for its main types, which may be useful to better understand the etiopathogenesis of this neoplasm. In addition, we identified a microRNA (miR-489) that is suggestive of differentiating among solid from unicystic ameloblastoma. PMID:29053755

  10. MicroRNA expression in a phosphaturic mesenchymal tumour

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    Darrell Green

    2017-12-01

    Full Text Available Phosphaturic mesenchymal tumours are a heterogeneous set of bone and soft tissue neoplasms that can cause a number of paraneoplastic syndromes such as tumour induced osteomalacia. The term phosphaturic comes from the common finding that these tumours secrete high levels of fibroblast growth factor 23 which causes renal phosphate wasting leading to hypophosphatemia. Phosphaturic mesenchymal tumours are rare and diagnosis is difficult. A very active 68 year old male presented with bone pain and muscle weakness. He was hypophosphataemic and total alkaline phosphatase was markedly elevated. The patient was placed on vitamin D supplementation but his condition progressed. In the fifth year of presentation the patient required the use of a wheelchair and described “explosive” bone pain on physical contact. Serum 1,25 dihydroxyvitamin D was low and serum fibroblast growth factor 23 was significantly elevated, raising suspicion of a phosphaturic mesenchymal tumour. A lesion was detected in his left femoral head and the patient underwent a total hip replacement. The patient displayed a rapid improvement to his condition and during a three year follow up period he returned to an active lifestyle. As molecular testing may help provide a robust diagnosis and is particularly useful in rare diseases we took a next generation sequencing approach to identify a differential expression of small RNAs in the resected tumour. Small RNAs are non-coding RNA molecules that play a key role in regulation of gene expression and can be used as specific biomarkers. We found an upregulation of miR-197. We also found a downregulation of miR-20b, miR-144 and miR-335 which is a small RNA profile typical of osteosarcoma. MiR-21, the most frequently upregulated microRNA in cancer, was downregulated. We conclude that the specific small RNA profile is typical of osteosarcoma except for the downregulation of oncogenic miR-21. Transcriptional plasticity of miR-197, which is

  11. Quantification of microRNA-21 and microRNA-125b in melanoma tissue

    DEFF Research Database (Denmark)

    Wandler, Anne; Riber-Hansen, Rikke; Hager, Henrik

    2017-01-01

    Although microRNAs (miRNAs) have emerged as potent mediators of melanoma development and progression, a precise understanding of their oncogenic role remains unclear. In this study, we analysed formalin-fixed and paraffin-embedded tissues from two separate melanoma cohorts and from a series...... the important involvement of different miRNAs in melanoma biology and may serve as solid basics for further miRNA investigations in melanoma formalin-fixed and paraffin-embedded tissue. In particular, there is increased expression of miR-21 in melanomas compared with benign nevi....

  12. Quark matter

    Energy Technology Data Exchange (ETDEWEB)

    Csernai, L.; Kampert, K. H.

    1994-10-15

    Precisely one decade ago the GSI (Darmstadt)/LBL (Berkeley) Collaboration at the Berkeley Bevalac reported clear evidence for collective sidewards flow in high energy heavy ion collisions. This milestone observation clearly displayed the compression and heating up of nuclear matter, providing new insights into how the behaviour of nuclear matter changes under very different conditions. This year, evidence for azimuthally asymmetric transverse flow at ten times higher projectile energy (11 GeV per nucleon gold on gold collisions) was presented by the Brookhaven E877 collaboration at the recent European Research Conference on ''Physics of High Energy Heavy Ion Collisions'', held in Helsinki from 17-22 June.

  13. Genome-wide annotation of porcine microRNA genes and transcriptome profiling during Actinobacillus infection

    DEFF Research Database (Denmark)

    Nielsen, Mathilde

    MicroRNAs are small single stranded non-coding RNA molecules which contributes to the regulation of gene expression by primarily binding to the 3´end of protein coding mRNA, hereby inhibiting the translation process or promting degradation of the mRNA. The main focus of this PhD project was to ex......MicroRNAs are small single stranded non-coding RNA molecules which contributes to the regulation of gene expression by primarily binding to the 3´end of protein coding mRNA, hereby inhibiting the translation process or promting degradation of the mRNA. The main focus of this PhD project...

  14. Profile of cerebrospinal microRNAs in fibromyalgia.

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    Jan L Bjersing

    Full Text Available Fibromyalgia (FM is characterized by chronic pain and reduced pain threshold. The pathophysiology involves disturbed neuroendocrine function, including impaired function of the growth hormone/insulin-like growth factor-1 axis. Recently, microRNAs have been shown to be important regulatory factors in a number of diseases. The aim of this study was to try to identify cerebrospinal microRNAs with expression specific for FM and to determine their correlation to pain and fatigue.The genome-wide profile of microRNAs in cerebrospinal fluid was assessed in ten women with FM and eight healthy controls using real-time quantitative PCR. Pain thresholds were examined by algometry. Levels of pain (FIQ pain were rated on a 0-100 mm scale (fibromyalgia impact questionnaire, FIQ. Levels of fatigue (FIQ fatigue were rated on a 0-100 mm scale using FIQ and by multidimensional fatigue inventory (MFI-20 general fatigue (MFIGF.Expression levels of nine microRNAs were significantly lower in patients with FM patients compared to healthy controls. The microRNAs identified were miR-21-5p, miR-145-5p, miR-29a-3p, miR-99b-5p, miR-125b-5p, miR-23a-3p, 23b-3p, miR-195-5p, miR-223-3p. The identified microRNAs with significantly lower expression in FM were assessed with regard to pain and fatigue. miR-145-5p correlated positively with FIQ pain (r=0.709, p=0.022, n=10 and with FIQ fatigue (r=0.687, p=0.028, n=10.To our knowledge, this is the first study to show a disease-specific pattern of cerebrospinal microRNAs in FM. We have identified nine microRNAs in cerebrospinal fluid that differed between FM patients and healthy controls. One of the identified microRNAs, miR-145 was associated with the cardinal symptoms of FM, pain and fatigue.

  15. Profile of cerebrospinal microRNAs in fibromyalgia.

    Science.gov (United States)

    Bjersing, Jan L; Lundborg, Christopher; Bokarewa, Maria I; Mannerkorpi, Kaisa

    2013-01-01

    Fibromyalgia (FM) is characterized by chronic pain and reduced pain threshold. The pathophysiology involves disturbed neuroendocrine function, including impaired function of the growth hormone/insulin-like growth factor-1 axis. Recently, microRNAs have been shown to be important regulatory factors in a number of diseases. The aim of this study was to try to identify cerebrospinal microRNAs with expression specific for FM and to determine their correlation to pain and fatigue. The genome-wide profile of microRNAs in cerebrospinal fluid was assessed in ten women with FM and eight healthy controls using real-time quantitative PCR. Pain thresholds were examined by algometry. Levels of pain (FIQ pain) were rated on a 0-100 mm scale (fibromyalgia impact questionnaire, FIQ). Levels of fatigue (FIQ fatigue) were rated on a 0-100 mm scale using FIQ and by multidimensional fatigue inventory (MFI-20) general fatigue (MFIGF). Expression levels of nine microRNAs were significantly lower in patients with FM patients compared to healthy controls. The microRNAs identified were miR-21-5p, miR-145-5p, miR-29a-3p, miR-99b-5p, miR-125b-5p, miR-23a-3p, 23b-3p, miR-195-5p, miR-223-3p. The identified microRNAs with significantly lower expression in FM were assessed with regard to pain and fatigue. miR-145-5p correlated positively with FIQ pain (r=0.709, p=0.022, n=10) and with FIQ fatigue (r=0.687, p=0.028, n=10). To our knowledge, this is the first study to show a disease-specific pattern of cerebrospinal microRNAs in FM. We have identified nine microRNAs in cerebrospinal fluid that differed between FM patients and healthy controls. One of the identified microRNAs, miR-145 was associated with the cardinal symptoms of FM, pain and fatigue.

  16. Intra-tumor heterogeneity of microRNA-92a, microRNA-375 and microRNA-424 in colorectal cancer

    DEFF Research Database (Denmark)

    Jepsen, Rikke Karlin; Novotny, Guy Wayne; Klarskov, Louise Laurberg

    2016-01-01

    Various microRNAs (miRNAs) have been investigated in order to improve diagnostics and risk assessment in colorectal cancer (CRC). To clarify the potential of miRNA profiling in CRC, knowledge of intra-tumor heterogeneity in expression levels is crucial. The study aim was to estimate the intra...

  17. Application of TALE-Based Approach for Dissecting Functional MicroRNA-302/367 in Cellular Reprogramming.

    Science.gov (United States)

    Zhang, Zhonghui; Wu, Wen-Shu

    2018-01-01

    MicroRNAs are small 18-24 nt single-stranded noncoding RNA molecules involved in many biological processes, including stemness maintenance and cellular reprogramming. Current methods used in loss-of-function studies of microRNAs have several limitations. Here, we describe a new approach for dissecting miR-302/367 functions by transcription activator-like effectors (TALEs), which are natural effector proteins secreted by Xanthomonas and Ralstonia bacteria. Knockdown of the miR-302/367 cluster uses the Kruppel-associated box repressor domain fused with specific TALEs designed to bind the miR-302/367 cluster promoter. Knockout of the miR-302/367 cluster uses two pairs of TALE nucleases (TALENs) to delete the miR-302/367 cluster in human primary cells. Together, both TALE-based transcriptional repressor and TALENs are two promising approaches for loss-of-function studies of microRNA cluster in human primary cells.

  18. Circulating MicroRNAs in Serum from Cattle Challenged with Bovine Viral Diarrhea Virus‡

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    Tasia M. Taxis

    2017-06-01

    Full Text Available Bovine viral diarrhea virus (BVDV is an RNA virus that is often associated with respiratory disease in cattle. MicroRNAs have been proposed as indicators of exposure to respiratory pathogens. The objective of this study was to identify microRNAs in cattle that had been challenged with a non-cytopathic field strain of BVDV. Five colostrum deprived neonate Holstein calves were inoculated with BVDV (challenged and 4 were mock challenged (control. Serum from all calves was collected at four different times: prior to challenge (day 0 and at 4, 9, and 16 days post-challenge. RNA was extracted from sera, and expression, via read counts, of small non-coding RNAs were obtained using next-generation sequencing. A total of 905,861 sequences identified 427 microRNAs. Sixty-two microRNAs had >1,000 total reads across all samples. Bta-miR-339a, bta-miR-185, bta-miR-486, Bta-miR-92a, bta-miR-30e-5p, bta-let-7c, and bta-miR-2284x were significantly different (P < 0.05 across time regardless of challenge status. Bta-miR-423-5p (P = 0.008 and bta-miR-151-3p (P = 0.005 were significantly different between challenged and control animals across time. In challenged animals, bta-miR-423-5p peaked in number of reads by day 4 and steadily declined from day 4 to day 16. In control animals, bta-miR-423-5p declined from day 0 to day 9 and increased in number by day 16. By day 16, both challenged and control animals had similar levels of bta-miR-423-5p, and these levels were similar to day 0 levels. Bta-miR-151-3p peaked at day 9 in challenged animals, while control animals decreased across time. By day 16, the number of reads of bta-miR-151-3p were similar between challenged and control animals. The level in challenged animals had returned to day 0 levels by day 16, whereas the levels for control animals was significantly lower (P = 0.006 than day 0. Further studies are needed to establish if bta-miR-423-5p or bta-miR-151-3p could be used as a biomarker for exposure to

  19. MicroRNAs in Obesity, Metabolic Syndrome and Diabetes Mellitus

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    Anna Meiliana

    2011-04-01

    Full Text Available BACKGROUND: MicroRNAs (miRNAs are small regulatory RNAs that play important roles in development of diseases. Several studies have provided evidences showing that miRNAs affect pathways that are fundamental for metabolic control in adipocyte and skeletal muscle differentiations. Some miRNAs have been implicated in lipid, amino acid, and glucose homeostasis. This leads to the possibility that miRNAs may contribute to common metabolic diseases and point to novel therapeutic opportunities based on targeting of miRNAs. CONTENT: miRNAs have been recognized as a class of epigenetic regulators of metabolism and energy homeostasis, primarily because the simultaneous regulation of a large number of target genes can be accomplished by a single miRNA. Emerging evidences suggest that miRNAs play a key role in the pathological development of obesity by affecting adipocyte differentiation. miRNAs have been implicated as novel protagonists in the pathogenesis of Diabetes Mellitus (DM, regulation of insulin production, secretion and action. They also appear to play a role in the development of diabetic complications such as nephropathy and cardiac hypertrophy. SUMMARY: Involvement of miRNAs in glucose and lipid metabolism has provided strong evidences to confirm their roles as key players in regulation of complex metabolic pathways. Additionally, it indicates potential outlook for novel therapeutic strategies in the management of obesity, metabolic syndrome and DM. Further research in this field is needed to ascertain the full potential of miRNAs as novel metabolic biomarkers and potent therapeutic agents against obesity and its metabolic disorders. KEYWORDS: obesity, metabolic syndrome, diabetes, miRNAs, adipogenesis, insulin, pancreatic cells.

  20. MicroRNA and Male Infertility: A Potential for Diagnosis

    Directory of Open Access Journals (Sweden)

    Yahya Khazaie

    2014-07-01

    Full Text Available MicroRNAs (miRNAs are small non-coding single stranded RNA molecules that are physiologically produced in eukaryotic cells to regulate or mostly down-regulate genes by pairing with their complementary base-sequence in related mRNA molecules in the cytoplasm. It has been reported that other than its function in many physiological cell processes, dysregulation of miRNAs plays a role in the development of many diseases. In this short review, the association between miRNAs and some male reproductive disorders is surveyed. Male factor Infertility is a devastating problem from which a notable percentage of couples suffer. However, the molecular mechanism of many infertility disorders has not been clearly elucidated. Since miRNAs have an important role in numerous biological cell processes and cellular dysfunctions, it is of interest to review the related literature on the role of miRNAs in the male reproductive organs. Aberrant expression of specific miRNAs is associated with certain male reproductive dysfunctions. For this reason, assessment of expression of such miRNAs may serve as a suitable molecular biomarker for diagnosis of those male infertility disorders. The presence of a single nucleotide polymorphism (SNP at the miRNAs’ binding site in its targeted mRNA has been reported to have an association with idiopathic male infertility. Also, a relation with male infertility has been shown with SNP in the genes of the factors necessary for miRNA biogenesis. Therefore, focusing on the role of miRNAs in male reproductive disorders can further elucidate the molecular mechanisms of male infertility and generate the potential for locating efficient biomarkers and therapeutic agents for these disorders.

  1. Challenges and Opportunities of MicroRNAs in Lymphomas

    Directory of Open Access Journals (Sweden)

    Giacoma De Tullio

    2014-09-01

    Full Text Available MicroRNAs (miRNAs are small non-coding RNAs that control the expression of many target messenger RNAs (mRNAs involved in normal cell functions (differentiation, proliferation and apoptosis. Consequently their aberrant expression and/or functions are related to pathogenesis of many human diseases including cancers. Haematopoiesis is a highly regulated process controlled by a complex network of molecular mechanisms that simultaneously regulate commitment, differentiation, proliferation, and apoptosis of hematopoietic stem cells (HSC. Alterations on this network could affect the normal haematopoiesis, leading to the development of haematological malignancies such as lymphomas. The incidence of lymphomas is rising and a significant proportion of patients are refractory to standard therapies. Accurate diagnosis, prognosis and therapy still require additional markers to be used for diagnostic and prognostic purpose and evaluation of clinical outcome. The dysregulated expression or function of miRNAs in various types of lymphomas has been associated with lymphoma pathogenesis. Indeed, many recent findings suggest that almost all lymphomas seem to have a distinct and specific miRNA profile and some miRNAs are related to therapy resistance or have a distinct kinetics during therapy. MiRNAs are easily detectable in fresh or paraffin-embedded diagnostic tissue and serum where they are highly stable and quantifiable within the diagnostic laboratory at each consultation. Accordingly they could be specific biomarkers for lymphoma diagnosis, as well as useful for evaluating prognosis or disease response to the therapy, especially for evaluation of early relapse detection and for greatly assisting clinical decisions making. Here we summarize the current knowledge on the role of miRNAs in normal and aberrant lymphopoiesis in order to highlight their clinical value as specific diagnosis and prognosis markers of lymphoid malignancies or for prediction of therapy

  2. Self-interacting warm dark matter

    International Nuclear Information System (INIS)

    Hannestad, Steen; Scherrer, Robert J.

    2000-01-01

    It has been shown by many independent studies that the cold dark matter scenario produces singular galactic dark halos, in strong contrast with observations. Possible remedies are that either the dark matter is warm so that it has significant thermal motion or that the dark matter has strong self-interactions. We combine these ideas to calculate the linear mass power spectrum and the spectrum of cosmic microwave background (CMB) fluctuations for self-interacting warm dark matter. Our results indicate that such models have more power on small scales than is the case for the standard warm dark matter model, with a CMB fluctuation spectrum which is nearly indistinguishable from standard cold dark matter. This enhanced small-scale power may provide better agreement with the observations than does standard warm dark matter. (c) 2000 The American Physical Society

  3. Dark Matter

    Indian Academy of Sciences (India)

    As if this was not enough, it turns out that if our knowledge of ... are thought to contain dark matter, although the evidences from them are the .... protons, electrons, neutrons ... ratio of protons to neutrons was close to unity then as they were in ...

  4. Quantum matter

    International Nuclear Information System (INIS)

    Buechler, Hans Peter; Calcarco, Tommaso; Dressel, Martin

    2008-01-01

    The following topics are dealt with: Artificial atoms and molecules, tailored from solids, fractional flux quanta, molecular magnets, controlled interaction in quantum gases, the theory of quantum correlations in mott matter, cold gases, and mesoscopic systems, Bose-Einstein condensates on the chip, on the route to the quantum computer, a quantum computer in diamond. (HSI)

  5. Molecule Matters

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 4. Molecule Matters – van der Waals Molecules - History and Some Perspectives on Intermolecular Forces. E Arunan. Feature Article Volume 14 Issue 4 April 2009 pp 346-356 ...

  6. Molecule Matters

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 16; Issue 12. Molecule Matters - Dinitrogen. A G Samuelson J Jabadurai. Volume 16 Issue 12 ... Author Affiliations. A G Samuelson1 J Jabadurai1. Department of Inroganic and Physical Chemistry, Indian Institute of Science, Bangalore 560 012, India.

  7. Interstellar matter

    International Nuclear Information System (INIS)

    Mezger, P.G.

    1978-01-01

    An overview of the formation of our galaxy is presented followed by a summary of recent work in star formation and related topics. Selected discussions are given on interstellar matter including absorption characteristics of dust, the fully ionised component of the ISM and the energy density of lyc-photons in the solar neighbourhood and the diffuse galactic IR radiation

  8. Dark Matter

    Indian Academy of Sciences (India)

    The study of gas clouds orbiting in the outer regions of spiral galaxies has revealed that their gravitational at- traction is much larger than the stars alone can provide. Over the last twenty years, astronomers have been forced to postulate the presence of large quantities of 'dark matter' to explain their observations. They are ...

  9. Molecule Matters

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 9. Molecule Matters - A Chromium Compound with a Quintuple Bond. K C Kumara Swamy. Feature Article Volume 11 Issue 9 September 2006 pp 72-75. Fulltext. Click here to view fulltext PDF. Permanent link:

  10. Methods for small RNA preparation for digital gene expression profiling by next-generation sequencing

    NARCIS (Netherlands)

    Linsen, S.E.V.; Cuppen, E.

    2012-01-01

    Digital gene expression (DGE) profiling techniques are playing an eminent role in the detection, localization, and differential expression quantification of many small RNA species, including microRNAs (1-3). Procedures in small RNA library preparation techniques typically include adapter ligation by

  11. Alternative dark matter candidates. Axions

    International Nuclear Information System (INIS)

    Ringwald, Andreas

    2017-01-01

    The axion is arguably one of the best motivated candidates for dark matter. For a decay constant >or similar 10 9 GeV, axions are dominantly produced non-thermally in the early universe and hence are ''cold'', their velocity dispersion being small enough to fit to large scale structure. Moreover, such a large decay constant ensures the stability at cosmological time scales and its behaviour as a collisionless fluid at cosmological length scales. Here, we review the state of the art of axion dark matter predictions and of experimental efforts to search for axion dark matter in laboratory experiments.

  12. Matter-Wave Tractor Beams

    DEFF Research Database (Denmark)

    Gorlach, Alexey A.; Gorlach, Maxim A.; Lavrinenko, Andrei

    2017-01-01

    Optical and acoustic tractor beams are currently the focus of intense research due to their counterintuitive property of exerting a pulling force on small scattering objects. In this Letter we propose a matter-wave tractor beam and utilize the de Broglie waves of nonrelativistic matter particles...... are compared, and the matter-wave pulling force is found to have exclusive properties of dragging slow particles in short-range potentials. We envisage that the use of tractor beams could lead to the unprecedented precision in manipulation with atomic-scale quantum objects....

  13. Alternative dark matter candidates. Axions

    Energy Technology Data Exchange (ETDEWEB)

    Ringwald, Andreas

    2017-01-15

    The axion is arguably one of the best motivated candidates for dark matter. For a decay constant >or similar 10{sup 9} GeV, axions are dominantly produced non-thermally in the early universe and hence are ''cold'', their velocity dispersion being small enough to fit to large scale structure. Moreover, such a large decay constant ensures the stability at cosmological time scales and its behaviour as a collisionless fluid at cosmological length scales. Here, we review the state of the art of axion dark matter predictions and of experimental efforts to search for axion dark matter in laboratory experiments.

  14. Dark Matter

    International Nuclear Information System (INIS)

    Audouze, J.; Tran Thanh Van, J.

    1988-01-01

    The book begins with the papers devoted to the experimental search of signatures of the dark matter which governs the evolution of the Universe as a whole. A series of contributions describe the presently considered experimental techniques (cryogenic detectors, supraconducting detectors...). A real dialogue concerning these techniques has been instaured between particle physicists and astrophysicists. After the progress report of the particle physicists, the book provides the reader with an updated situation concerning the research in cosmology. The second part of the book is devoted to the analysis of the backgrounds at different energies such as the possible role of the cooling flows in the constitution of massive galactic halos. Any search of dark matter implies necessarily the analysis of the spatial distributions of the large scale structures of the Universe. This report is followed by a series of statistical analyses of these distributions. These analyses concern mainly universes filled up with cold dark matter. The last paper of this third part concerns the search of clustering in the spatial distribution of QSOs. The presence of dark matter should affect the solar neighborhood and related to the existence of galactic haloes. The contributions are devoted to the search of such local dark matter. Primordial nucleosynthesis provides a very powerful tool to set up quite constraining limitations on the overall baryonic density. Even if on takes into account the inhomogeneities in density possibly induced by the Quark-Hadron transition, this baryonic density should be much lower than the overall density deduced from the dynamical models of Universe or the inflationary theories

  15. Proanthocyanidins modulate microRNA expression in human HepG2 cells.

    Directory of Open Access Journals (Sweden)

    Anna Arola-Arnal

    Full Text Available Mi(croRNAs are small non-coding RNAs of 18-25 nucleotides in length that modulate gene expression at the post-transcriptional level. These RNAs have been shown to be involved in a several biological processes, human diseases and metabolic disorders. Proanthocyanidins, which are the most abundant polyphenol class in the human diet, have positive health effects on a variety of metabolic disorders such as inflammation, obesity, diabetes and insulin resistance. The present study aimed to evaluate whether proanthocyanidin-rich natural extracts modulate miRNA expression. Using microarray analysis and Q-PCR, we investigated miRNA expression in HepG2 cells treated with proanthocyanidins. Our results showed that when HepG2 cells were treated with grape seed proanthocyanidin extract (GSPE, cocoa proanthocyanidin extract (CPE or pure epigallocatechin gallate isolated from green tea (EGCG, fifteen, six and five differentially expressed miRNAs, respectively, were identified out of 904 mRNAs. Specifically, miR-30b* was downregulated by the three treatments, and treatment with GSPE or CPE upregulated miR-1224-3p, miR-197 and miR-532-3p. Therefore, these results provide evidence of the capacity of dietary proanthocyanidins to influence microRNA expression, suggesting a new mechanism of action of proanthocyanidins.

  16. The Role of Exportin-5 in MicroRNA Biogenesis and Cancer

    Directory of Open Access Journals (Sweden)

    Ke Wu

    2018-04-01

    Full Text Available MicroRNAs (miRNAs are conserved small non-coding RNAs that play an important role in the regulation of gene expression and participate in a variety of biological processes. The biogenesis of miRNAs is tightly controlled at multiple steps, such as transcription of miRNA genes, processing by Drosha and Dicer, and transportation of precursor miRNAs (pre-miRNAs from the nucleus to the cytoplasm by exportin-5 (XPO5. Given the critical role of nuclear export of pre-miRNAs in miRNA biogenesis, any alterations of XPO5, resulting from either genetic mutation, epigenetic change, abnormal expression level or posttranslational modification, could affect miRNA expression and thus have profound effects on tumorigenesis. Importantly, XPO5 phosphorylation by ERK kinase and its cis/trans isomerization by the prolyl isomerase Pin1 impair XPO5′s nucleo-to-cytoplasmic transport ability of pre-miRNAs, leading to downregulation of mature miRNAs in hepatocellular carcinoma. In this review, we focus on how XPO5 transports pre-miRNAs in the cells and summarize the dysregulation of XPO5 in human tumors. Keywords: Exportin-5, MicroRNA, Biogenesis, Dysregulation, Cancer

  17. Computational study of ‘HUB’ microRNA in human cardiac diseases

    Science.gov (United States)

    Krishnan, Remya; Nair, Achuthsankar S.; Dhar, Pawan K.

    2017-01-01

    MicroRNAs (miRNAs) are small non-coding RNAs ~22 nucleotides long that do not encode for proteins but have been reported to influence gene expression in normal and abnormal health conditions. Though a large body of scientific literature on miRNAs exists, their network level profile linking molecules with their corresponding phenotypes, is less explored. Here, we studied a network of 191 human miRNAs reported to play a role in 30 human cardiac diseases. Our aim was to study miRNA network properties like hubness and preferred associations, using data mining, network graph theory and statistical analysis. A total of 16 miRNAs were found to have a disease node connectivity of >5 edges (i.e., they were linked to more than 5 diseases) and were considered hubs in the miRNAcardiac disease network. Alternatively, when diseases were considered as hubs, >10 of miRNAs showed up on each ‘disease hub node’. Of all the miRNAs associated with diseases, 19 miRNAs (19/24= 79.1% of upregulated events) were found to be upregulated in atherosclerosis. The data suggest micro RNAs as early stage biological markers in cardiac conditions with potential towards microRNA based therapeutics. PMID:28479745

  18. Alterations of MicroRNAs in Solid Cancers and Their Prognostic Value

    International Nuclear Information System (INIS)

    Chira, Panagiota; Vareli, Katerina; Sainis, Ioannis; Papandreou, Christos; Briasoulis, Evangelos

    2010-01-01

    MicroRNAs (miRNAs) are evolutionarily conserved, naturally abundant, small, regulatory non-coding RNAs that inhibit gene expression at the post-transcriptional level in a sequence-specific manner. Each miRNA represses the protein expression of several coding genes in a manner proportional to the sequence complementarity with the target transcripts. MicroRNAs play key regulatory roles in organismal development and homeostasis. They control fundamental biological processes, such as stem-cell regulation and cellular metabolism, proliferation, differentiation, stress resistance, and apoptosis. Differential miRNA expression is found in malignant tumors in comparison to normal tissue counterparts. This indicates that miRNA deregulation contributes to the initiation and progression of cancer. Currently, miRNA expression signatures are being rigorously investigated in various tumor types, with the aim of developing novel, efficient biomarkers that can improve clinical management of cancer patients. This review discusses deregulated miRNAs in solid tumors, and focuses on their emerging prognostic potential

  19. MicroRNAs and hepatitis C virus: Toward the end of miR-122 supremacy

    Directory of Open Access Journals (Sweden)

    Hoffmann Thomas

    2012-06-01

    Full Text Available Abstract The most common etiologic agents causing chronic hepatitis are hepatitis C and B viruses (HCV and HBV, respectively. Chronic infection caused by HCV is considered one of the major causative agents of liver cirrhosis and hepatocellular carcinoma worldwide. In combination with the increasing rate of new HCV infections, the lack of a current vaccine and/or an effective treatment for this virus continues to be a major public health challenge. The development of new treatments requires a better understanding of the virus and its interaction with the different components of the host cell. MicroRNAs (miRNAs are small non-coding RNAs functioning as negative regulators of gene expression and represent an interesting lead to study HCV infection and to identify new therapeutic targets. Until now, microRNA-122 (miR-122 and its implication in HCV infection have been the focus of different published studies and reviews. Here we will review recent advances in the relationship between HCV infection and miRNAs, showing that some of them emerge in publications as challengers against the supremacy of miR-122.

  20. An update on the microRNAs and their targets in unicellular red alga porphyridium cruentum

    International Nuclear Information System (INIS)

    Barozai, M.Y.K.

    2018-01-01

    MicroRNAs (miRNAs) are small, non-coding and regulatory RNAs about approx 21 nucleotides in length. The miRNAs are reported in large number of higher eukaryotic plant species. But very little data of miRNAs in algae is available. Porphyridium cruentum is unicellular red alga famous as a source for polyunsaturated fatty acids, proteins and polysaccharide contents. The present study is aimed to update the microRNAs and their targets in this important algal species. A comparative genomics approach was applied to update the miRNAs in P. cruentum. This effort resulted in a total of 49 miRNAs belonging to 46 families in P. cruentum. Their precursor-miRNAs were observed with a range of 40 to 351 nucleotides (nt). The mature miRNA sequences showed a range of 17-24 nts. The minimum free energies by stem loop structures of these miRNAs are found with an average of -32 Kcalmol-1. A total of 13 targets, including important proteins like; Ribulose-1,5-bisphosphate carboxylase oxygenase, Light-harvesting complex I, Oxygen-evolving enhancer protein, Phycobiliproteins, Granule-bound starch synthase and Carbonic anhydrase were also predicted for these miRNAs. (author)

  1. Tissue-specific regulation of mouse MicroRNA genes in endoderm-derived tissues

    OpenAIRE

    Gao, Yan; Schug, Jonathan; McKenna, Lindsay B.; Le Lay, John; Kaestner, Klaus H.; Greenbaum, Linda E.

    2010-01-01

    MicroRNAs fine-tune the activity of hundreds of protein-coding genes. The identification of tissue-specific microRNAs and their promoters has been constrained by the limited sensitivity of prior microRNA quantification methods. Here, we determine the entire microRNAome of three endoderm-derived tissues, liver, jejunum and pancreas, using ultra-high throughput sequencing. Although many microRNA genes are expressed at comparable levels, 162 microRNAs exhibited striking tissue-specificity. After...

  2. MicroRNA mimicry blocks pulmonary fibrosis

    Science.gov (United States)

    Montgomery, Rusty L; Yu, Guoying; Latimer, Paul A; Stack, Christianna; Robinson, Kathryn; Dalby, Christina M; Kaminski, Naftali; van Rooij, Eva

    2014-01-01

    Over the last decade, great enthusiasm has evolved for microRNA (miRNA) therapeutics. Part of the excitement stems from the fact that a miRNA often regulates numerous related mRNAs. As such, modulation of a single miRNA allows for parallel regulation of multiple genes involved in a particular disease. While many studies have shown therapeutic efficacy using miRNA inhibitors, efforts to restore or increase the function of a miRNA have been lagging behind. The miR-29 family has gained a lot of attention for its clear function in tissue fibrosis. This fibroblast-enriched miRNA family is downregulated in fibrotic diseases which induces a coordinate increase of many extracellular matrix genes. Here, we show that intravenous injection of synthetic RNA duplexes can increase miR-29 levels in vivo for several days. Moreover, therapeutic delivery of these miR-29 mimics during bleomycin-induced pulmonary fibrosis restores endogenous miR-29 function whereby decreasing collagen expression and blocking and reversing pulmonary fibrosis. Our data support the feasibility of using miRNA mimics to therapeutically increase miRNAs and indicate miR-29 to be a potent therapeutic miRNA for treating pulmonary fibrosis. PMID:25239947

  3. MicroRNAs in addiction: adaptation's middlemen?

    Science.gov (United States)

    Li, M D; van der Vaart, A D

    2011-12-01

    A central question in addiction is how drug-induced changes in synaptic signaling are converted into long-term neuroadaptations. Emerging evidence reveals that microRNAs (miRNAs) have a distinct role in this process through rapid response to cellular signals and dynamic regulation of local mRNA transcripts. Because each miRNA can target hundreds of mRNAs, relative changes in the expression of miRNAs can greatly impact cellular responsiveness, synaptic plasticity and transcriptional events. These diverse consequences of miRNA action occur through coordination with genes implicated in addictions, the most compelling of these being the neurotrophin BDNF, the transcription factor cAMP-responsive element-binding protein (CREB) and the DNA-binding methyl CpG binding protein 2 (MeCP2). In this study, we review the recent progress in the understanding of miRNAs in general mechanisms of plasticity and neuroadaptation and then focus on specific examples of miRNA regulation in the context of addiction. We conclude that miRNA-mediated gene regulation is a conserved means of converting environmental signals into neuronal response, which holds significant implications for addiction and other psychiatric illnesses.

  4. MicroRNA delivery for regenerative medicine.

    Science.gov (United States)

    Peng, Bo; Chen, Yongming; Leong, Kam W

    2015-07-01

    MicroRNA (miRNA) directs post-transcriptional regulation of a network of genes by targeting mRNA. Although relatively recent in development, many miRNAs direct differentiation of various stem cells including induced pluripotent stem cells (iPSCs), a major player in regenerative medicine. An effective and safe delivery of miRNA holds the key to translating miRNA technologies. Both viral and nonviral delivery systems have seen success in miRNA delivery, and each approach possesses advantages and disadvantages. A number of studies have demonstrated success in augmenting osteogenesis, improving cardiogenesis, and reducing fibrosis among many other tissue engineering applications. A scaffold-based approach with the possibility of local and sustained delivery of miRNA is particularly attractive since the physical cues provided by the scaffold may synergize with the biochemical cues induced by miRNA therapy. Herein, we first briefly cover the application of miRNA to direct stem cell fate via replacement and inhibition therapies, followed by the discussion of the promising viral and nonviral delivery systems. Next we present the unique advantages of a scaffold-based delivery in achieving lineage-specific differentiation and tissue development. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Transcriptome dynamics of the microRNA inhibition response

    DEFF Research Database (Denmark)

    Wen, Jiayu; Leucci, Elenora; Vendramin, Roberto

    2015-01-01

    We report a high-resolution time series study of transcriptome dynamics following antimiR-mediated inhibition of miR-9 in a Hodgkin lymphoma cell-line-the first such dynamic study of the microRNA inhibition response-revealing both general and specific aspects of the physiological response. We show...... validate the key observations with independent time series qPCR and we experimentally validate key predicted miR-9 targets. Methodologically, we developed sensitive functional data analytic predictive methods to analyse the weak response inherent in microRNA inhibition experiments. The methods...... of this study will be applicable to similar high-resolution time series transcriptome analyses and provides the context for more accurate experimental design and interpretation of future microRNA inhibition studies....

  6. The impact of co-combustion of polyethylene plastics and wood in a small residential boiler on emissions of gaseous pollutants, particulate matter, PAHs and 1,3,5- triphenylbenzene.

    Science.gov (United States)

    Tomsej, Tomas; Horak, Jiri; Tomsejova, Sarka; Krpec, Kamil; Klanova, Jana; Dej, Milan; Hopan, Frantisek

    2018-04-01

    The aim of this study was to simulate a banned but widely spread practice of co-combustion of plastic with wood in a small residential boiler and to quantify its impact on emissions of gaseous pollutants, particulate matter (PM), polycyclic aromatic hydrocarbons (PAHs), and 1,3,5-triphenylbenzene (135TPB), a new tracer of polyethylene plastic combustion. Supermarket polyethylene shopping bags (PE) and polyethylene terephthalate bottles (PET) were burnt as supplementary fuels with beech logs (BL) in an old-type 20 kW over-fire boiler both at a nominal and reduced heat output. An impact of co-combustion was more pronounced at the nominal heat output: an increase in emissions of PM, total organic carbon (TOC), toxic equivalent (TEQ) of 7 carcinogenic PAHs (c-PAHs) and a higher ratio of c-PAHs TEQ in particulate phase was observed during co-combustion of both plastics. 135TPB was found in emissions from both plastics both at a nominal and reduced output. In contrast to findings reported in the literature, 135TPB was a dominant compound detected by mass spectrometry on m/z 306 exclusively in emissions from co-combustion of PE. Surprisingly, six other even more abundant compounds of unknown identity were found on this m/z in emissions from co-combustion of PET. One of these unknown compounds was identified as p-quaterphenyl (pQ). Principal component analysis revealed strong correlation among 135TPB, pQ and five unknown compounds. pQ seems to be suitable tracers of polyethylene terephthalate plastic co-combustion, while 135TPB proved its suitability to be an all-purpose tracer of polyethylene plastics combustion. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Gravitational waves in cold dark matter

    Science.gov (United States)

    Flauger, Raphael; Weinberg, Steven

    2018-06-01

    We study the effects of cold dark matter on the propagation of gravitational waves of astrophysical and primordial origin. We show that the dominant effect of cold dark matter on gravitational waves from astrophysical sources is a small frequency dependent modification of the propagation speed of gravitational waves. However, the magnitude of the effect is too small to be detected in the near future. We furthermore show that the spectrum of primordial gravitational waves in principle contains detailed information about the properties of dark matter. However, depending on the wavelength, the effects are either suppressed because the dark matter is highly nonrelativistic or because it contributes a small fraction of the energy density of the universe. As a consequence, the effects of cold dark matter on primordial gravitational waves in practice also appear too small to be detectable.

  8. Detection of plant microRNAs in honey.

    Directory of Open Access Journals (Sweden)

    Angelo Gismondi

    Full Text Available For the first time in the literature, our group has managed to demonstrate the existence of plant RNAs in honey samples. In particular, in our work, different RNA extraction procedures were performed in order to identify a purification method for nucleic acids from honey. Purity, stability and integrity of the RNA samples were evaluated by spectrophotometric, PCR and electrophoretic analyses. Among all honey RNAs, we specifically revealed the presence of both plastidial and nuclear plant transcripts: RuBisCO large subunit mRNA, maturase K messenger and 18S ribosomal RNA. Surprisingly, nine plant microRNAs (miR482b, miR156a, miR396c, miR171a, miR858, miR162a, miR159c, miR395a and miR2118a were also detected and quantified by qPCR. In this context, a comparison between microRNA content in plant samples (i.e. flowers, nectars and their derivative honeys was carried out. In addition, peculiar microRNA profiles were also identified in six different monofloral honeys. Finally, the same plant microRNAs were investigated in other plant food products: tea, cocoa and coffee. Since plant microRNAs introduced by diet have been recently recognized as being able to modulate the consumer's gene expression, our research suggests that honey's benefits for human health may be strongly correlated to the bioactivity of plant microRNAs contained in this matrix.

  9. Disposal Of Waste Matter

    International Nuclear Information System (INIS)

    Kim, Jeong Hyeon; Lee, Seung Mu

    1989-02-01

    This book deals with disposal of waste matter management of soiled waste matter in city with introduction, definition of waste matter, meaning of management of waste matter, management system of waste matter, current condition in the country, collect and transportation of waste matter disposal liquid waste matter, industrial waste matter like plastic, waste gas sludge, pulp and sulfuric acid, recycling technology of waste matter such as recycling system of Black clawson, Monroe and Rome.

  10. Expression of MicroRNA-146a and MicroRNA-155 in Placental Villi in Early- and Late-Onset Preeclampsia.

    Science.gov (United States)

    Nizyaeva, N V; Kulikova, G V; Nagovitsyna, M N; Kan, N E; Prozorovskaya, K N; Shchegolev, A I; Sukhikh, G T

    2017-07-01

    We studied the expression of microRNA-146a and microRNA-155 in placental villi from 18 women (26-39 weeks of gestation) of reproductive age with early- or late-onset preeclampsia. The reference group consisted of women with physiological pregnancy and full-term gestation and with preterm birth after caesarian section on gestation week 26-31. MicroRNA-146a and microRNA-155 were detected by in situ hybridization with digoxigenin on paraffin sections. It was found that the expression of microRNA-146a in both syncytiotrophoblast of the intermediate villi and syncytial knots was lower at late-onset preeclampsia than at physiologic pregnancy of full-term period (p=0.037 and p=0.001 respectively). The expression of microRNA-155 in syncytiotrophoblast of intermediate placental villi in early-onset preeclampsia was higher than in group with preterm delivery (p=0.003). However, in syncytiotrophoblast of intermediate villi and in syncytial knots, the expression of microRNA-155 was lower at late-onset preeclampsia in comparison with full-term physiological pregnancy (p=0.005). In addition, the expression of microRNA-146a and microRNA-155 did not increase in the later terms in preeclampsia, while in the reference groups demonstrating gradual increase in the expression of these markers with increasing gestational age. Expression microRNA-146a and microRNA-155 little differed in early- and late-onset preeclampsia. These findings suggest that different variants of preeclampsia are probably characterized by common pathogenetic pathways. Damaged trophoblast cannot maintain of microRNAs synthesis at the required level, which determines the formation of a vicious circle in preeclampsia and further progression of the disease.

  11. MicroRNAs and potential target interactions in psoriasis

    DEFF Research Database (Denmark)

    Zibert, John Robert; Løvendorf, Marianne B.; Litman, Thomas

    2010-01-01

    BACKGROUND: Psoriasis is a chronic inflammatory skin disease often seen in patients with a genetic susceptibility. MicroRNAs (miRNA) are endogenous, short RNA molecules that can bind to parts of mRNA target genes, thus inhibiting their translation and causing accelerated turnover or transcript...... degradation. MicroRNAs are important in the pathogenesis of human diseases such as immunological disorders, as they regulate a broad range of biological processes. OBJECTIVE: We investigated miRNA-mRNA interactions in involved (PP) and non-involved (PN) psoriatic skin compared with healthy skin (NN). METHODS...

  12. MicroRNA in oral cancer research: future prospects.

    Science.gov (United States)

    Sarode, Sachin C; Sarode, Gargi S; Patil, Shankargouda

    2014-09-01

    MicroRNA (miRNA) and related therapeutic approaches hold great promise in the field of cancer managements. Various studies on epithelial malignancies have shown encouraging results on various fronts. Its association with invasion, tumor growth, epithelial mesenchymal transition (EMT), angiogenesis, cancer stem cells (CSCs), metastasis and refects the diversified role of miRNA. Moreover, miRNA plays an important role in determining the prognosis of the patients. MicroRNAs interactions with each other and with external factors [human papilloma virus (HPV) (like oncoproteins)] intrigue us to explore more deep into this fascinating world.(1.)

  13. MicroRNAs as potential therapeutic targets in kidney disease

    Science.gov (United States)

    Gomez, Ivan G; Grafals, Monica; Portilla, Didier; Duffield, Jeremy S

    2014-01-01

    One cornerstone of Chronic Kidney Disease (CKD) is fibrosis, as kidneys are susceptible due to their high vascularity and predisposition to ischemia. Presently, only therapies targeting the angiotensin receptor are used in clinical practice to retard the progression of CKD. Thus, there is a pressing need for new therapies designed to treat the damaged kidney. Several independent laboratories have identified a number of microRNAs that are dysregulated in human and animal models of CKD. We will explore the evidence suggesting that by blocking the activity of such dysregulated microRNAs, new therapeutics could be developed to treat the progression of CKD. PMID:23660218

  14. MicroRNA 101b is downregulated in the prefrontal cortex of a genetic model of depression and targets the glutamate transporter SLC1A1 (EAAT3) in vitro

    DEFF Research Database (Denmark)

    Wei, Ya Bin; Melas, Philippe A; Villaescusa, J Carlos

    2016-01-01

    Background: MicroRNAs (miRNAs) are small regulatory molecules that cause translational repression by base pairing with target mRNAs. Cumulative evidence suggests that changes in miRNA expression may in part underlie the pathophysiology and treatment of neuropsychiatric disorders, including major ...

  15. Quark matter

    International Nuclear Information System (INIS)

    Csernai, L.; Kampert, K.H.

    1994-01-01

    Precisely one decade ago the GSI (Darmstadt)/LBL (Berkeley) Collaboration at the Berkeley Bevalac reported clear evidence for collective sidewards flow in high energy heavy ion collisions. This milestone observation clearly displayed the compression and heating up of nuclear matter, providing new insights into how the behaviour of nuclear matter changes under very different conditions. This year, evidence for azimuthally asymmetric transverse flow at ten times higher projectile energy (11 GeV per nucleon gold on gold collisions) was presented by the Brookhaven E877 collaboration at the recent European Research Conference on ''Physics of High Energy Heavy Ion Collisions'', held in Helsinki from 17-22 June

  16. MicroRNA-21 Increases Proliferation and Cisplatin Sensitivity of Osteosarcoma-Derived Cells.

    Directory of Open Access Journals (Sweden)

    Vanita Vanas

    Full Text Available Osteosarcoma is the most common primary bone tumor and poor prognosis for osteosarcoma patients is mainly due to chemotherapy resistance. MicroRNAs are important to maintain pathophysiological mechanisms of cancer and influence cell sensitivity to chemotherapy. In this study, we tested the functions of microRNA-21 for malignant features as well as for drug resistance of osteosarcoma. We used Northern blot to measure microRNA-21 levels in osteosarcoma-derived cell lines. MicroRNA-21 activity was modulated by either expressing a sponge to decrease its activity in an osteosarcoma-derived cell line expressing high levels of microRNA-21 or by introducing pri-microRNA-21 in a cell line with low endogenous levels. Cell migration was determined in a scratch assay and cell proliferation was measured by performing growth curve analysis. Sensitivity of the cells towards chemotherapeutics was investigated by performing cell viability assays and calculating the IC50 values. While cell migration was unaffected by modulated microRNA-21 levels, microRNA-21 inhibition slowed proliferation and exogenously expressed microRNA-21 promoted this process. Modulated microRNA-21 activity failed to effect sensitivity of osteosarcoma-derived cell lines to doxorubicin or methotrexate. Contrarily, reduction of microRNA-21 activity resulted in enhanced resistance towards cisplatin while ectopic expression of microRNA-21 showed the opposite effect. Increased microRNA-21 levels repressed the expression of Sprouty2 and ectopic expression of Sprouty2 was able to largely rescue the observed effects of microRNA-21 in osteosarcoma. In summary, our data indicate that in osteosarcoma microRNA-21 expression is an important component for regulation of cell proliferation and for determining sensitivity to cisplatin.

  17. Curcumin increases the sensitivity of Paclitaxel-resistant NSCLC cells to Paclitaxel through microRNA-30c-mediated MTA1 reduction.

    Science.gov (United States)

    Lu, Yimin; Wang, Jun; Liu, Lei; Yu, Lequn; Zhao, Nian; Zhou, Xingju; Lu, Xudong

    2017-04-01

    Non-small-cell lung cancer is one of the most lethal cancers in the worldwide. Although Paclitaxel-based combinational therapies have long been used as a standard treatment in aggressive non-small-cell lung cancers, Paclitaxel resistance emerges as a major clinical problem. It has been demonstrated that Curcumin from Curcuma longa as a traditional Chinese medicine can inhibit cancer cell proliferation. However, the role of Curcumin in Paclitaxel-resistant non-small-cell lung cancer cells is not clear. In this study, we investigated the effect of Curcumin on the Paclitaxel-resistant non-small-cell lung cancer cells and found that Curcumin treatment markedly increased the sensitivity of Paclitaxel-resistant non-small-cell lung cancer cells to Paclitaxel. Mechanically, the study revealed that Curcumin could reduce the expression of metastasis-associated gene 1 (MTA1) gene through upregulation of microRNA-30c in Paclitaxel-resistant non-small-cell lung cancer cells. During the course, MTA1 reduction sensitized Paclitaxel-resistant non-small-cell lung cancer cells and enhanced the effect of Paclitaxel. Taken together, our studies indicate that Curcumin increases the sensitivity of Paclitaxel-resistant non-small-cell lung cancer cells to Paclitaxel through microRNA-30c-mediated MTA1 reduction. Curcumin might be a potential adjuvant for non-small-cell lung cancer patients during Paclitaxel treatment.

  18. Frontotemporal Lobar Degeneration and microRNAs

    Directory of Open Access Journals (Sweden)

    Paola ePiscopo

    2016-02-01

    Full Text Available Frontotemporal lobar degeneration (FTLD includes a spectrum of disorders characterized by changes of personality and social behaviour and, often, a gradual and progressive language dysfunction. In the last years, several efforts have been fulfilled in identifying both genetic mutations and pathological proteins associated with FTLD. The molecular bases undergoing the onset and progression of the disease remain still unknown. Recent literature prompts an involvement of RNA metabolism in FTLD, particularly miRNAs. Dysregulation of miRNAs in several disorders, including neurodegenerative diseases, and increasing importance of circulating miRNAs in different pathologies has suggested to implement the study of their possible application as biological markers and new therapeutic targets; moreover, miRNA-based therapy is becoming a powerful tool to deepen the function of a gene, the mechanism of a disease, and validate therapeutic targets. Regarding FTLD, different studies showed that miRNAs are playing an important role. For example, several reports have evaluated miRNA regulation of the progranulin gene suggesting that it is under their control, as described for miR-29b, miR-107 and miR-659. More recently, it has been demonstrated that TMEM106B gene, which protein is elevated in FTLD-TDP brains, is repressed by miR-132/212 cluster; this post-transcriptional mechanism increases intracellular levels of progranulin, affecting its pathways. These findings if confirmed could suggest that these microRNAs have a role as potential targets for some related-FTLD genes. In this review, we focus on the emerging roles of the miRNAs in the pathogenesis of FTLD.

  19. microRNA expression during trophectoderm specification.

    Directory of Open Access Journals (Sweden)

    Srinivas R Viswanathan

    2009-07-01

    Full Text Available Segregation of the trophectoderm from the inner cell mass of the embryo represents the first cell-fate decision of mammalian development. Transcription factors essential for specifying trophectoderm have been identified, but the role of microRNAs (miRNAs in modulating this fate-choice has been largely unexplored. We have compared miRNA expression in embryonic stem cell (ESC-derived trophectoderm and in staged murine embryos to identify a set of candidate miRNAs likely to be involved in trophectoderm specification.We profiled embryonic stem cells (ESCs as they were induced to differentiate into trophectodermal cells by ectopic expression of HRas/Q61L. We also profiled murine embryos at progressive stages of preimplantation development (zygote, 2-cell, 4-cell, 8-cell, morula, and blastocyst, which includes the time window in which the trophectoderm is specified in vivo Q61L/H.We describe miRNA expression changes that occur during trophectoderm specification and validate that our in vitro system faithfully recapitulates trophectoderm specification in vivo. By comparing our in vitro and in vivo datasets, we have identified a minimal set of candidate miRNAs likely to play a role in trophectoderm specification. These miRNAs are predicted to regulate a host of development-associated target genes, and many of these miRNAs have previously reported roles in development and differentiation. Additionally, we highlight a number of miRNAs whose tight developmental regulation may reflect a functional role in other stages of embryogenesis. Our embryo profiling data may be useful to investigators studying trophectoderm specification and other stages of preimplantation development.

  20. NPK macronutrients and microRNA homeostasis.

    Science.gov (United States)

    Kulcheski, Franceli R; Côrrea, Régis; Gomes, Igor A; de Lima, Júlio C; Margis, Rogerio

    2015-01-01

    Macronutrients are essential elements for plant growth and development. In natural, non-cultivated systems, the availability of macronutrients is not a limiting factor of growth, due to fast recycling mechanisms. However, their availability might be an issue in modern agricultural practices, since soil has been frequently over exploited. From a crop management perspective, the nitrogen (N), phosphorus (P), and potassium (K) are three important limiting factors and therefore frequently added as fertilizers. NPK are among the nutrients that have been reported to alter post-embryonic root developmental processes and consequently, impairs crop yield. To cope with nutrients scarcity, plants have evolved several mechanisms involved in metabolic, physiological, and developmental adaptations. In this scenario, microRNAs (miRNAs) have emerged as additional key regulators of nutrients uptake and assimilation. Some studies have demonstrated the intrinsic relation between miRNAs and their targets, and how they can modulate plants to deal with the NPK availability. In this review, we focus on miRNAs and their regulation of targets involved in NPK metabolism. In general, NPK starvation is related with miRNAs that are involved in root-architectural changes and uptake activity modulation. We further show that several miRNAs were discovered to be involved in plant-microbe symbiosis during N and P uptake, and in this way we present a global view of some studies that were conducted in the last years. The integration of current knowledge about miRNA-NPK signaling may help future studies to focus in good candidates genes for the development of important tools for plant nutritional breeding.

  1. MicroRNA of the fifth-instar posterior silk gland of silkworm identified by Solexa sequencing

    Directory of Open Access Journals (Sweden)

    Jisheng Li

    2014-12-01

    Full Text Available No special studies have been focused on the microRNA (miRNA in the fifth-instar posterior silk gland of Bombyx mori. Here, using next-generation sequencing, we acquired 93.2 million processed reads from 10 small RNA libraries. In this paper, we tried to thoroughly describe how our dataset generated from deep sequencing which was recently published in BMC genomics. Results showed that our findings are largely enriched silkworm miRNA depository and may benefit us to reveal the miRNA functions in the process of silk production.

  2. Circulating microRNAs in patients with Shiga-Toxin-producing E. coli O104:H4 induced hemolytic uremic syndrome.

    Directory of Open Access Journals (Sweden)

    Johan M Lorenzen

    Full Text Available BACKGROUND: In early May 2011, an outbreak of hemorrhagic colitis associated with hemolytic-uremic syndrome (HUS first developed in Northern Germany and spread to 15 other countries in Europe. The outbreak-strain O104:H4, which combined virulence factors of typical enteroaggregative and Shiga-Toxin-producing E. coli was associated with an unusual high rate of hemolytic uremic syndrome. Also an unexpected high rate of coma and seizures leading to mechanical ventilation and ICU treatment was observed. MicroRNAs are small ribonucleotides orchestrating gene expression. We tested whether circulating microRNAs in serum of HUS patients during the 2011 epidemics are altered in this patient cohort and related to clinical manifestations. METHODOLOGY/PRINCIPAL FINDINGS: We profiled microRNAs using RNA isolated from serum of patients and healthy age-matched controls. The results were validated in 38 patients at baseline, 29 patients during follow-up and 21 age-matched healthy controls by miRNA-specific quantitative RT-PCR. Circulating levels of miR-24, miR-126 were increased in HUS patients versus controls. There was no association between these microRNAs and renal function or the need for renal replacement therapy. In contrast, levels of miR-126 were associated with neurological symptoms at baseline and during follow-up. In addition, miR-126 (on admission and miR-24 (on admission and during follow-up were associated with platelet count. CONCLUSIONS/SIGNIFICANCE: Circulating microRNAs are strongly altered in this patient cohort and associated with neurological symptoms as well as platelet count.

  3. Subgenomic analysis of microRNAs in polyploid wheat

    Czech Academy of Sciences Publication Activity Database

    Kantar, M.; Akpinar, B. A.; Valárik, Miroslav; Lucas, S. J.; Doležel, Jaroslav; Hernandez, P.; Budak, H.

    2012-01-01

    Roč. 12, č. 3 (2012), s. 465-479 ISSN 1438-793X Grant - others:GA MŠk(CZ) ED0007/01/01 Program:ED Institutional research plan: CEZ:AV0Z50380511 Keywords : Triticum aestivum * microRNA * miRNA prediction Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.292, year: 2012

  4. MicroRNA-449a deficiency promotes colon carcinogenesis.

    Science.gov (United States)

    Niki, Masanori; Nakajima, Kohei; Ishikawa, Daichi; Nishida, Jun; Ishifune, Chieko; Tsukumo, Shin-Ichi; Shimada, Mitsuo; Nagahiro, Shinji; Mitamura, Yoshinori; Yasutomo, Koji

    2017-09-06

    MicroRNAs have broad roles in tumorigenesis and cell differentiation through regulation of target genes. Notch signaling also controls cell differentiation and tumorigenesis. However, the mechanisms through which Notch mediates microRNA expression are still unclear. In this study, we aimed to identify microRNAs regulated by Notch signaling. Our analysis found that microRNA-449a (miR-449a) was indirectly regulated by Notch signaling. Although miR-449a-deficient mice did not show any Notch-dependent defects in immune cell development, treatment of miR-449a-deficient mice with azoxymethane (AOM) or dextran sodium sulfate (DSS) increased the numbers and sizes of colon tumors. These effects were associated with an increase in intestinal epithelial cell proliferation following AOM/DSS treatment. In patients with colon cancer, miR-449a expression was inversely correlated with disease-free survival and histological scores and was positively correlated with the expression of MLH1 for which loss-of function mutations have been shown to be involved in colon cancer. Colon tissues of miR-449a-deficient mice showed reduced Mlh1 expression compared with those of wild-type mice. Thus, these data suggested that miR-449a acted as a key regulator of colon tumorigenesis by controlling the proliferation of intestinal epithelial cells. Additionally, activation of miR-449a may represent an effective therapeutic strategy and prognostic marker in colon cancer.

  5. Circulating microRNAs as diagnostic biomarkers for cardiovascular diseases

    NARCIS (Netherlands)

    Tijsen, Anke J.; Pinto, Yigal M.; Creemers, Esther E.

    2012-01-01

    Tijsen AJ, Pinto YM, Creemers EE. Circulating microRNAs as diagnostic biomarkers for cardiovascular diseases. Am J Physiol Heart Circ Physiol 303: H1085-H1095, 2012. First published August 31, 2012; doi:10.1152/ajpheart.00191.2012.-One of the major challenges in cardiovascular disease is the

  6. microRNA-101 is a potent inhibitor of autophagy

    DEFF Research Database (Denmark)

    Frankel, Lisa B; Wen, Jiayu; Lees, Michael

    2011-01-01

    performed a functional screen in search of microRNAs (miRNAs), which regulate the autophagic flux in breast cancer cells. In this study, we identified the tumour suppressive miRNA, miR-101, as a potent inhibitor of basal, etoposide- and rapamycin-induced autophagy. Through transcriptome profiling, we...

  7. The therapeutic potential of MicroRNAs in cancer

    DEFF Research Database (Denmark)

    Thorsen, Stine Buch; Obad, Susanna; Jensen, Niels Frank

    2012-01-01

    MicroRNAs (miRNAs) have been uncovered as important posttranscriptional regulators of nearly every biological process in the cell. Furthermore, mounting evidence implies that miRNAs play key roles in the pathogenesis of cancer and that many miRNAs can function either as oncogenes or tumor...

  8. Pharmacogenomics genes show varying perceptibility to microRNA regulation

    DEFF Research Database (Denmark)

    Rukov, Jakob Lewin; Vinther, Jeppe; Shomron, Noam

    2011-01-01

    The aim of pharmacogenomics is to identify individual differences in genome and transcriptome composition and their effect on drug efficacy. MicroRNAs (miRNAs) are short noncoding RNAs that negatively regulate expression of the majority of animal genes, including many genes involved in drug...

  9. Brain expressed microRNAs implicated in schizophrenia etiology

    DEFF Research Database (Denmark)

    Hansen, Thomas; Olsen, Line; Lindow, Morten

    2007-01-01

    Protein encoding genes have long been the major targets for research in schizophrenia genetics. However, with the identification of regulatory microRNAs (miRNAs) as important in brain development and function, miRNAs genes have emerged as candidates for schizophrenia-associated genetic factors...

  10. MicroRNAs, the DNA damage response and cancer

    International Nuclear Information System (INIS)

    Wouters, Maikel D.; Gent, Dik C. van; Hoeijmakers, Jan H.J.; Pothof, Joris

    2011-01-01

    Many carcinogenic agents such as ultra-violet light from the sun and various natural and man-made chemicals act by damaging the DNA. To deal with these potentially detrimental effects of DNA damage, cells induce a complex DNA damage response (DDR) that includes DNA repair, cell cycle checkpoints, damage tolerance systems and apoptosis. This DDR is a potent barrier against carcinogenesis and defects within this response are observed in many, if not all, human tumors. DDR defects fuel the evolution of precancerous cells to malignant tumors, but can also induce sensitivity to DNA damaging agents in cancer cells, which can be therapeutically exploited by the use of DNA damaging treatment modalities. Regulation of and coordination between sub-pathways within the DDR is important for maintaining genome stability. Although regulation of the DDR has been extensively studied at the transcriptional and post-translational level, less is known about post-transcriptional gene regulation by microRNAs, the topic of this review. More specifically, we highlight current knowledge about DNA damage responsive microRNAs and microRNAs that regulate DNA damage response genes. We end by discussing the role of DNA damage response microRNAs in cancer etiology and sensitivity to ionizing radiation and other DNA damaging therapeutic agents.

  11. MicroRNA related polymorphisms and breast cancer risk

    NARCIS (Netherlands)

    S. Khan (Sofia); D. Greco (Dario); K. Michailidou (Kyriaki); R.L. Milne (Roger); T.A. Muranen (Taru); T. Heikkinen (Tuomas); K. Aaltonen (Kirsimari); J. Dennis (Joe); M.K. Bolla (Manjeet); J. Liu (Jianjun); P. Hall (Per); A. Irwanto (Astrid); M.K. Humphreys (Manjeet); J. Li (Jingmei); K. Czene (Kamila); J. Chang-Claude (Jenny); R. Hein (Rebecca); A. Rudolph (Anja); P. Seibold (Petra); D. Flesch-Janys (Dieter); O. Fletcher (Olivia); J. Peto (Julian); I. dos Santos Silva (Isabel); N. Johnson (Nichola); L.J. Gibson (Lorna); A. Aitken; J.L. Hopper (John); H. Tsimiklis (Helen); M. Bui (Minh); E. Makalic (Enes); D.F. Schmidt (Daniel); M.C. Southey (Melissa); C. Apicella (Carmel); J. Stone (Jennifer); Q. Waisfisz (Quinten); E.J. Meijers-Heijboer (Hanne); M.A. Adank (Muriel); R.B. van der Luijt (Rob); A. Meindl (Alfons); R.K. Schmutzler (Rita); B. Müller-Myhsok (B.); P. Lichtner (Peter); C. Turnbull (Clare); N. Rahman (Nazneen); S.J. Chanock (Stephen); D. Hunter (David); A. Cox (Angela); S.S. Cross (Simon); M.W.R. Reed (Malcolm); M.K. Schmidt (Marjanka); A. Broeks (Annegien); L.J. van 't Veer (Laura); F.B.L. Hogervorst (Frans); P.A. Fasching (Peter); A. Schrauder (André); A.B. Ekici (Arif); M.W. Beckmann (Matthias); S.E. Bojesen (Stig); B.G. Nordestgaard (Børge); S.F. Nielsen (Sune); H. Flyger (Henrik); J. Benítez (Javier); P.M. Zamora (Pilar M.); J.I.A. Perez (Jose Ignacio Arias); C.A. Haiman (Christopher); B.E. Henderson (Brian); F.R. Schumacher (Fredrick); L.L. March (Loic Le); P.D.P. Pharoah (Paul); A.M. Dunning (Alison); M. Shah (Mitul); R.N. Luben (Robert); J. Brown (Judith); F.J. Couch (Fergus); X. Wang (X.); C. Vachon (Celine); J.E. Olson (Janet); D. Lambrechts (Diether); M. Moisse (Matthieu); R. Paridaens (Robert); M.R. Christiaens (Marie Rose); P. Guénel (Pascal); T. Truong (Thérèse); P. Laurent-Puig (Pierre); C. Mulot (Claire); F. Marme (Frederick); B. Burwinkel (Barbara); A. Schneeweiss (Andreas); C. Sohn (Christof); E.J. Sawyer (Elinor); I.P. Tomlinson (Ian); M. Kerin (Michael); N. Miller (Nicola); I.L. Andrulis (Irene); J.A. Knight (Julia); S. Tchatchou (Srine); A.-M. Mulligan (Anna-Marie); T. Dörk (Thilo); N.V. Bogdanova (Natalia); N.N. Antonenkova (Natalia); H. Anton-Culver (Hoda); H. Darabi (Hatef); M. Eriksson (Mats); M. García-Closas (Montserrat); J.D. Figueroa (Jonine); J. Lissowska (Jolanta); L.A. Brinton (Louise); P. Devilee (Peter); R.A.E.M. Tollenaar (Rob); C.M. Seynaeve (Caroline); C.J. van Asperen (Christi); V. Kristensen (Vessela); S. Slager (Susan); A.E. Tol (Ama E.); C.B. Ambrosone (Christine); D. Yannoukakos (Drakoulis); A. Lindblom (Annika); S. Margolin (Sara); P. Radice (Paolo); P. Peterlongo (Paolo); M. Barile (Monica); P. Mariani (Paolo); M.J. Hooning (Maartje); J.W.M. Martens (John); J.M. Collée (Margriet); A. Jager (Agnes); A. Jakubowska (Anna); J. Lubinski (Jan); K. Jaworska-Bieniek (Katarzyna); K. Durda (Katarzyna); G.G. Giles (Graham); C.A. McLean (Catriona Ann); H. Brauch (Hiltrud); T. Brüning (Thomas); Y.-D. Ko (Yon-Dschun); H. Brenner (Hermann); A.K. Dieffenbach (Aida Karina); V. Arndt (Volker); C. Stegmaier (Christa); A.J. Swerdlow (Anthony ); A. Ashworth (Alan); N. Orr (Nick); M. Jones (Michael); J. Simard (Jacques); M.S. Goldberg (Mark); F. Labrèche (France); M. Dumont (Martine); R. Winqvist (Robert); K. Pykäs (Katri); A. Jukkola-Vuorinen (Arja); M. Grip (Mervi); V. Kataja (Vesa); V-M. Kosma (Veli-Matti); J.M. Hartikainen (J.); A. Mannermaa (Arto); U. Hamann (Ute); G. Chenevix-Trench (Georgia); C. Blomqvist (Carl); K. Aittomäki (Kristiina); D.F. Easton (Douglas); H. Nevanlinna (Heli)

    2014-01-01

    textabstractGenetic variations, such as single nucleotide polymorphisms (SNPs) in microRNAs (miRNA) or in the miRNA binding sites may affect the miRNA dependent gene expression regulation, which has been implicated in various cancers, including breast cancer, and may alter individual susceptibility

  12. Evolution of microRNA diversity and regulation in animals

    NARCIS (Netherlands)

    Berezikov, E.

    2011-01-01

    In the past decade, microRNAs (miRNAs) have been uncovered as key regulators of gene expression at the post-transcriptional level. The ancient origin of miRNAs, their dramatic expansion in bilaterian animals and their function in providing robustness to transcriptional programmes suggest that miRNAs

  13. MicroRNA Changes in Cerebrospinal Fluid After Subarachnoid Hemorrhage

    DEFF Research Database (Denmark)

    Bache, Søren; Rasmussen, Rune; Rossing, Maria

    2017-01-01

    BACKGROUND AND PURPOSE: Delayed cerebral ischemia (DCI) accounts for a major part of the morbidity and mortality after aneurysmal subarachnoid hemorrhage (SAH). MicroRNAs (miRNAs) are pathophysiologically involved in acute cerebral ischemia. This study compared miRNA profiles in cerebrospinal fluid...

  14. One dark matter mystery: halos in the cosmic web

    Science.gov (United States)

    Gaite, Jose

    2015-01-01

    The current cold dark matter cosmological model explains the large scale cosmic web structure but is challenged by the observation of a relatively smooth distribution of matter in galactic clusters. We consider various aspects of modeling the dark matter around galaxies as distributed in smooth halos and, especially, the smoothness of the dark matter halos seen in N-body cosmological simulations. We conclude that the problems of the cold dark matter cosmology on small scales are more serious than normally admitted.

  15. One dark matter mystery: halos in the cosmic web

    International Nuclear Information System (INIS)

    Gaite, Jose

    2015-01-01

    The current cold dark matter cosmological model explains the large scale cosmic web structure but is challenged by the observation of a relatively smooth distribution of matter in galactic clusters. We consider various aspects of modeling the dark matter around galaxies as distributed in smooth halos and, especially, the smoothness of the dark matter halos seen in N-body cosmological simulations. We conclude that the problems of the cold dark matter cosmology on small scales are more serious than normally admitted

  16. Media Matter

    Directory of Open Access Journals (Sweden)

    Holger Pötzsch

    2017-02-01

    Full Text Available The present contribution maps materialist advances in media studies. Based on the assumption that matter and materiality constitute significant aspects of communication processes and practices, I introduce four fields of inquiry - technology, political economy, ecology, and the body - and argue that these perspectives enable a more comprehensive understanding of the implications of contemporary technologically afforded forms of interaction. The article shows how each perspective can balance apologetic and apocalyptic approaches to the impact of in particular digital technologies, before it demonstrates the applicability of an integrated framework with reference to the techno-politics of NSA surveillance and the counter-practices of WikiLeaks.

  17. Play Matters

    DEFF Research Database (Denmark)

    Sicart (Vila), Miguel Angel

    ? In Play Matters, Miguel Sicart argues that to play is to be in the world; playing is a form of understanding what surrounds us and a way of engaging with others. Play goes beyond games; it is a mode of being human. We play games, but we also play with toys, on playgrounds, with technologies and design......, but not necessarily fun. Play can be dangerous, addictive, and destructive. Along the way, Sicart considers playfulness, the capacity to use play outside the context of play; toys, the materialization of play--instruments but also play pals; playgrounds, play spaces that enable all kinds of play; beauty...

  18. Characterization and identification of microRNA core promoters in four model species.

    Directory of Open Access Journals (Sweden)

    Xuefeng Zhou

    2007-03-01

    Full Text Available MicroRNAs are short, noncoding RNAs that play important roles in post-transcriptional gene regulation. Although many functions of microRNAs in plants and animals have been revealed in recent years, the transcriptional mechanism of microRNA genes is not well-understood. To elucidate the transcriptional regulation of microRNA genes, we study and characterize, in a genome scale, the promoters of intergenic microRNA genes in Caenorhabditis elegans, Homo sapiens, Arabidopsis thaliana, and Oryza sativa. We show that most known microRNA genes in these four species have the same type of promoters as protein-coding genes have. To further characterize the promoters of microRNA genes, we developed a novel promoter prediction method, called common query voting (CoVote, which is more effective than available promoter prediction methods. Using this new method, we identify putative core promoters of most known microRNA genes in the four model species. Moreover, we characterize the promoters of microRNA genes in these four species. We discover many significant, characteristic sequence motifs in these core promoters, several of which match or resemble the known cis-acting elements for transcription initiation. Among these motifs, some are conserved across different species while some are specific to microRNA genes of individual species.

  19. miRBase: integrating microRNA annotation and deep-sequencing data.

    Science.gov (United States)

    Kozomara, Ana; Griffiths-Jones, Sam

    2011-01-01

    miRBase is the primary online repository for all microRNA sequences and annotation. The current release (miRBase 16) contains over 15,000 microRNA gene loci in over 140 species, and over 17,000 distinct mature microRNA sequences. Deep-sequencing technologies have delivered a sharp rise in the rate of novel microRNA discovery. We have mapped reads from short RNA deep-sequencing experiments to microRNAs in miRBase and developed web interfaces to view these mappings. The user can view all read data associated with a given microRNA annotation, filter reads by experiment and count, and search for microRNAs by tissue- and stage-specific expression. These data can be used as a proxy for relative expression levels of microRNA sequences, provide detailed evidence for microRNA annotations and alternative isoforms of mature microRNAs, and allow us to revisit previous annotations. miRBase is available online at: http://www.mirbase.org/.

  20. Circulating microRNAs as novel biomarkers for the early diagnosis of acute coronary syndrome.

    Science.gov (United States)

    Deddens, J C; Colijn, J M; Oerlemans, M I F J; Pasterkamp, G; Chamuleau, S A; Doevendans, P A; Sluijter, J P G

    2013-12-01

    Small non-coding microRNAs (miRNAs) are important physiological regulators of post-transcriptional gene expression. miRNAs not only reside in the cytoplasm but are also stably present in several extracellular compartments, including the circulation. For that reason, miRNAs are proposed as diagnostic biomarkers for various diseases. Early diagnosis of acute coronary syndrome (ACS), especially non-ST elevated myocardial infarction and unstable angina pectoris, is essential for optimal treatment outcome, and due to the ongoing need for additional identifiers, miRNAs are of special interest as biomarkers for ACS. This review highlights the nature and cellular release mechanisms of circulating miRNAs and therefore their potential role in the diagnosis of myocardial infarction. We will give an update of clinical studies addressing the role of circulating miRNA expression after myocardial infarction and explore the diagnostic value of this potential biomarker.

  1. Tumor suppressor microRNAs are downregulated in myelodysplastic syndrome with spliceosome mutations

    DEFF Research Database (Denmark)

    Aslan, Derya; Garde, Christian; Nygaard, Mette Katrine

    2016-01-01

    Spliceosome mutations are frequently observed in patients with myelodysplastic syndromes (MDS). However, it is largely unknown how these mutations contribute to the disease. MicroRNAs (miRNAs) are small noncoding RNAs, which have been implicated in most human cancers due to their role in post...... the most downregulated miRNAs were several tumor-suppressor miRNAs, including several let-7 family members, miR-423, and miR-103a. Finally, we observed that the predicted targets of the most downregulated miRNAs were involved in apoptosis, hematopoiesis, and acute myeloid leukemia among other cancer......- and metabolic pathways. Our data indicate that spliceosome mutations may play an important role in MDS pathophysiology by affecting the expression of tumor suppressor miRNA genes involved in the development and progression of MDS....

  2. MicroRNA-133 mediates cardiac diseases: Mechanisms and clinical implications

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Yi; Liang, Yan [Guangdong Key Laboratory for Research and Development of Natural Drugs, Guangdong Medical University, Zhanjiang 524023, Guangdong (China); Zhang, Jin-fang [Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong (China); Fu, Wei-ming, E-mail: fuweiming76@smu.edu.cn [School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515 (China)

    2017-05-15

    MicroRNAs (miRNAs) belong to the family of small non-coding RNAs that mediate gene expression by post-transcriptional regulation. Increasing evidence have demonstrated that miR-133 is enriched in muscle tissues and myogenic cells, and its aberrant expression could induce the occurrence and development of cardiac disorders, such as cardiac hypertrophy, heart failure, etc. In this review, we summarized the regulatory roles of miR-133 in cardiac disorders and the underlying mechanisms, which suggest that miR-133 may be a potential diagnostic and therapeutic tool for cardiac disorders. - Highlights: • miR-218 is frequently downregulated in multiple cancers. • miR-218 plays pivotal roles in carcinogenesis. • miR-218 mediates proliferation, apoptosis, metastasis, invasion, etc. • miR-218 mediates tumorigenesis and metastasis via multiple pathways.

  3. Computational Identification of MicroRNAs and Their Targets from Finger Millet (Eleusine coracana).

    Science.gov (United States)

    Usha, S; Jyothi, M N; Suchithra, B; Dixit, Rekha; Rai, D V; Nagesh Babu, R

    2017-03-01

    MicroRNAs are endogenous small RNAs regulating intrinsic normal growth and development of plant. Discovering miRNAs, their targets and further inferring their functions had become routine process to comprehend the normal biological processes of miRNAs and their roles in plant development. In this study, we used homology-based analysis with available expressed sequence tag of finger millet (Eleusine coracana) to predict conserved miRNAs. Three potent miRNAs targeting 88 genes were identified. The newly identified miRNAs were found to be homologous with miR166 and miR1310. The targets recognized were transcription factors and enzymes, and GO analysis showed these miRNAs played varied roles in gene regulation. The identification of miRNAs and their targets is anticipated to hasten the pace of key epigenetic regulators in plant development.

  4. New opportunities for the regulation of secondary metabolism in plants: focus on microRNAs.

    Science.gov (United States)

    Bulgakov, Victor P; Avramenko, Tatiana V

    2015-09-01

    Plant cell cultures are of particular interest in industrial applications as a source of biologically active substances. It is difficult, however, to achieve stable production of secondary metabolites for many plant cell cultures using classical techniques. Novel approaches should be developed for removal of the inhibitor blocks that prevent pathway activation and shift the regulatory balance to the activation of entire biosynthetic pathways. MicroRNAs (miRNAs) are small RNAs that play important regulatory roles in various biological processes. Only recently miRNAs have been demonstrated as active in secondary metabolism regulation. In this work, we summarize recent data on the emerging approaches based on regulation of secondary metabolism by miRNAs.

  5. Implications of microRNAs in Colorectal Cancer Development, Diagnosis, Prognosis and Therapeutics

    Directory of Open Access Journals (Sweden)

    Haiyan eZhai

    2011-11-01

    Full Text Available MicroRNAs (miRNAs are a class of non-coding small RNAs with critical regulatory functions as post-transcriptional regulators. Due to the fundamental importance and broad impact of miRNAs on multiple genes and pathways, dysregulated miRNAs have been associated with human diseases, including cancer. Colorectal cancer (CRC is among the most deadly diseases, and miRNAs offer a new frontier for target discovery and novel biomarkers for both diagnosis and prognosis. In this review, we summarize the recent advancement of miRNA research in CRC, in particular, the roles of miRNAs in colorectal cancer stem cells, EMT, chemoresistance, therapeutics, diagnosis and prognosis.

  6. MicroRNAs as putative mediators of treatment response in prostate cancer.

    LENUS (Irish Health Repository)

    O'Kelly, Fardod

    2012-05-22

    MicroRNAs (miRNAs) are an abundant class of noncoding RNAs that function to regulate post-transcriptional gene expression, predominantly by translational repression. In addition to their role in prostate cancer initiation and progression, recent evidence suggests that miRNAs might also participate in treatment response across a range of therapies including radiation treatment, chemotherapy and androgen suppression. The mechanism of this regulation is thought to be multifactorial and is currently poorly understood. To date, only a small number of studies have examined the functional role of miRNAs in response to prostate cancer treatment. Elucidating the role of miRNAs in treatment response following radiotherapy, chemotherapy and androgen suppression will provide new avenues of investigation for the development of novel therapies for the treatment of prostate cancer.

  7. The Role of MicroRNAs in Bovine Infection and Immunity

    Directory of Open Access Journals (Sweden)

    Nathan eLawless

    2014-11-01

    Full Text Available MicroRNAs (miRNAs are a class of small, non-coding RNAs that are recognised as critical regulators of immune gene expression during infection. Many immunologically significant human miRNAs have been found to be conserved in agriculturally important species, including cattle. Discovering how bovine miRNAs mediate the immune defence during infection is critical to understanding the aetiology of the most prevalent bovine diseases. Here, we review current knowledge of miRNAs in the bovine genome, and discuss the advances in understanding of miRNAs as regulators of immune cell function, and bovine immune response activation, regulation, and resolution. Finally, we consider the future perspectives on miRNAs in bovine viral disease, their role as potential biomarkers and in therapy.

  8. MetastamiRs: Non-Coding MicroRNAs Driving Cancer Invasion and Metastasis

    Directory of Open Access Journals (Sweden)

    Sergio Rodriguez-Cuevas

    2012-01-01

    Full Text Available MicroRNAs (miRNAs are small non-coding RNAs of ~22 nucleotides that function as negative regulators of gene expression by either inhibiting translation or inducing deadenylation-dependent degradation of target transcripts. Notably, deregulation of miRNAs expression is associated with the initiation and progression of human cancers where they act as oncogenes or tumor suppressors contributing to tumorigenesis. Abnormal miRNA expression may provide potential diagnostic and prognostic tumor biomarkers and new therapeutic targets in cancer. Recently, several miRNAs have been shown to initiate invasion and metastasis by targeting multiple proteins that are major players in these cellular events, thus they have been denominated as metastamiRs. Here, we present a review of the current knowledge of miRNAs in cancer with a special focus on metastamiRs. In addition we discuss their potential use as novel specific markers for cancer progression.

  9. Functional studies of microRNAs in neural stem cells: problems and perspectives.

    Directory of Open Access Journals (Sweden)

    Malin eÅkerblom

    2012-02-01

    Full Text Available In adult mammals, neural stem cells (NSCs are found in two niches of the brain; the subventricular zone at the lateral ventricle and the subgranular zone of the dentate gyrus in the hippocampus. Neurogenesis is a complex process that is tightly controlled on a molecular level. Recently, microRNAs (miRNAs have been implicated to play a central role in the regulation of NCSs. miRNAs are small, endogenously expressed RNAs that regulate gene expression at the post-transcriptional level. However, functional studies of miRNAs are complicated due to current technical limitations. In this review we describe recent findings about miRNAs in NSCs looking closely at miR-124, miR-9 and let-7. We also highlight technical strategies used to investigate miRNA function, accentuating limitations and potentials.

  10. The role of micro-RNAs in hepatocellular carcinoma: from molecular biology to treatment.

    Science.gov (United States)

    D'Anzeo, Marco; Faloppi, Luca; Scartozzi, Mario; Giampieri, Riccardo; Bianconi, Maristella; Del Prete, Michela; Silvestris, Nicola; Cascinu, Stefano

    2014-05-19

    Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide and the third leading cause of cancer deaths. microRNAs (miRNAs) are evolutionary conserved small non-coding RNA that negatively regulate gene expression and protein translation. Recent evidences have shown that they are involved in many biological processes, from development and cell-cycle regulation to apoptosis. miRNAs can behave as tumor suppressor or promoter of oncogenesis depending on the cellular function of their targets. Moreover, they are frequently dysregulated in HCC. In this review we summarize the latest findings of miRNAs regulation in HCC and their role as potentially diagnostic and prognostic biomarkers for HCC. We highlight development of miRNAs as potential therapeutic targets for HCC.

  11. High responders to resistance exercise training demonstrate differential regulation of skeletal muscle microRNA expression

    DEFF Research Database (Denmark)

    Davidsen, Peter K; Gallagher, Iain J; Hartman, Joseph W

    2011-01-01

    MicroRNAs (miRNA), small noncoding RNA molecules, may regulate protein synthesis, while resistance exercise training (RT) is an efficient strategy for stimulating muscle protein synthesis in vivo. However, RT increases muscle mass, with a very wide range of effectiveness in humans. We therefore...... determined the expression level of 21 abundant miRNAs to determine whether variation in these miRNAs was able to explain the variation in RT-induced gains in muscle mass. Vastus lateralis biopsies were obtained from the top and bottom ~20% of responders from 56 young men who undertook a 5 day/wk RT program...... for 12 wk. Training-induced muscle mass gain was determined by dual-energy X-ray absorptiometry, and fiber size was evaluated by histochemistry. The expression level of each miRNA was quantified using TaqMan-based quantitative PCR, with the analysis carried out in a blinded manner. Gene ontology...

  12. MicroRNA-133 mediates cardiac diseases: Mechanisms and clinical implications

    International Nuclear Information System (INIS)

    Liu, Yi; Liang, Yan; Zhang, Jin-fang; Fu, Wei-ming

    2017-01-01

    MicroRNAs (miRNAs) belong to the family of small non-coding RNAs that mediate gene expression by post-transcriptional regulation. Increasing evidence have demonstrated that miR-133 is enriched in muscle tissues and myogenic cells, and its aberrant expression could induce the occurrence and development of cardiac disorders, such as cardiac hypertrophy, heart failure, etc. In this review, we summarized the regulatory roles of miR-133 in cardiac disorders and the underlying mechanisms, which suggest that miR-133 may be a potential diagnostic and therapeutic tool for cardiac disorders. - Highlights: • miR-218 is frequently downregulated in multiple cancers. • miR-218 plays pivotal roles in carcinogenesis. • miR-218 mediates proliferation, apoptosis, metastasis, invasion, etc. • miR-218 mediates tumorigenesis and metastasis via multiple pathways.

  13. A non-canonical landscape of the microRNA system

    Directory of Open Access Journals (Sweden)

    Gabriel Adelman Cipolla

    2014-09-01

    Full Text Available Microribonucleic acids, best known as microRNAs or miRNAs, are small, non-coding RNAs with important regulatory roles in eukaryotic cells. Here, I present a broad review about highly relevant but generally non-depicted features of miRNAs, among which stand out the non-conventional miRNA seed sites, the unusual messenger RNA (mRNA target regions, the non-canonical miRNA-guided mechanisms of gene expression regulation and the recently identified new class of miRNA ligands. Furthermore, I address the miRNA uncommon genomic location, transcription, and subcellular localization. Altogether, these unusual features and roles place the miRNA system as a very diverse, complex and intriguing biological mechanism.

  14. Knockdown of Rice microRNA166 by Short Tandem Target Mimic (STTM).

    Science.gov (United States)

    Teotia, Sachin; Zhang, Dabing; Tang, Guiliang

    2017-01-01

    Small RNAs, including microRNAs (miRNAs), are abundant in plants and play key roles in controlling plant development and physiology. miRNAs regulate the expression of the target genes involved in key plant processes. Due to functional redundancy among miRNA family members in plants, an ideal approach to silence the expression of all members simultaneously, for their functional characterization, is desirable. Target mimic (TM) was the first approach to achieve this goal. Short tandem target mimic (STTM) is a potent approach complementing TM for silencing miRNAs in plants. STTMs have been successfully used in dicots to block miRNA functions. Here, we describe in detail the protocol for designing STTM construct to block miRNA functions in rice. Such approach can be applied to silence miRNAs in other monocots as well.

  15. Computational Characterization of Exogenous MicroRNAs that Can Be Transferred into Human Circulation.

    Directory of Open Access Journals (Sweden)

    Jiang Shu

    Full Text Available MicroRNAs have been long considered synthesized endogenously until very recent discoveries showing that human can absorb dietary microRNAs from animal and plant origins while the mechanism remains unknown. Compelling evidences of microRNAs from rice, milk, and honeysuckle transported to human blood and tissues have created a high volume of interests in the fundamental questions that which and how exogenous microRNAs can be transferred into human circulation and possibly exert functions in humans. Here we present an integrated genomics and computational analysis to study the potential deciding features of transportable microRNAs. Specifically, we analyzed all publicly available microRNAs, a total of 34,612 from 194 species, with 1,102 features derived from the microRNA sequence and structure. Through in-depth bioinformatics analysis, 8 groups of discriminative features have been used to characterize human circulating microRNAs and infer the likelihood that a microRNA will get transferred into human circulation. For example, 345 dietary microRNAs have been predicted as highly transportable candidates where 117 of them have identical sequences with their homologs in human and 73 are known to be associated with exosomes. Through a milk feeding experiment, we have validated 9 cow-milk microRNAs in human plasma using microRNA-sequencing analysis, including the top ranked microRNAs such as bta-miR-487b, miR-181b, and miR-421. The implications in health-related processes have been illustrated in the functional analysis. This work demonstrates the data-driven computational analysis is highly promising to study novel molecular characteristics of transportable microRNAs while bypassing the complex mechanistic details.

  16. Computational Characterization of Exogenous MicroRNAs that Can Be Transferred into Human Circulation

    Science.gov (United States)

    Shu, Jiang; Chiang, Kevin; Zempleni, Janos; Cui, Juan

    2015-01-01

    MicroRNAs have been long considered synthesized endogenously until very recent discoveries showing that human can absorb dietary microRNAs from animal and plant origins while the mechanism remains unknown. Compelling evidences of microRNAs from rice, milk, and honeysuckle transported to human blood and tissues have created a high volume of interests in the fundamental questions that which and how exogenous microRNAs can be transferred into human circulation and possibly exert functions in humans. Here we present an integrated genomics and computational analysis to study the potential deciding features of transportable microRNAs. Specifically, we analyzed all publicly available microRNAs, a total of 34,612 from 194 species, with 1,102 features derived from the microRNA sequence and structure. Through in-depth bioinformatics analysis, 8 groups of discriminative features have been used to characterize human circulating microRNAs and infer the likelihood that a microRNA will get transferred into human circulation. For example, 345 dietary microRNAs have been predicted as highly transportable candidates where 117 of them have identical sequences with their homologs in human and 73 are known to be associated with exosomes. Through a milk feeding experiment, we have validated 9 cow-milk microRNAs in human plasma using microRNA-sequencing analysis, including the top ranked microRNAs such as bta-miR-487b, miR-181b, and miR-421. The implications in health-related processes have been illustrated in the functional analysis. This work demonstrates the data-driven computational analysis is highly promising to study novel molecular characteristics of transportable microRNAs while bypassing the complex mechanistic details. PMID:26528912

  17. Cool quark matter

    CERN Document Server

    Kurkela, Aleksi

    2016-07-20

    We generalize the state-of-the-art perturbative Equation of State of cold quark matter to nonzero temperatures, needed in the description of neutron star mergers and core collapse processes. The new result is accurate to order g^5 in the gauge coupling, and is based on a novel framework for dealing with the infrared sensitive soft field modes of the theory. The zero Matsubara mode sector is treated using a dimensionally reduced effective theory, while the soft non-zero modes are resummed using the Hard Thermal Loop approximation. This combination of known effective descriptions offers unprecedented access to small but nonzero temperatures, both in and out of beta equilibrium.

  18. Dark matter and dark radiation

    International Nuclear Information System (INIS)

    Ackerman, Lotty; Buckley, Matthew R.; Carroll, Sean M.; Kamionkowski, Marc

    2009-01-01

    We explore the feasibility and astrophysical consequences of a new long-range U(1) gauge field ('dark electromagnetism') that couples only to dark matter, not to the standard model. The dark matter consists of an equal number of positive and negative charges under the new force, but annihilations are suppressed if the dark-matter mass is sufficiently high and the dark fine-structure constant α-circumflex is sufficiently small. The correct relic abundance can be obtained if the dark matter also couples to the conventional weak interactions, and we verify that this is consistent with particle-physics constraints. The primary limit on α-circumflex comes from the demand that the dark matter be effectively collisionless in galactic dynamics, which implies α-circumflex -3 for TeV-scale dark matter. These values are easily compatible with constraints from structure formation and primordial nucleosynthesis. We raise the prospect of interesting new plasma effects in dark-matter dynamics, which remain to be explored.

  19. Dark matter from split seesaw

    International Nuclear Information System (INIS)

    Kusenko, Alexander; Takahashi, Fuminobu; Yanagida, Tsutomu T.

    2010-01-01

    The seesaw mechanism in models with extra dimensions is shown to be generically consistent with a broad range of Majorana masses. The resulting democracy of scales implies that the seesaw mechanism can naturally explain the smallness of neutrino masses for an arbitrarily small right-handed neutrino mass. If the scales of the seesaw parameters are split, with two right-handed neutrinos at a high scale and one at a keV scale, one can explain the matter-antimatter asymmetry of the universe, as well as dark matter. The dark matter candidate, a sterile right-handed neutrino with mass of several keV, can account for the observed pulsar velocities and for the recent data from Chandra X-ray Observatory, which suggest the existence of a 5 keV sterile right-handed neutrino.

  20. Serum microRNA-1 and microRNA-133a levels reflect myocardial steatosis in uncomplicated type 2 diabetes

    NARCIS (Netherlands)

    Gonzalo-Calvo, D. de; Meer, R.W. van der; Rijzewijk, L.J.; Smit, J.W.A.; Revuelta-Lopez, E.; Nasarre, L.; Escola-Gil, J.C.; Lamb, H.J.; Llorente-Cortes, V.

    2017-01-01

    Using in vitro, in vivo and patient-based approaches, we investigated the potential of circulating microRNAs (miRNAs) as surrogate biomarkers of myocardial steatosis, a hallmark of diabetic cardiomyopathy. We analysed the cardiomyocyte-enriched miRNA signature in serum from patients with

  1. Annotation of mammalian primary microRNAs

    Directory of Open Access Journals (Sweden)

    Enright Anton J

    2008-11-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are important regulators of gene expression and have been implicated in development, differentiation and pathogenesis. Hundreds of miRNAs have been discovered in mammalian genomes. Approximately 50% of mammalian miRNAs are expressed from introns of protein-coding genes; the primary transcript (pri-miRNA is therefore assumed to be the host transcript. However, very little is known about the structure of pri-miRNAs expressed from intergenic regions. Here we annotate transcript boundaries of miRNAs in human, mouse and rat genomes using various transcription features. The 5' end of the pri-miRNA is predicted from transcription start sites, CpG islands and 5' CAGE tags mapped in the upstream flanking region surrounding the precursor miRNA (pre-miRNA. The 3' end of the pri-miRNA is predicted based on the mapping of polyA signals, and supported by cDNA/EST and ditags data. The predicted pri-miRNAs are also analyzed for promoter and insulator-associated regulatory regions. Results We define sets of conserved and non-conserved human, mouse and rat pre-miRNAs using bidirectional BLAST and synteny analysis. Transcription features in their flanking regions are used to demarcate the 5' and 3' boundaries of the pri-miRNAs. The lengths and boundaries of primary transcripts are highly conserved between orthologous miRNAs. A significant fraction of pri-miRNAs have lengths between 1 and 10 kb, with very few introns. We annotate a total of 59 pri-miRNA structures, which include 82 pre-miRNAs. 36 pri-miRNAs are conserved in all 3 species. In total, 18 of the confidently annotated transcripts express more than one pre-miRNA. The upstream regions of 54% of the predicted pri-miRNAs are found to be associated with promoter and insulator regulatory sequences. Conclusion Little is known about the primary transcripts of intergenic miRNAs. Using comparative data, we are able to identify the boundaries of a significant proportion of

  2. MicroRNA profiling in intraocular medulloepitheliomas.

    Directory of Open Access Journals (Sweden)

    Deepak P Edward

    Full Text Available To study the differential expression of microRNA (miRNA profiles between intraocular medulloepithelioma (ME and normal control tissue (CT.Total RNA was extracted from formalin fixed paraffin embedded (FFPE intraocular ME (n=7 and from age matched ciliary body controls (n=8. The clinical history and phenotype was recorded. MiRNA profiles were determined using the Affymetrix GeneChip miRNA Arrays analyzed using expression console 1.3 software. Validation of significantly dysregulated miRNA was confirmed by quantitative real-time PCR. The web-based DNA Intelligent Analysis (DIANA-miRPath v2.0 was used to perform enrichment analysis of differentially expressed (DE miRNA gene targets in Kyoto Encyclopedia of Genes and Genomes (KEGG pathway.The pathologic evaluation revealed one benign (benign non-teratoid, n=1 and six malignant tumors (malignant teratoid, n=2; malignant non-teratoid, n = 4. A total of 88 miRNAs were upregulated and 43 miRNAs were downregulated significantly (P<0.05 in the tumor specimens. Many of these significantly dysregulated miRNAs were known to play various roles in carcinogenesis and tumor behavior. RT-PCR validated three significantly upregulated miRNAs and three significantly downregulated miRNAs namely miR-217, miR-216a, miR-216b, miR-146a, miR-509-3p and miR-211. Many DE miRNAs that were significant in ME tumors showed dysregulation in retinoblastoma, glioblastoma, and precursor, normal and reactive human cartilage. Enriched pathway analysis suggested a significant association of upregulated miRNAs with 15 pathways involved in prion disease and several types of cancer. The pathways involving significantly downregulated miRNAs included the toll-like receptor (TLR (p<4.36E-16 and Nuclear Factor kappa B (NF-κB signaling pathways (p<9.00E-06.We report significantly dysregulated miRNAs in intraocular ME tumors, which exhibited abnormal profiles in other cancers as well such as retinoblastoma and glioblastoma. Pathway analysis

  3. Quark matter formation in dense stellar objects

    Indian Academy of Sciences (India)

    Although not much is known about the density at which the phase transition takes place at small temperatures, it is expected to occur around the nuclear densities of few times nuclear matter density. Also, there is a strong reason to believe that the quark matter formed after the phase transition is in colour superconducting ...

  4. Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies

    Directory of Open Access Journals (Sweden)

    Fedele Vita

    2006-06-01

    Full Text Available Abstract Background Recent studies indicate that microRNAs (miRNAs are mechanistically involved in the development of various human malignancies, suggesting that they represent a promising new class of cancer biomarkers. However, previously reported methods for measuring miRNA expression consume large amounts of tissue, prohibiting high-throughput miRNA profiling from typically small clinical samples such as excision or core needle biopsies of breast or prostate cancer. Here we describe a novel combination of linear amplification and labeling of miRNA for highly sensitive expression microarray profiling requiring only picogram quantities of purified microRNA. Results Comparison of microarray and qRT-PCR measured miRNA levels from two different prostate cancer cell lines showed concordance between the two platforms (Pearson correlation R2 = 0.81; and extension of the amplification, labeling and microarray platform was successfully demonstrated using clinical core and excision biopsy samples from breast and prostate cancer patients. Unsupervised clustering analysis of the prostate biopsy microarrays separated advanced and metastatic prostate cancers from pooled normal prostatic samples and from a non-malignant precursor lesion. Unsupervised clustering of the breast cancer microarrays significantly distinguished ErbB2-positive/ER-negative, ErbB2-positive/ER-positive, and ErbB2-negative/ER-positive breast cancer phenotypes (Fisher exact test, p = 0.03; as well, supervised analysis of these microarray profiles identified distinct miRNA subsets distinguishing ErbB2-positive from ErbB2-negative and ER-positive from ER-negative breast cancers, independent of other clinically important parameters (patient age; tumor size, node status and proliferation index. Conclusion In sum, these findings demonstrate that optimized high-throughput microRNA expression profiling offers novel biomarker identification from typically small clinical samples such as breast

  5. MicroRNA modulation in complex regional pain syndrome

    Directory of Open Access Journals (Sweden)

    Orlova Irina A

    2011-11-01

    Full Text Available Abstract Background Aberrant expression of small noncoding RNAs called microRNAs (miRNAs is a common feature of several human diseases. The objective of the study was to identify miRNA modulation in patients with complex regional pain syndrome (CRPS a chronic pain condition resulting from dysfunction in the central and/or peripheral nervous systems. Due to a multitude of inciting pathologies, symptoms and treatment conditions, the CRPS patient population is very heterogeneous. Our goal was to identify differentially expressed miRNAs in blood and explore their utility in patient stratification. Methods We profiled miRNAs in whole blood from 41 patients with CRPS and 20 controls using TaqMan low density array cards. Since neurogenic inflammation is known to play a significant role in CRPS we measured inflammatory markers including chemokines, cytokines, and their soluble receptors in blood from the same individuals. Correlation analyses were performed for miRNAs, inflammatory markers and other parameters including disease symptoms, medication, and comorbid conditions. Results Three different groups emerged from miRNA profiling. One group was comprised of 60% of CRPS patients and contained no control subjects. miRNA profiles from the remaining patients were interspersed among control samples in the other two groups. We identified differential expression of 18 miRNAs in CRPS patients. Analysis of inflammatory markers showed that vascular endothelial growth factor (VEGF, interleukin1 receptor antagonist (IL1Ra and monocyte chemotactic protein-1 (MCP1 were significantly elevated in CRPS patients. VEGF and IL1Ra showed significant correlation with the patients reported pain levels. Analysis of the patients who were clustered according to their miRNA profile revealed correlations that were not significant in the total patient population. Correlation analysis of miRNAs detected in blood with additional parameters identified miRNAs associated with

  6. Identification of microRNA genes in three opisthorchiids.

    Directory of Open Access Journals (Sweden)

    Vladimir Y Ovchinnikov

    2015-04-01

    Full Text Available Opisthorchis felineus, O. viverrini, and Clonorchis sinensis (family Opisthorchiidae are parasitic flatworms that pose a serious threat to humans in some countries and cause opisthorchiasis/clonorchiasis. Chronic disease may lead to a risk of carcinogenesis in the biliary ducts. MicroRNAs (miRNAs are small noncoding RNAs that control gene expression at post-transcriptional level and are implicated in the regulation of various cellular processes during the parasite- host interplay. However, to date, the miRNAs of opisthorchiid flukes, in particular those essential for maintaining their complex biology and parasitic mode of existence, have not been satisfactorily described.Using a SOLiD deep sequencing-bioinformatic approach, we identified 43 novel and 18 conserved miRNAs for O. felineus (miracidia, metacercariae and adult worms, 20 novel and 16 conserved miRNAs for O. viverrini (adult worms, and 33 novel and 18 conserved miRNAs for C. sinensis (adult worms. The analysis of the data revealed differences in the expression level of conserved miRNAs among the three species and among three the developmental stages of O. felineus. Analysis of miRNA genes revealed two gene clusters, one cluster-like region and one intronic miRNA in the genome. The presence and structure of the two gene clusters were validated using a PCR-based approach in the three flukes.This study represents a comprehensive description of miRNAs in three members of the family Opistorchiidae, significantly expands our knowledge of miRNAs in multicellular parasites and provides a basis for understanding the structural and functional evolution of miRNAs in these metazoan parasites. Results of this study also provides novel resources for deeper understanding the complex parasite biology, for further research on the pathogenesis and molecular events of disease induced by the liver flukes. The present data may also facilitate the development of novel approaches for the prevention and

  7. Species-independent MicroRNA Gene Discovery

    KAUST Repository

    Kamanu, Timothy K.

    2012-12-01

    MicroRNA (miRNA) are a class of small endogenous non-coding RNA that are mainly negative transcriptional and post-transcriptional regulators in both plants and animals. Recent studies have shown that miRNA are involved in different types of cancer and other incurable diseases such as autism and Alzheimer’s. Functional miRNAs are excised from hairpin-like sequences that are known as miRNA genes. There are about 21,000 known miRNA genes, most of which have been determined using experimental methods. miRNA genes are classified into different groups (miRNA families). This study reports about 19,000 unknown miRNA genes in nine species whereby approximately 15,300 predictions were computationally validated to contain at least one experimentally verified functional miRNA product. The predictions are based on a novel computational strategy which relies on miRNA family groupings and exploits the physics and geometry of miRNA genes to unveil the hidden palindromic signals and symmetries in miRNA gene sequences. Unlike conventional computational miRNA gene discovery methods, the algorithm developed here is species-independent: it allows prediction at higher accuracy and resolution from arbitrary RNA/DNA sequences in any species and thus enables examination of repeat-prone genomic regions which are thought to be non-informative or ’junk’ sequences. The information non-redundancy of uni-directional RNA sequences compared to information redundancy of bi-directional DNA is demonstrated, a fact that is overlooked by most pattern discovery algorithms. A novel method for computing upstream and downstream miRNA gene boundaries based on mathematical/statistical functions is suggested, as well as cutoffs for annotation of miRNA genes in different miRNA families. Another tool is proposed to allow hypotheses generation and visualization of data matrices, intra- and inter-species chromosomal distribution of miRNA genes or miRNA families. Our results indicate that: miRNA and mi

  8. Friend or Foe: MicroRNAs in the p53 network.

    Science.gov (United States)

    Luo, Zhenghua; Cui, Ri; Tili, Esmerina; Croce, Carlo

    2018-04-10

    The critical tumor suppressor gene TP53 is either lost or mutated in more than half of human cancers. As an important transcriptional regulator, p53 modulates the expression of many microRNAs. While wild-type p53 uses microRNAs to suppress cancer development, microRNAs that are activated by gain-of-function mutant p53 confer oncogenic properties. On the other hand, the expression of p53 is tightly controlled by a fine-tune machinery including microRNAs. MicroRNAs can target the TP53 gene directly or other factors in the p53 network so that expression and function of either the wild-type or the mutant forms of p53 is downregulated. Therefore, depending on the wild-type or mutant p53 context, microRNAs contribute substantially to suppress or exacerbate tumor development. Copyright © 2018. Published by Elsevier B.V.

  9. Marginal Matter

    Science.gov (United States)

    van Hecke, Martin

    2013-03-01

    All around us, things are falling apart. The foam on our cappuccinos appears solid, but gentle stirring irreversibly changes its shape. Skin, a biological fiber network, is firm when you pinch it, but soft under light touch. Sand mimics a solid when we walk on the beach but a liquid when we pour it out of our shoes. Crucially, a marginal point separates the rigid or jammed state from the mechanical vacuum (freely flowing) state - at their marginal points, soft materials are neither solid nor liquid. Here I will show how the marginal point gives birth to a third sector of soft matter physics: intrinsically nonlinear mechanics. I will illustrate this with shock waves in weakly compressed granular media, the nonlinear rheology of foams, and the nonlinear mechanics of weakly connected elastic networks.

  10. MicroRNA-33 promotes the replicative senescence of mouse embryonic fibroblasts by suppressing CDK6

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Shun; Huang, Haijiao; Li, Nanhong; Zhang, Bing; Jia, Yubin; Yang, Yukun; Yuan, Yuan; Xiong, Xing-dong; Wang, Dengchuan; Zheng, Hui-ling [Institute of Aging Research, Guangdong Medical University, Dongguan (China); Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan (China); Institute of Biochemistry & Molecular Biology, Guangdong Medical University, Zhanjiang (China); Liu, Xinguang, E-mail: xgliu64@126.com [Institute of Aging Research, Guangdong Medical University, Dongguan (China); Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan (China); Institute of Biochemistry & Molecular Biology, Guangdong Medical University, Zhanjiang (China)

    2016-05-13

    MicroRNAs are a large class of tiny noncoding RNAs, which have emerged as critical regulators of gene expression, and thus are involved in multiple cellular processes, including cellular senescence. MicroRNA-33 has previously been established to exert crucial effect on cell proliferation, lipid metabolism and cholesterol metabolism. Nonetheless, the association between microRNA-33 and cellular senescence and its underlying molecular mechanism are far to be elucidated. The present study has attempted to probe into the effect of microRNA-33 on MEFs senescence. Our data unveiled that microRNA-33 was dramatically down-regulated in senescent MEFs compared to the young MEFs, and ectopic expression of microRNA-33 promoted MEFs senescence, while knock-down of microRNA-33 exhibited a protective effect against senescence phenotype. Moreover, we verified CDK6 as a direct target of microRNA-33 in mouse. Silencing of CDK6 induced the premature senescence phenotype of MEFs similarly as microRNA-33, while enforced expression of CDK6 significantly reverse the senescence-induction effect of microRNA-33. Taken together, our results suggested that microRNA-33 enhanced the replicative senescence of MEFs potentially by suppressing CDK6 expression. -- Highlights: •MicroRNA-33 was dramatically down-regulated in senescent MEF cells. •Altered expression of microRNA-33 exerted a critical role in MEFs senescence. •MicroRNA-33 promoted the replicative senescence of MEFs via targeting of CDK6.

  11. MicroRNA-33 promotes the replicative senescence of mouse embryonic fibroblasts by suppressing CDK6

    International Nuclear Information System (INIS)

    Xu, Shun; Huang, Haijiao; Li, Nanhong; Zhang, Bing; Jia, Yubin; Yang, Yukun; Yuan, Yuan; Xiong, Xing-dong; Wang, Dengchuan; Zheng, Hui-ling; Liu, Xinguang

    2016-01-01

    MicroRNAs are a large class of tiny noncoding RNAs, which have emerged as critical regulators of gene expression, and thus are involved in multiple cellular processes, including cellular senescence. MicroRNA-33 has previously been established to exert crucial effect on cell proliferation, lipid metabolism and cholesterol metabolism. Nonetheless, the association between microRNA-33 and cellular senescence and its underlying molecular mechanism are far to be elucidated. The present study has attempted to probe into the effect of microRNA-33 on MEFs senescence. Our data unveiled that microRNA-33 was dramatically down-regulated in senescent MEFs compared to the young MEFs, and ectopic expression of microRNA-33 promoted MEFs senescence, while knock-down of microRNA-33 exhibited a protective effect against senescence phenotype. Moreover, we verified CDK6 as a direct target of microRNA-33 in mouse. Silencing of CDK6 induced the premature senescence phenotype of MEFs similarly as microRNA-33, while enforced expression of CDK6 significantly reverse the senescence-induction effect of microRNA-33. Taken together, our results suggested that microRNA-33 enhanced the replicative senescence of MEFs potentially by suppressing CDK6 expression. -- Highlights: •MicroRNA-33 was dramatically down-regulated in senescent MEF cells. •Altered expression of microRNA-33 exerted a critical role in MEFs senescence. •MicroRNA-33 promoted the replicative senescence of MEFs via targeting of CDK6.

  12. MicroRNA expression profiles of cancer stem cells in head and neck squamous cell carcinoma

    OpenAIRE

    YATA, KAZUYA; BEDER, LEVENT BEKIR; TAMAGAWA, SHUNJI; HOTOMI, MUNEKI; HIROHASHI, YOSHIHIKO; GRENMAN, REIDAR; YAMANAKA, NOBORU

    2015-01-01

    Increasing evidence indicates that cancer stem cells have essential roles in tumor initiation, progression, metastasis and resistance to chemo-radiation. Recent research has pointed out biological importance of microRNAs in cancer stem cell dysregulation. Total number of mature microRNAs in human genome increased to more than 2,500 with the recent up-date of the database. However, currently no information is available regarding microRNA expression profiles of cancer stem cells in head and nec...

  13. Identification of rat lung-specific microRNAs by microRNA microarray: valuable discoveries for the facilitation of lung research

    Directory of Open Access Journals (Sweden)

    Chintagari Narendranath

    2007-01-01

    Full Text Available Abstract Background An important mechanism for gene regulation utilizes small non-coding RNAs called microRNAs (miRNAs. These small RNAs play important roles in tissue development, cell differentiation and proliferation, lipid and fat metabolism, stem cells, exocytosis, diseases and cancers. To date, relatively little is known about functions of miRNAs in the lung except lung cancer. Results In this study, we utilized a rat miRNA microarray containing 216 miRNA probes, printed in-house, to detect the expression of miRNAs in the rat lung compared to the rat heart, brain, liver, kidney and spleen. Statistical analysis using Significant Analysis of Microarray (SAM and Tukey Honestly Significant Difference (HSD revealed 2 miRNAs (miR-195 and miR-200c expressed specifically in the lung and 9 miRNAs co-expressed in the lung and another organ. 12 selected miRNAs were verified by Northern blot analysis. Conclusion The identified lung-specific miRNAs from this work will facilitate functional studies of miRNAs during normal physiological and pathophysiological processes of the lung.

  14. The Emerging Role of MicroRNA-155 in Cardiovascular Diseases

    Directory of Open Access Journals (Sweden)

    Richard Y. Cao

    2016-01-01

    Full Text Available MicroRNAs have been demonstrated to be involved in human diseases, including cardiovascular diseases. Growing evidences suggest that microRNA-155, a typical multifunctional microRNA, plays a crucial role in hematopoietic lineage differentiation, immunity, inflammation, viral infections, and vascular remodeling, which is linked to cardiovascular diseases such as coronary artery disease, abdominal aortic aneurysm, heart failure, and diabetic heart disease. The effects of microRNA-155 in different cell types through different target genes result in different mechanisms in diseases. MicroRNA-155 has been intensively studied in atherosclerosis and coronary artery disease. Contradictory results of microRNA-155 either promoting or preventing the pathophysiological process of atherosclerosis illustrate the complexity of this pleiotropic molecule. Therefore, more comprehensive studies of the underlying mechanisms of microRNA-155 involvement in cardiovascular diseases are required. Furthermore, a recent clinical trial of Miravirsen targeting microRNA-122 sheds light on exploiting microRNA-155 as a novel target to develop effective therapeutic strategies for cardiovascular diseases in the near future.

  15. Identification and characteristics of microRNAs from Bombyx mori

    Directory of Open Access Journals (Sweden)

    Gao Xiaolian

    2008-05-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are small RNA molecules that regulate gene expression by targeting messenger RNAs (mRNAs and causing mRNA cleavage or translation blockage. Of the 355 Arthropod miRNAs that have been identified, only 21 are B. mori miRNAs that were predicted computationally; of these, only let-7 has been confirmed by Northern blotting. Results Combining a computational method based on sequence homology searches with experimental identification based on microarray assays and Northern blotting, we identified 46 miRNAs, an additional 21 plausible miRNAs, and a novel small RNA in B. mori. The latter, bmo-miR-100-like, was identified using the known miRNA aga-miR-100 as a probe; bmo-miR-100-like was detected by microarray assay and Northern blotting, but its precursor sequences did not fold into a hairpin structure. Among these identified miRNAs, we found 12 pairs of miRNAs and miRNA*s. Northern blotting revealed that some B. mori miRNA genes were expressed only during specific stages, indicating that B. mori miRNA genes (e.g., bmo-miR-277 have developmentally regulated patterns of expression. We identified two miRNA gene clusters in the B. mori genome. bmo-miR-2b, which is found in the gene cluster bmo-miR-2a-1/bmo-miR-2a-1*/bmo-miR-2a-2/bmo-miR-2b/bmo-miR-13a*/bmo-miR-13b, encodes a newly identified member of the mir-2 family. Moreover, we found that methylation can increase the sensitivity of a DNA probe used to detect a miRNA by Northern blotting. Functional analysis revealed that 11 miRNAs may regulate 13 B. mori orthologs of the 25 known Drosophila miRNA-targeted genes according to the functional conservation. We predicted the binding sites on the 1671 3'UTR of B. mori genes; 547 targeted genes, including 986 target sites, were predicted. Of these target sites, 338 had perfect base pairing to the seed region of 43 miRNAs. From the predicted genes, 61 genes, each of them with multiple predicted target sites, should be

  16. Design, Construction, and Validation of Artificial MicroRNA Vectors Using Agrobacterium-Mediated Transient Expression System.

    Science.gov (United States)

    Bhagwat, Basdeo; Chi, Ming; Han, Dianwei; Tang, Haifeng; Tang, Guiliang; Xiang, Yu

    2016-01-01

    Artificial microRNA (amiRNA) technology utilizes microRNA (miRNA) biogenesis pathway to produce artificially selected small RNAs using miRNA gene backbone. It provides a feasible strategy for inducing loss of gene function, and has been applied in functional genomics study, improvement of crop quality and plant virus disease resistance. A big challenge in amiRNA applications is the unpredictability of silencing efficacy of the designed amiRNAs and not all constructed amiRNA candidates would be expressed effectively in plant cells. We and others found that high efficiency and specificity in RNA silencing can be achieved by designing amiRNAs with perfect or almost perfect sequence complementarity to their targets. In addition, we recently demonstrated that Agrobacterium-mediated transient expression system can be used to validate amiRNA constructs, which provides a simple, rapid and effective method to select highly expressible amiRNA candidates for stable genetic transformation. Here, we describe the methods for design of amiRNA candidates with perfect or almost perfect base-pairing to the target gene or gene groups, incorporation of amiRNA candidates in miR168a gene backbone by one step inverse PCR amplification, construction of plant amiRNA expression vectors, and assay of transient expression of amiRNAs in Nicotiana benthamiana through agro-infiltration, small RNA extraction, and amiRNA Northern blot.

  17. MicroRNAs and fetal brain development: Implications for ethanol teratology during the second trimester period of neurogenesis.

    Directory of Open Access Journals (Sweden)

    Rajesh eMiranda

    2012-05-01

    Full Text Available Maternal ethanol consumption during pregnancy can lead to a stereotypic cluster of fetal craniofacial, cardiovascular, skeletal and neurological deficits that are collectively termed the Fetal Alcohol Spectrum Disorder (FASD. Fetal ethanol exposure is a leading non-genetic cause of mental retardation. Mechanisms underlying the etiology of ethanol teratology are varied and complex. This review will focus on the developing brain as an important and vulnerable ethanol target. Near the end of the first trimester, and during the second trimester, fetal neural stem cells (NSCs produce most of the neurons of the adult brain, and ethanol has been shown to influence NSC renewal and maturation. We will discuss the neural developmental and teratological implications of the biogenesis and function of microRNAs (miRNAs, a class of small non-protein-coding RNAs that control the expression of gene networks by translation repression. A small but growing body of research has identified ethanol-sensitive miRNAs at different stages of NSC and brain maturation. While many microRNAs appear to be vulnerable to ethanol at specific developmental stages, a few, like the miR-9 family, appear to exhibit broad vulnerability to ethanol across multiple stages of NSC differentiation. An assessment of the regulation and function of these miRNAs provides important clues about the mechanisms that underlie fetal vulnerability to alterations in the maternal-fetal environment and yields insights into the genesis of FASD.

  18. Identification and Characterization of MicroRNAs in the Liver of Blunt Snout Bream (Megalobrama amblycephala Infected by Aeromonas hydrophila

    Directory of Open Access Journals (Sweden)

    Lei Cui

    2016-11-01

    Full Text Available MicroRNAs (miRNAs are small RNA molecules that play key roles in regulation of various biological processes. In order to better understand the biological significance of miRNAs in the context of Aeromonas hydrophila infection in Megalobrama amblycephala, small RNA libraries obtained from fish liver at 0 (non-infection, 4, and 24 h post infection (poi were sequenced using Illumina deep sequencing technology. A total of 11,244,207, 9,212,958, and 7,939,157 clean reads were obtained from these three RNA libraries, respectively. Bioinformatics analysis identified 171 conserved miRNAs and 62 putative novel miRNAs. The existence of ten randomly selected novel miRNAs was validated by RT-PCR. Pairwise comparison suggested that 61 and 44 miRNAs were differentially expressed at 4 and 24 h poi, respectively. Furthermore, the expression profiles of nine randomly selected miRNAs were validated by qRT-PCR. MicroRNA target prediction, gene ontology (GO annotation, and Kyoto Encylopedia of Genes and Genomes (KEGG analysis indicated that a variety of biological pathways could be affected by A. hydrophila infection. Additionally, transferrin (TF and transferrin receptor (TFR genes were confirmed to be direct targets of miR-375. These results will expand our knowledge of the role of miRNAs in the immune response of M. amblycephala to A. hydrophila infection, and facilitate the development of effective strategies against A. hydrophila infection in M. amblycephala.

  19. Make dark matter charged again

    Energy Technology Data Exchange (ETDEWEB)

    Agrawal, Prateek; Cyr-Racine, Francis-Yan; Randall, Lisa; Scholtz, Jakub, E-mail: prateekagrawal@fas.harvard.edu, E-mail: fcyrraci@physics.harvard.edu, E-mail: randall@physics.harvard.edu, E-mail: jscholtz@physics.harvard.edu [Department of Physics, Harvard University, Cambridge, MA 02138 (United States)

    2017-05-01

    We revisit constraints on dark matter that is charged under a U(1) gauge group in the dark sector, decoupled from Standard Model forces. We find that the strongest constraints in the literature are subject to a number of mitigating factors. For instance, the naive dark matter thermalization timescale in halos is corrected by saturation effects that slow down isotropization for modest ellipticities. The weakened bounds uncover interesting parameter space, making models with weak-scale charged dark matter viable, even with electromagnetic strength interaction. This also leads to the intriguing possibility that dark matter self-interactions within small dwarf galaxies are extremely large, a relatively unexplored regime in current simulations. Such strong interactions suppress heat transfer over scales larger than the dark matter mean free path, inducing a dynamical cutoff length scale above which the system appears to have only feeble interactions. These effects must be taken into account to assess the viability of darkly-charged dark matter. Future analyses and measurements should probe a promising region of parameter space for this model.

  20. A microRNA feedback loop regulates global microRNA abundance during aging.

    Science.gov (United States)

    Inukai, Sachi; Pincus, Zachary; de Lencastre, Alexandre; Slack, Frank J

    2018-02-01

    Expression levels of many microRNAs (miRNAs) change during aging, notably declining globally in a number of organisms and tissues across taxa. However, little is known about the mechanisms or the biological relevance for this change. We investigated the network of genes that controls miRNA transcription and processing during C. elegans aging. We found that miRNA biogenesis genes are highly networked with transcription factors and aging-associated miRNAs. In particular, miR-71, known to influence life span and itself up-regulated during aging, represses alg-1 /Argonaute expression post-transcriptionally during aging. Increased ALG-1 abundance in mir-71 loss-of-function mutants led to globally increased miRNA expression. Interestingly, these mutants demonstrated widespread mRNA expression dysregulation and diminished levels of variability both in gene expression and in overall life span. Thus, the progressive molecular decline often thought to be the result of accumulated damage over an organism's life may be partially explained by a miRNA-directed mechanism of age-associated decline. © 2018 Inukai et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.