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Sample records for micrornas show mutually

  1. Mutual antagonism between hepatitis B viral mRNA and host microRNA let-7.

    PubMed

    Takata, Akemi; Otsuka, Motoyuki; Ohno, Motoko; Kishikawa, Takahiro; Yoshikawa, Takeshi; Koike, Kazuhiko

    2016-01-01

    The interplay between viral and host factors plays a major role in viral pathogenesis. Hepatitis B virus (HBV) infection is a global health problem that leads to liver cirrhosis and hepatocellular carcinoma (HCC). Although HBV proteins have been studied extensively about their implication in hepatocarcinogenesis, the molecular mechanisms of oncogenesis are still largely unknown. A recent concept in gene regulation, in which competitive endogenous RNAs compete for common microRNAs (miRNAs), suggests that mRNA targets are key elements in the regulation of miRNA availability. Here, we show that HBV mRNA in the preS2 region can be targeted by host miRNA let-7 g. This leads to the sequestration of let-7 g and inhibition of let-7 g function. The expression of HBV transcripts, including the preS2 region, de-repressed let-7 g targets, which may contribute to long-term oncogenesis. HBV transcript-expressing transgenic mice, but not non-targeted transcript-expressing mice, were more prone to chemically induced hepatoocarcinogenesis. Let-7 target protein expression was upregulated in human HCC tissues derived from HBV-infected patients. On the other hand, let-7 g inhibited HBV preS2 protein expression and viral products. These results suggest that the interplay between viral intermediate transcripts during HBV replication and host miRNAs is crucial to the pathogenesis of chronic viral infection. PMID:26979389

  2. Mutual antagonism between hepatitis B viral mRNA and host microRNA let-7

    PubMed Central

    Takata, Akemi; Otsuka, Motoyuki; Ohno, Motoko; Kishikawa, Takahiro; Yoshikawa, Takeshi; Koike, Kazuhiko

    2016-01-01

    The interplay between viral and host factors plays a major role in viral pathogenesis. Hepatitis B virus (HBV) infection is a global health problem that leads to liver cirrhosis and hepatocellular carcinoma (HCC). Although HBV proteins have been studied extensively about their implication in hepatocarcinogenesis, the molecular mechanisms of oncogenesis are still largely unknown. A recent concept in gene regulation, in which competitive endogenous RNAs compete for common microRNAs (miRNAs), suggests that mRNA targets are key elements in the regulation of miRNA availability. Here, we show that HBV mRNA in the preS2 region can be targeted by host miRNA let-7 g. This leads to the sequestration of let-7 g and inhibition of let-7 g function. The expression of HBV transcripts, including the preS2 region, de-repressed let-7 g targets, which may contribute to long-term oncogenesis. HBV transcript-expressing transgenic mice, but not non-targeted transcript-expressing mice, were more prone to chemically induced hepatoocarcinogenesis. Let-7 target protein expression was upregulated in human HCC tissues derived from HBV-infected patients. On the other hand, let-7 g inhibited HBV preS2 protein expression and viral products. These results suggest that the interplay between viral intermediate transcripts during HBV replication and host miRNAs is crucial to the pathogenesis of chronic viral infection. PMID:26979389

  3. A simple coculture system shows mutualism between anaerobic faecalibacteria and epithelial Caco-2 cells

    PubMed Central

    Sadaghian Sadabad, Mehdi; von Martels, Julius Z. H.; Khan, Muhammed Tanweer; Blokzijl, Tjasso; Paglia, Giuseppe; Dijkstra, Gerard; Harmsen, Hermie J. M.; Faber, Klaas Nico

    2015-01-01

    Most gut bacteria are obligate anaerobes and are important for human health. However, little mechanistic insight is available on the health benefits of specific anaerobic gut bacteria. A main obstacle in generating such knowledge is the lack of simple and robust coculturing methods for anaerobic bacteria and oxygen-requiring human cells. Here, we describe the development of a coculture system for intestinal Caco-2 cells and an anaerobic symbiont, Faecalibacterium prausnitzii, making use of 50 mL culture tubes. F. prausnitzii was grown in 40 mL YCFAG-agar with glass-adhered Caco-2 cells placed on top in 10 mL DMEM medium. Grown for 18–36 h in a humidified incubator at 37 °C and 5% CO2, coverslip-attached Caco-2 cells promoted growth and metabolism of F. prausnitzii, while F. prausnitzii suppressed inflammation and oxidative stress in Caco-2 cells. F. prausnitzii did not compromise Caco-2 cell viability. Exogenously added porcine mucin also promoted growth of F. prausnitzii, suggesting that it may be part of the mechanism of Caco-2-stimulated growth of F. prausnitzii. This ‘Human oxygen-Bacteria anaerobic‘ (HoxBan) coculturing system uniquely establishes host-microbe mutualism of a beneficial anaerobic gut microbe in vitro and principally allows the analysis of host-microbe interactions of pure and mixed cultures of bacteria and human cells. PMID:26667159

  4. Modulation of microRNAs in two genetically disparate chicken lines showing different necrotic enteritis disease susceptibility

    Technology Transfer Automated Retrieval System (TEKTRAN)

    MicroRNAs (miRNA) play a critical role in post-transcriptional regulation by influencing the 3'-UTR of target genes. Using two inbred White Leghorn chicken lines, line 6.3 and line 7.2 showing Marek’s disease-resistant and -susceptible phenotypes, respectively, we used small RNA high-throughput sequ...

  5. Mutual induction of transcription factor PPARγ and microRNAs miR-145 and miR-329

    PubMed Central

    Dharap, Ashutosh; Pokrzywa, Courtney; Murali, Shruthi; Kaimal, Balarama; Vemuganti, Raghu

    2016-01-01

    MicroRNAs (miRNAs) are small non-coding RNAs that are known to control mRNA translation. Most miRNAs are transcribed from specific genes with well-defined promoters located throughout the genome. The mechanisms that control miRNA expression under normal and pathological conditions are not yet understood clearly. Peroxisome proliferator activated receptor (PPAR) γ is a ligand-activated transcription factor that is extensively distributed in the CNS. PPARγ activation induces neuroprotection by modulating genes that contain peroxisome proliferator response elements (PPREs) in their promoters. We presently evaluated if PPARγ modulates miRNA expression. When adult rats were treated with PPARγ agonist rosiglitazone, expression of 28 miRNAs altered significantly (12 up- and 16 down-regulated; 3 to 119 fold) in the cerebral cortex compared to vehicle-treated controls. In silico analysis showed 1 to 5 PPREs in the putative promoter regions (within 1 Kb upstream of the transcription start site) of these miRNA genes. Cotransfection with a PPARγ constitutively expressing vector significantly induced the miR-145 and miR-329 promoter vectors (each have 4 PPREs) which was curtailed by point mutations of PPREs in their promoters. Interestingly, the PPARγ promoter has binding sites for both these miRNAs and transfection with miR-329 mimic and miR-145 mimic induced the PPARγ expression. Thus, these studies show a cyclical induction of miRNAs and PPARγ indicating that the pleiotropic beneficial effects of PPARγ agonists might be modulated in part by miRNAs and their down-stream mRNAs. PMID:26119485

  6. MicroRNAs of Gallid and Meleagrid herpesviruses show generally conserved genomic locations and are virus-specific.

    PubMed

    Waidner, Lisa A; Morgan, Robin W; Anderson, Amy S; Bernberg, Erin L; Kamboj, Sachin; Garcia, Maricarmen; Riblet, Silva M; Ouyang, Ming; Isaacs, Grace K; Markis, Milos; Meyers, Blake C; Green, Pamela J; Burnside, Joan

    2009-05-25

    Many herpesviruses, including Marek's disease viruses (MDV1 and MDV2), encode microRNAs. In this study, we report microRNAs of two related herpesviruses, infectious laryngotracheitis virus (ILTV) and herpesvirus of turkeys (HVT), as well as additional MDV2 microRNAs. The genome locations, but not microRNA sequences, are conserved among all four of these avian herpesviruses. Most are clustered in the repeats flanking the unique long region (I/TR(L)), except in ILTV which lacks these repeats. Two abundant ILTV microRNAs are antisense to the immediate early gene ICP4. A homologue of host microRNA, gga-miR-221, was found among the HVT microRNAs. Additionally, a cluster of HVT microRNAs was found in a region containing two locally duplicated segments, resulting in paralogous HVT microRNAs with 96-100% identity. The prevalence of microRNAs in the genomic repeat regions as well as in local repeats suggests the importance of genetic plasticity in herpesviruses for microRNA evolution and preservation of function. PMID:19328516

  7. Homeologs of the Nicotiana benthamiana Antiviral ARGONAUTE1 Show Different Susceptibilities to microRNA168-Mediated Control1[OPEN

    PubMed Central

    Gursinsky, Torsten; Gambino, Giorgio; Friedrich, Susann; Behrens, Sven-Erik

    2015-01-01

    The plant ARGONAUTE1 protein (AGO1) is a central functional component of the posttranscriptional regulation of gene expression and the RNA silencing-based antiviral defense. By genomic and molecular approaches, we here reveal the presence of two homeologs of the AGO1-like gene in Nicotiana benthamiana, NbAGO1-1H and NbAGO1-1L. Both homeologs retain the capacity to transcribe messenger RNAs (mRNAs), which mainly differ in one 18-nucleotide insertion/deletion (indel). The indel does not modify the frame of the open reading frame, and it is located eight nucleotides upstream of the target site of a microRNA, miR168, which is an important modulator of AGO1 expression. We demonstrate that there is a differential accumulation of the two NbAGO1-1 homeolog mRNAs at conditions where miR168 is up-regulated, such as during a tombusvirus infection. The data reported suggest that the indel affects the miR168-guided regulation of NbAGO1 mRNA. The two AGO1 homeologs show full functionality in reconstituted, catalytically active RNA-induced silencing complexes following the incorporation of small interfering RNAs. Virus-induced gene silencing experiments suggest a specific involvement of the NbAGO1 homeologs in symptom development. The results provide an example of the diversity of microRNA target regions in NbAGO1 homeolog genes, which has important implications for improving resilience measures of the plant during viral infections. PMID:26015446

  8. Homeologs of the Nicotiana benthamiana Antiviral ARGONAUTE1 Show Different Susceptibilities to microRNA168-Mediated Control.

    PubMed

    Gursinsky, Torsten; Pirovano, Walter; Gambino, Giorgio; Friedrich, Susann; Behrens, Sven-Erik; Pantaleo, Vitantonio

    2015-07-01

    The plant ARGONAUTE1 protein (AGO1) is a central functional component of the posttranscriptional regulation of gene expression and the RNA silencing-based antiviral defense. By genomic and molecular approaches, we here reveal the presence of two homeologs of the AGO1-like gene in Nicotiana benthamiana, NbAGO1-1H and NbAGO1-1L. Both homeologs retain the capacity to transcribe messenger RNAs (mRNAs), which mainly differ in one 18-nucleotide insertion/deletion (indel). The indel does not modify the frame of the open reading frame, and it is located eight nucleotides upstream of the target site of a microRNA, miR168, which is an important modulator of AGO1 expression. We demonstrate that there is a differential accumulation of the two NbAGO1-1 homeolog mRNAs at conditions where miR168 is up-regulated, such as during a tombusvirus infection. The data reported suggest that the indel affects the miR168-guided regulation of NbAGO1 mRNA. The two AGO1 homeologs show full functionality in reconstituted, catalytically active RNA-induced silencing complexes following the incorporation of small interfering RNAs. Virus-induced gene silencing experiments suggest a specific involvement of the NbAGO1 homeologs in symptom development. The results provide an example of the diversity of microRNA target regions in NbAGO1 homeolog genes, which has important implications for improving resilience measures of the plant during viral infections. PMID:26015446

  9. Modulation of microRNAs in two genetically disparate chicken lines showing different necrotic enteritis disease susceptibility.

    PubMed

    Dinh, Hue; Hong, Yeong Ho; Lillehoj, Hyun S

    2014-05-15

    MicroRNAs (miRNA) play a critical role in post-transcriptional regulation by influencing the 3'-UTR of target genes. Using two inbred White Leghorn chicken lines, line 6.3 and line 7.2 showing Marek's disease-resistant and -susceptible phenotypes, respectively, we used small RNA high-throughput sequencing (HTS) to investigate whether miRNAs are differently expressed in these two chicken lines after inducing necrotic enteritis (NE). The 12 miRNAs, selected from the most down-regulated or up-regulated miRNAs following NE induction, were confirmed by their expressions in real-time PCR. Among these miRNAs, miR-215, miR-217, miR-194, miR-200a, miR-200b, miR-216a, miR-216b, and miR-429 were highly expressed in intestine derived from line 7.2, whereas, miR-1782 and miR-499 were down-regulated. In spleen, miR-34b and miR-1684 were the most up-regulated miRNAs in line 6.3. Notably, five out of six target genes, CXCR5, BCL2, GJA1, TCF12, and TAB3 were differentially expressed between line 6.3 and line 7.2, and showed suppression in the MD-susceptible chicken line. Their expression levels were conversely correlated with those of miRNA obtained from both HTS and quantitative real-time PCR. These results suggest that some miRNAs are differentially altered in response to NE and they modulate the expression of their target genes in the two inbred lines. Collectively, HTS analysis of intestinal miRNAs from NE-afflicted inbred chickens showing different disease phenotypes led to the identification of host immunity genes regulated by miRNA. Future studies of the function of these miRNAs and their target genes in the host will lead to enhanced understanding of molecular mechanisms controlling host-pathogen interaction in NE. PMID:24629767

  10. MicroRNAs of the mesothorax in Qinlingacris elaeodes, an alpine grasshopper showing a wing polymorphism with unilateral wing form.

    PubMed

    Li, R; Jiang, G F; Ren, Q P; Wang, Y T; Zhou, X M; Zhou, C F; Qin, D Z

    2016-04-01

    MicroRNAs (miRNAs) are now recognized as key post-transcriptional regulators in regulation of phenotypic diversity. Qinlingacris elaeodes is a species of the alpine grasshopper, which is endemic to China. Adult individuals have three wing forms: wingless, unilateral-winged and short-winged. This is an ideal species to investigate the phenotypic plasticity, development and evolution of insect wings because of its case of unilateral wing form in both the sexes. We sequenced a small RNA library prepared from mesothoraxes of the adult grasshoppers using the Illumina deep sequencing technology. Approximately 12,792,458 raw reads were generated, of which the 854,580 high-quality reads were used only for miRNA identification. In this study, we identified 49 conserved miRNAs belonging to 41 families and 69 species-specific miRNAs. Moreover, seven miRNA*s were detected both for conserved miRNAs and species-specific miRNAs, which were supported by hairpin forming precursors based on polymerase chain reaction. This is the first description of miRNAs in alpine grasshoppers. The results provide a useful resource for further studies on molecular regulation and evolution of miRNAs in grasshoppers. These findings not only enrich the miRNAs for insects but also lay the groundwork for the study of post-transcriptional regulation of wing forms. PMID:26693589

  11. Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress.

    PubMed

    Akpinar, Bala Ani; Kantar, Melda; Budak, Hikmet

    2015-09-01

    MicroRNAs, small regulatory molecules with significant impacts on the transcriptional network of all living organisms, have been the focus of several studies conducted mostly on modern wheat cultivars. In this study, we investigated miRNA repertoires of modern durum wheat and its wild relatives, with differing degrees of drought tolerance, to identify miRNA candidates and their targets involved in drought stress response. Root transcriptomes of Triticum turgidum ssp. durum variety Kızıltan and two Triticum turgidum ssp. dicoccoides genotypes TR39477 and TTD-22 under control and drought conditions were assembled from individual RNA-Seq reads and used for in silico identification of miRNAs. A total of 66 miRNAs were identified from all species, across all conditions, of which 46 and 38 of the miRNAs identified from modern durum wheat and wild genotypes, respectively, had not been previously reported. Genotype- and/or stress-specific miRNAs provide insights into our understanding of the complex drought response. Particularly, miR1435, miR5024, and miR7714, identified only from drought-stress roots of drought-tolerant genotype TR39477, can be candidates for future studies to explore and exploit the drought response to develop tolerant varieties. PMID:26174050

  12. Global Profiling in Vestibular Schwannomas Shows Critical Deregulation of MicroRNAs and Upregulation in Those Included in Chromosomal Region 14q32

    PubMed Central

    Torres-Martin, Miguel; Lassaletta, Luis; de Campos, Jose M.; Isla, Alberto; Gavilan, Javier; Pinto, Giovanny R.; Burbano, Rommel R.; Latif, Farida; Melendez, Barbara; Castresana, Javier S.; Rey, Juan A.

    2013-01-01

    Background Vestibular schwannomas are benign tumors that arise from Schwann cells in the VIII cranial pair and usually present NF2 gene mutations and/or loss of heterozygosity on chromosome 22q. Deregulation has also been found in several genes, such as ERBB2 and NRG1. MicroRNAs are non-coding RNAs approximately 21 to 23 nucleotides in length that regulate mRNAs, usually by degradation at the post-transcriptional level. Methods We used microarray technology to test the deregulation of miRNAs and other non-coding RNAs present in GeneChip miRNA 1.0 (Affymetrix) over 16 vestibular schwannomas and 3 control-nerves, validating 10 of them by qRT-PCR. Findings Our results showed the deregulation of 174 miRNAs, including miR-10b, miR-206, miR-183 and miR-204, and the upregulation of miR-431, miR-221, miR-21 and miR-720, among others. The results also showed an aberrant expression of other non-coding RNAs. We also found a general upregulation of the miRNA cluster located at chromosome 14q32. Conclusion Our results suggest that several miRNAs are involved in tumor formation and/or maintenance and that global upregulation of the 14q32 chromosomal site contains miRNAs that may represent a therapeutic target for this neoplasm. PMID:23776562

  13. Integration-Free Human Induced Pluripotent Stem Cells From Type 1 Diabetes Patient Skin Fibroblasts Show Increased Abundance of Pancreas-Specific microRNAs

    PubMed Central

    Liu, Jun; Joglekar, Mugdha V.; Sumer, Huseyin; Hardikar, Anandwardhan A.; Teede, Halena; Verma, Paul J.

    2014-01-01

    Type 1 diabetes (T1D) is a disease that is typically associated with multigenetic changes as well as environmental triggers. Disease-specific induced pluripotent stem cells (iPSCs) are preferable cell sources to study T1D, as they are derived from patient cells and therefore capture the disease genotype in a stem cell line. The purpose of this study was to generate integration-free iPSCs from adult skin fibroblasts with T1D. iPSCs were generated by transfection of synthetic mRNAs encoding transcription factors OCT4, SOX2, KLF4, c-MYC, and LIN28. Phase-contrast microscopy, immunocytochemistry, karyotyping, bisulfite genomic sequencing, reverse transcription-polymerase chain reaction, and teratoma formation assay were used to determine reprogramming efficiency, pluripotency, and differentiation potential. Following 18 consecutive days of synthetic mRNA transfections, the T1D patient skin fibroblasts underwent morphological changes, and the aggregated clumps exhibited a human embryonic stem cell (ESC)-like morphology with a high nucleus/cytoplasm ratio. Highly efficient generation of iPSCs was achieved using the mRNA reprogramming approach. The disease-specific iPSCs expressed pluripotency markers, maintained a normal karyotype, and formed teratomas containing tissues representative of the three germ layers when injected into immune-deficient mice. Of interest, the iPSCs showed upregulations of pancreas-specific microRNAs, compared with parental fibroblasts. These data indicate that T1D patient skin fibroblasts can be reprogrammed to pluripotency using a synthetic mRNA approach. These cells can serve as a useful tool for the identification of genes that are involved in autoimmune reactions as well as generating patient-matched β-cells for cell-based therapy. PMID:26858889

  14. MicroRNA processing without Dicer

    PubMed Central

    2010-01-01

    The canonical processing of precursor microRNAs requires the endonuclease Dicer. A recent study shows that microRNAs can be processed independently of Dicer but instead require Argonaute 2. PMID:20565849

  15. The Evolution of Interspecific Mutualisms

    NASA Astrophysics Data System (ADS)

    Doebeli, Michael; Knowlton, Nancy

    1998-07-01

    Interspecific mutualisms are widespread, but how they evolve is not clear. The Iterated Prisoner's Dilemma is the main theoretical tool to study cooperation, but this model ignores ecological differences between partners and assumes that amounts exchanged cannot themselves evolve. A more realistic model incorporating these features shows that strategies that succeed with fixed exchanges (e.g., Tit-for-Tat) cannot explain mutualism when exchanges vary because the amount exchanged evolves to 0. For mutualism to evolve, increased investments in a partner must yield increased returns, and spatial structure in competitive interactions is required. Under these biologically plausible assumptions, mutualism evolves with surprising ease. This suggests that, contrary to the basic premise of past theoretical analyses, overcoming a potential host's initial defenses may be a bigger obstacle for mutualism than the subsequent recurrence and spread of noncooperative mutants.

  16. Mutually unbiased bases

    NASA Astrophysics Data System (ADS)

    Chaturvedi, S.

    2002-08-01

    After a brief review of the notion of a full set of mutually unbiased bases in an N-dimensional Hilbert space, we summarize the work of Wootters and Fields (W K Wootters and B C Fields, Ann. Phys. 191, 363 (1989)) which gives an explicit construction for such bases for the case N=pr, where p is a prime. Further, we show how, by exploiting certain freedom in the Wootters-Fields construction, the task of explicitly writing down such bases can be simplified for the case when p is an odd prime. In particular, we express the results entirely in terms of the character vectors of the cyclic group G of order p. We also analyse the connection between mutually unbiased bases and the representations of G.

  17. Covariant mutually unbiased bases

    NASA Astrophysics Data System (ADS)

    Carmeli, Claudio; Schultz, Jussi; Toigo, Alessandro

    2016-06-01

    The connection between maximal sets of mutually unbiased bases (MUBs) in a prime-power dimensional Hilbert space and finite phase-space geometries is well known. In this article, we classify MUBs according to their degree of covariance with respect to the natural symmetries of a finite phase-space, which are the group of its affine symplectic transformations. We prove that there exist maximal sets of MUBs that are covariant with respect to the full group only in odd prime-power dimensional spaces, and in this case, their equivalence class is actually unique. Despite this limitation, we show that in dimension 2r covariance can still be achieved by restricting to proper subgroups of the symplectic group, that constitute the finite analogues of the oscillator group. For these subgroups, we explicitly construct the unitary operators yielding the covariance.

  18. Evolution of mutualism between species

    SciTech Connect

    Post, W.M.; Travis, C.C.; DeAngelis, D.L.

    1980-01-01

    Recent theoretical work on mutualism, the interaction between species populations that is mutually beneficial, is reviewed. Several ecological facts that should be addressed in the construction of dynamic models for mutualism are examined. Basic terminology is clarified. (PSB)

  19. Behavioral Ecology: Manipulative Mutualism.

    PubMed

    Hughes, David P

    2015-09-21

    A new study reveals that an apparent mutualism between lycaenid caterpillars and their attendant ants may not be all it seems, as the caterpillars produce secretions that modify the brains and behavior of their attendant ants. PMID:26394105

  20. Mutually Exclusive, Complementary, or . . .

    ERIC Educational Resources Information Center

    Schloemer, Cathy G.

    2016-01-01

    Whether students are beginning their study of probability or are well into it, distinctions between complementary sets and mutually exclusive sets can be confusing. Cathy Schloemer writes in this article that for years she used typical classroom examples but was not happy with the student engagement or the level of understanding they produced.…

  1. Mutual Adaptaion in Action

    ERIC Educational Resources Information Center

    Siskin, Leslie Santee

    2016-01-01

    Building on an expanded concept of mutual adaptation, this chapter explores a distinctive and successful aspect of International Baccalaureate's effort to scale up, as they moved to expand their programs and support services in Title I schools. Based on a three-year, mixed-methods study, it offers a case where we see not only local adaptations…

  2. Pervasive microRNA Duplication in Chelicerates: Insights from the Embryonic microRNA Repertoire of the Spider Parasteatoda tepidariorum

    PubMed Central

    Leite, Daniel J.; Ninova, Maria; Hilbrant, Maarten; Arif, Saad; Griffiths-Jones, Sam; Ronshaugen, Matthew; McGregor, Alistair P.

    2016-01-01

    MicroRNAs are small (∼22 nt) noncoding RNAs that repress translation and therefore regulate the production of proteins from specific target mRNAs. microRNAs have been found to function in diverse aspects of gene regulation within animal development and many other processes. Among invertebrates, both conserved and novel, lineage specific, microRNAs have been extensively studied predominantly in holometabolous insects such as Drosophila melanogaster. However little is known about microRNA repertoires in other arthropod lineages such as the chelicerates. To understand the evolution of microRNAs in this poorly sampled subphylum, we characterized the microRNA repertoire expressed during embryogenesis of the common house spider Parasteatoda tepidariorum. We identified a total of 148 microRNAs in P. tepidariorum representing 66 families. Approximately half of these microRNA families are conserved in other metazoans, while the remainder are specific to this spider. Of the 35 conserved microRNAs families 15 had at least two copies in the P. tepidariorum genome. A BLAST-based approach revealed a similar pattern of duplication in other spiders and a scorpion, but not among other chelicerates and arthropods, with the exception of a horseshoe crab. Among the duplicated microRNAs we found examples of lineage-specific tandem duplications, and the duplication of entire microRNA clusters in three spiders, a scorpion, and in a horseshoe crab. Furthermore, we found that paralogs of many P. tepidariorum microRNA families exhibit arm switching, which suggests that duplication was often followed by sub- or neofunctionalization. Our work shows that understanding the evolution of microRNAs in the chelicerates has great potential to provide insights into the process of microRNA duplication and divergence and the evolution of animal development. PMID:27324919

  3. Pervasive microRNA Duplication in Chelicerates: Insights from the Embryonic microRNA Repertoire of the Spider Parasteatoda tepidariorum.

    PubMed

    Leite, Daniel J; Ninova, Maria; Hilbrant, Maarten; Arif, Saad; Griffiths-Jones, Sam; Ronshaugen, Matthew; McGregor, Alistair P

    2016-01-01

    MicroRNAs are small (∼22 nt) noncoding RNAs that repress translation and therefore regulate the production of proteins from specific target mRNAs. microRNAs have been found to function in diverse aspects of gene regulation within animal development and many other processes. Among invertebrates, both conserved and novel, lineage specific, microRNAs have been extensively studied predominantly in holometabolous insects such as Drosophila melanogaster However little is known about microRNA repertoires in other arthropod lineages such as the chelicerates. To understand the evolution of microRNAs in this poorly sampled subphylum, we characterized the microRNA repertoire expressed during embryogenesis of the common house spider Parasteatoda tepidariorum We identified a total of 148 microRNAs in P. tepidariorum representing 66 families. Approximately half of these microRNA families are conserved in other metazoans, while the remainder are specific to this spider. Of the 35 conserved microRNAs families 15 had at least two copies in the P. tepidariorum genome. A BLAST-based approach revealed a similar pattern of duplication in other spiders and a scorpion, but not among other chelicerates and arthropods, with the exception of a horseshoe crab. Among the duplicated microRNAs we found examples of lineage-specific tandem duplications, and the duplication of entire microRNA clusters in three spiders, a scorpion, and in a horseshoe crab. Furthermore, we found that paralogs of many P. tepidariorum microRNA families exhibit arm switching, which suggests that duplication was often followed by sub- or neofunctionalization. Our work shows that understanding the evolution of microRNAs in the chelicerates has great potential to provide insights into the process of microRNA duplication and divergence and the evolution of animal development. PMID:27324919

  4. Phenological shifts and the fate of mutualisms

    PubMed Central

    Rafferty, Nicole E.; CaraDonna, Paul J.; Bronstein, Judith L.

    2014-01-01

    Climate change is altering the timing of life history events in a wide array of species, many of which are involved in mutualistic interactions. Because many mutualisms can form only if partner species are able to locate each other in time, differential phenological shifts are likely to influence their strength, duration and outcome. At the extreme, climate change-driven shifts in phenology may result in phenological mismatch: the partial or complete loss of temporal overlap of mutualistic species. We have a growing understanding of how, when, and why phenological change can alter one type of mutualism–pollination. However, as we show here, there has been a surprising lack of attention to other types of mutualism. We generate a set of predictions about the characteristics that may predispose mutualisms in general to phenological mismatches. We focus not on the consequences of such mismatches but rather on the likelihood that mismatches will develop. We explore the influence of three key characteristics of mutualism: 1) intimacy, 2) seasonality and duration, and 3) obligacy and specificity. We predict that the following characteristics of mutualism may increase the likelihood of phenological mismatch: 1) a non-symbiotic life history in which co-dispersal is absent; 2) brief, seasonal interactions; and 3) facultative, generalized interactions. We then review the limited available data in light of our a priori predictions and point to mutualisms that are more and less likely to be at risk of becoming phenologically mismatched, emphasizing the need for research on mutualisms other than plant–pollinator interactions. Future studies should explicitly focus on mutualism characteristics to determine whether and how changing phenologies will affect mutualistic interactions. PMID:25883391

  5. Certainty relations, mutual entanglement, and nondisplaceable manifolds

    NASA Astrophysics Data System (ADS)

    Puchała, Zbigniew; Rudnicki, Łukasz; Chabuda, Krzysztof; Paraniak, Mikołaj; Życzkowski, Karol

    2015-09-01

    We derive explicit bounds for the average entropy characterizing measurements of a pure quantum state of size N in L orthogonal bases. Lower bounds lead to novel entropic uncertainty relations, while upper bounds allow us to formulate universal certainty relations. For L =2 the maximal average entropy saturates at logN because there exists a mutually coherent state, but certainty relations are shown to be nontrivial for L ≥3 measurements. In the case of a prime power dimension, N =pk , and the number of measurements L =N +1 , the upper bound for the average entropy becomes minimal for a collection of mutually unbiased bases. An analogous approach is used to study entanglement with respect to L different splittings of a composite system linked by bipartite quantum gates. We show that, for any two-qubit unitary gate U ∈U(4 ) there exist states being mutually separable or mutually entangled with respect to both splittings (related by U ) of the composite system. The latter statement follows from the fact that the real projective space R P3⊂C P3 is nondisplaceable by a unitary transformation. For L =3 splittings the maximal sum of L entanglement entropies is conjectured to achieve its minimum for a collection of three mutually entangled bases, formed by two mutually entangling gates.

  6. microRNA Profiling of Amniotic Fluid: Evidence of Synergy of microRNAs in Fetal Development

    PubMed Central

    Li, Tianpeng; Ling, Shucai

    2016-01-01

    Amniotic fluid (AF) continuously exchanges molecules with the fetus, playing critical roles in fetal development especially via its complex components. Among these components, microRNAs are thought to be transferred between cells loaded in microvesicles. However, the functions of AF microRNAs remain unknown. To date, few studies have examined microRNAs in amniotic fluid. In this study, we employed miRCURY Locked Nucleotide Acid arrays to profile the dynamic expression of microRNAs in AF from mice on embryonic days E13, E15, and E17. At these times, 233 microRNAs were differentially expressed (p< 0.01), accounting for 23% of the total Mus musculus microRNAs. These differentially-expressed microRNAs were divided into two distinct groups based on their expression patterns. Gene ontology analysis showed that the intersectional target genes of these differentially-expressed microRNAs were mainly distributed in synapse, synaptosome, cell projection, and cytoskeleton. Pathway analysis revealed that the target genes of the two groups of microRNAs were synergistically enriched in axon guidance, focal adhesion, and MAPK signaling pathways. MicroRNA-mRNA network analysis and gene- mapping showed that these microRNAs synergistically regulated cell motility, cell proliferation and differentiation, and especially the axon guidance process. Cancer pathways associated with growth and proliferation were also enriched in AF. Taken together, the results of this study are the first to show the functions of microRNAs in AF during fetal development, providing novel insights into interpreting the roles of AF microRNAs in fetal development. PMID:27166676

  7. Defense mutualisms enhance plant diversification.

    PubMed

    Weber, Marjorie G; Agrawal, Anurag A

    2014-11-18

    The ability of plants to form mutualistic relationships with animal defenders has long been suspected to influence their evolutionary success, both by decreasing extinction risk and by increasing opportunity for speciation through an expanded realized niche. Nonetheless, the hypothesis that defense mutualisms consistently enhance plant diversification across lineages has not been well tested due to a lack of phenotypic and phylogenetic information. Using a global analysis, we show that the >100 vascular plant families in which species have evolved extrafloral nectaries (EFNs), sugar-secreting organs that recruit arthropod mutualists, have twofold higher diversification rates than families that lack species with EFNs. Zooming in on six distantly related plant clades, trait-dependent diversification models confirmed the tendency for lineages with EFNs to display increased rates of diversification. These results were consistent across methodological approaches. Inference using reversible-jump Markov chain Monte Carlo (MCMC) to model the placement and number of rate shifts revealed that high net diversification rates in EFN clades were driven by an increased number of positive rate shifts following EFN evolution compared with sister clades, suggesting that EFNs may be indirect facilitators of diversification. Our replicated analysis indicates that defense mutualisms put lineages on a path toward increased diversification rates within and between clades, and is concordant with the hypothesis that mutualistic interactions with animals can have an impact on deep macroevolutionary patterns and enhance plant diversity. PMID:25349406

  8. Defense mutualisms enhance plant diversification

    PubMed Central

    Weber, Marjorie G.; Agrawal, Anurag A.

    2014-01-01

    The ability of plants to form mutualistic relationships with animal defenders has long been suspected to influence their evolutionary success, both by decreasing extinction risk and by increasing opportunity for speciation through an expanded realized niche. Nonetheless, the hypothesis that defense mutualisms consistently enhance plant diversification across lineages has not been well tested due to a lack of phenotypic and phylogenetic information. Using a global analysis, we show that the >100 vascular plant families in which species have evolved extrafloral nectaries (EFNs), sugar-secreting organs that recruit arthropod mutualists, have twofold higher diversification rates than families that lack species with EFNs. Zooming in on six distantly related plant clades, trait-dependent diversification models confirmed the tendency for lineages with EFNs to display increased rates of diversification. These results were consistent across methodological approaches. Inference using reversible-jump Markov chain Monte Carlo (MCMC) to model the placement and number of rate shifts revealed that high net diversification rates in EFN clades were driven by an increased number of positive rate shifts following EFN evolution compared with sister clades, suggesting that EFNs may be indirect facilitators of diversification. Our replicated analysis indicates that defense mutualisms put lineages on a path toward increased diversification rates within and between clades, and is concordant with the hypothesis that mutualistic interactions with animals can have an impact on deep macroevolutionary patterns and enhance plant diversity. PMID:25349406

  9. Mutual information and spontaneous symmetry breaking

    NASA Astrophysics Data System (ADS)

    Hamma, A.; Giampaolo, S. M.; Illuminati, F.

    2016-01-01

    We show that the metastable, symmetry-breaking ground states of quantum many-body Hamiltonians have vanishing quantum mutual information between macroscopically separated regions and are thus the most classical ones among all possible quantum ground states. This statement is obvious only when the symmetry-breaking ground states are simple product states, e.g., at the factorization point. On the other hand, symmetry-breaking states are in general entangled along the entire ordered phase, and to show that they actually feature the least macroscopic correlations compared to their symmetric superpositions is highly nontrivial. We prove this result in general, by considering the quantum mutual information based on the two-Rényi entanglement entropy and using a locality result stemming from quasiadiabatic continuation. Moreover, in the paradigmatic case of the exactly solvable one-dimensional quantum X Y model, we further verify the general result by considering also the quantum mutual information based on the von Neumann entanglement entropy.

  10. MicroRNA fingerprints during human megakaryocytopoiesis

    PubMed Central

    Garzon, Ramiro; Pichiorri, Flavia; Palumbo, Tiziana; Iuliano, Rodolfo; Cimmino, Amelia; Aqeilan, Rami; Volinia, Stefano; Bhatt, Darshna; Alder, Hansjuerg; Marcucci, Guido; Calin, George A.; Liu, Chang-Gong; Bloomfield, Clara D.; Andreeff, Michael; Croce, Carlo M.

    2006-01-01

    microRNAs are a highly conserved class of noncoding RNAs with important regulatory functions in proliferation, apoptosis, development, and differentiation. To discover novel regulatory pathways during megakaryocytic differentiation, we performed microRNA expression profiling of in vitro-differentiated megakaryocytes derived from CD34+ hematopoietic progenitors. The main finding was down-regulation of miR-10a, miR-126, miR-106, miR-10b, miR-17 and miR-20. Hypothetically, the down-regulation of microRNAs unblocks target genes involved in differentiation. We confirmed in vitro and in vivo that miR-130a targets the transcription factor MAFB, which is involved in the activation of the GPIIB promoter, a key protein for platelet physiology. In addition, we found that miR-10a expression in differentiated megakaryocytes is inverse to that of HOXA1, and we showed that HOXA1 is a direct target of miR-10a. Finally, we compared the microRNA expression of megakaryoblastic leukemic cell lines with that of in vitro differentiated megakaryocytes and CD34+ progenitors. This analysis revealed up-regulation of miR-101, miR-126, miR-99a, miR-135, and miR-20. Our data delineate the expression of microRNAs during megakaryocytopoiesis and suggest a regulatory role of microRNAs in this process by targeting megakaryocytic transcription factors. PMID:16549775

  11. Nutrient loading alters the performance of key nutrient exchange mutualisms.

    PubMed

    Shantz, Andrew A; Lemoine, Nathan P; Burkepile, Deron E

    2016-01-01

    Nutrient exchange mutualisms between phototrophs and heterotrophs, such as plants and mycorrhizal fungi or symbiotic algae and corals, underpin the functioning of many ecosystems. These relationships structure communities, promote biodiversity and help maintain food security. Nutrient loading may destabilise these mutualisms by altering the costs and benefits each partner incurs from interacting. Using meta-analyses, we show a near ubiquitous decoupling in mutualism performance across terrestrial and marine environments in which phototrophs benefit from enrichment at the expense of their heterotrophic partners. Importantly, heterotroph identity, their dependence on phototroph-derived C and the type of nutrient enrichment (e.g. nitrogen vs. phosphorus) mediated the responses of different mutualisms to enrichment. Nutrient-driven changes in mutualism performance may alter community organisation and ecosystem processes and increase costs of food production. Consequently, the decoupling of nutrient exchange mutualisms via alterations of the world's nitrogen and phosphorus cycles may represent an emerging threat of global change. PMID:26549314

  12. Entanglement in Mutually Unbiased Bases

    NASA Astrophysics Data System (ADS)

    Wiesniak, Marcin; Paterek, Tomasz; Zeilinger, Anton

    2011-03-01

    Higher-dimensional Hilbert spaces are still not fully explored. One issue concerns mutually unbiased bases (MUBs). For primes and their powers (e.g.), full sets of MUBs are known. The question of existence of all MUBs in composite dimensions is still open. We show that for all full sets of MUBs of a given dimension a certain entanglement measure of the bases is constant. This fact could be an argument either for or against the existence of full sets of MUBs in some dimensions and tells us that almost all MUBs are maximally entangled for high-dimensional composite systems, whereas this is not the case for prime dimensions. We present a new construction of MUBs in squared prime dimensions. We use only one entangling operation, which simplifies possible experiments. The construction gives only product states and maximally entangled states. Research supported by ERC Advanced Grant QIT4QAD and FWF SFB-grant F4007 of the Austrian Science Fund.

  13. Estimating mutual information.

    PubMed

    Kraskov, Alexander; Stögbauer, Harald; Grassberger, Peter

    2004-06-01

    We present two classes of improved estimators for mutual information M(X,Y), from samples of random points distributed according to some joint probability density mu(x,y). In contrast to conventional estimators based on binnings, they are based on entropy estimates from k -nearest neighbor distances. This means that they are data efficient (with k=1 we resolve structures down to the smallest possible scales), adaptive (the resolution is higher where data are more numerous), and have minimal bias. Indeed, the bias of the underlying entropy estimates is mainly due to nonuniformity of the density at the smallest resolved scale, giving typically systematic errors which scale as functions of k/N for N points. Numerically, we find that both families become exact for independent distributions, i.e. the estimator M(X,Y) vanishes (up to statistical fluctuations) if mu(x,y)=mu(x)mu(y). This holds for all tested marginal distributions and for all dimensions of x and y. In addition, we give estimators for redundancies between more than two random variables. We compare our algorithms in detail with existing algorithms. Finally, we demonstrate the usefulness of our estimators for assessing the actual independence of components obtained from independent component analysis (ICA), for improving ICA, and for estimating the reliability of blind source separation. PMID:15244698

  14. [Biological mutualism, concepts and models].

    PubMed

    Perru, Olivier

    2011-01-01

    Mutualism is a biological association for a mutual benefit between two different species. In this paper, firstly, we examine the history and signification of mutualism in relation to symbiosis. Then, we consider the link between concepts and models of mutualism. Models of mutualism depend on different concepts we use: If mutualism is situated at populations' level, it will be expressed by Lotka-Volterra models, concerning exclusively populations' size. If mutualism is considered as a resources' exchange or a biological market increasing the fitness of these organisms, it will be described at an individual level by a cost-benefit model. Our analysis will be limited to the history and epistemology of Lotka-Volterra models and we hypothesize that these models are adapted at first to translate dynamic evolutions of mutualism. They render stability or variations of size and assume that there are clear distinctions and a state of equilibrium between populations of different species. Italian mathematician Vito Volterra demonstrated that biological associations consist in a constant relation between some species. In 1931 and 1935, Volterra described the general form of antagonistic or mutualistic biological associations by the same differential equations. We recognize that these equations have been more used to model competition or prey-predator interactions, but a simple sign change allows describing mutualism. The epistemological problem is the following: Volterra's equations help us to conceptualize a global phenomenon. However, mutualistic interactions may have stronger effects away from equilibrium and these effects may be better understood at individual level. We conclude that, between 1985 and 2000, some researchers carried on working and converting Lotka-Volterra models but this description appeared as insufficient. So, other researchers adopted an economical viewpoint, considering mutualism as a biological market. PMID:22288336

  15. Grief and Palliative Care: Mutuality

    PubMed Central

    Moon, Paul J

    2013-01-01

    Grief and palliative care are interrelated and perhaps mutually inclusive. Conceptually and practically, grief intimately relates to palliative care, as both domains regard the phenomena of loss, suffering, and a desire for abatement of pain burden. Moreover, the notions of palliative care and grief may be construed as being mutually inclusive in terms of one cueing the other. As such, the discussions in this article will center on the conceptualizations of the mutuality between grief and palliative care related to end-of-life circumstances. Specifically, the complementarity of grief and palliative care, as well as a controvertible view thereof, will be considered. PMID:25278758

  16. Mutual diffusion in a binary isotopic mixture.

    PubMed

    Sharma, Raman; Tankeshwar, K

    2010-11-17

    The mass dependence of the mutual diffusion coefficient, in a binary equimolar mixture of Lennard-Jones fluids, is studied within Mori's memory function formalism. A phenomenological form of the memory function is used to study the time evolution of the self- and relative velocity correlation functions. The diffusion coefficients are calculated from the relevant velocity correlation functions using the Green-Kubo integral formula. Like the self-diffusion coefficient, the mutual diffusion coefficient is also found to be weakly dependent on the mass ratio. The present study shows that the minimum value that the mutual diffusion coefficient in an equimolar mixture of isotopic fluids can have is √(1/2) times the self-diffusion coefficient of any of the species when in isolation. Further, the contribution of the dynamic/distinct cross correlations to the mutual diffusion coefficient is found to be small and positive for the whole range of the mass ratio which is consistent with earlier molecular dynamics results. PMID:21339621

  17. [Human cerebral image registration using generalized mutual information].

    PubMed

    Zhang, Jingzhou; Li, Ting; Zhang, Jia

    2008-12-01

    Medical image registration is a highlight of actual research on medical image processing. Based onsimilarity measure of Shannon entropy, a new generalized distance measurement based on Rényi entropy applied to image rigid registration is introduced and is called here generalized mutual information (GMI). It is used in three dimensional cerebral image registration experiments. The simulation results show that generalized distance measurement and Shannon entropy measurement apply to different areas; that the registration measure based o n generalized distance is a natural extension of mutual information of Shannon entropy. The results prove that generalized mutual information uses less time than simple mutual information does, and the new similarity measure manifests higher degree of consistency between the two cerebral registration images. Also, the registration results provide the clinical diagnoses with more important references. In conclusion, generalized mutual information has satisfied the demands of clinical application to a wide extent. PMID:19166197

  18. Nanopore-based detection of circulating microRNAs in lung cancer patients

    NASA Astrophysics Data System (ADS)

    Wang, Yong; Zheng, Dali; Tan, Qiulin; Wang, Michael X.; Gu, Li-Qun

    2011-10-01

    MicroRNAs are short RNA molecules that regulate gene expression, and have been investigated as potential biomarkers because their expression levels are correlated with various diseases. However, detecting microRNAs in the bloodstream remains difficult because current methods are not sufficiently selective or sensitive. Here, we show that a nanopore sensor based on the α-haemolysin protein can selectively detect microRNAs at the single molecular level in plasma samples from lung cancer patients without the need for labels or amplification of the microRNA. The sensor, which uses a programmable oligonucleotide probe to generate a target-specific signature signal, can quantify subpicomolar levels of cancer-associated microRNAs and can distinguish single-nucleotide differences between microRNA family members. This approach is potentially useful for quantitative microRNA detection, the discovery of disease markers and non-invasive early diagnosis of cancer.

  19. Mutual Orbits of Transneptunian Binaries

    NASA Astrophysics Data System (ADS)

    Grundy, William M.; Noll, K. S.; Roe, H. G.; Porter, S. B.; Trujillo, C. A.; Benecchi, S. D.; Buie, M. W.

    2012-10-01

    We report the latest results from a program of high spatial resolution imaging to resolve the individual components of binary transneptunian objects. These observations use Hubble Space Telescope and also laser guide star adaptive optics systems on Keck and Gemini telescopes on Mauna Kea. From relative astrometry over multiple epochs, we determine the mutual orbits of the components, and thus the total masses of the systems. Accurate masses anchor subsequent detailed investigations into the physical characteristics of these systems. For instance, dynamical masses enable computation of bulk densities for systems where the component sizes can be estimated from other measurements. Additionally, patterns in the ensemble characteristics of binary orbits offer clues to circumstances in the protoplanetary nebula when these systems formed, as well as carrying imprints of various subsequent dynamical evolution processes. The growing ensemble of known orbits shows intriguing patterns that can shed light on the evolution of this population of distant objects. This work has been supported by an NSF Planetary Astronomy grant and by several Hubble Space Telescope and NASA Keck data analysis grants. The research makes use of data from the Gemini Observatory obtained through NOAO survey program 11A-0017, from a large number of Hubble Space Telescope programs, and from several NASA Keck programs.

  20. 26 CFR 1.831-3 - Tax on insurance companies (other than life or mutual), mutual marine insurance companies, mutual...

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 26 Internal Revenue 8 2010-04-01 2010-04-01 false Tax on insurance companies (other than life or...-3 Tax on insurance companies (other than life or mutual), mutual marine insurance companies, mutual... insurance companies, other than life or mutual or foreign insurance companies not carrying on an...

  1. Principles of microRNA Regulation Revealed Through Modeling microRNA Expression Quantitative Trait Loci

    PubMed Central

    Budach, Stefan; Heinig, Matthias; Marsico, Annalisa

    2016-01-01

    Extensive work has been dedicated to study mechanisms of microRNA-mediated gene regulation. However, the transcriptional regulation of microRNAs themselves is far less well understood, due to difficulties determining the transcription start sites of transient primary transcripts. This challenge can be addressed using expression quantitative trait loci (eQTLs) whose regulatory effects represent a natural source of perturbation of cis-regulatory elements. Here we used previously published cis-microRNA-eQTL data for the human GM12878 cell line, promoter predictions, and other functional annotations to determine the relationship between functional elements and microRNA regulation. We built a logistic regression model that classifies microRNA/SNP pairs into eQTLs or non-eQTLs with 85% accuracy; shows microRNA-eQTL enrichment for microRNA precursors, promoters, enhancers, and transcription factor binding sites; and depletion for repressed chromatin. Interestingly, although there is a large overlap between microRNA eQTLs and messenger RNA eQTLs of host genes, 74% of these shared eQTLs affect microRNA and host expression independently. Considering microRNA-only eQTLs we find a significant enrichment for intronic promoters, validating the existence of alternative promoters for intragenic microRNAs. Finally, in line with the GM12878 cell line derived from B cells, we find genome-wide association (GWA) variants associated to blood-related traits more likely to be microRNA eQTLs than random GWA and non-GWA variants, aiding the interpretation of GWA results. PMID:27260304

  2. MicroRNA-21 Increases Proliferation and Cisplatin Sensitivity of Osteosarcoma-Derived Cells

    PubMed Central

    Vanas, Vanita; Haigl, Barbara; Stockhammer, Verena; Sutterlüty-Fall, Hedwig

    2016-01-01

    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. PMID:27513462

  3. MicroRNA-21 Increases Proliferation and Cisplatin Sensitivity of Osteosarcoma-Derived Cells.

    PubMed

    Vanas, Vanita; Haigl, Barbara; Stockhammer, Verena; Sutterlüty-Fall, Hedwig

    2016-01-01

    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. PMID:27513462

  4. Mutual information analysis of JPEG2000 contexts

    NASA Astrophysics Data System (ADS)

    Liu, Zhen; Karam, Lina J.

    2003-05-01

    Context-based arithmetic coding has been widely adopted in image and video compression and is a key component of the new JPEG2000 image compression standard. In this paper, the contexts used in JPEG2000 are analyzed using the mutual information, which has a direct link with the compression performance. We first show that, when combining the contexts, the mutual information between the contexts and the encoded data will decrease unless the conditional probability distributions of the combined contexts are the same. Given I, the initial number of contexts, and F, the final desired number of contexts, there are S(I, F) possible context classification schemes where S(I, F) is called the Stirling number of the second kind. The optimal classification scheme is the one that gives the maximum mutual information. Instead of exhaustive search, the optimal classification scheme can be obtained through a modified Generalized Lloyd algorithm with the relative entropy as the distortion metric. For binary arithmetic coding, the search complexity can be reduced by using the dynamic programming. Our experimental results show that the JPEG2000 contexts capture very well the correlations among the wavelet coefficients. At the same time, the number of contexts used as part of the standard can be reduced without loss in the coding performance.

  5. Observations of Pluto-Charon mutual events

    SciTech Connect

    Blanco, C.; Di Martino, M.; Ferreri, W.; Osservatorio Astronomico, Turin )

    1989-07-01

    As part of the planned 'Pluto-Charon Mutual Eclipse Season Campaign', one mutual event was observed at the ESO Observatory on July 10, 1986 and seven mutual events were observed at the Serra La Nave stellar station of Catania Astrophysical Observatory from April 29 to July 21, 1987. At ESO the measurements were performed at the 61-cm Bochum telescope equipped with a photon-counting system and U, B, V, filters; at Serra La Nave the Cassegrain focus of the 91-cm reflector was equipped with a photon-counting system and B and V filters. The observed light losses and contact times do not show relevant systematic deviations from the predicted ones. An examination of the behavior of the B and V light curves gives slight indications of a different slope of the B and V light loss of the same event for a superior or an inferior event, and shows that the superior events are shallower at wavelengths longer than B. 6 refs.

  6. Spatial Mutual Information Based Hyperspectral Band Selection for Classification

    PubMed Central

    2015-01-01

    The amount of information involved in hyperspectral imaging is large. Hyperspectral band selection is a popular method for reducing dimensionality. Several information based measures such as mutual information have been proposed to reduce information redundancy among spectral bands. Unfortunately, mutual information does not take into account the spatial dependency between adjacent pixels in images thus reducing its robustness as a similarity measure. In this paper, we propose a new band selection method based on spatial mutual information. As validation criteria, a supervised classification method using support vector machine (SVM) is used. Experimental results of the classification of hyperspectral datasets show that the proposed method can achieve more accurate results. PMID:25918742

  7. Quantum Conditional Mutual Information, Reconstructed States, and State Redistribution.

    PubMed

    Brandão, Fernando G S L; Harrow, Aram W; Oppenheim, Jonathan; Strelchuk, Sergii

    2015-07-31

    We give two strengthenings of an inequality for the quantum conditional mutual information of a tripartite quantum state recently proved by Fawzi and Renner, connecting it with the ability to reconstruct the state from its bipartite reductions. Namely, we show that the conditional mutual information is an upper bound on the regularized relative entropy distance between the quantum state and its reconstructed version. It is also an upper bound for the measured relative entropy distance of the state to its reconstructed version. The main ingredient of the proof is the fact that the conditional mutual information is the optimal quantum communication rate in the task of state redistribution. PMID:26274402

  8. Bio-barcode gel assay for microRNA

    NASA Astrophysics Data System (ADS)

    Lee, Hyojin; Park, Jeong-Eun; Nam, Jwa-Min

    2014-02-01

    MicroRNA has been identified as a potential biomarker because expression level of microRNA is correlated with various cancers. Its detection at low concentrations would be highly beneficial for cancer diagnosis. Here, we develop a new type of a DNA-modified gold nanoparticle-based bio-barcode assay that uses a conventional gel electrophoresis platform and potassium cyanide chemistry and show this assay can detect microRNA at aM levels without enzymatic amplification. It is also shown that single-base-mismatched microRNA can be differentiated from perfectly matched microRNA and the multiplexed detection of various combinations of microRNA sequences is possible with this approach. Finally, differently expressed microRNA levels are selectively detected from cancer cells using the bio-barcode gel assay, and the results are compared with conventional polymerase chain reaction-based results. The method and results shown herein pave the way for practical use of a conventional gel electrophoresis for detecting biomolecules of interest even at aM level without polymerase chain reaction amplification.

  9. Duplicate gene divergence by changes in microRNA binding sites in Arabidopsis and Brassica.

    PubMed

    Wang, Sishuo; Adams, Keith L

    2015-03-01

    Gene duplication provides large numbers of new genes that can lead to the evolution of new functions. Duplicated genes can diverge by changes in sequences, expression patterns, and functions. MicroRNAs play an important role in the regulation of gene expression in many eukaryotes. After duplication, two paralogs may diverge in their microRNA binding sites, which might impact their expression and function. Little is known about conservation and divergence of microRNA binding sites in duplicated genes in plants. We analyzed microRNA binding sites in duplicated genes in Arabidopsis thaliana and Brassica rapa. We found that duplicates are more often targeted by microRNAs than singletons. The vast majority of duplicated genes in A. thaliana with microRNA binding sites show divergence in those sites between paralogs. Analysis of microRNA binding sites in genes derived from the ancient whole-genome triplication in B. rapa also revealed extensive divergence. Paralog pairs with divergent microRNA binding sites show more divergence in expression patterns compared with paralog pairs with the same microRNA binding sites in Arabidopsis. Close to half of the cases of binding site divergence are caused by microRNAs that are specific to the Arabidopsis genus, indicating evolutionarily recent gain of binding sites after target gene duplication. We also show rapid evolution of microRNA binding sites in a jacalin gene family. Our analyses reveal a dynamic process of changes in microRNA binding sites after gene duplication in Arabidopsis and highlight the role of microRNA regulation in the divergence and contrasting evolutionary fates of duplicated genes. PMID:25644246

  10. Hierarchical clustering using mutual information

    NASA Astrophysics Data System (ADS)

    Kraskov, A.; Stögbauer, H.; Andrzejak, R. G.; Grassberger, P.

    2005-04-01

    We present a conceptually simple method for hierarchical clustering of data called mutual information clustering (MIC) algorithm. It uses mutual information (MI) as a similarity measure and exploits its grouping property: The MI between three objects X, Y, and Z is equal to the sum of the MI between X and Y, plus the MI between Z and the combined object (XY). We use this both in the Shannon (probabilistic) version of information theory and in the Kolmogorov (algorithmic) version. We apply our method to the construction of phylogenetic trees from mitochondrial DNA sequences and to the output of independent components analysis (ICA) as illustrated with the ECG of a pregnant woman.

  11. MicroRNA Expression in the Glaucomatous Retina

    PubMed Central

    Jayaram, Hari; Cepurna, William O.; Johnson, Elaine C.; Morrison, John C.

    2015-01-01

    Purpose MicroRNAs are small, endogenous noncoding RNAs that modulate posttranscriptional gene expression. Although the contribution of microRNAs to the pathogenesis of glaucomatous damage is unknown, supporting evidence from central nervous system (CNS) research suggests they may play a role. It was therefore hypothesized that microRNAs known to be altered in CNS injury are also altered in experimental glaucoma. Methods Intraocular pressure (IOP) was elevated in rats by unilateral injection of hypertonic saline and IOP monitored for 5 weeks. After rats were killed, retrobulbar optic nerve sections were graded for damage. MicroRNA was extracted from whole retinae of eyes with advanced nerve damage (n = 8) and from normal, noninjected control eyes (n = 8). Quantitative PCRs were performed using a panel of 17 microRNAs, reported from CNS research to be implicated in mechanisms also linked to glaucomatous damage. Computationally and experimentally derived gene targets were identified for the differentially expressed microRNAs. These were then integrated with existing gene array data. Functional interpretation was performed using the Molecular Signatures Database and DAVID Functional Annotation Clustering. Results Eight microRNAs were significantly downregulated in glaucomatous retinae compared with controls (miR-181c, miR-497, miR-204, let-7a, miR-29b, miR-16, miR106b, and miR-25); miR-27a was significantly upregulated. Enrichment of targets associated with extracellular matrix/cell proliferation, immune system, and regulation of apoptosis were observed. Cholesterol homeostasis and mTORC-1 pathways showed reduced expression. Conclusions MicroRNAs are differentially expressed in retinae of eyes with advanced glaucomatous damage compared with normal controls. Integrating microRNA with gene expression data may improve understanding of the complex biological responses produced by chronically elevated IOP. PMID:26720444

  12. Mutual Gains Means Everyone Wins.

    ERIC Educational Resources Information Center

    Flaherty, Bernard L.

    1997-01-01

    Mutual gains negotiation is an innovative system that emphasizes interests instead of positions and problem solving instead of preconceived solutions. The process can reverse social disintegration, reverse worker alienation, and address a shifting educational environment. It can resolve difficult labor-management problems such as contracting out,…

  13. Mutual Respect and Civic Education

    ERIC Educational Resources Information Center

    Bird, Colin

    2010-01-01

    Contemporary theories of civic education frequently appeal to an ideal of mutual respect in the context of ethical, ethical and religious disagreement. This paper critically examines two recently popular criticisms of this ideal. The first, coming from a postmodern direction, charges that the ideal is hypocritical in its effort to be maximally…

  14. Mutual impedance of nonplanar-skew sinusoidal dipoles

    NASA Technical Reports Server (NTRS)

    Richmond, J. H.; Geary, N. H.

    1975-01-01

    The mutual impedance expressions for parallel dipoles in terms of sine-integrals and cosine-integrals have been published by King (1957). The investigation reported provides analogous expressions for nonparallel dipoles. The expressions presented are most useful when the monopoles are close together. The theory of moment methods shows an approach for employing the mutual impedance of filamentary sinusoidal dipoles to calculate the impedance and scattering properties of straight and bent wires with small but finite diameter.

  15. Mutual impedance of nonplanar-skew sinusoidal dipoles

    NASA Technical Reports Server (NTRS)

    Richmond, J. H.; Geary, N. H.

    1974-01-01

    The mutual impedance of nonplanar-skew sinusoidal dipoles is presented as a summation of several exponential integrals with complex arguments. Mathematical models are developed to show the near-zone field of the sinusoidal dipole. The mutual impedance of coupled dipoles is expressed as the sum of four monopole-mobopole impedances to simplify the analysis procedure. The subroutines for solving the parameters of the dipoles are discussed.

  16. Computational Characterization of Exogenous MicroRNAs that Can Be Transferred into Human Circulation

    PubMed Central

    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. Computational Characterization of Exogenous MicroRNAs that Can Be Transferred into Human Circulation.

    PubMed

    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

  18. Mutuality and the social regulation of neural threat responding

    PubMed Central

    Coan, James A.; Kasle, Shelley; Jackson, Alice; Schaefer, Hillary S.; Davidson, Richard J.

    2014-01-01

    Recent studies have shown that the presence of a caring relational partner can attenuate neural responses to threat. Here we report reanalyzed data from Coan, Schaefer, and Davidson (2006), investigating the role of relational mutuality in the neural response to threat. Mutuality reflects the degree to which couple members show mutual interest in the sharing of internal feelings, thoughts, aspirations, and joys – a vital form of responsiveness in attachment relationships. We predicted that wives who were high (versus low) in perceived mutuality, and who attended the study session with their husbands, would show reduced neural threat reactivity in response to mild electric shocks. We also explored whether this effect would depend on physical contact (handholding). As predicted, we observed that higher mutuality scores corresponded with decreased neural threat responding in the right dorsolateral prefrontal cortex and supplementary motor cortex. These effects were independent of hand-holding condition. These findings suggest that higher perceived mutuality corresponds with decreased self-regulatory effort and attenuated preparatory motor activity in response to threat cues, even in the absence of direct physical contact with social resources. PMID:23547803

  19. 26 CFR 1.831-3 - Tax on insurance companies (other than life or mutual), mutual marine insurance companies, mutual...

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 26 Internal Revenue 8 2012-04-01 2012-04-01 false Tax on insurance companies (other than life or... Companies § 1.831-3 Tax on insurance companies (other than life or mutual), mutual marine insurance...) All insurance companies, other than life or mutual or foreign insurance companies not carrying on...

  20. 26 CFR 1.831-3 - Tax on insurance companies (other than life or mutual), mutual marine insurance companies, mutual...

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 26 Internal Revenue 8 2011-04-01 2011-04-01 false Tax on insurance companies (other than life or... Companies § 1.831-3 Tax on insurance companies (other than life or mutual), mutual marine insurance...) All insurance companies, other than life or mutual or foreign insurance companies not carrying on...

  1. 26 CFR 1.831-3 - Tax on insurance companies (other than life or mutual), mutual marine insurance companies, mutual...

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 26 Internal Revenue 8 2013-04-01 2013-04-01 false Tax on insurance companies (other than life or... Companies § 1.831-3 Tax on insurance companies (other than life or mutual), mutual marine insurance...) All insurance companies, other than life or mutual or foreign insurance companies not carrying on...

  2. 26 CFR 1.831-3 - Tax on insurance companies (other than life or mutual), mutual marine insurance companies, mutual...

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 26 Internal Revenue 8 2014-04-01 2014-04-01 false Tax on insurance companies (other than life or... Companies § 1.831-3 Tax on insurance companies (other than life or mutual), mutual marine insurance...) All insurance companies, other than life or mutual or foreign insurance companies not carrying on...

  3. Mutual impedance computation between printed dipoles

    NASA Astrophysics Data System (ADS)

    Alexopoulos, N. G.; Rana, I. E.

    1981-01-01

    The mutual impedance between microstrip dipoles printed on a grounded substrate is computed. Results for the microstrip dipoles in broadside, collinear, and echelon arrangements are presented. The significance of surface wave to mutual coupling is discussed.

  4. Pluto-charon mutual events

    SciTech Connect

    Binzel, R.P. )

    1989-11-01

    Since 1985, planetary astronomers have been working to take advantage of a once-per-century apparent alignment between Pluto and its satellite, Charon, which has allowed mutual occultation and transit events to be observed. There events, which will cease in 1990, have permitted the first precise determinations of their individual radii, densities, and surface compositions. In addition, information on their surface albedo distributions can be obtained.

  5. MicroRNAs Form Triplexes with Double Stranded DNA at Sequence-Specific Binding Sites; a Eukaryotic Mechanism via which microRNAs Could Directly Alter Gene Expression

    PubMed Central

    Grace, Christy R.; Ferreira, Antonio M.; Waddell, M. Brett; Ridout, Granger; Naeve, Deanna; Leuze, Michael; LoCascio, Philip F.; Panetta, John C.; Wilkinson, Mark R.; Pui, Ching-Hon; Naeve, Clayton W.; Uberbacher, Edward C.; Bonten, Erik J.; Evans, William E.

    2016-01-01

    MicroRNAs are important regulators of gene expression, acting primarily by binding to sequence-specific locations on already transcribed messenger RNAs (mRNA) and typically down-regulating their stability or translation. Recent studies indicate that microRNAs may also play a role in up-regulating mRNA transcription levels, although a definitive mechanism has not been established. Double-helical DNA is capable of forming triple-helical structures through Hoogsteen and reverse Hoogsteen interactions in the major groove of the duplex, and we show physical evidence (i.e., NMR, FRET, SPR) that purine or pyrimidine-rich microRNAs of appropriate length and sequence form triple-helical structures with purine-rich sequences of duplex DNA, and identify microRNA sequences that favor triplex formation. We developed an algorithm (Trident) to search genome-wide for potential triplex-forming sites and show that several mammalian and non-mammalian genomes are enriched for strong microRNA triplex binding sites. We show that those genes containing sequences favoring microRNA triplex formation are markedly enriched (3.3 fold, p<2.2 × 10−16) for genes whose expression is positively correlated with expression of microRNAs targeting triplex binding sequences. This work has thus revealed a new mechanism by which microRNAs could interact with gene promoter regions to modify gene transcription. PMID:26844769

  6. MicroRNAs Form Triplexes with Double Stranded DNA at Sequence-Specific Binding Sites; a Eukaryotic Mechanism via which microRNAs Could Directly Alter Gene Expression.

    PubMed

    Paugh, Steven W; Coss, David R; Bao, Ju; Laudermilk, Lucas T; Grace, Christy R; Ferreira, Antonio M; Waddell, M Brett; Ridout, Granger; Naeve, Deanna; Leuze, Michael; LoCascio, Philip F; Panetta, John C; Wilkinson, Mark R; Pui, Ching-Hon; Naeve, Clayton W; Uberbacher, Edward C; Bonten, Erik J; Evans, William E

    2016-02-01

    MicroRNAs are important regulators of gene expression, acting primarily by binding to sequence-specific locations on already transcribed messenger RNAs (mRNA) and typically down-regulating their stability or translation. Recent studies indicate that microRNAs may also play a role in up-regulating mRNA transcription levels, although a definitive mechanism has not been established. Double-helical DNA is capable of forming triple-helical structures through Hoogsteen and reverse Hoogsteen interactions in the major groove of the duplex, and we show physical evidence (i.e., NMR, FRET, SPR) that purine or pyrimidine-rich microRNAs of appropriate length and sequence form triple-helical structures with purine-rich sequences of duplex DNA, and identify microRNA sequences that favor triplex formation. We developed an algorithm (Trident) to search genome-wide for potential triplex-forming sites and show that several mammalian and non-mammalian genomes are enriched for strong microRNA triplex binding sites. We show that those genes containing sequences favoring microRNA triplex formation are markedly enriched (3.3 fold, p<2.2 × 10(-16)) for genes whose expression is positively correlated with expression of microRNAs targeting triplex binding sequences. This work has thus revealed a new mechanism by which microRNAs could interact with gene promoter regions to modify gene transcription. PMID:26844769

  7. MicroRNAs form triplexes with double stranded DNA at sequence-specific binding sites; a eukaryotic mechanism via which microRNAs could directly alter gene expression

    DOE PAGESBeta

    Paugh, Steven W.; Coss, David R.; Bao, Ju; Laudermilk, Lucas T.; Grace, Christy R.; Ferreira, Antonio M.; Waddell, M. Brett; Ridout, Granger; Naeve, Deanna; Leuze, Michael Rex; et al

    2016-02-04

    MicroRNAs are important regulators of gene expression, acting primarily by binding to sequence-specific locations on already transcribed messenger RNAs (mRNA). Recent studies indicate that microRNAs may also play a role in up-regulating mRNA transcription levels, although a definitive mechanism has not been established. Double-helical DNA is capable of forming triple-helical structures through Hoogsteen and reverse Hoogsteen interactions in the major groove of the duplex, and we show physical evidence that microRNAs form triple-helical structures with duplex DNA, and identify microRNA sequences that favor triplex formation. We developed an algorithm (Trident) to search genome-wide for potential triplex-forming sites and show thatmore » several mammalian and non-mammalian genomes are enriched for strong microRNA triplex binding sites. We show that those genes containing sequences favoring microRNA triplex formation are markedly enriched (3.3 fold, p<2.2 x 10-16) for genes whose expression is positively correlated with expression of microRNAs targeting triplex binding sequences. As a result, this work has thus revealed a new mechanism by which microRNAs can interact with gene promoter regions to modify gene transcription.« less

  8. 76 FR 20458 - Mutual Holding Company

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-12

    ... Office of Thrift Supervision Mutual Holding Company AGENCY: Office of Thrift Supervision (OTS), Treasury... collection. Title of Proposal: Mutual Holding Company. OMB Number: 1550-0072. Form Numbers: MHC-1 (OTS Form... whether the applicant meets the statutory and regulatory criteria to form a mutual holding company...

  9. Parents Helping Parents: Mutual Parenting Network Handbook.

    ERIC Educational Resources Information Center

    Simkinson, Charles H.; Redmond, Robert F.

    Guidelines for mutual parenting are provided in this handbook. "Mutual parenting" means that everyone in the community shares the responsibility for the safety and well-being of the community's youngsters. Several topics are discussed in the 15 brief chapters of the handbook. Chapters 1 through 3 focus on the formation of a mutual parenting…

  10. Are adolescents' mutually hostile interactions at home reproduced in other everyday life contexts?

    PubMed

    Trifan, Tatiana Alina; Stattin, Håkan

    2015-03-01

    Children involved in mutually hostile interactions at home are at risk of experiencing adjustment problems in other everyday life contexts. However, little is known about whether the pattern of mutual hostility at home is reproduced by high-conflict youths in other interpersonal contexts. In this study, we examined whether adolescents involved in mutually hostile interactions with their parents encounter similar mutually hostile interactions in other interpersonal contexts. We used a longitudinal design, following mid-adolescents over 1 year (N = 2,009, 51% boys, Mage = 14.06, SD = 0.73). The adolescents were 7th and 8th grade students in a mid-sized town in Sweden. The results showed that the youths involved in mutual hostility at home were more likely to be involved in mutual hostility at school and in their free-time. A longitudinal relationship between mutual hostility at home and mutual hostility in other contexts was confirmed. Being involved in mutually hostile interactions at home at Time 1 increased adolescents' likelihood of getting involved in mutually hostile interactions with peers at school and in free-time at Time 2. Overall, the results point to the important role played by experiencing mutual hostility at home in maladaptive behaviors across everyday settings. PMID:25348950

  11. "The Show"

    ERIC Educational Resources Information Center

    Gehring, John

    2004-01-01

    For the past 16 years, the blue-collar city of Huntington, West Virginia, has rolled out the red carpet to welcome young wrestlers and their families as old friends. They have come to town chasing the same dream for a spot in what many of them call "The Show". For three days, under the lights of an arena packed with 5,000 fans, the state's best…

  12. Characteristics of microRNA co-target networks

    NASA Astrophysics Data System (ADS)

    Lee, Chang-Yong

    2011-07-01

    The database of microRNAs and their predicted target genes in humans were used to extract a microRNA co-target network. Based on the finding that more than two miRNAs can target the same gene, we constructed a microRNA co-target network and analyzed it from the perspective of the complex network. We found that a network having a positive assortative mixing can be characterized by small-world and scale-free characteristics which are found in most complex networks. The network was further analyzed by the nearest-neighbor average connectivity, and it was shown that the more assortative a microRNA network is, the wider the range of increasing average connectivity. In particular, an assortative network has a power-law relationship of the average connectivity with a positive exponent. A percolation analysis of the network showed that, although the network is diluted, there is no percolation transition in the network. From these findings, we infer that the microRNAs in the network are clustered together, forming a core group. The same analyses carried out on different species confirmed the robustness of the main results found in the microRNA networks of humans.

  13. MicroRNAs: Clinical Relevance in Colorectal Cancer

    PubMed Central

    Thomas, Joe; Ohtsuka, Masahisa; Pichler, Martin; Ling, Hui

    2015-01-01

    Colorectal cancer is one of the most common cancer diagnoses and causes of mortality worldwide. MicroRNAs are a class of small, non-coding regulatory RNAs that have shown strong associations with colorectal cancer. Through the repression of target messenger RNAs, microRNAs modulate many cellular pathways, such as those involved in cell proliferation, apoptosis, and differentiation. The utilization of microRNAs has shown significant promise in the diagnosis and prognosis of colorectal cancer, owing to their unique expression profile associations with cancer types and malignancies. Moreover, microRNA therapeutics with mimics or antagonists show great promise in preclinical studies, which encourages further development of their clinical use for colorectal cancer patients. The unique ability of microRNAs to affect multiple downstream pathways represents a novel approach for cancer therapy. Although still early in its development, we believe that microRNAs can be used in the near future as biomarkers and therapeutic targets for colorectal cancer. PMID:26602923

  14. Phenotypic MicroRNA Microarrays

    PubMed Central

    Kwon, Yong-Jun; Heo, Jin Yeong; Kim, Hi Chul; Kim, Jin Yeop; Liuzzi, Michel; Soloveva, Veronica

    2013-01-01

    Microarray technology has become a very popular approach in cases where multiple experiments need to be conducted repeatedly or done with a variety of samples. In our lab, we are applying our high density spots microarray approach to microscopy visualization of the effects of transiently introduced siRNA or cDNA on cellular morphology or phenotype. In this publication, we are discussing the possibility of using this micro-scale high throughput process to study the role of microRNAs in the biology of selected cellular models. After reverse-transfection of microRNAs and siRNA, the cellular phenotype generated by microRNAs regulated NF-κB expression comparably to the siRNA. The ability to print microRNA molecules for reverse transfection into cells is opening up the wide horizon for the phenotypic high content screening of microRNA libraries using cellular disease models.

  15. Arabidopsis microRNA expression regulation in a wide range of abiotic stress responses

    PubMed Central

    Barciszewska-Pacak, Maria; Milanowska, Kaja; Knop, Katarzyna; Bielewicz, Dawid; Nuc, Przemyslaw; Plewka, Patrycja; Pacak, Andrzej M.; Vazquez, Franck; Karlowski, Wojciech; Jarmolowski, Artur; Szweykowska-Kulinska, Zofia

    2015-01-01

    Arabidopsis microRNA expression regulation was studied in a wide array of abiotic stresses such as drought, heat, salinity, copper excess/deficiency, cadmium excess, and sulfur deficiency. A home-built RT-qPCR mirEX platform for the amplification of 289 Arabidopsis microRNA transcripts was used to study their response to abiotic stresses. Small RNA sequencing, Northern hybridization, and TaqMan® microRNA assays were performed to study the abundance of mature microRNAs. A broad response on the level of primary miRNAs (pri-miRNAs) was observed. However, stress response at the level of mature microRNAs was rather confined. The data presented show that in most instances, the level of a particular mature miRNA could not be predicted based on the level of its pri-miRNA. This points to an essential role of posttranscriptional regulation of microRNA expression. New Arabidopsis microRNAs responsive to abiotic stresses were discovered. Four microRNAs: miR319a/b, miR319b.2, and miR400 have been found to be responsive to several abiotic stresses and thus can be regarded as general stress-responsive microRNA species. PMID:26089831

  16. Propagating Resource Constraints Using Mutual Exclusion Reasoning

    NASA Technical Reports Server (NTRS)

    Frank, Jeremy; Sanchez, Romeo; Do, Minh B.; Clancy, Daniel (Technical Monitor)

    2001-01-01

    One of the most recent techniques for propagating resource constraints in Constraint Based scheduling is Energy Constraint. This technique focuses in precedence based scheduling, where precedence relations are taken into account rather than the absolute position of activities. Although, this particular technique proved to be efficient on discrete unary resources, it provides only loose bounds for jobs using discrete multi-capacity resources. In this paper we show how mutual exclusion reasoning can be used to propagate time bounds for activities using discrete resources. We show that our technique based on critical path analysis and mutex reasoning is just as effective on unary resources, and also shows that it is more effective on multi-capacity resources, through both examples and empirical study.

  17. Plant-based microRNA presences in mice and human sera to breast milk

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant foods contain hundreds of thousands of different small RNAs, including microRNAs (miRNAs). A microRNA (miRNA) is a tiny (19-24 nucleotide) piece of RNA that attaches to a specific protein-making mRNA, thus inhibiting protein production. A recent finding shows that a miRNA in rice survives dige...

  18. No effect of diffraction on Pluto-Charon mutual events

    NASA Technical Reports Server (NTRS)

    Tholen, D. J.; Hubbard, W. B.

    1988-01-01

    Mulholland and Gustafson (1987) made the interesting suggestion that observations of Pluto-Charon mutual events might show significant dependence on both wavelength and telescope aperture because of diffraction effects. In this letter, observations are presented that show the predicted effects to be absent and demonstrate that the parameters of the system are such that the events can be accurately analyzed with geometrical optics.

  19. Population dynamics and mutualism: Functional responses of benefits and costs

    USGS Publications Warehouse

    Holland, J. Nathaniel; DeAngelis, Donald L.; Bronstein, Judith L.

    2002-01-01

    We develop an approach for studying population dynamics resulting from mutualism by employing functional responses based on density‐dependent benefits and costs. These functional responses express how the population growth rate of a mutualist is modified by the density of its partner. We present several possible dependencies of gross benefits and costs, and hence net effects, to a mutualist as functions of the density of its partner. Net effects to mutualists are likely a monotonically saturating or unimodal function of the density of their partner. We show that fundamental differences in the growth, limitation, and dynamics of a population can occur when net effects to that population change linearly, unimodally, or in a saturating fashion. We use the mutualism between senita cactus and its pollinating seed‐eating moth as an example to show the influence of different benefit and cost functional responses on population dynamics and stability of mutualisms. We investigated two mechanisms that may alter this mutualism's functional responses: distribution of eggs among flowers and fruit abortion. Differences in how benefits and costs vary with density can alter the stability of this mutualism. In particular, fruit abortion may allow for a stable equilibrium where none could otherwise exist.

  20. Graph-state formalism for mutually unbiased bases

    NASA Astrophysics Data System (ADS)

    Spengler, Christoph; Kraus, Barbara

    2013-11-01

    A pair of orthonormal bases is called mutually unbiased if all mutual overlaps between any element of one basis and an arbitrary element of the other basis coincide. In case the dimension, d, of the considered Hilbert space is a power of a prime number, complete sets of d+1 mutually unbiased bases (MUBs) exist. Here we present a method based on the graph-state formalism to construct such sets of MUBs. We show that for n p-level systems, with p being prime, one particular graph suffices to easily construct a set of pn+1 MUBs. In fact, we show that a single n-dimensional vector, which is associated with this graph, can be used to generate a complete set of MUBs and demonstrate that this vector can be easily determined. Finally, we discuss some advantages of our formalism regarding the analysis of entanglement structures in MUBs, as well as experimental realizations.

  1. A parallel genome-wide mRNA and microRNA profiling of the frontal cortex of HIV patients with and without HIV-associated dementia shows the role of axon guidance and downstream pathways in HIV-mediated neurodegeneration

    PubMed Central

    2012-01-01

    Background HIV-associated dementia (HAD) is the most common dementia type in young adults less than 40 years of age. Although the neurotoxins, oxidative/metabolic stress and impaired activity of neurotrophic factors are believed to be underlying reasons for the development of HAD, the genomic basis, which ultimately defines the virus-host interaction and leads to neurologic manifestation of HIV disease is lacking. Therefore, identifying HIV fingerprints on the host gene machinery and its regulation by microRNA holds a great promise and potential for improving our understanding of HAD pathogenesis, its diagnosis and therapy. Results A parallel profiling of mRNA and miRNA of the frontal cortex autopsies from HIV positive patients with and without dementia was performed using Illumina Human-6 BeadChip and Affymetrix version 1.0 miRNA array, respectively. The gene ontology and pathway analysis of the two data sets showed high concordance between miRNA and mRNAs, revealing significant interference with the host axon guidance and its downstream signalling pathways in HAD brains. Moreover, the differentially expressed (DE) miRNAs identified in this study, in particular miR-137, 153 and 218, based on which most correlations were built cumulatively targeted neurodegeneration related pathways, implying their future potential in diagnosis, prognosis and possible therapies for HIV-mediated and possibly other neurodegenerative diseases. Furthermore, this relationship between DE miRNAs and DE mRNAs was also reflected in correlation analysis using Bayesian networks by splitting-averaging strategy (SA-BNs), which revealed 195 statistically significant correlated miRNA-mRNA pairs according to Pearson’s correlation test (P<0.05). Conclusions Our study provides the first evidence on unambiguous support for intrinsic functional relationship between mRNA and miRNA in the context of HIV-mediated neurodegeneration, which shows that neurologic manifestation in HIV patients possibly

  2. Mutual information in classical spin models

    NASA Astrophysics Data System (ADS)

    Wilms, Johannes; Troyer, Matthias; Verstraete, Frank

    2011-10-01

    The total many-body correlations present in finite temperature classical spin systems are studied using the concept of mutual information. As opposed to zero-temperature quantum phase transitions, the total correlations are not maximal at the phase transition, but reach a maximum in the high-temperature paramagnetic phase. The Shannon mutual information and the Renyi mutual information in both Ising and Potts models in two dimensions are calculated numerically by combining matrix product state algorithms and Monte Carlo sampling techniques.

  3. Mutual enhancement of diverse terminologies

    PubMed Central

    Hardiker, Nicholas R.; Casey, Anne; Coenen, Amy; Konicek, Debra

    2006-01-01

    The purpose of this study was to map the North American Nursing Diagnosis Association (NANDA) nursing diagnoses to the International Classification for Nursing Practice Version 1.0 (ICNP®) and to compare the resulting representations and relationships to those within SNOMED® Clinical Terms (CT). Independent reviewers reached agreement on 25 (i.e. 64%) of the 39 parent-child relationships identified via the mappings between NANDA entities. Other parent-child relationships were more questionable and are in need of further discussion. This work does not seek to promote one terminology over any other. Rather, this collaborative effort has the potential to mutually enhance all three terminologies involved in the study: ICNP®, SNOMED® CT and NANDA. In doing so it provides an example of the type of collaborative effort that is needed to facilitate the development of tools to support interoperability at a global level. PMID:17238355

  4. MicroRNA expression profiling using microarrays.

    PubMed

    Love, Cassandra; Dave, Sandeep

    2013-01-01

    MicroRNAs are small noncoding RNAs which are able to regulate gene expression at both the transcriptional and translational levels. There is a growing recognition of the role of microRNAs in nearly every tissue type and cellular process. Thus there is an increasing need for accurate quantitation of microRNA expression in a variety of tissues. Microarrays provide a robust method for the examination of microRNA expression. In this chapter, we describe detailed methods for the use of microarrays to measure microRNA expression and discuss methods for the analysis of microRNA expression data. PMID:23666707

  5. Occurrence and characteristics of mutual interference between LIDAR scanners

    NASA Astrophysics Data System (ADS)

    Kim, Gunzung; Eom, Jeongsook; Park, Seonghyeon; Park, Yongwan

    2015-05-01

    The LIDAR scanner is at the heart of object detection of the self-driving car. Mutual interference between LIDAR scanners has not been regarded as a problem because the percentage of vehicles equipped with LIDAR scanners was very rare. With the growing number of autonomous vehicle equipped with LIDAR scanner operated close to each other at the same time, the LIDAR scanner may receive laser pulses from other LIDAR scanners. In this paper, three types of experiments and their results are shown, according to the arrangement of two LIDAR scanners. We will show the probability that any LIDAR scanner will interfere mutually by considering spatial and temporal overlaps. It will present some typical mutual interference scenario and report an analysis of the interference mechanism.

  6. Empirical study of the tails of mutual fund size

    NASA Astrophysics Data System (ADS)

    Schwarzkopf, Yonathan; Farmer, J. Doyne

    2010-06-01

    The mutual fund industry manages about a quarter of the assets in the U.S. stock market and thus plays an important role in the U.S. economy. The question of how much control is concentrated in the hands of the largest players is best quantitatively discussed in terms of the tail behavior of the mutual fund size distribution. We study the distribution empirically and show that the tail is much better described by a log-normal than a power law, indicating less concentration than, for example, personal income. The results are highly statistically significant and are consistent across fifteen years. This contradicts a recent theory concerning the origin of the power law tails of the trading volume distribution. Based on the analysis in a companion paper, the log-normality is to be expected, and indicates that the distribution of mutual funds remains perpetually out of equilibrium.

  7. Thermalization of mutual information in hyperscaling violating backgrounds

    NASA Astrophysics Data System (ADS)

    Tanhayi, M. Reza

    2016-03-01

    We study certain features of scaling behaviors of the mutual information during a process of thermalization, more precisely we extend the time scaling behavior of mutual information which has been discussed in [1] to time-dependent hyperscaling violating geometries. We use the holographic description of entanglement entropy for two disjoint system consisting of two parallel strips whose widths are much larger than the separation between them. We show that during the thermalization process, the dynamical exponent plays a crucial rule in reading the general time scaling behavior of mutual information (e.g., at the pre-local-equilibration regime). It is shown that the scaling violating parameter can be employed to define an effective dimension.

  8. Mutual information-based facial expression recognition

    NASA Astrophysics Data System (ADS)

    Hazar, Mliki; Hammami, Mohamed; Hanêne, Ben-Abdallah

    2013-12-01

    This paper introduces a novel low-computation discriminative regions representation for expression analysis task. The proposed approach relies on interesting studies in psychology which show that most of the descriptive and responsible regions for facial expression are located around some face parts. The contributions of this work lie in the proposition of new approach which supports automatic facial expression recognition based on automatic regions selection. The regions selection step aims to select the descriptive regions responsible or facial expression and was performed using Mutual Information (MI) technique. For facial feature extraction, we have applied Local Binary Patterns Pattern (LBP) on Gradient image to encode salient micro-patterns of facial expressions. Experimental studies have shown that using discriminative regions provide better results than using the whole face regions whilst reducing features vector dimension.

  9. The Effects of Perceived Mutual Understanding in Interpersonal Communication.

    ERIC Educational Resources Information Center

    Gordon, Ron

    To investigate the effects of mutual perceived understanding on the communicators, 86 undergraduate students in a speech communication course were asked to use a 382 item checklist to identify those feelings and sensations that described their own experiences of intense communication. Analysis of subjects' responses showed that 63 items were…

  10. Conflict Management: A Premarital Training Program in Mutual Problem Solving.

    ERIC Educational Resources Information Center

    Ridley, Carl A.; And Others

    1981-01-01

    Evaluated the effectiveness of a structured educational program to train premarital couples in communication and mutual problem-solving skills. Couples (N=26) participated in a problem-solving training program, while similar couples (N=28) participated in a relationship discussion group. The problem-solving group showed a greater increase in…

  11. A conformation-induced fluorescence method for microRNA detection.

    PubMed

    Aw, Sherry S; Tang, Melissa Xm; Teo, Yin Nah; Cohen, Stephen M

    2016-06-01

    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 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 microRNA 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 microRNA resulted in large changes in fluorescence intensity. The median fold change in fluorescence observed for the sensors tested was ∼50-fold. Pandan RNA sensors exhibit good signal-to-noise ratios, and can detect their target microRNAs within complex RNA mixtures. PMID:26951376

  12. A conformation-induced fluorescence method for microRNA detection

    PubMed Central

    Aw, Sherry S.; Tang, Melissa XM; Teo, Yin Nah; Cohen, Stephen M.

    2016-01-01

    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 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 microRNA 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 microRNA resulted in large changes in fluorescence intensity. The median fold change in fluorescence observed for the sensors tested was ∼50-fold. Pandan RNA sensors exhibit good signal-to-noise ratios, and can detect their target microRNAs within complex RNA mixtures. PMID:26951376

  13. A parallel strategy for predicting the secondary structure of polycistronic microRNAs.

    PubMed

    Han, Dianwei; Tang, Guiliang; Zhang, Jun

    2013-01-01

    The biogenesis of a functional microRNA is largely dependent on the secondary structure of the microRNA precursor (pre-miRNA). Recently, it has been shown that microRNAs are present in the genome as the form of polycistronic transcriptional units in plants and animals. It will be important to design efficient computational methods to predict such structures for microRNA discovery and its applications in gene silencing. In this paper, we propose a parallel algorithm based on the master-slave architecture to predict the secondary structure from an input sequence. We conducted some experiments to verify the effectiveness of our parallel algorithm. The experimental results show that our algorithm is able to produce the optimal secondary structure of polycistronic microRNAs. PMID:23467060

  14. The Competitive Strategy of Mutual Learning.

    ERIC Educational Resources Information Center

    Kelner, Stephen P.; Slavin, Lois

    1998-01-01

    Defines and discusses mutual learning in organizations. Suggests that the idea of people and companies sharing knowledge is becoming a competitive strategy because mutual learning enables executives and employees to increase their capacity to work together, accelerate organizational learning, and avoid mistakes. (JOW)

  15. Victimization within Mutually Antipathetic Peer Relationships

    ERIC Educational Resources Information Center

    Card, Noel A.; Hodges, Ernest V. E.

    2007-01-01

    Children's victimization experiences within relationships characterized by mutual animosity were examined among 210 6th- and 7th-grade boys and girls. Participants reported that a greater proportion of mutual antipathies, relative to other peers, victimized them. Moreover, the receipt of victimization within antipathetic relationships was greater…

  16. [Maintaining solidarity: is mutuality the solution?].

    PubMed

    Gevers, J K M; Ploem, M C

    2013-01-01

    Solidarity is essentially the willingness to contribute to the community and its demands, which may even involve contributing more than one is expecting to receive. Another principle is mutuality: this refers to a balance between rights and obligations or between mutual obligations. In its advisory document 'The importance of mutuality......solidarity takes work!', The Dutch Council for Public Health and Health Care underlines the importance of ensuring solidarity within the Dutch health care system, e.g. by encouraging patients to take responsibility for their own health, possibly by introducing elements of mutuality. In our contribution, we comment on the Council's advice. Although we fully agree with the overall conclusion that solidarity should be maintained within the system, we do not see how the introduction of increased mutuality will contribute to this goal. PMID:23945438

  17. Resource Availability Modulates the Cooperative and Competitive Nature of a Microbial Cross-Feeding Mutualism.

    PubMed

    Hoek, Tim A; Axelrod, Kevin; Biancalani, Tommaso; Yurtsev, Eugene A; Liu, Jinghui; Gore, Jeff

    2016-08-01

    Mutualisms between species play an important role in ecosystem function and stability. However, in some environments, the competitive aspects of an interaction may dominate the mutualistic aspects. Although these transitions could have far-reaching implications, it has been difficult to study the causes and consequences of this mutualistic-competitive transition in experimentally tractable systems. Here, we study a microbial cross-feeding mutualism in which each yeast strain supplies an essential amino acid for its partner strain. We find that, depending upon the amount of freely available amino acid in the environment, this pair of strains can exhibit an obligatory mutualism, facultative mutualism, competition, parasitism, competitive exclusion, or failed mutualism leading to extinction of the population. A simple model capturing the essential features of this interaction explains how resource availability modulates the interaction and predicts that changes in the dynamics of the mutualism in deteriorating environments can provide advance warning that collapse of the mutualism is imminent. We confirm this prediction experimentally by showing that, in the high nutrient competitive regime, the strains rapidly reach a common carrying capacity before slowly reaching the equilibrium ratio between the strains. However, in the low nutrient regime, before collapse of the obligate mutualism, we find that the ratio rapidly reaches its equilibrium and it is the total abundance that is slow to reach equilibrium. Our results provide a general framework for how mutualisms may transition between qualitatively different regimes of interaction in response to changes in nutrient availability in the environment. PMID:27557335

  18. Resource Availability Modulates the Cooperative and Competitive Nature of a Microbial Cross-Feeding Mutualism

    PubMed Central

    Hoek, Tim A.; Axelrod, Kevin; Biancalani, Tommaso; Yurtsev, Eugene A.; Gore, Jeff

    2016-01-01

    Mutualisms between species play an important role in ecosystem function and stability. However, in some environments, the competitive aspects of an interaction may dominate the mutualistic aspects. Although these transitions could have far-reaching implications, it has been difficult to study the causes and consequences of this mutualistic–competitive transition in experimentally tractable systems. Here, we study a microbial cross-feeding mutualism in which each yeast strain supplies an essential amino acid for its partner strain. We find that, depending upon the amount of freely available amino acid in the environment, this pair of strains can exhibit an obligatory mutualism, facultative mutualism, competition, parasitism, competitive exclusion, or failed mutualism leading to extinction of the population. A simple model capturing the essential features of this interaction explains how resource availability modulates the interaction and predicts that changes in the dynamics of the mutualism in deteriorating environments can provide advance warning that collapse of the mutualism is imminent. We confirm this prediction experimentally by showing that, in the high nutrient competitive regime, the strains rapidly reach a common carrying capacity before slowly reaching the equilibrium ratio between the strains. However, in the low nutrient regime, before collapse of the obligate mutualism, we find that the ratio rapidly reaches its equilibrium and it is the total abundance that is slow to reach equilibrium. Our results provide a general framework for how mutualisms may transition between qualitatively different regimes of interaction in response to changes in nutrient availability in the environment. PMID:27557335

  19. 12 CFR 575.3 - Mutual holding company reorganizations.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false Mutual holding company reorganizations. 575.3... COMPANIES § 575.3 Mutual holding company reorganizations. A mutual savings association may reorganize to become a mutual holding company, or join in a mutual holding company reorganization as an...

  20. Identification of Reference Genes for Relative Quantification of Circulating MicroRNAs in Bovine Serum

    PubMed Central

    Bae, In-Seon; Chung, Ki Yong; Yi, Jongmin; Kim, Tae Il; Choi, Hwa-Sik; Cho, Young-Moo; Choi, Inho; Kim, Sang Hoon

    2015-01-01

    Circulating microRNAs in body fluids have been implicated as promising biomarkers for physiopathology disorders. Currently, the expression levels of circulating microRNAs are estimated by reverse transcription quantitative real-time polymerase chain reaction. Use of appropriate reference microRNAs for normalization is critical for accurate microRNA expression analysis. However, no study has systematically investigated reference genes for evaluating circulating microRNA expression in cattle. In this study, we describe the identification and characterization of appropriate reference microRNAs for use in the normalization of circulating microRNA levels in bovine serum. We evaluated the expression stability of ten candidate reference genes in bovine serum by using reverse transcription quantitative real-time polymerase chain reaction. Data were analyzed using geNorm, NormFinder, and BestKeeper statistical algorithms. The results consistently showed that a combination of miR-93 and miR-127 provided the most stably expressed reference. The suitability of these microRNAs was validated, and even when compared among different genders or breeds, the combination of miR-93 and miR-127 was ranked as the most stable microRNA reference. Therefore, we conclude that this combination is the optimal endogenous reference for reverse transcription quantitative real-time polymerase chain reaction-based detection of microRNAs in bovine serum. The data presented in this study are crucial to successful biomarker discovery and validation for the diagnosis of physiopathological conditions in cattle. PMID:25826387

  1. Dicer–TRBP complex formation ensures accurate mammalian microRNA biogenesis

    PubMed Central

    Wilson, Ross C.; Tambe, Akshay; Kidwell, Mary Anne; Noland, Cameron L.; Schneider, Catherine P.; Doudna, Jennifer A.

    2014-01-01

    Summary RNA-mediated gene silencing in human cells requires the accurate generation of ∼22-nucleotide microRNAs (miRNAs) from double-stranded RNA substrates by the endonuclease Dicer. Although the phylogenetically conserved RNA-binding proteins TRBP and PACT are known to contribute to this process, their mode of Dicer binding and their genome-wide effects on miRNA processing have not been determined. We solved the crystal structure of a human Dicer–TRBP interaction complex comprising two domains of previously unknown structure. Interface residues conserved between TRBP and PACT show that the proteins bind to Dicer in a similar manner and by mutual exclusion. Based on the structure, a catalytically active Dicer that cannot bind TRBP or PACT was designed and introduced into Dicer-deficient mammalian cells, revealing selective defects in guide strand selection. These results demonstrate the role of Dicer-associated RNA binding proteins in maintenance of gene silencing fidelity. PMID:25557550

  2. microRNA-451 inhibited cell proliferation, migration and invasion through regulation of MIF in renal cell carcinoma

    PubMed Central

    Tang, Yan; Wan, Wei; Wang, Lijuan; Ji, Shishun; Zhang, Juanjuan

    2015-01-01

    The expression and functions of microRNA-451 have been studied in many human cancers. However, up to date, there is no study of microRNA-451 in renal cell carcinoma. In the present study, we aimed to investigate the expression, biological functions and molecular mechanisms of microRNA-451 in renal cell carcinoma. microRNA-451 expression level in renal cell carcinoma tissues and cell lines was measured using quantitative Real-time PCR. By using CCK8 assay, cell migration and invasion assay, we explored the functions of microRNA-451 in renal cell carcinoma. Dual-Luciferase report assay, quantitative Real-time PCR and western blot were performed to explore the molecular mechanisms of microRNA-451 functions in renal cell carcinoma. Functional assays were also performed to explore the effects of endogenous MIF in renal cell carcinoma. In this study, we showed for the first time that microRNA-451 was significantly down-regulated in renal cell carcinomas tissues and cell lines. microRNA-451 expression level was correlated with histological grade and lymph node metastasis. In addition, microRNA-451 inhibited proliferation, migration and invasion of renal cell carcinomas cells. Moreover, MIF was identified as a target of microRNA-451, and down-regulation of MIF could mimic the suppressive functions of microRNA-451 in renal cell carcinomas, suggesting that microRNA-451 might be a novel therapeutic strategy for the treatment of renal cell carcinomas. PMID:26884830

  3. Generalized mutual information and Tsirelson's bound

    SciTech Connect

    Wakakuwa, Eyuri; Murao, Mio

    2014-12-04

    We introduce a generalization of the quantum mutual information between a classical system and a quantum system into the mutual information between a classical system and a system described by general probabilistic theories. We apply this generalized mutual information (GMI) to a derivation of Tsirelson's bound from information causality, and prove that Tsirelson's bound can be derived from the chain rule of the GMI. By using the GMI, we formulate the 'no-supersignalling condition' (NSS), that the assistance of correlations does not enhance the capability of classical communication. We prove that NSS is never violated in any no-signalling theory.

  4. MicroRNAs and Epithelial Immunity

    PubMed Central

    Liu, Jun; Drescher, Kristen M.; Chen, Xian-Ming

    2009-01-01

    MicroRNAs are required for development and maintenance of the epithelial barrier. It is hypothesized that microRNAs are involved in regulating epithelial anti-microbial defenses by targeting key epithelial effector molecules and/or influencing intracellular signaling pathways. Additionally, aberrant microRNA expression has been implicated in the pathogenesis of various diseases at the skin and mucosa. Increased understanding of the role of microRNAs in epithelial immunoregulation and identification of microRNAs of pathogenetic significance will enhance our understanding of epithelial immunobiology and immunopathology. PMID:19811319

  5. Functional analysis of mutual behavior in laboratory rats (Rattus norvegicus)

    PubMed Central

    Tan, Lavinia; Hackenberg, Timothy D.

    2015-01-01

    Three pairs of rats were trained to synchronize their lever pressing according to a mutual reinforcement contingency, in which alternating lever presses that fell within a 500-ms window were reinforced with food. In Experiment 1, rats worked in adjacent chambers separated by a transparent barrier, and the effects of the mutual reinforcement contingency were compared to those under yoked-control conditions that provided the same rate of food reinforcement but without the temporal coordination response requirement. In Experiment 2, coordinated behavior was compared with and without a barrier, and across different barrier types: transparent, opaque, wire mesh. In Experiment 3, the effects of social familiarity were assessed by switching partners, enabling a comparison of coordinated behavior with familiar and unfamiliar partners. The overall pattern of results shows that the coordinated behavior of two rats was (a) maintained by mutual reinforcement contingencies, (b) unrelated to the type or presence of a barrier separating the rats, and (c) sufficiently flexible to adjust to the presence and behavior of an unfamiliar partner. Taken as a whole, the study illustrates a promising approach to conceptualizing and analyzing behavioral mechanisms of mutual behavior, an important component of an integrated study of social behavior. PMID:26479279

  6. Functional analysis of mutual behavior in laboratory rats (Rattus norvegicus).

    PubMed

    Tan, Lavinia; Hackenberg, Timothy D

    2016-02-01

    Three pairs of rats were trained to synchronize their lever pressing according to a mutual reinforcement contingency, in which alternating lever presses that fell within a 500-ms window were reinforced with food. In Experiment 1, rats worked in adjacent chambers separated by a transparent barrier, and the effects of the mutual reinforcement contingency were compared with those under yoked-control conditions that provided the same rate of food reinforcement but without the temporal coordination response requirement. In Experiment 2, coordinated behavior was compared with and without a barrier, and across different barrier types: transparent, opaque, wire mesh. In Experiment 3, the effects of social familiarity were assessed by switching partners, enabling a comparison of coordinated behavior with familiar and unfamiliar partners. The overall pattern of results shows that the coordinated behavior of 2 rats was (a) maintained by mutual reinforcement contingencies, (b) unrelated to the type or presence of a barrier separating the rats, and (c) sufficiently flexible to adjust to the presence and behavior of an unfamiliar partner. Taken as a whole, the study illustrates a promising approach to conceptualizing and analyzing behavioral mechanisms of mutual behavior, an important component of an integrated study of social behavior. PMID:26479279

  7. Quadratic mutual information for dimensionality reduction and classification

    NASA Astrophysics Data System (ADS)

    Gray, David M.; Principe, José C.

    2010-04-01

    A research area based on the application of information theory to machine learning has attracted considerable interest in the last few years. This research area has been coined information-theoretic learning within the community. In this paper we apply elements of information-theoretic learning to the problem of automatic target recognition (ATR). A number of researchers have previously shown the benefits of designing classifiers based on maximizing the mutual information between the class data and the class labels. Following prior research in information-theoretic learning, in the current results we show that quadratic mutual information, derived using a special case of the more general Renyi's entropy, can be used for classifier design. In this implementation, a simple subspace projection classifier is formulated to find the optimal projection weights such that the quadratic mutual information between the class data and the class labels is maximized. This subspace projection accomplishes a dimensionality reduction of the raw data set wherein information about the class membership is retained while irrelevant information is discarded. A subspace projection based on this criterion preserves as much class discriminability as possible within the subspace. For this paper, laser radar images are used to demonstrate the results. Classification performance against this data set is compared for a gradient descent MLP classifier and a quadratic mutual information MLP classifier.

  8. 76 FR 71437 - Mutual Savings Association Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-17

    ... Office of the Comptroller of the Currency Mutual Savings Association Advisory Committee AGENCY... Mutual Savings Association Advisory Committee (MSAAC or Committee) formerly administered by the Office of... of and challenges facing mutual savings associations. The OCC is seeking nominations of...

  9. Mycorrhiza: A Common Form of Mutualism.

    ERIC Educational Resources Information Center

    Medve, Richard J.

    1978-01-01

    Mycorrhizae are among the most common examples of mutualism. This article discusses their structure, symbolic relationship, factors affecting formation and applying research. Questions are posed and answers suggested. (MA)

  10. PARma: identification of microRNA target sites in AGO-PAR-CLIP data.

    PubMed

    Erhard, Florian; Dölken, Lars; Jaskiewicz, Lukasz; Zimmer, Ralf

    2013-01-01

    PARma is a complete data analysis software for AGO-PAR-CLIP experiments to identify target sites of microRNAs as well as the microRNA binding to these sites. It integrates specific characteristics of the experiments into a generative model. The model and a novel pattern discovery tool are iteratively applied to data to estimate seed activity probabilities, cluster confidence scores and to assign the most probable microRNA. Based on differential PAR-CLIP analysis and comparison to RIP-Chip data, we show that PARma is more accurate than existing approaches. PARma is available from http://www.bio.ifi.lmu.de/PARma. PMID:23895117

  11. PARma: identification of microRNA target sites in AGO-PAR-CLIP data

    PubMed Central

    2013-01-01

    PARma is a complete data analysis software for AGO-PAR-CLIP experiments to identify target sites of microRNAs as well as the microRNA binding to these sites. It integrates specific characteristics of the experiments into a generative model. The model and a novel pattern discovery tool are iteratively applied to data to estimate seed activity probabilities, cluster confidence scores and to assign the most probable microRNA. Based on differential PAR-CLIP analysis and comparison to RIP-Chip data, we show that PARma is more accurate than existing approaches. PARma is available from http://www.bio.ifi.lmu.de/PARma PMID:23895117

  12. Clamping of RNA with PNA enables targeting of microRNA.

    PubMed

    Ghidini, Alice; Bergquist, Helen; Murtola, Merita; Punga, Tanel; Zain, Rula; Strömberg, Roger

    2016-06-21

    To be able to target microRNAs also at stages where these are in a double stranded or hairpin form we have studied BisPNA designed to clamp the target and give sufficient affinity to allow for strand invasion. We show that BisPNA complexes are more stable with RNA than with DNA. In addition, 24-mer BisPNA (AntimiR) constructs form complexes with a hairpin RNA that is a model of the microRNA miR-376b, suggesting that PNA-clamping may be an effective way of targeting microRNAs. PMID:27203783

  13. MicroRNA In Lung Cancer: Novel Biomarkers and Potential Tools for Treatment

    PubMed Central

    Inamura, Kentaro; Ishikawa, Yuichi

    2016-01-01

    Lung cancer is the leading cause of cancer death in men and women worldwide. The lack of specific and sensitive tools for early diagnosis as well as still-inadequate targeted therapies contribute to poor outcomes. MicroRNAs are small non-coding RNAs, which regulate gene expression post-transcriptionally by translational repression or degradation of target mRNAs. A growing body of evidence suggests various roles of microRNAs including development and progression of lung cancer. In lung cancer, several studies have showed that certain microRNA profiles classified lung cancer subtypes, and that specific microRNA expression signatures distinguished between better-prognosis and worse-prognosis lung cancers. Furthermore, microRNAs circulate in body fluids, and therefore may serve as promising biomarkers for early diagnosis of lung cancer as well as for predicting prognosis of patients. In the present review, we briefly summarize microRNAs in the development and progression of lung cancer, focusing on possible applications of microRNAs as novel biomarkers and tools for treatment. PMID:27005669

  14. MicroRNAs 15a and 16 regulate tumor proliferation in multiple myeloma

    PubMed Central

    Roccaro, Aldo M.; Sacco, Antonio; Thompson, Brian; Leleu, Xavier; Azab, Abdel Kareem; Azab, Feda; Runnels, Judith; Jia, Xiaoying; Ngo, Hai T.; Melhem, Molly R.; Lin, Charles P.; Ribatti, Domenico; Rollins, Barrett J.; Witzig, Thomas E.; Anderson, Kenneth C.

    2009-01-01

    Detailed genomic studies have shown that cytogenetic abnormalities contribute to multiple myeloma (MM) pathogenesis and disease progression. Nevertheless, little is known about the characteristics of MM at the epigenetic level and specifically how microRNAs regulate MM progression in the context of the bone marrow milieu. Therefore, we performed microRNA expression profiling of bone marrow derived CD138+ MM cells versus their normal cellular counterparts and validated data by qRT-PCR. We identified a MM-specific microRNA signature characterized by down-expression of microRNA-15a/-16 and overexpression of microRNA-222/-221/-382/-181a/-181b (P < .01). We investigated the functional role of microRNA-15a and -16 and showed that they regulate proliferation and growth of MM cells in vitro and in vivo by inhibiting AKT serine/threonine-protein-kinase (AKT3), ribosomal-protein-S6, MAP-kinases, and NF-κB-activator MAP3KIP3. Moreover, miRNA-15a and -16 exerted their anti-MM activity even in the context of the bone marrow milieu in vitro and in vivo. These data indicate that microRNAs play a pivotal role in the biology of MM and represent important targets for novel therapies in MM. PMID:19401561

  15. DNA methylation, microRNAs, and their crosstalk as potential biomarkers in hepatocellular carcinoma

    PubMed Central

    Anwar, Sumadi Lukman; Lehmann, Ulrich

    2014-01-01

    Epigenetic alterations have been identified as a major characteristic in human cancers. Advances in the field of epigenetics have contributed significantly in refining our knowledge of molecular mechanisms underlying malignant transformation. DNA methylation and microRNA expression are epigenetic mechanisms that are widely altered in human cancers including hepatocellular carcinoma (HCC), the third leading cause of cancer related mortality worldwide. Both DNA methylation and microRNA expression patterns are regulated in developmental stage specific-, cell type specific- and tissue-specific manner. The aberrations are inferred in the maintenance of cancer stem cells and in clonal cell evolution during carcinogenesis. The availability of genome-wide technologies for DNA methylation and microRNA profiling has revolutionized the field of epigenetics and led to the discovery of a number of epigenetically silenced microRNAs in cancerous cells and primary tissues. Dysregulation of these microRNAs affects several key signalling pathways in hepatocarcinogenesis suggesting that modulation of DNA methylation and/or microRNA expression can serve as new therapeutic targets for HCC. Accumulative evidence shows that aberrant DNA methylation of certain microRNA genes is an event specifically found in HCC which correlates with unfavorable outcomes. Therefore, it can potentially serve as a biomarker for detection as well as for prognosis, monitoring and predicting therapeutic responses in HCC. PMID:24976726

  16. The Regulatory Roles of MicroRNAs in Bone Remodeling and Perspectives as Biomarkers in Osteoporosis

    PubMed Central

    Sun, Mengge; Zhou, Xiaoya; Chen, Lili; Huang, Shishu; Leung, Victor; Wu, Nan; Pan, Haobo; Zhen, Wanxin; Lu, William; Peng, Songlin

    2016-01-01

    MicroRNAs are involved in many cellular and molecular activities and played important roles in many biological and pathological processes, such as tissue formation, cancer development, diabetes, neurodegenerative diseases, and cardiovascular diseases. Recently, it has been reported that microRNAs can modulate the differentiation and activities of osteoblasts and osteoclasts, the key cells that are involved in bone remodeling process. Meanwhile, the results from our and other research groups showed that the expression profiles of microRNAs in the serum and bone tissues are significantly different in postmenopausal women with or without fractures compared to the control. Therefore, it can be postulated that microRNAs might play important roles in bone remodeling and that they are very likely to be involved in the pathological process of postmenopausal osteoporosis. In this review, we will present the updated research on the regulatory roles of microRNAs in osteoblasts and osteoclasts and the expression profiles of microRNAs in osteoporosis and osteoporotic fracture patients. The perspective of serum microRNAs as novel biomarkers in bone loss disorders such as osteoporosis has also been discussed. PMID:27073801

  17. Female partners of men who use pornography: are honesty and mutual use associated with relationship satisfaction?

    PubMed

    Resch, Marley N; Alderson, Kevin G

    2014-01-01

    The authors discuss findings pertaining to male pornography use and female partners' relationship satisfaction and distress. The authors investigated honesty regarding pornography use and mutual consumption between partners, along with honesty and mutual use as predictors of satisfaction. Female participants (N = 340) in committed relationships completed the Pornography Distress Scale and Couples Satisfaction Index online. Participants reporting more honesty showed higher satisfaction and lower levels of distress, and participants disclosing mutual use showed lower levels of distress, although no differences were reported in satisfaction. Honesty regarding pornography use significantly predicted relationship dissatisfaction. Directions for future research and counseling implications are discussed. PMID:23898992

  18. Seed microRNA Research

    Technology Transfer Automated Retrieval System (TEKTRAN)

    MicroRNAs (miRNAs) are key regulatory molecules that play critical roles in gene expression. The biological functions of miRNAs are important for developmental processes in plants and animals. Little is known about the functions of miRNAs in seeds. To gain a better understand-ing of the regulation o...

  19. [Mutual inhibition between positive and negative emotions].

    PubMed

    Shimokawa, A

    1994-02-01

    The purpose of this study is to examine the relationship between positive and negative emotions. In study 1, 62 emotional items were selected in order to measure subjective emotional experiences. In study 2, comics, photos and poems were randomly presented to 1,220 college students to induce emotion. Subjects were asked to rate their momentary emotional intensity on two set of 5-point scales (general emotional intensity scale and 62 specific emotional intensity scale). In analysis 1, positive correlations were suggested between general emotional intensity scale and some of the specific emotional intensity scales which were activated by stimuli. In analysis 2, 10 positive and 10 negative emotional items were extracted from 62 items by factor analysis. In analysis 3, 4 and 5, it became clear that the distribution of frequency of correlations of 10 positive x 10 negative items changed according to the general emotional intensity scale. That is, from low to moderate levels of GEIS, the two kinds of emotion had no or slightly positive correlation, but at high level they became to be negatively correlated. From the facts described above, it is concluded that positive and negative emotions is not always independent, but show mutual inhibition in case of high intensity level of one of each emotions. PMID:8201808

  20. microRNA Response to Listeria monocytogenes Infection in Epithelial Cells

    PubMed Central

    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

  1. Detecting entanglement of continuous variables with three mutually unbiased bases

    NASA Astrophysics Data System (ADS)

    Paul, E. C.; Tasca, D. S.; Rudnicki, Łukasz; Walborn, S. P.

    2016-07-01

    An uncertainty relation is introduced for a symmetric arrangement of three mutually unbiased bases in continuous-variable phase space, and then used to derive a bipartite entanglement criterion based on the variance of global operators composed of these three phase-space variables. We test this criterion using spatial variables of photon pairs and show that the entangled photons are correlated in three pairs of bases.

  2. Mutualism with sea anemones triggered the adaptive radiation of clownfishes

    PubMed Central

    2012-01-01

    Background Adaptive radiation is the process by which a single ancestral species diversifies into many descendants adapted to exploit a wide range of habitats. The appearance of ecological opportunities, or the colonisation or adaptation to novel ecological resources, has been documented to promote adaptive radiation in many classic examples. Mutualistic interactions allow species to access resources untapped by competitors, but evidence shows that the effect of mutualism on species diversification can greatly vary among mutualistic systems. Here, we test whether the development of obligate mutualism with sea anemones allowed the clownfishes to radiate adaptively across the Indian and western Pacific oceans reef habitats. Results We show that clownfishes morphological characters are linked with ecological niches associated with the sea anemones. This pattern is consistent with the ecological speciation hypothesis. Furthermore, the clownfishes show an increase in the rate of species diversification as well as rate of morphological evolution compared to their closest relatives without anemone mutualistic associations. Conclusions The effect of mutualism on species diversification has only been studied in a limited number of groups. We present a case of adaptive radiation where mutualistic interaction is the likely key innovation, providing new insights into the mechanisms involved in the buildup of biodiversity. Due to a lack of barriers to dispersal, ecological speciation is rare in marine environments. Particular life-history characteristics of clownfishes likely reinforced reproductive isolation between populations, allowing rapid species diversification. PMID:23122007

  3. MicroRNAs in rheumatoid arthritis.

    PubMed

    Salehi, Eisa; Eftekhari, Rahil; Oraei, Mona; Gharib, Alvand; Bidad, Katayoon

    2015-04-01

    The role of genetic and epigenetic factors in the development of rheumatic diseases has been an interesting field of research over the past decades all around the world. Research on the role of microRNAs (miRNAs) in rheumatoid arthritis (RA) has been active and ongoing, and investigations have attempted to use miRNAs as biomarkers in disease diagnosis, prognosis, and treatment. This review focuses on experimental researches in the field of miRNAs and RA to present the data available up to this date and includes researches searched by keywords "microRNA" and "rheumatoid arthritis" in PubMed from 2008 to January 2015. All references were also searched for related papers. miRNAs are shown to act as proinflammatory or anti-inflammatory agents in diverse cell types, and their role seems to be regulatory in most instances. Researchers have evaluated miRNAs in patients compared to controls or have investigated their role by overexpressing or silencing them. Multiple targets have been identified in vivo, in vitro, or in silico, and the researches still continue to show their efficacy in clinical settings. PMID:25736037

  4. 12 CFR 575.3 - Mutual holding company reorganizations.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 5 2011-01-01 2011-01-01 false Mutual holding company reorganizations. 575.3 Section 575.3 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY MUTUAL HOLDING COMPANIES § 575.3 Mutual holding company reorganizations. A mutual savings association may reorganize...

  5. 12 CFR 575.3 - Mutual holding company reorganizations.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 6 2014-01-01 2012-01-01 true Mutual holding company reorganizations. 575.3 Section 575.3 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY MUTUAL HOLDING COMPANIES § 575.3 Mutual holding company reorganizations. A mutual savings association may reorganize...

  6. 78 FR 64600 - Mutual Savings Association Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-29

    ... Office of the Comptroller of the Currency Mutual Savings Association Advisory Committee AGENCY... Mutual Savings Association Advisory Committee (MSAAC). DATES: A public meeting of the MSAAC will be held... mutual savings associations and other issues of concern to the existing mutual savings...

  7. 75 FR 77048 - Mutual Savings Association Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-10

    ... Office of Thrift Supervision Mutual Savings Association Advisory Committee AGENCY: Department of the... Thrift Supervision has determined that the renewal of the ] Charter of the OTS Mutual Savings Association... facing mutual savings associations. DATES: The Charter of the OTS Mutual Savings Association...

  8. Group Differences in the Mutual Gaze of Chimpanzees (Pan Troglodytes)

    ERIC Educational Resources Information Center

    Bard, Kim A.; Myowa-Yamakoshi, Masako; Tomonaga, Masaki; Tanaka, Masayuki; Costall, Alan; Matsuzawa, Tetsuro

    2005-01-01

    A comparative developmental framework was used to determine whether mutual gaze is unique to humans and, if not, whether common mechanisms support the development of mutual gaze in chimpanzees and humans. Mother-infant chimpanzees engaged in approximately 17 instances of mutual gaze per hour. Mutual gaze occurred in positive, nonagonistic…

  9. 12 CFR 544.5 - Federal mutual savings association bylaws.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 5 2011-01-01 2011-01-01 false Federal mutual savings association bylaws. 544.5 Section 544.5 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY FEDERAL MUTUAL SAVINGS ASSOCIATIONS-CHARTER AND BYLAWS Bylaws § 544.5 Federal mutual savings association bylaws. (a) General. A Federal mutual...

  10. 12 CFR 144.1 - Federal mutual charter.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 12 Banks and Banking 1 2012-01-01 2012-01-01 false Federal mutual charter. 144.1 Section 144.1 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY FEDERAL MUTUAL SAVINGS ASSOCIATIONS-CHARTER AND BYLAWS Charter § 144.1 Federal mutual charter. A Federal mutual savings association shall have a charter in the following...

  11. 12 CFR 544.1 - Federal mutual charter.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 5 2011-01-01 2011-01-01 false Federal mutual charter. 544.1 Section 544.1 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY FEDERAL MUTUAL SAVINGS ASSOCIATIONS-CHARTER AND BYLAWS Charter § 544.1 Federal mutual charter. A Federal mutual savings association shall have a charter in the following...

  12. 12 CFR 144.1 - Federal mutual charter.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 12 Banks and Banking 1 2013-01-01 2013-01-01 false Federal mutual charter. 144.1 Section 144.1 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY FEDERAL MUTUAL SAVINGS ASSOCIATIONS-CHARTER AND BYLAWS Charter § 144.1 Federal mutual charter. A Federal mutual savings association shall have a charter in the following...

  13. 12 CFR 544.1 - Federal mutual charter.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 12 Banks and Banking 6 2013-01-01 2012-01-01 true Federal mutual charter. 544.1 Section 544.1 Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY FEDERAL MUTUAL SAVINGS ASSOCIATIONS-CHARTER AND BYLAWS Charter § 544.1 Federal mutual charter. A Federal mutual savings association shall have a charter in the following...

  14. microRNAs and microRNA Targets Involved in Alfalfa Stem Development

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To examine the possible involvement of microRNAs in alfalfa stem development, we hybridized 32P-labled total microRNAs purified from elongating and post-elongation stem internodes (ES and PES, respectively) of the alfalfa Clone 252 to a microRNA dot blot that contains a total of 70 reference anti-mi...

  15. microRNAs and Endometrial Pathophysiology.

    PubMed

    Chill, Henry H; Dior, Uri P; Kogan, Liron; Revel, Ariel

    2015-01-01

    Embryo implantation requires a reciprocal interaction between the blastocyst and endometrium and is associated with complex regulatory mechanisms. Since their discovery, microRNAs became prominent candidates providing missing links for many biological pathways. In recent years, microRNAs were implicated as one of the important players in regulation of various biological and physiological endometrial related processes. This chapter aims to present recent knowledge pertaining to the diverse aspects of microRNAs in the embryo-endometrial relationship. We will focus on the role of microRNAs in decidualization and their part in natural and stimulated cycles. Next, we will present recent studies deliberating the role of microRNAs in recurrent pregnancy loss and in the important phenomenon of recurrent implantation failure. Lastly, demonstrating an important aspect of embryo implantation and invasion, we will outline few microRNA related shared pathways of implantation and carcinogenesis. PMID:26662990

  16. An efficient algorithm for direction finding against unknown mutual coupling.

    PubMed

    Wang, Weijiang; Ren, Shiwei; Ding, Yingtao; Wang, Haoyu

    2014-01-01

    In this paper, an algorithm of direction finding is proposed in the presence of unknown mutual coupling. The preliminary direction of arrival (DOA) is estimated using the whole array for high resolution. Further refinement can then be conducted by estimating the angularly dependent coefficients (ADCs) with the subspace theory. The mutual coupling coefficients are finally determined by solving the least squares problem with all of the ADCs utilized without discarding any. Simulation results show that the proposed method can achieve better performance at a low signal-to-noise ratio (SNR) with a small-sized array and is more robust, compared with the similar processes employing the initial DOA estimation and further improvement iteratively. PMID:25347587

  17. Modeling of a bipedal robot using mutually coupled Rayleigh oscillators.

    PubMed

    Filho, Armando C de Pina; Dutra, Max S; Raptopoulos, Luciano S C

    2005-01-01

    The objective of the work presented here was the modeling of a bipedal robot using a central pattern generator (CPG) formed by a set of mutually coupled Rayleigh oscillators. We analyzed a 2D model, with the three most important determinants of gait, that performs only motions parallel to the sagittal plane. Using oscillators with integer relation of frequency, we determined the transient motion and the stable limit cycles of the network formed by the three oscillators, showing the behavior of the knee angles and the hip angle. A comparison of the plotted graphs revealed that the system provided excellent results when compared to experimental analysis. Based on the results of the study, we come to the conclusion that the use of mutually coupled Rayleigh oscillators can represent an excellent method of signal generation, allowing their application for feedback control of a walking machine. PMID:15580522

  18. The Mutual Impedance Probe (RPC-MIP) onboard ROSETTA

    NASA Astrophysics Data System (ADS)

    Henri, Pierre; Lebreton, Jean-Pierre; Béghin, Christian; Décréau, Pierrette; Grard, Réjean; Hamelin, Michel; Mazelle, Christian; Randriamboarison, Orélien; Schmidt, Walter; Winterhalter, Daniel; Aouad, Youcef; Lagoutte, Dominique; Vallières, Xavier

    2014-05-01

    The ROSETTA mission will reach the comet 67P/Churyumov-Gerasimenko in August 2014 and enable, for the first time, the in situ survey of a comet activity during along orbit. On board the ROSETTA orbiter, the Mutual Impedance Probe (MIP) is one of the instruments of the Rosetta Plasma Consortium (RPC) that aims at monitoring the cometary plasma environment. MIP is a quadrupolar probe that measures the frequency response of the coupling impedance between two emitting and two receiving dipoles. The electron density and temperature are derived from the resonance peak and the interference pattern of the mutual impedance spectrum. We will describe this instrument and discuss the preliminary results obtained during the third ROSETTA Earth flyby to show its expected capabilities. The RPC switch ON for the post-hibernation recommissioning is planned at the end of March. The health status of the instrument will be discussed.

  19. An Efficient Algorithm for Direction Finding against Unknown Mutual Coupling

    PubMed Central

    Wang, Weijiang; Ren, Shiwei; Ding, Yingtao; Wang, Haoyu

    2014-01-01

    In this paper, an algorithm of direction finding is proposed in the presence of unknown mutual coupling. The preliminary direction of arrival (DOA) is estimated using the whole array for high resolution. Further refinement can then be conducted by estimating the angularly dependent coefficients (ADCs) with the subspace theory. The mutual coupling coefficients are finally determined by solving the least squares problem with all of the ADCs utilized without discarding any. Simulation results show that the proposed method can achieve better performance at a low signal-to-noise ratio (SNR) with a small-sized array and is more robust, compared with the similar processes employing the initial DOA estimation and further improvement iteratively. PMID:25347587

  20. Networks in financial markets based on the mutual information rate

    NASA Astrophysics Data System (ADS)

    Fiedor, Paweł

    2014-05-01

    In the last few years there have been many efforts in econophysics studying how network theory can facilitate understanding of complex financial markets. These efforts consist mainly of the study of correlation-based hierarchical networks. This is somewhat surprising as the underlying assumptions of research looking at financial markets are that they are complex systems and thus behave in a nonlinear manner, which is confirmed by numerous studies, making the use of correlations which are inherently dealing with linear dependencies only baffling. In this paper we introduce a way to incorporate nonlinear dynamics and dependencies into hierarchical networks to study financial markets using mutual information and its dynamical extension: the mutual information rate. We show that this approach leads to different results than the correlation-based approach used in most studies, on the basis of 91 companies listed on the New York Stock Exchange 100 between 2003 and 2013, using minimal spanning trees and planar maximally filtered graphs.

  1. Mutualisms in a changing world: an evolutionary perspective.

    PubMed

    Toby Kiers, E; Palmer, Todd M; Ives, Anthony R; Bruno, John F; Bronstein, Judith L

    2010-12-01

    Ecology Letters (2010) 13: 1459-1474 ABSTRACT: There is growing concern that rapid environmental degradation threatens mutualistic interactions. Because mutualisms can bind species to a common fate, mutualism breakdown has the potential to expand and accelerate effects of global change on biodiversity loss and ecosystem disruption. The current focus on the ecological dynamics of mutualism under global change has skirted fundamental evolutionary issues. Here, we develop an evolutionary perspective on mutualism breakdown to complement the ecological perspective, by focusing on three processes: (1) shifts from mutualism to antagonism, (2) switches to novel partners and (3) mutualism abandonment. We then identify the evolutionary factors that may make particular classes of mutualisms especially susceptible or resistant to breakdown and discuss how communities harbouring mutualisms may be affected by these evolutionary responses. We propose a template for evolutionary research on mutualism resilience and identify conservation approaches that may help conserve targeted mutualisms in the face of environmental change. PMID:20955506

  2. The functional consequences of age-related changes in microRNA expression in skeletal muscle.

    PubMed

    Soriano-Arroquia, Ana; House, Louise; Tregilgas, Luke; Canty-Laird, Elizabeth; Goljanek-Whysall, Katarzyna

    2016-06-01

    A common characteristic of ageing is disrupted homeostasis between growth and atrophy of skeletal muscle resulting in loss of muscle mass and function, which is associated with sarcopenia. Sarcopenia is related to impaired balance, increased falls and decline in quality of life of older people. Ageing-related transcriptome and proteome changes in skeletal muscle have been characterised, however the molecular mechanisms underlying sarcopenia are still not fully understood. microRNAs are novel regulators of gene expression known to modulate skeletal muscle development and homeostasis. Expression of numerous microRNAs is disrupted in skeletal muscle with age however, the functional consequences of this are not yet understood. Given that a single microRNA can simultaneously affect multiple signalling pathways, microRNAs are potent modulators of pathophysiological changes occurring during ageing. Here we use microRNA and transcript expression profiling together with microRNA functional assays to show that disrupted microRNA:target interactions play an important role in maintaining muscle homeostasis. We identified miR-181a as a regulator of the sirtuin1 (Sirt1) gene expression in skeletal muscle and show that the expression of miR-181a and its target gene is disrupted in skeletal muscle from old mice. Moreover, we show that miR-181a:Sirt1 interactions regulate myotube size. Our results demonstrate that disrupted microRNA:target interactions are likely related to the pathophysiological changes occurring in skeletal muscle during ageing. PMID:26922183

  3. Dispersal Mutualism Incorporated into Large-Scale, Infrequent Disturbances.

    PubMed

    Parker, V Thomas

    2015-01-01

    Because of their influence on succession and other community interactions, large-scale, infrequent natural disturbances also should play a major role in mutualistic interactions. Using field data and experiments, I test whether mutualisms have been incorporated into large-scale wildfire by whether the outcomes of a mutualism depend on disturbance. In this study a seed dispersal mutualism is shown to depend on infrequent, large-scale disturbances. A dominant shrubland plant (Arctostaphylos species) produces seeds that make up a persistent soil seed bank and requires fire to germinate. In post-fire stands, I show that seedlings emerging from rodent caches dominate sites experiencing higher fire intensity. Field experiments show that rodents (Perimyscus californicus, P. boylii) do cache Arctostaphylos fruit and bury most seed caches to a sufficient depth to survive a killing heat pulse that a fire might drive into the soil. While the rodent dispersal and caching behavior itself has not changed compared to other habitats, the environmental transformation caused by wildfire converts the caching burial of seed from a dispersal process to a plant fire adaptive trait, and provides the context for stimulating subsequent life history evolution in the plant host. PMID:26151560

  4. Dispersal Mutualism Incorporated into Large-Scale, Infrequent Disturbances

    PubMed Central

    Parker, V. Thomas

    2015-01-01

    Because of their influence on succession and other community interactions, large-scale, infrequent natural disturbances also should play a major role in mutualistic interactions. Using field data and experiments, I test whether mutualisms have been incorporated into large-scale wildfire by whether the outcomes of a mutualism depend on disturbance. In this study a seed dispersal mutualism is shown to depend on infrequent, large-scale disturbances. A dominant shrubland plant (Arctostaphylos species) produces seeds that make up a persistent soil seed bank and requires fire to germinate. In post-fire stands, I show that seedlings emerging from rodent caches dominate sites experiencing higher fire intensity. Field experiments show that rodents (Perimyscus californicus, P. boylii) do cache Arctostaphylos fruit and bury most seed caches to a sufficient depth to survive a killing heat pulse that a fire might drive into the soil. While the rodent dispersal and caching behavior itself has not changed compared to other habitats, the environmental transformation caused by wildfire converts the caching burial of seed from a dispersal process to a plant fire adaptive trait, and provides the context for stimulating subsequent life history evolution in the plant host. PMID:26151560

  5. Mutual inductance between piecewise-linear loops

    NASA Astrophysics Data System (ADS)

    Cristina Barroso, Ana; Silva, J. P.

    2013-11-01

    We consider a current-carrying wire loop made out of linear segments of arbitrary sizes and directions in three-dimensional space. We develop expressions to calculate its vector potential and magnetic field at all points in space. We then calculate the mutual inductance between two such (non-intersecting) piecewise-linear loops. As simple applications, we consider in detail the mutual inductance between two square wires of equal length that either lie in the same plane or lie in parallel horizontal planes with their centers on the same vertical axis. Our expressions can also be used to obtain approximations to the mutual inductance between wires of arbitrary three-dimensional shapes.

  6. Mutual information rate and bounds for it.

    PubMed

    Baptista, Murilo S; Rubinger, Rero M; Viana, Emilson R; Sartorelli, José C; Parlitz, Ulrich; Grebogi, Celso

    2012-01-01

    The amount of information exchanged per unit of time between two nodes in a dynamical network or between two data sets is a powerful concept for analysing complex systems. This quantity, known as the mutual information rate (MIR), is calculated from the mutual information, which is rigorously defined only for random systems. Moreover, the definition of mutual information is based on probabilities of significant events. This work offers a simple alternative way to calculate the MIR in dynamical (deterministic) networks or between two time series (not fully deterministic), and to calculate its upper and lower bounds without having to calculate probabilities, but rather in terms of well known and well defined quantities in dynamical systems. As possible applications of our bounds, we study the relationship between synchronisation and the exchange of information in a system of two coupled maps and in experimental networks of coupled oscillators. PMID:23112809

  7. Integrating plant carbon dynamics with mutualism ecology.

    PubMed

    Pringle, Elizabeth G

    2016-04-01

    71 I. 71 II. 72 III. 73 IV. 74 V. 74 74 References 74 SUMMARY: Plants reward microbial and animal mutualists with carbohydrates to obtain nutrients, defense, pollination, and dispersal. Under a fixed carbon budget, plants must allocate carbon to their mutualists at the expense of allocation to growth, reproduction, or storage. Such carbon trade-offs are indirectly expressed when a plant exhibits reduced growth or fecundity in the presence of its mutualist. Because carbon regulates the costs of all plant mutualisms, carbon dynamics are a common platform for integrating these costs in the face of ecological complexity and context dependence. The ecophysiology of whole-plant carbon allocation could thus elucidate the ecology and evolution of plant mutualisms. If mutualisms are costly to plants, then they must be important but frequently underestimated sinks in the terrestrial carbon cycle. PMID:26414800

  8. Distribution of Mutual Information in Multipartite States

    NASA Astrophysics Data System (ADS)

    Maziero, Jonas

    2014-06-01

    Using the relative entropy of total correlation, we derive an expression relating the mutual information of n-partite pure states to the sum of the mutual informations and entropies of its marginals and analyze some of its implications. Besides, by utilizing the extended strong subadditivity of von Neumann entropy, we obtain generalized monogamy relations for the total correlation in three-partite mixed states. These inequalities lead to a tight lower bound for this correlation in terms of the sum of the bipartite mutual informations. We use this bound to propose a measure for residual three-partite total correlation and discuss the non-applicability of this kind of quantifier to measure genuine multiparty correlations.

  9. Influence of predator mutual interference and prey refuge on Lotka-Volterra predator-prey dynamics

    NASA Astrophysics Data System (ADS)

    Chen, Liujuan; Chen, Fengde; Wang, Yiqin

    2013-11-01

    A Lotka-Volterra predator-prey model incorporating a constant number of prey using refuges and mutual interference for predator species is presented. By applying the divergency criterion and theories on exceptional directions and normal sectors, we show that the interior equilibrium is always globally asymptotically stable and two boundary equilibria are both saddle points. Our results indicate that prey refuge has no influence on the coexistence of predator and prey species of the considered model under the effects of mutual interference for predator species, which differently from the conclusion without predator mutual interference, thus improving some known ones. Numerical simulations are performed to illustrate the validity of our results.

  10. 26 CFR 1.831-1 - Tax on insurance companies (other than life or mutual), mutual marine insurance companies, and...

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 26 Internal Revenue 8 2011-04-01 2011-04-01 false Tax on insurance companies (other than life or... insurance companies (other than life or mutual), mutual marine insurance companies, and mutual fire insurance companies issuing perpetual policies. (a) All insurance companies, other than life or mutual...

  11. 26 CFR 1.831-1 - Tax on insurance companies (other than life or mutual), mutual marine insurance companies, and...

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 26 Internal Revenue 8 2013-04-01 2013-04-01 false Tax on insurance companies (other than life or... insurance companies (other than life or mutual), mutual marine insurance companies, and mutual fire insurance companies issuing perpetual policies. (a) All insurance companies, other than life or mutual...

  12. 26 CFR 1.831-1 - Tax on insurance companies (other than life or mutual), mutual marine insurance companies, and...

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 26 Internal Revenue 8 2014-04-01 2014-04-01 false Tax on insurance companies (other than life or... insurance companies (other than life or mutual), mutual marine insurance companies, and mutual fire insurance companies issuing perpetual policies. (a) All insurance companies, other than life or mutual...

  13. 26 CFR 1.831-1 - Tax on insurance companies (other than life or mutual), mutual marine insurance companies, and...

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 26 Internal Revenue 8 2012-04-01 2012-04-01 false Tax on insurance companies (other than life or... insurance companies (other than life or mutual), mutual marine insurance companies, and mutual fire insurance companies issuing perpetual policies. (a) All insurance companies, other than life or mutual...

  14. 26 CFR 1.831-1 - Tax on insurance companies (other than life or mutual), mutual marine insurance companies, and...

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 26 Internal Revenue 8 2010-04-01 2010-04-01 false Tax on insurance companies (other than life or... companies (other than life or mutual), mutual marine insurance companies, and mutual fire insurance companies issuing perpetual policies. (a) All insurance companies, other than life or mutual or...

  15. Conceptual Alignment: How Brains Achieve Mutual Understanding.

    PubMed

    Stolk, Arjen; Verhagen, Lennart; Toni, Ivan

    2016-03-01

    We share our thoughts with other minds, but we do not understand how. Having a common language certainly helps, but infants' and tourists' communicative success clearly illustrates that sharing thoughts does not require signals with a pre-assigned meaning. In fact, human communicators jointly build a fleeting conceptual space in which signals are a means to seek and provide evidence for mutual understanding. Recent work has started to capture the neural mechanisms supporting those fleeting conceptual alignments. The evidence suggests that communicators and addressees achieve mutual understanding by using the same computational procedures, implemented in the same neuronal substrate, and operating over temporal scales independent from the signals' occurrences. PMID:26792458

  16. Magnetic circuitry mutual coupling probe

    NASA Technical Reports Server (NTRS)

    Anthony, P. L.

    1972-01-01

    Development of magnetic probe for nondestructive testing of multilayer printed circuit boards to determine existence of opens or shorts is reported. Components of probe are described and procedures for operation are discussed. Two illustrations are provided to show magnetic circuits and principles of operation.

  17. A consumer-resource approach to the density-dependent population dynamics of mutualism

    USGS Publications Warehouse

    Holland, J. Nathaniel; DeAngelis, Donald L.

    2010-01-01

    Like predation and competition, mutualism is now recognized as a consumer resource (C-R) interaction, including, in particular, bi-directional (e.g., coral, plant- mycorrhizae) and uni-directional (e.g., ant-plant defense, plant-pollinator) C-R mutualisms. Here, we develop general theory for the density-dependent population dynamics of mutualism based on the C-R mechanism of interspecific interaction. To test the influence of C-R interactions on the dynamics and stability of bi- and uni-directional C-R mutualisms, we developed simple models that link consumer functional response of one mutualistic species with the resources supplied by another. Phase-plane analyses show that the ecological dynamics of C-R mutualisms are stable in general. Most transient behavior leads to an equilibrium of mutualistic coexistence, at which both species densities are greater than in the absence of interactions. However, due to the basic nature of C-R interactions, certain density-dependent conditions can lead to C-R dynamics characteristic of predator-prey interactions, in which one species overexploits and causes the other to go extinct. Consistent with empirical phenomena, these results suggest that the C-R interaction can provide a broad mechanism for understanding density-dependent population dynamics of mutualism. By unifying predation, competition, and mutualism under the common ecological framework of consumer-resource theory, we may also gain a better understanding of the universal features of interspecific interactions in general.

  18. Identification and Pathway Analysis of microRNAs with No Previous Involvement in Breast Cancer

    PubMed Central

    Rebollar-Vega, Rosa; Quintanar-Jurado, Valeria; Maffuz-Aziz, Antonio; Jimenez-Sanchez, Gerardo; Bautista-Piña, Veronica; Arellano-Llamas, Rocio; Hidalgo-Miranda, Alfredo

    2012-01-01

    microRNA expression signatures can differentiate normal and breast cancer tissues and can define specific clinico-pathological phenotypes in breast tumors. In order to further evaluate the microRNA expression profile in breast cancer, we analyzed the expression of 667 microRNAs in 29 tumors and 21 adjacent normal tissues using TaqMan Low-density arrays. 130 miRNAs showed significant differential expression (adjusted P value = 0.05, Fold Change = 2) in breast tumors compared to the normal adjacent tissue. Importantly, the role of 43 of these microRNAs has not been previously reported in breast cancer, including several evolutionary conserved microRNA*, showing similar expression rates to that of their corresponding leading strand. The expression of 14 microRNAs was replicated in an independent set of 55 tumors. Bioinformatic analysis of mRNA targets of the altered miRNAs, identified oncogenes like ERBB2, YY1, several MAP kinases, and known tumor-suppressors like FOXA1 and SMAD4. Pathway analysis identified that some biological process which are important in breast carcinogenesis are affected by the altered microRNA expression, including signaling through MAP kinases and TP53 pathways, as well as biological processes like cell death and communication, focal adhesion and ERBB2-ERBB3 signaling. Our data identified the altered expression of several microRNAs whose aberrant expression might have an important impact on cancer-related cellular pathways and whose role in breast cancer has not been previously described. PMID:22438871

  19. MicroRNA modulation combined with sunitinib as a novel therapeutic strategy for pancreatic cancer

    PubMed Central

    Passadouro, Marta; Pedroso de Lima, Maria C; Faneca, Henrique

    2014-01-01

    Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive and mortal cancer, characterized by a set of known mutations, invasive features, and aberrant microRNA expression that have been associated with hallmark malignant properties of PDAC. The lack of effective PDAC treatment options prompted us to investigate whether microRNAs would constitute promising therapeutic targets toward the generation of a gene therapy approach with clinical significance for this disease. In this work, we show that the developed human serum albumin–1-palmitoyl-2-oleoyl-sn-glycero-3-ethylphosphocholine:cholesterol/anti-microRNA oligonucleotides (+/−) (4/1) nanosystem exhibits the ability to efficiently deliver anti-microRNA oligonucleotides targeting the overexpressed microRNAs miR-21, miR-221, miR-222, and miR-10 in PDCA cells, promoting an almost complete abolishment of microRNA expression. Silencing of these microRNAs resulted in a significant increase in the levels of their targets. Moreover, the combination of microRNA silencing, namely miR-21, with low amounts of the chemotherapeutic drug sunitinib resulted in a strong and synergistic antitumor effect, showing that this combined strategy could be of great importance for therapeutic application in PDAC. PMID:25061297

  20. MitomiRs, chloromiRs and modelling of the microRNA inhibition.

    PubMed

    Demongeot, J; Hazgui, H; Bandiera, S; Cohen, O; Henrion-Caude, A

    2013-09-01

    MicroRNAs are non-coding parts of nuclear and mitochondrial genomes, preventing the weakest part of the genetic regulatory networks from being expressed and preventing the appearance of a too many attractors in these networks. They have also a great influence on the chromatin clock, which ensures the updating of the genetic regulatory networks. The post-transcriptional inhibitory activity by the microRNAs, which is partly unspecific, is due firstly to their possibly direct negative action during translation by hybridizing tRNAs, especially those inside the mitochondrion, hence slowing mitochondrial respiration, and secondly to their action on a large number of putative m-RNA targets like those involved in immunetworks; We show that the circuits in the core of the interaction graphs are responsible for the small number of dedicated attractors that correspond to genetically controlled functions, partly due to a general filtering by the microRNAs. We analyze this influence as well as their impact on important functions like the control by the p53 network over the apoptosis/proliferation system and the homeostasis of the energy metabolism. In this last case, we show the role of two kinds of microRNAs, both involved in the control of the mitochondrial genome: (1) nuclear microRNAs, called mitoMirs, inhibiting mitochondrial genes and (2) putative mitochondrial microRNAs inhibiting the tRNAs functioning. PMID:23982306

  1. MicroRNA-338 and microRNA-21 co-transfection for the treatment of rat sciatic nerve injury.

    PubMed

    Wang, Jianyong; Muheremu, Aikeremujiang; Zhang, Ming; Gong, Kai; Huang, Chuyi; Ji, Yuchen; Wei, Yujun; Ao, Qiang

    2016-06-01

    The objective of this study is to find if co-transfecting microRNA-338 and microRNA-21 into the neurons in the spinal cord can promote functional recovery after peripheral nerve injury in rats. Animals were divided into three groups: 20 animals in the GFP control vector group (group A), 20 animals in the GFP experimental vector group (group B) and ten animals in the normal control group. Right sciatic nerves of animals in groups A and B were transected and were bridged with collagen nerve conduits with 10 mm distance between the stumps. 3 µl GFP control vector or 3 µl lentiviral vectors encoding the sequence of microRNA-338 and microRNA-21 were injected in the conduit. 8 weeks after the surgery, the treatment effect was evaluated by functional analysis, electrophysiological analysis, immunohistochemical analysis as well as transmitting electronic microscope observations in all the rats. Animals treated with microRNA-338 and microRNA-21 showed significantly better recovery than GFP control group animals by means of functional analysis (Sciatic nerve index -47.7 ± 2.5 vs -59.4 ± 3.7), electrophysiological analysis (Conduction velocity 20.5 ± 2.8 vs 10.5 ± 1.4 m/s), ratio of wet weight of the gastrocnemius muscles (0.83 ± 0.03 vs 0.55 ± 0.06), axon diameter (5.0 ± 1.8 µm vs 4.0 ± 2.2), myelin sheath thickness (1.4 ± 0.43 vs 0.80 ± 0.31 µm) and G-ratio (0.80 ± 0.06 vs 0.75 ± 0.04). Lentiviral vectors encoding microRNA 338 and 21 might be explored in the future as potential therapeutic intervention to promote nerve regeneration. PMID:26909749

  2. Why power matters: creating a foundation of mutual support in couple relationships.

    PubMed

    Knudson-Martin, Carmen

    2013-03-01

    Research shows that equal power helps couples create intimacy and relationship success. However, though couples increasingly desire equal relationships, cultural models of mutual support are not well developed. Clinicians often approach heterosexual couple therapy as though partners are inherently equal, thus reinforcing unacknowledged gender inequities. This article examines research that shows why power imbalances are destructive to intimate relationships and focuses on four gender-related aspects of mutual support: (a) shared relational responsibility, (b) mutual vulnerability, (c) mutual attunement, and (d) shared influence. Case examples illustrate how socio-emotional attunement, interrupting the flow of power, and introducing alternative relational experience help couple therapists identify and address power disparities in these important relational processes. Encouraging the powerful person to take relational initiative and introducing alternative gender discourse are especially important. PMID:25408086

  3. Oscillatory dynamics in a bacterial cross-protection mutualism.

    PubMed

    Yurtsev, Eugene Anatoly; Conwill, Arolyn; Gore, Jeff

    2016-05-31

    Cooperation between microbes can enable microbial communities to survive in harsh environments. Enzymatic deactivation of antibiotics, a common mechanism of antibiotic resistance in bacteria, is a cooperative behavior that can allow resistant cells to protect sensitive cells from antibiotics. Understanding how bacterial populations survive antibiotic exposure is important both clinically and ecologically, yet the implications of cooperative antibiotic deactivation on the population and evolutionary dynamics remain poorly understood, particularly in the presence of more than one antibiotic. Here, we show that two Escherichia coli strains can form an effective cross-protection mutualism, protecting each other in the presence of two antibiotics (ampicillin and chloramphenicol) so that the coculture can survive in antibiotic concentrations that inhibit growth of either strain alone. Moreover, we find that daily dilutions of the coculture lead to large oscillations in the relative abundance of the two strains, with the ratio of abundances varying by nearly four orders of magnitude over the course of the 3-day period of the oscillation. At modest antibiotic concentrations, the mutualistic behavior enables long-term survival of the oscillating populations; however, at higher antibiotic concentrations, the oscillations destabilize the population, eventually leading to collapse. The two strains form a successful cross-protection mutualism without a period of coevolution, suggesting that similar mutualisms may arise during antibiotic treatment and in natural environments such as the soil. PMID:27194723

  4. Oscillatory dynamics in a bacterial cross-protection mutualism

    PubMed Central

    Yurtsev, Eugene Anatoly; Conwill, Arolyn; Gore, Jeff

    2016-01-01

    Cooperation between microbes can enable microbial communities to survive in harsh environments. Enzymatic deactivation of antibiotics, a common mechanism of antibiotic resistance in bacteria, is a cooperative behavior that can allow resistant cells to protect sensitive cells from antibiotics. Understanding how bacterial populations survive antibiotic exposure is important both clinically and ecologically, yet the implications of cooperative antibiotic deactivation on the population and evolutionary dynamics remain poorly understood, particularly in the presence of more than one antibiotic. Here, we show that two Escherichia coli strains can form an effective cross-protection mutualism, protecting each other in the presence of two antibiotics (ampicillin and chloramphenicol) so that the coculture can survive in antibiotic concentrations that inhibit growth of either strain alone. Moreover, we find that daily dilutions of the coculture lead to large oscillations in the relative abundance of the two strains, with the ratio of abundances varying by nearly four orders of magnitude over the course of the 3-day period of the oscillation. At modest antibiotic concentrations, the mutualistic behavior enables long-term survival of the oscillating populations; however, at higher antibiotic concentrations, the oscillations destabilize the population, eventually leading to collapse. The two strains form a successful cross-protection mutualism without a period of coevolution, suggesting that similar mutualisms may arise during antibiotic treatment and in natural environments such as the soil. PMID:27194723

  5. Multiple occurrences of mutualism in the yucca moth lineage.

    PubMed Central

    Pellmyr, O; Thompson, J N

    1992-01-01

    The complex mutualism between yuccas and the moths that pollinate their flowers is regarded as one of the most obvious cases of coevolution. Studies of related genera show that at least two of the critical behavioral and life history traits suggested to have resulted from coevolved mutualism in yucca moths are plesiomorphic to the family. Another trait, oviposition into flowers, has evolved repeatedly within the family. One species with these traits, Greya politella, feeds on and pollinates plants of a different family, but pollination occurs through a different component of the oviposition behavior than in the yucca moths. Major differences compared with yucca moths and their hosts are that G. politella only passively pollinates its host and that copollinators often contribute to pollination. This analysis suggests that evolution of mutualism between yuccas and yucca moths may have required few behavioral and life history changes in the moths. The truly coevolved features of this interaction appear to be the evolution of active pollination by the moths, the associated morphological structures in the moths for carrying pollen, and the exclusion of copollinators by yuccas. Images PMID:11607287

  6. Track-to-Track Data Association using Mutual Information

    NASA Astrophysics Data System (ADS)

    Hussein, I.; Roscoe, C.; Wilkins, M.; Schumacher, P.

    In this paper, we build on recent work to further investigate the use of mutual information to solve various association problems in space situational awareness. Specifically, we solve the track-to-track association (TTTA) problem where we seek to associate a given set of tracks at one point in time with another set of tracks at a different time instance. Both sets of tracks are uncertain and are probabilistically described using multivariate normal distributions. This allows for a closed-form solution, based on the unscented transform and on mutual information. Future work will focus on developing a similar solution when uncertainty is analytic but not Gaussian or when it is completely non-analytic -e.g., when the uncertainty is described using a particle cloud. The proposed solution is inspired by a similar solution based on the unscented transform and mutual information for the observation-to-observation association (OTOA) problem that was developed by the authors in the past. This solution can be adjusted to address the classical observation-to-track association problem (OTTA), which will be the focus of future research. We will demonstrate the main result in simulation for LEO, MEO, GTO, and GEO orbit regimes to show general applicability.

  7. Synchronization in human musical rhythms and mutually interacting complex systems

    PubMed Central

    Hennig, Holger

    2014-01-01

    Though the music produced by an ensemble is influenced by multiple factors, including musical genre, musician skill, and individual interpretation, rhythmic synchronization is at the foundation of musical interaction. Here, we study the statistical nature of the mutual interaction between two humans synchronizing rhythms. We find that the interbeat intervals of both laypeople and professional musicians exhibit scale-free (power law) cross-correlations. Surprisingly, the next beat to be played by one person is dependent on the entire history of the other person’s interbeat intervals on timescales up to several minutes. To understand this finding, we propose a general stochastic model for mutually interacting complex systems, which suggests a physiologically motivated explanation for the occurrence of scale-free cross-correlations. We show that the observed long-term memory phenomenon in rhythmic synchronization can be imitated by fractal coupling of separately recorded or synthesized audio tracks and thus applied in electronic music. Though this study provides an understanding of fundamental characteristics of timing and synchronization at the interbrain level, the mutually interacting complex systems model may also be applied to study the dynamics of other complex systems where scale-free cross-correlations have been observed, including econophysics, physiological time series, and collective behavior of animal flocks. PMID:25114228

  8. Mutualism breakdown in breadfruit domestication

    PubMed Central

    Xing, Xiaoke; Koch, Alexander M.; Jones, A. Maxwell P.; Ragone, Diane; Murch, Susan; Hart, Miranda M.

    2012-01-01

    During the process of plant domestication, below-ground communities are rarely considered. Some studies have attempted to understand the changes in root symbionts owing to domestication, but little is known about how it influences mycorrhizal response in domesticated crops. We hypothesized that selection for above-ground traits may also result in decreased mycorrhizal abundance in roots. Breadfruit (Artocarpus sp.) has a long domestication history, with a strong geographical movement of cultivars from west to east across the Melanesian and Polynesian islands. Our results clearly show a decrease in arbuscular mycorrhizas (AMs) along a domestication gradient from wild to recently derived cultivars. We showed that the vesicular and arbuscular colonization rate decreased significantly in more recently derived breadfruit cultivars. In addition, molecular analyses of breadfruit roots indicated that AM fungal species richness also responded along the domestication gradient. These results suggest that human-driven selection for plant cultivars can have unintended effects on below-ground mutualists, with potential impacts on the stress tolerance of crops and long-term food security. PMID:21920983

  9. Clinical evaluation of circulating microRNA-25 level change in sepsis and its potential relationship with oxidative stress

    PubMed Central

    Yao, Liqiong; Liu, Zhiwu; Zhu, Jinhong; Li, Bin; Chai, Chen; Tian, Yunlin

    2015-01-01

    Objective: to investigated the circulating microRNA expression profile in sepsis and its clinical evaluation. Methods: 70 patients with sepsis and 30 patients with SIRS were selected and their blood samples were collected. Using liquid bead array with 3 statistical analysis approaches analyzed the circulating microRNA expression profiles, for confirming the data of liquid bead array, qRT-PCR was performed. The prognostic value of the changed microRNA in sepsis was determined and compared with CRP and PCT by analyzing the receiver operating characteristic (ROC) curves. To reveal whether the selected microRNAs could predict the outcome of patients, 28 d survival rate were calculated using Kaplan-Meier curves. Furthermore, the level of malondialdehyde (MDA), activity of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) in plasma were detected and the relationship with the changed microRNA was determined. Results: By integrating data from liquid bead array, we ultimately identified 6 microRNAs that were consistently changed in both of 3 statistical analysis approaches, however, only the change of microRNA-25 was significant according to the qPCR’s result. The area under ROC curve showed that the clinical accuracy of microRNA-25 for sepsis diagnosis was better than CRP and PCT (AUG=0.806, 0.676 and 0.726, P<0.05).The decrease in level of microRNA-25 was correlated with the severity of sepsis, SOFA score, CRP and PCT level, meanwhile, microRNA-25 level can be used for predicting the prognosis of patients, the patients with microRNA-25 level ≤0.492 had a lower 28 d survival rate. Moreover, Decreased microRNA-25 level was related to the level of oxidative stress indicators in sepsis patients. Conclusions: microRNA-25 can be used as a biomarker for the diagnosis and assessment of sepsis. Meanwhile, microRNA-25 level may be associated with oxidative stress in patients with sepsis, and it is expected to become a target for anti-oxidation therapy. PMID

  10. Mutual diffusion of interacting membrane proteins.

    PubMed Central

    Abney, J R; Scalettar, B A; Owicki, J C

    1989-01-01

    The generalized Stokes-Einstein equation is used, together with the two-dimensional pressure equation, to analyze mutual diffusion in concentrated membrane systems. These equations can be used to investigate the role that both direct and hydrodynamic interactions play in determining diffusive behavior. Here only direct interactions are explicitly incorporated into the theory at high densities; however, both direct and hydrodynamic interactions are analyzed for some dilute solutions. We look at diffusion in the presence of weak attractions, soft repulsions, and hard-core repulsions. It is found that, at low densities, attractions retard mutual diffusion while repulsions enhance it. Mechanistically, attractions tend to tether particles together and oppose the dissipation of gradients or fluctuations in concentration, while repulsions provide a driving force that pushes particles apart. At higher concentrations, changes in the structure of the fluid enhance mutual diffusion even in the presence of attractions. It is shown that the theoretical description of postelectrophoresis relaxation and fluorescence correlation spectroscopy experiments must be modified if interacting systems are studied. The effects of interactions on mutual diffusion coefficients have probably already been seen in postelectrophoresis relaxation experiments. PMID:2775829

  11. 76 FR 36625 - Mutual Holding Company

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-22

    ... Office of Thrift Supervision Mutual Holding Company AGENCY: Office of Thrift Supervision (OTS), Treasury... Thrift Supervision, 1700 G Street, NW., Washington, DC 20552, by fax to (202) 906-6518, or by e-mail to...'s Office, Office of Thrift Supervision, 1700 G Street, NW., Washington, DC 20552....

  12. Mutual Group Hypnosis: A Social Interaction Analysis.

    ERIC Educational Resources Information Center

    Sanders, Shirley

    Mutual Group Hypnosis is discussed in terms of its similarity to group dynamics in general and in terms of its similarity to a social interaction program (Role Modeling) designed to foster the expression of warmth and acceptance among group members. Hypnosis also fosters a regression to prelogical thought processes in the service of the ego. Group…

  13. Mutual information image registration based on improved bee evolutionary genetic algorithm

    NASA Astrophysics Data System (ADS)

    Xu, Gang; Tu, Jingzhi

    2009-07-01

    In recent years, the mutual information is regarded as a more efficient similarity metrics in the image registration. According to the features of mutual information image registration, the Bee Evolution Genetic Algorithm (BEGA) is chosen for optimizing parameters, which imitates swarm mating. Besides, we try our best adaptively set the initial parameters to improve the BEGA. The programming result shows the wonderful precision of the algorithm.

  14. MicroRNA Profiling of Primary Cutaneous Large B-Cell Lymphomas

    PubMed Central

    Koens, Lianne; Qin, Yongjun; Leung, Wai Y.; Corver, Willem E.; Jansen, Patty M.; Willemze, Rein; Vermeer, Maarten H.; Tensen, Cornelis P.

    2013-01-01

    Aberrant expression of microRNAs is widely accepted to be pathogenetically involved in nodal diffuse large B-cell lymphomas (DLBCLs). However, the microRNAs profiles of primary cutaneous large B-cell lymphomas (PCLBCLs) are not yet described. Its two main subtypes, i.e., primary cutaneous diffuse large B-cell lymphoma, leg type (PCLBCL-LT) and primary cutaneous follicle center lymphoma (PCFCL) are characterized by an activated B-cell (ABC)-genotype and a germinal center B-cell (GCB)-genotype, respectively. We performed high-throughput sequencing analysis on frozen tumor biopsies from 19 cases of PCFCL and PCLBCL-LT to establish microRNA profiles. Cluster analysis of the complete microRNome could not distinguish between the two subtypes, but 16 single microRNAs were found to be differentially expressed. Single microRNA RT-qPCR was conducted on formalin-fixed paraffin-embedded tumor biopsies of 20 additional cases, confirming higher expression of miR-9-5p, miR-31-5p, miR-129-2-3p and miR-214-3p in PCFCL as compared to PCLBCL-LT. MicroRNAs previously described to be higher expressed in ABC-type as compared to GCB-type nodal DLBCL were not differentially expressed between PCFCL and PCLBCL-LT. In conclusion, PCFCL and PCLBCL-LT differ in their microRNA profiles. In contrast to their gene expression profile, they only show slight resemblance with the microRNA profiles found in GCB- and ABC-type nodal DLBCL. PMID:24358187

  15. Polychlorinated biphenyl exposure alters the expression profile of microRNAs associated with vascular diseases.

    PubMed

    Wahlang, Banrida; Petriello, Michael C; Perkins, Jordan T; Shen, Shu; Hennig, Bernhard

    2016-09-01

    Exposure to persistent organic pollutants, including polychlorinated biphenyls (PCBs) is correlated with multiple vascular complications including endothelial cell dysfunction and atherosclerosis. PCB-induced activation of the vasculature subsequently leads to oxidative stress and induction of pro-inflammatory cytokines and adhesion proteins. Gene expression of these cytokines/proteins is known to be regulated by small, endogenous oligonucleotides known as microRNAs that interact with messenger RNA. MicroRNAs are an acknowledged component of the epigenome, but the role of environmentally-driven epigenetic changes such as toxicant-induced changes in microRNA profiles is currently understudied. The objective of this study was to determine the effects of PCB exposure on microRNA expression profile in primary human endothelial cells using the commercial PCB mixture Aroclor 1260. Samples were analyzed using Affymetrix GeneChip® miRNA 4.0 arrays for high throughput detection and selected microRNA gene expression was validated (RT-PCR). Microarray analysis identified 557 out of 6658 microRNAs that were changed with PCB exposure (p<0.05). In-silico analysis using MetaCore database identified 21 of these microRNAs to be associated with vascular diseases. Further validation showed that Aroclor 1260 increased miR-21, miR-31, miR-126, miR-221 and miR-222 expression levels. Upregulated miR-21 has been reported in cardiac injury while miR-126 and miR-31 modulate inflammation. Our results demonstrated evidence of altered microRNA expression with PCB exposure, thus providing novel insights into mechanisms of PCB toxicity. PMID:27288564

  16. MicroRNA profiling of primary cutaneous large B-cell lymphomas.

    PubMed

    Koens, Lianne; Qin, Yongjun; Leung, Wai Y; Corver, Willem E; Jansen, Patty M; Willemze, Rein; Vermeer, Maarten H; Tensen, Cornelis P

    2013-01-01

    Aberrant expression of microRNAs is widely accepted to be pathogenetically involved in nodal diffuse large B-cell lymphomas (DLBCLs). However, the microRNAs profiles of primary cutaneous large B-cell lymphomas (PCLBCLs) are not yet described. Its two main subtypes, i.e., primary cutaneous diffuse large B-cell lymphoma, leg type (PCLBCL-LT) and primary cutaneous follicle center lymphoma (PCFCL) are characterized by an activated B-cell (ABC)-genotype and a germinal center B-cell (GCB)-genotype, respectively. We performed high-throughput sequencing analysis on frozen tumor biopsies from 19 cases of PCFCL and PCLBCL-LT to establish microRNA profiles. Cluster analysis of the complete microRNome could not distinguish between the two subtypes, but 16 single microRNAs were found to be differentially expressed. Single microRNA RT-qPCR was conducted on formalin-fixed paraffin-embedded tumor biopsies of 20 additional cases, confirming higher expression of miR-9-5p, miR-31-5p, miR-129-2-3p and miR-214-3p in PCFCL as compared to PCLBCL-LT. MicroRNAs previously described to be higher expressed in ABC-type as compared to GCB-type nodal DLBCL were not differentially expressed between PCFCL and PCLBCL-LT. In conclusion, PCFCL and PCLBCL-LT differ in their microRNA profiles. In contrast to their gene expression profile, they only show slight resemblance with the microRNA profiles found in GCB- and ABC-type nodal DLBCL. PMID:24358187

  17. Sensitive detection of melanoma metastasis using circulating microRNA expression profiles.

    PubMed

    Shiiyama, Rie; Fukushima, Satoshi; Jinnin, Masatoshi; Yamashita, Junji; Miyashita, Azusa; Nakahara, Satoshi; Kogi, Ai; Aoi, Jun; Masuguchi, Shinichi; Inoue, Yuji; Ihn, Hironobu

    2013-10-01

    Numerous studies have indicated that the serum levels of microRNAs are useful for the diagnosis or evaluation of activity in human diseases. However, determining the level of only one of the nearly 2000 microRNAs identified so far may be less significant. Accordingly, we examined the possibility that the expression pattern of multiple microRNAs in each patient may be a more reliable disease marker for melanoma, especially metastatic disease, focusing on the interaction among microRNAs. Six microRNAs (miR-9, miR-145, miR-150, miR-155, miR-203, and miR-205) were evaluated using real-time PCR in 11 patients with metastatic melanoma and in 16 patients without melanoma. The expression of the six microRNAs was significantly different between the patients with metastasis and those without it. MiR-9 and miR-205 and miR-203 and miR-205 showed significant correlations, and the combination of miR-9, miR-145, miR-150, miR-155, and miR-205 was more sensitive than when each miR was used individually to distinguish the patients with metastasis from those without it. This is the first report demonstrating the expression profiles of multiple microRNAs in melanoma patients. Clarifying the involvement of the microRNA network in the pathogenesis of melanoma may contribute to the development of new diagnostic tools and to advancing the understanding of this disease. PMID:23863473

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

    PubMed Central

    Virant-Klun, Irma; Ståhlberg, Anders; Kubista, Mikael; Skutella, Thomas

    2016-01-01

    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. PMID:26664407

  19. microRNAs as cancer biomarkers.

    PubMed

    Flatmark, Kjersti; Høye, Eirik; Fromm, Bastian

    2016-01-01

    Since their discovery in 1993, microRNAs (miRNAs) have been identified as important gene regulators in many biological processes and as key molecular players in human disease, including cancer where they show specific pathogenic deregulation. Their remarkable chemical stability, the availability of very sensitive miRNA detection methods and the fact that miRNAs can be extracted from and detected in various kinds of clinically relevant samples, such as solid tissues, body fluids and secretions make them excellent candidate biomarkers. However, no miRNA has yet entered the level of practical clinical relevance. We present a brief background and some key aspects and challenges of miRNAs as cancer biomarkers, we discuss shortfalls and identify possible routes towards the use of miRNAs as reliable biomarkers for cancer. PMID:27542003

  20. MicroRNAs as biomarkers in leukemia

    PubMed Central

    Wang, Xinxin; Zhu, Baohua; Huang, Zunnan; Chen, Liyong

    2014-01-01

    Current diagnostic and prognostic markers still exhibit biological limitation and seeking novel molecular biomarkers is crucial for early clinical diagnosis and in the development of novel strategies for leukemia therapy. Emerging evidence showed that dysregulated microRNAs (miRNAs) play important roles in cancer including leukemia. In this review, we summarized recent progress on the role of miRNAs in leukemia, mainly focusing on recent findings that suggest the potential of miRNAs as biomarkers for diagnosis and prognosis. Notably, the circulating miRNAs were also discussed for the fact that they can be detected in body fluids, and thus represent a novel source of promising biomarkers that may be applied to clinical settings.

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

    PubMed Central

    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 and computational analysis, validated using 3′-UTR-luciferase reporter plasmids. Protein levels were assessed by western blot and functional analysis by cell adhesion. Results We identified 990 known miRNAs and 1621 potential novel miRNAs in human osteoarthritic chondrocytes, 60 of the latter were expressed in all samples assayed. MicroRNA-140-3p was the most highly expressed microRNA in osteoarthritic cartilage. Sixteen novel candidate miRNAs were analysed further, of which six remained after northern blot analysis. Three novel miRNAs were regulated across models of chondrogenesis, chondrocyte differentiation or cartilage injury. One sequence (novel #11), annotated in rodents as microRNA-3085-3p, was preferentially expressed in cartilage, dependent on chondrocyte differentiation and, in man, is located in an intron of the cartilage-expressed gene CRTAC-1. This microRNA was shown to target the ITGA5 gene directly (which encodes integrin alpha5) and inhibited adhesion to fibronectin (dependent on alpha5beta1 integrin). Conclusion Deep sequencing has uncovered many potential microRNA candidates expressed in human cartilage. At least three of these show potential functional interest in cartilage homeostasis and osteoarthritis (OA). Particularly, novel #11 (microRNA-3085-3p) which has been identified for the first time in man. PMID:26497608

  2. Dense registration of CHRIS-Proba and Ikonos images using multi-dimensional mutual information maximization

    NASA Astrophysics Data System (ADS)

    Cariou, Claude; Chehdi, Kacem

    2013-10-01

    We investigate the potential of multidimensional mutual information for the registration of multi-spectral remote sensing images. We devise a gradient flow algorithm which iteratively maximizes the multidimensional mutual information with respect to a differentiable displacement map, accounting for partial derivatives of the multivariate joint distribution and the multivariate marginal of the float image with respect to each variable of the mutual information derivative. The resulting terms are shown to weight the band specific gradients of the warp image, and we propose in addition to compute them with a method based on the k-nearest neighbours. We apply our method to the registration of Ikonos and CHRIS-Proba images over the region of Baabdat, Lebanon, for purposes of cedar pines detection. A comparison between (crossed) single band and multi-band registration results obtained shows that using the multidimensional mutual information brings a significant gain in positional accuracy and is suitable for multispectral remote sensing image registration.

  3. MicroRNA involvement in glioblastoma pathogenesis

    SciTech Connect

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

    2009-08-14

    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.

  4. Hardware device binding and mutual authentication

    SciTech Connect

    Hamlet, Jason R; Pierson, Lyndon G

    2014-03-04

    Detection and deterrence of device tampering and subversion by substitution may be achieved by including a cryptographic unit within a computing device for binding multiple hardware devices and mutually authenticating the devices. The cryptographic unit includes a physically unclonable function ("PUF") circuit disposed in or on the hardware device, which generates a binding PUF value. The cryptographic unit uses the binding PUF value during an enrollment phase and subsequent authentication phases. During a subsequent authentication phase, the cryptographic unit uses the binding PUF values of the multiple hardware devices to generate a challenge to send to the other device, and to verify a challenge received from the other device to mutually authenticate the hardware devices.

  5. Automotive radar - investigation of mutual interference mechanisms

    NASA Astrophysics Data System (ADS)

    Goppelt, M.; Blöcher, H.-L.; Menzel, W.

    2010-09-01

    In the past mutual interference between automotive radar sensors has not been regarded as a major problem. With an increasing number of such systems, however, this topic is receiving more and more attention. The investigation of mutual interference and countermeasures is therefore one topic of the joint project "Radar on Chip for Cars" (RoCC) funded by the German Federal Ministry of Education and Research (BMBF). RoCC's goal is to pave the way for the development of high-performance, low-cost 79 GHz radar sensors based on Silicon-Germanium (SiGe) Monolithic Microwave Integrated Circuits (MMICs). This paper will present some generic interference scenarios and report on the current status of the analysis of interference mechanisms.

  6. 47 CFR 90.165 - Procedures for mutually exclusive applications.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... SPECIAL RADIO SERVICES PRIVATE LAND MOBILE RADIO SERVICES Applications and Authorizations Special Rules Governing Facilities Used to Provide Commercial Mobile Radio Services § 90.165 Procedures for mutually exclusive applications. Mutually exclusive commercial mobile radio service applications are processed...

  7. 47 CFR 90.165 - Procedures for mutually exclusive applications.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... SPECIAL RADIO SERVICES PRIVATE LAND MOBILE RADIO SERVICES Applications and Authorizations Special Rules Governing Facilities Used to Provide Commercial Mobile Radio Services § 90.165 Procedures for mutually exclusive applications. Mutually exclusive commercial mobile radio service applications are processed...

  8. 47 CFR 90.165 - Procedures for mutually exclusive applications.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... SPECIAL RADIO SERVICES PRIVATE LAND MOBILE RADIO SERVICES Applications and Authorizations Special Rules Governing Facilities Used to Provide Commercial Mobile Radio Services § 90.165 Procedures for mutually exclusive applications. Mutually exclusive commercial mobile radio service applications are processed...

  9. 47 CFR 90.165 - Procedures for mutually exclusive applications.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... SPECIAL RADIO SERVICES PRIVATE LAND MOBILE RADIO SERVICES Applications and Authorizations Special Rules Governing Facilities Used to Provide Commercial Mobile Radio Services § 90.165 Procedures for mutually exclusive applications. Mutually exclusive commercial mobile radio service applications are processed...

  10. 47 CFR 90.165 - Procedures for mutually exclusive applications.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... SPECIAL RADIO SERVICES PRIVATE LAND MOBILE RADIO SERVICES Applications and Authorizations Special Rules Governing Facilities Used to Provide Commercial Mobile Radio Services § 90.165 Procedures for mutually exclusive applications. Mutually exclusive commercial mobile radio service applications are processed...

  11. Frontotemporal Lobar Degeneration and MicroRNAs

    PubMed Central

    Piscopo, Paola; Albani, Diego; Castellano, Anna E.; Forloni, Gianluigi; Confaloni, Annamaria

    2016-01-01

    Frontotemporal lobar degeneration (FTLD) includes a spectrum of disorders characterized by changes of personality and social behavior 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 microRNAs (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. PMID:26903860

  12. Entanglement patterns in mutually unbiased basis sets

    SciTech Connect

    Lawrence, Jay

    2011-08-15

    A few simply stated rules govern the entanglement patterns that can occur in mutually unbiased basis sets (MUBs) and constrain the combinations of such patterns that can coexist in full complements of MUBs. We consider Hilbert spaces of prime power dimensions (D=p{sup N}), as realized by systems of N prime-state particles, where full complements of D+1 MUBs are known to exist, and we assume only that MUBs are eigenbases of generalized Pauli operators, without using any particular construction. The general rules include the following: (1) In any MUB, a given particle appears either in a pure state or totally entangled and (2) in any full MUB complement, each particle is pure in (p+1) bases (not necessarily the same ones) and totally entangled in the remaining (p{sup N}-p). It follows that the maximum number of product bases is p+1 and, when this number is realized, all remaining (p{sup N}-p) bases in the complement are characterized by the total entanglement of every particle. This ''standard distribution'' is inescapable for two-particle systems (of any p), where only product and generalized Bell bases are admissible MUB types. This and the following results generalize previous results for qubits [Phys. Rev. A 65. 032320 (2002); Phys. Rev. A 72, 062310 (2005)] and qutrits [Phys. Rev. A 70, 012302 (2004)], drawing particularly upon [Phys. Rev. A 72, 062310 (2005)]. With three particles there are three MUB types, and these may be combined in (p+2) different ways to form full complements. With N=4, there are 6 MUB types for p=2, but new MUB types become possible with larger p, and these are essential to realizing full complements. With this example, we argue that new MUB types that show new entanglement patterns should enter with every step in N and, also, when N is a prime plus 1, at a critical p value, p=N-1. Such MUBs should play critical roles in filling complements.

  13. MicroRNA-143/-145 in Cardiovascular Diseases

    PubMed Central

    Zhao, Wang; Zhao, Shui-Ping; Zhao, Yu-Hong

    2015-01-01

    MicroRNAs (miRNAs) play an essential role in the onset and development of many cardiovascular diseases. Increasing evidence shows that miRNAs can be used as potential diagnostic biomarkers for cardiovascular diseases, and miRNA-based therapy may be a promising therapy for the treatment of cardiovascular diseases. The microRNA-143/-145 (miR-143/-145) cluster is essential for differentiation of vascular smooth muscle cells (VSMCs) and determines VSMC phenotypic switching. In this review, we summarize the recent progress in knowledge concerning the function of miR-143/-145 in the cardiovascular system and their role in cardiovascular diseases. We discuss the potential role of miR-143/-145 as valuable biomarkers for cardiovascular diseases and explore the potential strategy of targeting miR-143 and miR-145. PMID:26221598

  14. Mutual synchronization of weakly coupled gyrotrons

    SciTech Connect

    Rozental, R. M.; Glyavin, M. Yu.; Sergeev, A. S.; Zotova, I. V.; Ginzburg, N. S.

    2015-09-15

    The processes of synchronization of two weakly coupled gyrotrons are studied within the framework of non-stationary equations with non-fixed longitudinal field structure. With the allowance for a small difference of the free oscillation frequencies of the gyrotrons, we found a certain range of parameters where mutual synchronization is possible while a high electronic efficiency is remained. It is also shown that synchronization regimes can be realized even under random fluctuations of the parameters of the electron beams.

  15. Combating isolation: Building mutual mentoring networks

    NASA Astrophysics Data System (ADS)

    Cox, Anne J.

    2015-12-01

    Women physicists can often feel isolated at work. Support from a grant through the ADVANCE program of the National Science Foundation (U.S. government funding) created mutual mentoring networks aimed at combating isolation specifically for women faculty at undergraduate-only institutions. This paper will discuss the organization of one such network, what contributed to its success, some of the outcomes, and how it might be implemented in other contexts.

  16. Asymmetric Mutualism in Two- and Three-Dimensional Range Expansions

    NASA Astrophysics Data System (ADS)

    Lavrentovich, Maxim O.; Nelson, David R.

    2014-04-01

    Genetic drift at the frontiers of two-dimensional range expansions of microorganisms can frustrate local cooperation between different genetic variants, demixing the population into distinct sectors. In a biological context, mutualistic or antagonistic interactions will typically be asymmetric between variants. By taking into account both the asymmetry and the interaction strength, we show that the much weaker demixing in three dimensions allows for a mutualistic phase over a much wider range of asymmetric cooperative benefits, with mutualism prevailing for any positive, symmetric benefit. We also demonstrate that expansions with undulating fronts roughen dramatically at the boundaries of the mutualistic phase, with severe consequences for the population genetics along the transition lines.

  17. Altered Spinal MicroRNA-146a and the MicroRNA-183 Cluster Contribute to Osteoarthritic Pain in Knee Joints

    PubMed Central

    Li, Xin; Kroin, Jeffrey S; Kc, Ranjan; Gibson, Gary; Chen, Di; Corbett, Grant T; Pahan, Kalipada; Fayyaz, Sana; Kim, Jae-Sung; van Wijnen, Andre J.; Suh, Joon; Kim, Su-Gwan; Im, Hee-Jeong

    2015-01-01

    Objective Examine whether altered expression of microRNAs in central nervous system components is pathologically linked to chronic knee joint pain in osteoarthritis. Methods A surgical animal model for knee joint OA was generated by medial meniscus transection in rats followed by behavioral pain tests. Relationships between pathological changes in knee joint and development of chronic joint pain were examined by histology and imaging analyses. Alterations in microRNAs associated with OA-evoked pain sensation were determined in bilateral lumbar dorsal root ganglia (DRG) and the spinal dorsal horn by microRNA array followed by individual microRNA analyses. Gain- and loss-of-function studies of selected microRNAs (miR-146a and miR-183 cluster) were conducted to identify target pain mediators regulated by these selective microRNAs in glial cells. Results The ipsilateral hind leg displayed significantly increased hyperalgesia after 4 weeks of surgery and sensitivity was sustained for the remainder of the 8 week experimental period (F=341, P<0.001). The development of OA-induced chronic pain was correlated with pathological changes in the knee joints as assessed by histological and imaging analyses. MicroRNA analyses showed that miR-146a and the miR-183 cluster were markedly reduced in the sensory neurons in DRG (L4/L5) and spinal cord from animals experiencing knee joint OA pain. The downregulation of miR-146a and/or the miR-183 cluster in the central compartments (DRG and spinal cord) are closely associated with the upregulation of inflammatory pain mediators. The corroboration between decreases in these signature microRNAs and their specific target pain mediators were further confirmed by gain- and loss-of-function analyses in glia, the major cellular component of the central nervous system (CNS). Conclusion MicroRNA therapy using miR-146a and the miR-183 cluster could be powerful therapeutic intervention for OA in alleviating joint pain and concomitantly regenerating

  18. 26 CFR 1.1502-42 - Mutual savings banks, etc.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 26 Internal Revenue 12 2012-04-01 2012-04-01 false Mutual savings banks, etc. 1.1502-42 Section 1... (CONTINUED) INCOME TAXES (CONTINUED) Special Taxes and Taxpayers § 1.1502-42 Mutual savings banks, etc. (a) In general. This section applies to mutual s avings banks and other institutions described in...

  19. 26 CFR 1.1502-42 - Mutual savings banks, etc.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 26 Internal Revenue 12 2014-04-01 2014-04-01 false Mutual savings banks, etc. 1.1502-42 Section 1... (CONTINUED) INCOME TAXES (CONTINUED) Special Taxes and Taxpayers § 1.1502-42 Mutual savings banks, etc. (a) In general. This section applies to mutual s avings banks and other institutions described in...

  20. 26 CFR 1.1502-42 - Mutual savings banks, etc.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 26 Internal Revenue 12 2013-04-01 2013-04-01 false Mutual savings banks, etc. 1.1502-42 Section 1... (CONTINUED) INCOME TAXES (CONTINUED) Special Taxes and Taxpayers § 1.1502-42 Mutual savings banks, etc. (a) In general. This section applies to mutual s avings banks and other institutions described in...

  1. 26 CFR 1.1502-42 - Mutual savings banks, etc.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 26 Internal Revenue 12 2011-04-01 2011-04-01 false Mutual savings banks, etc. 1.1502-42 Section 1... (CONTINUED) INCOME TAXES (CONTINUED) Special Taxes and Taxpayers § 1.1502-42 Mutual savings banks, etc. (a) In general. This section applies to mutual s avings banks and other institutions described in...

  2. 26 CFR 1.1502-42 - Mutual savings banks, etc.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 26 Internal Revenue 12 2010-04-01 2010-04-01 false Mutual savings banks, etc. 1.1502-42 Section 1... (CONTINUED) INCOME TAXES Special Taxes and Taxpayers § 1.1502-42 Mutual savings banks, etc. (a) In general. This section applies to mutual s avings banks and other institutions described in section 593(a)....

  3. 78 FR 26424 - Mutual Savings Association Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-06

    ... Office of the Comptroller of the Currency Mutual Savings Association Advisory Committee AGENCY: Office of... Mutual Savings Association Advisory Committee (MSAAC). DATES: A public meeting of the MSAAC will be held... savings associations, and other issues of concern to the existing mutual savings associations. On the...

  4. 77 FR 74052 - Mutual Savings Association Advisory Committee Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-12

    ... Office of the Comptroller of the Currency Mutual Savings Association Advisory Committee Meeting AGENCY... Mutual Savings Association Advisory Committee (MSAAC or Committee). DATES: A public meeting of the MSAAC... 8:30 a.m. EST. Agenda items include a discussion of the status of the mutual savings...

  5. An orb-weaver spider exploits an ant–acacia mutualism for enemy-free space

    PubMed Central

    Styrsky, John D

    2014-01-01

    Exploiters of protection mutualisms are assumed to represent an important threat for the stability of those mutualisms, but empirical evidence for the commonness or relevance of exploiters is limited. Here, I describe results from a manipulative study showing that an orb-weaver spider, Eustala oblonga, inhabits an ant-acacia for protection from predators. This spider is unique in the orb-weaver family in that it associates closely with both a specific host plant and ants. I tested the protective effect of acacia ants on E. oblonga by comparing spider abundance over time on acacias with ants and on acacias from which entire ant colonies were experimentally removed. Both juvenile and adult spider abundance significantly decreased over time on acacias without ants. Concomitantly, the combined abundance of potential spider predators increased over time on acacias without ants. These results suggest that ant protection of the ant-acacia Acacia melanocerus also protects the spiders, thus supporting the hypothesis that E. oblonga exploits the ant–acacia mutualism for enemy-free space. Although E. oblonga takes advantage of the protection services of ants, it likely exacts little to no cost and should not threaten the stability of the ant–acacia mutualism. Indeed, the potential threat of exploiter species to protection mutualisms in general may be limited to species that exploit the material rewards traded in such mutualisms rather than the protection services. PMID:24558583

  6. Evolutionary stability of mutualism: interspecific population regulation as an evolutionarily stable strategy

    USGS Publications Warehouse

    Holland, J. Nathaniel; DeAngelis, Donald L.; Schultz, Stewart T.

    2004-01-01

    Interspecific mutualisms are often vulnerable to instability because low benefit : cost ratios can rapidly lead to extinction or to the conversion of mutualism to parasite–host or predator–prey interactions. We hypothesize that the evolutionary stability of mutualism can depend on how benefits and costs to one mutualist vary with the population density of its partner, and that stability can be maintained if a mutualist can influence demographic rates and regulate the population density of its partner. We test this hypothesis in a model of mutualism with key features of senita cactus (Pachycereus schottii) – senita moth (Upiga virescens) interactions, in which benefits of pollination and costs of larval seed consumption to plant fitness depend on pollinator density. We show that plants can maximize their fitness by allocating resources to the production of excess flowers at the expense of fruit. Fruit abortion resulting from excess flower production reduces pre–adult survival of the pollinating seed–consumer, and maintains its density beneath a threshold that would destabilize the mutualism. Such a strategy of excess flower production and fruit abortion is convergent and evolutionarily stable against invasion by cheater plants that produce few flowers and abort few to no fruit. This novel mechanism of achieving evolutionarily stable mutualism, namely interspecific population regulation, is qualitatively different from other mechanisms invoking partner choice or selective rewards, and may be a general process that helps to preserve mutualistic interactions in nature.

  7. H19 derived microRNA-675 regulates cell proliferation and migration through CDK6 in glioma

    PubMed Central

    Li, Chao; Lei, Bingxi; Huang, Shuaibin; Zheng, Meiguang; Liu, Zhenghao; Li, Zhongjun; Deng, Yuefei

    2015-01-01

    The long non-coding RNA (LncRNA) H19 is one of the most highly abundant and conserved transcripts involved in the mammalian development and tumorigenesis. H19 is expressed in both embryonic cells and tumor cells, but its physical and pathological functions still need to be further studied. Our results showed that microRNA-675, a microRNA in the first exon of H19, expressed in glioma. Over-expression of microRNA-675 in a range of glioma cell lines resulted in their immoderate proliferation and migration. In addition, H19 derived microRNA-675 was down-regulated in the glioma, and CDK6, a pivotal regulator in cell cycle, was a target of microRNA-675. The survival of glioma patients with low CDK6 expression significantly increased as compared to patients with high CDK6 expression. Moreover, the CDK6 expression was inversely correlated with microRNA-675 expression in the glioma. Our results suggest that H19 derived microRNA-675 may regulate giloma cell proliferation and migration through CDK6, and predict a poor prognosis of glioma patients. PMID:26692922

  8. CRISPR/cas9, a novel genomic tool to knock down microRNA in vitro and in vivo.

    PubMed

    Chang, Hong; Yi, Bin; Ma, Ruixia; Zhang, Xiaoguo; Zhao, Hongyou; Xi, Yaguang

    2016-01-01

    MicroRNAs are small and non-coding RNA molecules with the master role in regulation of gene expression at post-transcriptional/translational levels. Many methods have been developed for microRNA loss-of-function study, such as antisense inhibitors and sponges; however, the robustness, specificity, and stability of these traditional strategies are not highly satisfied. CRISPR/cas9 system is emerging as a novel genome editing tool in biology/medicine research, but its indication in microRNA research has not been studied exclusively. In this study, we clone CRISPR/cas9 constructs with single-guide RNAs specifically targeting biogenesis processing sites of selected microRNAs; and we find that CRISPR/cas9 can robustly and specifically reduce the expression of these microRNAs up to 96%. CRISPR/cas9 also shows an exclusive benefit in control of crossing off-target effect on microRNAs in the same family or with highly conserved sequences. More significantly, for the first time, we demonstrate the long term stability of microRNA knockdown phenotype by CRISPR/cas9 in both in vitro and in vivo models. PMID:26924382

  9. miRepress: modelling gene expression regulation by microRNA with non-conventional binding sites

    PubMed Central

    Ghosal, Suman; Saha, Shekhar; Das, Shaoli; Sen, Rituparno; Goswami, Swagata; Jana, Siddhartha S.; Chakrabarti, Jayprokas

    2016-01-01

    Some earlier studies have reported an alternative mode of microRNA-target interaction. We detected target regions within mRNA transcripts from AGO PAR-CLIP that did not contain any conventional microRNA seed pairing but only had non-conventional binding sites with microRNA 3′ end. Our study from 7 set of data that measured global protein fold change after microRNA transfection pointed towards the association of target protein fold change with 6-mer and 7-mer target sites involving microRNA 3′ end. We developed a model to predict the degree of microRNA target regulation in terms of protein fold changes from the number of different conventional and non-conventional target sites present in the target, and found significant correlation of its output with protein expression changes. We validated the effect of non-conventional interactions with target by modulating the abundance of microRNA in a human breast cancer cell line MCF-7. The validation was done using luciferase assay and immunoblot analysis for our predicted non-conventional microRNA-target pair WNT1 (3′ UTR) and miR-367-5p and immunoblot analysis for another predicted non-conventional microRNA-target pair MYH10 (coding region) and miR-181a-5p. Both experiments showed inhibition of targets by transfection of microRNA mimics that were predicted to have only non-conventional sites. PMID:26923536

  10. Identification of a pan-cancer oncogenic microRNA superfamily anchored by a central core seed motif

    NASA Astrophysics Data System (ADS)

    Hamilton, Mark P.; Rajapakshe, Kimal; Hartig, Sean M.; Reva, Boris; McLellan, Michael D.; Kandoth, Cyriac; Ding, Li; Zack, Travis I.; Gunaratne, Preethi H.; Wheeler, David A.; Coarfa, Cristian; McGuire, Sean E.

    2013-11-01

    MicroRNAs modulate tumorigenesis through suppression of specific genes. As many tumour types rely on overlapping oncogenic pathways, a core set of microRNAs may exist, which consistently drives or suppresses tumorigenesis in many cancer types. Here we integrate The Cancer Genome Atlas (TCGA) pan-cancer data set with a microRNA target atlas composed of publicly available Argonaute Crosslinking Immunoprecipitation (AGO-CLIP) data to identify pan-tumour microRNA drivers of cancer. Through this analysis, we show a pan-cancer, coregulated oncogenic microRNA ‘superfamily’ consisting of the miR-17, miR-19, miR-130, miR-93, miR-18, miR-455 and miR-210 seed families, which cotargets critical tumour suppressors via a central GUGC core motif. We subsequently define mutations in microRNA target sites using the AGO-CLIP microRNA target atlas and TCGA exome-sequencing data. These combined analyses identify pan-cancer oncogenic cotargeting of the phosphoinositide 3-kinase, TGFβ and p53 pathways by the miR-17-19-130 superfamily members.

  11. CRISPR/cas9, a novel genomic tool to knock down microRNA in vitro and in vivo

    PubMed Central

    Chang, Hong; Yi, Bin; Ma, Ruixia; Zhang, Xiaoguo; Zhao, Hongyou; Xi, Yaguang

    2016-01-01

    MicroRNAs are small and non-coding RNA molecules with the master role in regulation of gene expression at post-transcriptional/translational levels. Many methods have been developed for microRNA loss-of-function study, such as antisense inhibitors and sponges; however, the robustness, specificity, and stability of these traditional strategies are not highly satisfied. CRISPR/cas9 system is emerging as a novel genome editing tool in biology/medicine research, but its indication in microRNA research has not been studied exclusively. In this study, we clone CRISPR/cas9 constructs with single-guide RNAs specifically targeting biogenesis processing sites of selected microRNAs; and we find that CRISPR/cas9 can robustly and specifically reduce the expression of these microRNAs up to 96%. CRISPR/cas9 also shows an exclusive benefit in control of crossing off-target effect on microRNAs in the same family or with highly conserved sequences. More significantly, for the first time, we demonstrate the long term stability of microRNA knockdown phenotype by CRISPR/cas9 in both in vitro and in vivo models. PMID:26924382

  12. Profiling Pre-MicroRNA and Mature MicroRNA Expressions Using a Single Microarray and Avoiding Separate Sample Preparation

    PubMed Central

    Gan, Lin; Denecke, Bernd

    2013-01-01

    Mature microRNA is a crucial component in the gene expression regulation network. At the same time, microRNA gene expression and procession is regulated in a precise and collaborated way. Pre-microRNAs mediate products during the microRNA transcription process, they can provide hints of microRNA gene expression regulation or can serve as alternative biomarkers. To date, little effort has been devoted to pre-microRNA expression profiling. In this study, three human and three mouse microRNA profile data sets, based on the Affymetrix miRNA 2.0 array, have been re-analyzed for both mature and pre-microRNA signals as a primary test of parallel mature/pre-microRNA expression profiling on a single platform. The results not only demonstrated a glimpse of pre-microRNA expression in human and mouse, but also the relationship of microRNA expressions between pre- and mature forms. The study also showed a possible application of currently available microRNA microarrays in profiling pre-microRNA expression in a time and cost effective manner.

  13. Gaining (mutual) information about quark/gluon discrimination

    NASA Astrophysics Data System (ADS)

    Larkoski, Andrew J.; Thaler, Jesse; Waalewijn, Wouter J.

    2014-11-01

    Discriminating quark jets from gluon jets is an important but challenging problem in jet substructure. In this paper, we use the concept of mutual information to illuminate the physics of quark/gluon tagging. Ideal quark/gluon separation requires only one bit of truth information, so even if two discriminant variables are largely uncorrelated, they can still share the same "truth overlap". Mutual information can be used to diagnose such situations, and thus determine which discriminant variables are redundant and which can be combined to improve performance. Using both parton showers and analytic resummation, we study a two-parameter family of generalized angularities, which includes familiar infrared and collinear (IRC) safe observables like thrust and broadening, as well as IRC unsafe variants like p {/T D } and hadron multiplicity. At leading-logarithmic (LL) order, the bulk of these variables exhibit Casimir scaling, such that their truth overlap is a universal function of the color factor ratio C A /C F . Only at next-to-leading-logarithmic (NLL) order can one see a difference in quark/gluon performance. For the IRC safe angularities, we show that the quark/gluon performance can be improved by combining angularities with complementary angular exponents. Interestingly, LL order, NLL order, Pythia 8, and Herwig++ all exhibit similar correlations between observables, but there are significant differences in the predicted quark/gluon discrimination power. For the IRC unsafe angularities, we show that the mutual information can be calculated analytically with the help of a nonperturbative "weighted-energy function", providing evidence for the complementarity of safe and unsafe observables for quark/gluon discrimination.

  14. MicroRNA-34b promoter hypermethylation induces CREB overexpression and contributes to myeloid transformation.

    PubMed

    Pigazzi, Martina; Manara, Elena; Bresolin, Silvia; Tregnago, Claudia; Beghin, Alessandra; Baron, Emma; Giarin, Emanuela; Cho, Er-Chieh; Masetti, Riccardo; Rao, Dinesh S; Sakamoto, Kathleen M; Basso, Giuseppe

    2013-04-01

    MicroRNA-34b down-regulation in acute myeloid leukemia was previously shown to induce CREB overexpression, thereby causing leukemia proliferation in vitro and in vivo. The role of microRNA-34b and CREB in patients with myeloid malignancies has never been evaluated. We examined microRNA-34b expression and the methylation status of its promoter in cells from patients diagnosed with myeloid malignancies. We used gene expression profiling to identify signatures of myeloid transformation. We established that microRNA-34b has suppressor ability and that CREB has oncogenic potential in primary bone marrow cell cultures and in vivo. MicroRNA-34b was found to be up-regulated in pediatric patients with juvenile myelomonocytic leukemia (n=17) and myelodysplastic syndromes (n=28), but was down-regulated in acute myeloid leukemia patients at diagnosis (n=112). Our results showed that hypermethylation of the microRNA-34b promoter occurred in 66% of cases of acute myeloid leukemia explaining the low microRNA-34b levels and CREB overexpression, whereas preleukemic myelodysplastic syndromes and juvenile myelomonocytic leukemia were not associated with hypermethylation or CREB overexpression. In paired samples taken from the same patients when they had myelodysplastic syndrome and again during the subsequent acute myeloid leukemia, we confirmed microRNA-34b promoter hypermethylation at leukemia onset, with 103 CREB target genes differentially expressed between the two disease stages. This subset of CREB targets was confirmed to associate with high-risk myelodysplastic syndromes in a separate cohort of patients (n=20). Seventy-eight of these 103 CREB targets were also differentially expressed between healthy samples (n=11) and de novo acute myeloid leukemia (n=72). Further, low microRNA-34b and high CREB expression levels induced aberrant myelopoiesis through CREB-dependent pathways in vitro and in vivo. In conclusion, we suggest that microRNA-34b controls CREB expression and

  15. MicroRNA Regulation of Epithelial to Mesenchymal Transition.

    PubMed

    Abba, Mohammed L; Patil, Nitin; Leupold, Jörg Hendrik; Allgayer, Heike

    2016-01-01

    Epithelial to mesenchymal transition (EMT) is a central regulatory program that is similar in many aspects to several steps of embryonic morphogenesis. In addition to its physiological role in tissue repair and wound healing, EMT contributes to chemo resistance, metastatic dissemination and fibrosis, amongst others. Classically, the morphological change from epithelial to mesenchymal phenotype is characterized by the appearance or loss of a group of proteins which have come to be recognized as markers of the EMT process. As with all proteins, these molecules are controlled at the transcriptional and translational level by transcription factors and microRNAs, respectively. A group of developmental transcription factors form the backbone of the EMT cascade and a large body of evidence shows that microRNAs are heavily involved in the successful coordination of mesenchymal transformation and vice versa, either by suppressing the expression of different groups of transcription factors, or otherwise acting as their functional mediators in orchestrating EMT. This article dissects the contribution of microRNAs to EMT and analyzes the molecular basis for their roles in this cellular process. Here, we emphasize their interaction with core transcription factors like the zinc finger enhancer (E)-box binding homeobox (ZEB), Snail and Twist families as well as some pluripotency transcription factors. PMID:26784241

  16. Silencing microRNA-155 ameliorates experimental autoimmune encephalomyelitis.

    PubMed

    Murugaiyan, Gopal; Beynon, Vanessa; Mittal, Akanksha; Joller, Nicole; Weiner, Howard L

    2011-09-01

    IFN-γ-producing Th1 and IL-17-producing Th17 cells are the key participants in various autoimmune diseases, including multiple sclerosis and its animal model, experimental autoimmune encephalomyelitis (EAE). Although both of these T cell subsets are known to be regulated by specific transcription factors and cytokines, the role of microRNAs that control these two inflammatory T cell subsets and whether targeting microRNAs can have therapeutic effects are not known. In this study, we show that microRNA-155 (Mir-155) expression is elevated in CD4(+) T cells during EAE, and Mir-155(-/-) mice had a delayed course and reduced severity of disease and less inflammation in the CNS. The attenuation of EAE in Mir-155(-/-) mice was associated with a decrease in Th1 and Th17 responses in the CNS and peripheral lymphoid organs. The T cell-intrinsic function of Mir-155(-/-) was demonstrated by the resistance of Mir-155(-/-) CD4(+) T cell-repleted Rag-1(-/-) mice to EAE. Finally, we found that anti-Mir-155 treatment reduced clinical severity of EAE when given before and after the appearance of clinical symptoms. These findings demonstrate that Mir-155 confers susceptibility to EAE by affecting inflammatory T cell responses and identify Mir-155 as a new target for therapeutic intervention in multiple sclerosis. PMID:21788439

  17. MicroRNA Regulation of Epithelial to Mesenchymal Transition

    PubMed Central

    Abba, Mohammed L.; Patil, Nitin; Leupold, Jörg Hendrik; Allgayer, Heike

    2016-01-01

    Epithelial to mesenchymal transition (EMT) is a central regulatory program that is similar in many aspects to several steps of embryonic morphogenesis. In addition to its physiological role in tissue repair and wound healing, EMT contributes to chemo resistance, metastatic dissemination and fibrosis, amongst others. Classically, the morphological change from epithelial to mesenchymal phenotype is characterized by the appearance or loss of a group of proteins which have come to be recognized as markers of the EMT process. As with all proteins, these molecules are controlled at the transcriptional and translational level by transcription factors and microRNAs, respectively. A group of developmental transcription factors form the backbone of the EMT cascade and a large body of evidence shows that microRNAs are heavily involved in the successful coordination of mesenchymal transformation and vice versa, either by suppressing the expression of different groups of transcription factors, or otherwise acting as their functional mediators in orchestrating EMT. This article dissects the contribution of microRNAs to EMT and analyzes the molecular basis for their roles in this cellular process. Here, we emphasize their interaction with core transcription factors like the zinc finger enhancer (E)-box binding homeobox (ZEB), Snail and Twist families as well as some pluripotency transcription factors. PMID:26784241

  18. Transcriptome dynamics of the microRNA inhibition response.

    PubMed

    Wen, Jiayu; Leucci, Elenora; Vendramin, Roberto; Kauppinen, Sakari; Lund, Anders H; Krogh, Anders; Parker, Brian J

    2015-07-27

    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 miR-9 inhibition inducing a multiphasic transcriptome response, with a direct target perturbation before 4 h, earlier than previously reported, amplified by a downstream peak at ∼32 h consistent with an indirect response due to secondary coherent regulation. Predictive modelling indicates a major role for miR-9 in post-transcriptional control of RNA processing and RNA binding protein regulation. Cluster analysis identifies multiple co-regulated gene regulatory modules. Functionally, we observe a shift over time from mRNA processing at early time points to translation at later time points. We 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. PMID:26089393

  19. Stage-Specific MicroRNAs and Their Role in the Anticancer Effects of Calorie Restriction in a Rat Model of ER-Positive Luminal Breast Cancer.

    PubMed

    Devlin, Kaylyn L; Sanford, Tiffany; Harrison, Lauren M; LeBourgeois, Paul; Lashinger, Laura M; Mambo, Elizabeth; Hursting, Stephen D

    2016-01-01

    MicroRNAs have emerged as ubiquitous post-transcriptional regulators that coordinate many fundamental processes within cells, including those commonly linked to cancer when dysregulated. Profiling microRNAs across stages of cancer progression provides focus as to which microRNAs are key players in cancer development and are therefore important to manipulate with interventions to delay cancer onset and progression. Calorie restriction is one of the most effective preventive interventions across many types of cancer, although its effects on microRNAs have not been well characterized. We used the dimethylbenz[a]-anthracene-induced model of luminal mammary cancer in Sprague Dawley rats to elucidate which microRNAs are linked to progression in this type of cancer and, subsequently, to study how calorie restriction affects such microRNAs. We identified eight microRNAs (miR-10a, miR-10b, miR-21, miR-124, miR-125b, miR-126, miR-145 and miR-200a) to be associated with DMBA-induced mammary tumor progression. Calorie restriction, which greatly increased tumor-free survival and decreased the overall size of tumors that did develop, significantly decreased the expression of one microRNA, miR-200a, which was positively associated with tumor progression. We further showed that inhibition of miR-200a function, mimicking the effect of calorie restriction on this microRNA, inhibited proliferation in both rat (LA7) and human (MCF7) luminal mammary cancer cell lines. These findings present, for the first time, a stage-specific profile of microRNAs in a rodent model of luminal mammary cancer. Furthermore, we have identified the regulation of miR-200a, a microRNA that is positively associated with progression in this model, as a possible mechanism contributing to the anticancer effects of calorie restriction. PMID:27433802

  20. Stage-Specific MicroRNAs and Their Role in the Anticancer Effects of Calorie Restriction in a Rat Model of ER-Positive Luminal Breast Cancer

    PubMed Central

    Devlin, Kaylyn L.; Sanford, Tiffany; Harrison, Lauren M.; LeBourgeois, Paul; Lashinger, Laura M.; Mambo, Elizabeth; Hursting, Stephen D.

    2016-01-01

    MicroRNAs have emerged as ubiquitous post-transcriptional regulators that coordinate many fundamental processes within cells, including those commonly linked to cancer when dysregulated. Profiling microRNAs across stages of cancer progression provides focus as to which microRNAs are key players in cancer development and are therefore important to manipulate with interventions to delay cancer onset and progression. Calorie restriction is one of the most effective preventive interventions across many types of cancer, although its effects on microRNAs have not been well characterized. We used the dimethylbenz[a]-anthracene-induced model of luminal mammary cancer in Sprague Dawley rats to elucidate which microRNAs are linked to progression in this type of cancer and, subsequently, to study how calorie restriction affects such microRNAs. We identified eight microRNAs (miR-10a, miR-10b, miR-21, miR-124, miR-125b, miR-126, miR-145 and miR-200a) to be associated with DMBA-induced mammary tumor progression. Calorie restriction, which greatly increased tumor-free survival and decreased the overall size of tumors that did develop, significantly decreased the expression of one microRNA, miR-200a, which was positively associated with tumor progression. We further showed that inhibition of miR-200a function, mimicking the effect of calorie restriction on this microRNA, inhibited proliferation in both rat (LA7) and human (MCF7) luminal mammary cancer cell lines. These findings present, for the first time, a stage-specific profile of microRNAs in a rodent model of luminal mammary cancer. Furthermore, we have identified the regulation of miR-200a, a microRNA that is positively associated with progression in this model, as a possible mechanism contributing to the anticancer effects of calorie restriction. PMID:27433802

  1. Ultrasensitive electrochemical detection of microRNA with star trigon structure and endonuclease mediated signal amplification.

    PubMed

    Miao, Peng; Wang, Bidou; Yu, Zhiqiang; Zhao, Jing; Tang, Yuguo

    2015-01-15

    MicroRNAs play important roles in gene regulation. They can be used as effective biomarkers for diagnosis and prognosis of diseases like cancers. Due to their intrinsic properties of short length, low abundance and sequence homology among family members, it is difficult to realize sensitive and selective detection with economical use of time and cost. Herein, we report an ultrasensitive electrochemical method for microRNA analysis employing two oligonucleotides and one endonuclease. Generally, a glassy carbon electrode is first covered with gold nanoparticles (AuNPs) mediated by poly(diallyldimethylammonium chloride) (PDDA). Then, thiolated capture probe (CP) with methylene blue (MB) labeled at 5' end is modified on the pretreated electrode. Hybridization occurs among target microRNA, CP and auxiliary probe (AP), forming a star trigon structure on the electrode surface. Subsequently, endonuclease recognizes and cleaves CP on CP/AP duplex, releasing microRNA and AP back to the solution. The two regenerated elements can then form another star trigon with other CP molecules, initiating cycles of CP cleavage and MB departure. Significant decrease of electrochemical signals is thus observed, which can be used to reflect the concentration of microRNA. This proposed method has a linear response to microRNA in a wide range from 100 aM to 1 nM and the sensitivity of attomolar level can be achieved. Moreover, it has high selectivity against single-base mismatch sequences and can be used directly in serum samples. Therefore, this method shows great feasibility for the detection of microRNA and may have potential applications in cancer diagnosis and prognosis. PMID:25127470

  2. Systematic analysis of the regulatory functions of microRNAs in chicken hepatic lipid metabolism

    PubMed Central

    Li, Hong; Ma, Zheng; Jia, Lijuan; Li, Yanmin; Xu, Chunlin; Wang, Taian; Han, Ruili; Jiang, Ruirui; Li, Zhuanjian; Sun, Guirong; Kang, Xiangtao; Liu, Xiaojun

    2016-01-01

    Laying performance is an important economic trait in hens, and this physiological process is largely influenced by the liver function. The livers of hens at 20- and 30-week-old stages were investigated using the next generation sequencing to identify the differences of microRNA expression profiles. Compared with the 20-week-old hens, 67 down- and 13 up-regulated microRNAs were verified to be significant differentially expressed (false discovery rate, FDR ≤ 0.05) (SDE) in the 30-week-old. We also identified 13 down- and 6 up-regulated novel differentially expressed (DE) microRNAs. miR-22-3p and miR-146b-5p, which exhibit critical roles in mammalian lipid metabolism, showed the most abundant expression and the highest fold-change, respectively. A total of 648 potential target genes of the SDE microRNAs were identified through an integrated analysis of microRNAs and the DE genes obtained in previous RNA-sequencing, including FADS1, FADS2, ELOVL6 and ACSL5, which are critical lipid metabolism-related regulators. Bioinformatic analyses revealed that target genes were mainly enriched in lipid-related metabolism processes. This work provides the first study of the expression patterns of hepatic microRNAs between 20- and 30-week old hens. The findings may serve as a fundamental resource for understanding the detailed functions of microRNAs in the molecular regulatory systems of lipid metabolism. PMID:27535581

  3. Systematic analysis of the regulatory functions of microRNAs in chicken hepatic lipid metabolism.

    PubMed

    Li, Hong; Ma, Zheng; Jia, Lijuan; Li, Yanmin; Xu, Chunlin; Wang, Taian; Han, Ruili; Jiang, Ruirui; Li, Zhuanjian; Sun, Guirong; Kang, Xiangtao; Liu, Xiaojun

    2016-01-01

    Laying performance is an important economic trait in hens, and this physiological process is largely influenced by the liver function. The livers of hens at 20- and 30-week-old stages were investigated using the next generation sequencing to identify the differences of microRNA expression profiles. Compared with the 20-week-old hens, 67 down- and 13 up-regulated microRNAs were verified to be significant differentially expressed (false discovery rate, FDR ≤ 0.05) (SDE) in the 30-week-old. We also identified 13 down- and 6 up-regulated novel differentially expressed (DE) microRNAs. miR-22-3p and miR-146b-5p, which exhibit critical roles in mammalian lipid metabolism, showed the most abundant expression and the highest fold-change, respectively. A total of 648 potential target genes of the SDE microRNAs were identified through an integrated analysis of microRNAs and the DE genes obtained in previous RNA-sequencing, including FADS1, FADS2, ELOVL6 and ACSL5, which are critical lipid metabolism-related regulators. Bioinformatic analyses revealed that target genes were mainly enriched in lipid-related metabolism processes. This work provides the first study of the expression patterns of hepatic microRNAs between 20- and 30-week old hens. The findings may serve as a fundamental resource for understanding the detailed functions of microRNAs in the molecular regulatory systems of lipid metabolism. PMID:27535581

  4. Aggressive mimicry coexists with mutualism in an aphid.

    PubMed

    Salazar, Adrián; Fürstenau, Benjamin; Quero, Carmen; Pérez-Hidalgo, Nicolás; Carazo, Pau; Font, Enrique; Martínez-Torres, David

    2015-01-27

    Understanding the evolutionary transition from interspecific exploitation to cooperation is a major challenge in evolutionary biology. Ant-aphid relationships represent an ideal system to this end because they encompass a coevolutionary continuum of interactions ranging from mutualism to antagonism. In this study, we report an unprecedented interaction along this continuum: aggressive mimicry in aphids. We show that two morphs clonally produced by the aphid Paracletus cimiciformis during its root-dwelling phase establish relationships with ants at opposite sides of the mutualism-antagonism continuum. Although one of these morphs exhibits the conventional trophobiotic (mutualistic) relationship with ants of the genus Tetramorium, aphids of the alternative morph are transported by the ants to their brood chamber and cared for as if they were true ant larvae. Gas chromatography-mass spectrometry analyses reveal that the innate cuticular hydrocarbon profile of the mimic morph resembles the profile of ant larvae more than that of the alternative, genetically identical nonmimic morph. Furthermore, we show that, once in the brood chamber, mimic aphids suck on ant larva hemolymph. These results not only add aphids to the limited list of arthropods known to biosynthesize the cuticular chemicals of their deceived hosts to exploit their resources but describe a remarkable case of plastic aggressive mimicry. The present work adds a previously unidentified dimension to the classical textbook paradigm of aphid-ant relationships by showcasing a complex system at the evolutionary interface between cooperation and exploitation. PMID:25583474

  5. Water Stress Strengthens Mutualism Among Ants, Trees, and Scale Insects

    PubMed Central

    Pringle, Elizabeth G.; Akçay, Erol; Raab, Ted K.; Dirzo, Rodolfo; Gordon, Deborah M.

    2013-01-01

    Abiotic environmental variables strongly affect the outcomes of species interactions. For example, mutualistic interactions between species are often stronger when resources are limited. The effect might be indirect: water stress on plants can lead to carbon stress, which could alter carbon-mediated plant mutualisms. In mutualistic ant–plant symbioses, plants host ant colonies that defend them against herbivores. Here we show that the partners' investments in a widespread ant–plant symbiosis increase with water stress across 26 sites along a Mesoamerican precipitation gradient. At lower precipitation levels, Cordia alliodora trees invest more carbon in Azteca ants via phloem-feeding scale insects that provide the ants with sugars, and the ants provide better defense of the carbon-producing leaves. Under water stress, the trees have smaller carbon pools. A model of the carbon trade-offs for the mutualistic partners shows that the observed strategies can arise from the carbon costs of rare but extreme events of herbivory in the rainy season. Thus, water limitation, together with the risk of herbivory, increases the strength of a carbon-based mutualism. PMID:24223521

  6. An invasive slug exploits an ant-seed dispersal mutualism.

    PubMed

    Meadley Dunphy, Shannon A; Prior, Kirsten M; Frederickson, Megan E

    2016-05-01

    Plant-animal mutualisms, such as seed dispersal, are often vulnerable to disruption by invasive species. Here, we show for the first time how a non-ant invasive species negatively affects seed dispersal by ants. We examined the effects of several animal species that co-occur in a temperate deciduous forest-including native and invasive seed-dispersing ants (Aphaenogaster rudis and Myrmica rubra, respectively), an invasive slug (Arion subfuscus), and native rodents-on a native myrmecochorous plant, Asarum canadense. We experimentally manipulated ant, slug, and rodent access to seed depots and measured seed removal. We also video-recorded depots to determine which other taxa interact with seeds. We found that A. rudis was the main disperser of seeds and that A. subfuscus consumed elaiosomes without dispersing seeds. Rodent visitation was rare, and rodent exclusion had no significant effect on seed or elaiosome removal. We then used data obtained from laboratory and field mesocosm experiments to determine how elaiosome robbing by A. subfuscus affects seed dispersal by A. rudis and M. rubra. We found that elaiosome robbing by slugs reduced seed dispersal by ants, especially in mesocosms with A. rudis, which picks up seeds more slowly than M. rubra. Taken together, our results show that elaiosome robbing by an invasive slug reduces seed dispersal by ants, suggesting that invasive slugs can have profound negative effects on seed dispersal mutualisms. PMID:26830293

  7. Gap junctions modulate glioma invasion by direct transfer of microRNA.

    PubMed

    Hong, Xiaoting; Sin, Wun Chey; Harris, Andrew L; Naus, Christian C

    2015-06-20

    The invasiveness of high-grade glioma is the primary reason for poor survival following treatment. Interaction between glioma cells and surrounding astrocytes are crucial to invasion. We investigated the role of gap junction mediated miRNA transfer in this context. By manipulating gap junctions with a gap junction inhibitor, siRNAs, and a dominant negative connexin mutant, we showed that functional glioma-glioma gap junctions suppress glioma invasion while glioma-astrocyte and astrocyte-astrocyte gap junctions promote it in an in vitro transwell invasion assay. After demonstrating that glioma-astrocyte gap junctions are permeable to microRNA, we compared the microRNA profiles of astrocytes before and after co-culture with glioma cells, identifying specific microRNAs as candidates for transfer through gap junctions from glioma cells to astrocytes. Further analysis showed that transfer of miR-5096 from glioma cells to astrocytes is through gap junctions; this transfer is responsible, in part, for the pro-invasive effect. Our results establish a role for glioma-astrocyte gap junction mediated microRNA signaling in modulation of glioma invasive behavior, and that gap junction coupling among astrocytes magnifies the pro-invasive signaling. Our findings reveal the potential for therapeutic interventions based on abolishing alteration of stromal cells by tumor cells via manipulation of microRNA and gap junction channel activity. PMID:25978028

  8. MicroRNA levels quantified in whole blood varies from PBMCs

    PubMed Central

    Atarod, Sadaf; Smith, Hannah; Dickinson, Anne; Wang, Xiao-Nong

    2015-01-01

    MicroRNAs are non-coding RNAs that negatively regulate mRNA expression and play significant roles in both health and disease. Differential microRNA expression has been used to aid diagnosis and discriminate disease stages. The accuracy and reliability of microRNA expression measurement is of utmost importance. Quantification of microRNA expression in human peripheral blood is commonly detected using total RNA extracted via different methods. To date, no convincing data are available showing whether microRNA quantification results can be influenced by the use of total RNA extracted from whole blood or peripheral blood mononuclear cells (PBMCs). This study examined miR-146a-5p and miR-155-5p expression using total RNA extracted in parallel from whole blood and PBMCs of 14 healthy volunteers. The data showed that the quantification of miRNA using total RNA extracted from whole blood varied from that of PBMCs, indicating that the miRNA expression was a result of all the different cell-types present in whole blood. Our results suggested that the source of total RNA and the statistical analyses performed are crucial considerations when designing miRNA research. PMID:26500764

  9. Partner selection in the mycorrhizal mutualism.

    PubMed

    Werner, Gijsbert D A; Kiers, E Toby

    2015-03-01

    Partner selection in the mycorrhizal symbiosis is thought to be a key factor stabilising the mutualism. Both plant hosts and mycorrhizal fungi have been shown to preferentially allocate resources to higher quality partners. This can help maintain underground cooperation, although it is likely that different plant species vary in the spatial precision with which they can select partners. Partner selection in the mycorrhizal symbiosis is presumably context-dependent and can be mediated by factors like (relative) resource abundance and resource fluctuations, competition among mycorrhizas, arrival order and cultivation history. Such factors complicate our current understanding of the importance of partner selection and its effectiveness in stimulating mutualistic cooperation. PMID:25421912

  10. Arithmetic, mutually unbiased bases and complementary observables

    NASA Astrophysics Data System (ADS)

    Sheppeard, M. D.

    2010-02-01

    Complementary observables in quantum mechanics may be viewed as Frobenius structures in a dagger monoidal category, such as the category of finite dimensional Hilbert spaces over the complex numbers. On the other hand, their properties crucially depend on the discrete Fourier transform and its associated quantum torus, requiring only the finite fields that underlie mutually unbiased bases. In axiomatic topos theory, the complex numbers are difficult to describe and should not be invoked unnecessarily. This paper surveys some fundamentals of quantum arithmetic using finite field complementary observables, with a view considering more general axiom systems.

  11. MicroRNAs and oncolytic viruses.

    PubMed

    Ruiz, Autumn J; Russell, Stephen J

    2015-08-01

    MicroRNAs regulate gene expression in mammalian cells and often exhibit tissue-specific expression patterns. Incorporation of microRNA target sequences can be used to control exogenous gene expression and viral tropism in specific tissues to enhance the therapeutic indices of oncolytic viruses expressing therapeutic transgenes. Continued development of this targeting strategy has resulted in the generation of unattenuated oncolytic viruses with enhanced potency, broad species-tropisms and reduced off-target toxicities in multiple-tissues simultaneously. Furthermore, oncolytic viruses have been used to enhance the delivery, duration and therapeutic efficacy of microRNA-based therapeutics designed to either restore or inhibit the function of dysregulated microRNAs in cancer cells. Recent efforts focused on combining oncolytic virotherapy and microRNA regulation have generated increasingly potent and safe cancer therapeutics. PMID:25863717

  12. MicroRNA in intervertebral disc degeneration.

    PubMed

    Li, Zheng; Yu, Xin; Shen, Jianxiong; Chan, Matthew T V; Wu, William Ka Kei

    2015-06-01

    Aetiology of intervertebral disc degeneration (IDD) is complex, with genetic, developmental, biochemical and biomechanical factors contributing to the disease process. It is becoming obvious that epigenetic processes influence evolution of IDD as strongly as the genetic background. Deregulated phenotypes of nucleus pulposus cells, including differentiation, migration, proliferation and apoptosis, are involved in all stages of progression of human IDD. Non-coding RNAs, including microRNAs, have recently been recognized as important regulators of gene expression. Research into roles of microRNAs in IDD has been very active over the past 5 years. Our review summarizes current research enlightenment towards understanding roles of microRNAs in regulating nucleus pulposus cell functions in IDD. These exciting findings support the notion that specific modulation of microRNAs may represent an attractive approach for management of IDD. PMID:25736871

  13. MicroRNA-146a suppresses ROCK1 allowing hyperphosphorylation of tau in Alzheimer’s disease

    PubMed Central

    Wang, Gang; Huang, Yue; Wang, Li-Ling; Zhang, Yong-Fang; Xu, Jing; Zhou, Yi; Lourenco, Guinevere F.; Zhang, Bei; Wang, Ying; Ren, Ru-Jing; Halliday, Glenda M.; Chen, Sheng-Di

    2016-01-01

    MicroRNA-146a is upregulated in the brains of patients with Alzheimer’s disease (AD). Here, we show that the rho-associated, coiled-coil containing protein kinase 1 (ROCK1) is a target of microRNA-146a in neural cells. Knockdown of ROCK1 mimicked the effects of microRNA-146a overexpression and induced abnormal tau phosphorylation, which was associated with inhibition of phosphorylation of the phosphatase and tensin homolog (PTEN). The ROCK1/PTEN pathway has been implicated in the neuronal hyperphosphorylation of tau that occurs in AD. To determine the function of ROCK1 in AD, brain tissue from 17 donors with low, intermediate or high probability of AD pathology were obtained and analyzed. Data showed that ROCK1 protein levels were reduced and ROCK1 colocalised with hyperphosphorylated tau in early neurofibrillary tangles. Intra-hippocampal delivery of a microRNA-146a specific inhibitor (antagomir) into 5xFAD mice showed enhanced hippocampal levels of ROCK1 protein and repressed tau hyperphosphorylation, partly restoring memory function in the 5xFAD mice. Our in vitro and in vivo results confirm that dysregulation of microRNA-146a biogenesis contributes to tau hyperphosphorylation and AD pathogenesis, and inhibition of this microRNA could be a viable novel in vivo therapy for AD. PMID:27221467

  14. Computational Systems Biology Approach Predicts Regulators and Targets of microRNAs and Their Genomic Hotspots in Apoptosis Process.

    PubMed

    Alanazi, Ibrahim O; Ebrahimie, Esmaeil

    2016-07-01

    Novel computational systems biology tools such as common targets analysis, common regulators analysis, pathway discovery, and transcriptomic-based hotspot discovery provide new opportunities in understanding of apoptosis molecular mechanisms. In this study, after measuring the global contribution of microRNAs in the course of apoptosis by Affymetrix platform, systems biology tools were utilized to obtain a comprehensive view on the role of microRNAs in apoptosis process. Network analysis and pathway discovery highlighted the crosstalk between transcription factors and microRNAs in apoptosis. Within the transcription factors, PRDM1 showed the highest upregulation during the course of apoptosis, with more than 9-fold expression increase compared to non-apoptotic condition. Within the microRNAs, MIR1208 showed the highest expression in non-apoptotic condition and downregulated by more than 6 fold during apoptosis. Common regulators algorithm showed that TNF receptor is the key upstream regulator with a high number of regulatory interactions with the differentially expressed microRNAs. BCL2 and AKT1 were the key downstream targets of differentially expressed microRNAs. Enrichment analysis of the genomic locations of differentially expressed microRNAs led us to the discovery of chromosome bands which were highly enriched (p < 0.01) with the apoptosis-related microRNAs, such as 13q31.3, 19p13.13, and Xq27.3 This study opens a new avenue in understanding regulatory mechanisms and downstream functions in the course of apoptosis as well as distinguishing genomic-enriched hotspots for apoptosis process. PMID:27178576

  15. Generalized mutual information of quantum critical chains

    NASA Astrophysics Data System (ADS)

    Alcaraz, F. C.; Rajabpour, M. A.

    2015-04-01

    We study the generalized mutual information I˜n of the ground state of different critical quantum chains. The generalized mutual information definition that we use is based on the well established concept of the Rényi divergence. We calculate this quantity numerically for several distinct quantum chains having either discrete Z (Q ) symmetries (Q -state Potts model with Q =2 ,3 ,4 and Z (Q ) parafermionic models with Q =5 ,6 ,7 ,8 and also Ashkin-Teller model with different anisotropies) or the U (1 ) continuous symmetries (Klein-Gordon field theory, X X Z and spin-1 Fateev-Zamolodchikov quantum chains with different anisotropies). For the spin chains these calculations were done by expressing the ground-state wave functions in two special bases. Our results indicate some general behavior for particular ranges of values of the parameter n that defines I˜n. For a system, with total size L and subsystem sizes ℓ and L -ℓ , the I˜n has a logarithmic leading behavior given by c/˜n4 log[L/π sin(π/ℓ L ) ] where the coefficient c˜n is linearly dependent on the central charge c of the underlying conformal field theory describing the system's critical properties.

  16. Permutation auto-mutual information of electroencephalogram in anesthesia

    NASA Astrophysics Data System (ADS)

    Liang, Zhenhu; Wang, Yinghua; Ouyang, Gaoxiang; Voss, Logan J.; Sleigh, Jamie W.; Li, Xiaoli

    2013-04-01

    Objective. The dynamic change of brain activity in anesthesia is an interesting topic for clinical doctors and drug designers. To explore the dynamical features of brain activity in anesthesia, a permutation auto-mutual information (PAMI) method is proposed to measure the information coupling of electroencephalogram (EEG) time series obtained in anesthesia. Approach. The PAMI is developed and applied on EEG data collected from 19 patients under sevoflurane anesthesia. The results are compared with the traditional auto-mutual information (AMI), SynchFastSlow (SFS, derived from the BIS index), permutation entropy (PE), composite PE (CPE), response entropy (RE) and state entropy (SE). Performance of all indices is assessed by pharmacokinetic/pharmacodynamic (PK/PD) modeling and prediction probability. Main results. The PK/PD modeling and prediction probability analysis show that the PAMI index correlates closely with the anesthetic effect. The coefficient of determination R2 between PAMI values and the sevoflurane effect site concentrations, and the prediction probability Pk are higher in comparison with other indices. The information coupling in EEG series can be applied to indicate the effect of the anesthetic drug sevoflurane on the brain activity as well as other indices. The PAMI of the EEG signals is suggested as a new index to track drug concentration change. Significance. The PAMI is a useful index for analyzing the EEG dynamics during general anesthesia.

  17. Remaining Flexible in Old Alliances: Functional Plasticity in Constrained Mutualisms

    PubMed Central

    Wheeler, Diana E.

    2009-01-01

    Central to any beneficial interaction is the capacity of partners to detect and respond to significant changes in the other. Recent studies of microbial mutualists show their close integration with host development, immune responses, and acclimation to a dynamic external environment. While the significance of microbial players is broadly appreciated, we are just beginning to understand the genetic, ecological, and physiological mechanisms that generate variation in symbiont functions, broadly termed “symbiont plasticity” here. Some possible mechanisms include shifts in symbiont community composition, genetic changes via DNA acquisition, gene expression fluctuations, and variation in symbiont densities. In this review, we examine mechanisms for plasticity in the exceptionally stable mutualisms between insects and bacterial endosymbionts. Despite the severe ecological and genomic constraints imposed by their specialized lifestyle, these bacteria retain the capacity to modulate functions depending on the particular requirements of the host. Focusing on the mutualism between Blochmannia and ants, we discuss the roles of gene expression fluctuations and shifts in bacterial densities in generating symbiont plasticity. This symbiont variation is best understood by considering ant colony as the host superorganism. In this eusocial host, the bacteria meet the needs of the colony and not necessarily the individual ants that house them. PMID:19435425

  18. Housekeeping Mutualisms: Do More Symbionts Facilitate Host Performance?

    PubMed Central

    Lemer, Sarah; Leray, Matthieu; Mills, Suzanne C.; Osenberg, Craig W.

    2012-01-01

    Mutualisms often involve one host supporting multiple symbionts, whose identity, density and intraguild interactions can influence the nature of the mutualism and performance of the host. However, the implications of multiple co-occurring symbionts on services to a host have rarely been quantified. In this study, we quantified effects of decapod symbionts on removal of sediment from their coral host. Our field survey showed that all common symbionts typically occur as pairs and never at greater abundances. Two species, the crab Trapezia serenei and the shrimp Alpheus lottini, were most common and co-occurred more often than expected by chance. We conducted a mesocosm experiment to test for effects of decapod identity and density on sediment removal. Alone, corals removed 10% of sediment, but removal increased to 30% and 48% with the presence of two and four symbionts, respectively. Per-capita effects of symbionts were independent of density and identity. Our results suggest that symbiont density is restricted by intraspecific competition. Thus, increased sediment removal from a coral host can only be achieved by increasing the number of species of symbionts on that coral, even though these species are functionally equivalent. Symbiont diversity plays a key role, not through added functionality but by overcoming density limitation likely imposed by intraspecific mating systems. PMID:22523536

  19. microRNAs in cancer

    PubMed Central

    Di Leva, Gianpiero; Garofalo, Michela; Croce, Carlo M.

    2014-01-01

    MicroRNAs are small non coding RNAs that typically inhibit the translation and stability of messanger RNAs (mRNAs), controlling genes involved in cellular processes such as inflammation, cell cycle regulation, stress response, differentiation, apoptosis, and migration. Thus, miRNAs have been implicated in the regulation of virtually all signaling circuits within a cell and their dysregulation has been shown to play an essential role in the development and progression of cancer. Here, after a brief description of the miRNA genomics, biogenesis and function, we discuss the effects of miRNA deregulation in the cellular pathways that lead to the progressive conversion of normal cells into cancer cells and the potential to develop new molecular miRNA-targeted therapies. PMID:24079833

  20. MicroRNAs and atherosclerosis

    PubMed Central

    Madrigal-Matute, Julio; Rotllan, Noemi; Aranda, Juan F.; Fernández-Hernando, Carlos

    2014-01-01

    MicroRNAs (miRNAs) are small (~22nucleotide) sequences of RNA that regulate gene expression at posttranscriptional level. MiRNA/mRNA base pairing complementarity provokes mRNA decay and consequent gene silencing. These endogenous gene expression inhibitors were primarily described in cancer but recent exciting findings have also demonstrated a key role in cardiovascular diseases (CVDs) including atherosclerosis. MiRNAs controls endothelial cell (EC), vascular smooth muscle cell (VSMC) and macrophage functions, and thereby regulate the progression of atherosclerosis. MiRNAs expression is modulated by different stimuli involved in every stage of atherosclerosis and conversely miRNAs modulates several pathways implicated in plaque development such as cholesterol metabolism. In the present review, we focus on the importance of miRNAs in atherosclerosis and we further discuss their potential use as biomarkers and therapeutic targets in CVDs. PMID:23512606

  1. The role of microRNA in myelodysplastic syndromes: beyond DNA methylation and histone modification.

    PubMed

    Milunović, Vibor; Mandac Rogulj, Inga; Planinc-Peraica, Ana; Bulycheva, Ekaterina; Kolonić Ostojić, Slobodanka

    2016-06-01

    Myelodysplastic syndromes (MDS) are heterogeneous group of hematologic disorders of mostly elderly and based on distinct clinical phenotypes. Current paradigm of their pathogenesis relies on somatic gene mutations combined with the predisposing defective osteohematopoietic niche, but due to the breakout in epigenetic research scientific focus has steered toward two most common epigenetic modifications: methylation mechanisms and histone modification. At the same time, relatively few studies have been undertaken regarding the third epigenetic pathway - microRNAs - in MDS. The main aim of this review is to provide the basics of microRNA biology and function in oncogenesis, showing the complexity of mechanisms behind this single-stranded 22 nucleotides long RNA molecule, with further focus on its implication in MDS pathology and clinical context. By extensive literature search, we have shown enough evidence for their deregulation in MDS. However, few studies have addressed the issue on pathogenic events in MDS and its association with specific microRNAs. Preliminary research in clinical setting has shown the possible utility of microRNAs in terms of prognosis and therapy, although we are only beginning to understand various implications of microRNAs in MDS and further extensive research is warranted to answer multiple questions arising from interconnection of this epigenetic mechanism in MDS. PMID:26773284

  2. Sequence-based design of bioactive small molecules that target precursor microRNAs

    PubMed Central

    Velagapudi, Sai Pradeep; Gallo, Steven M.; Disney, Matthew D.

    2014-01-01

    Oligonucleotides are designed to target RNA using base pairing rules, however, they are hampered by poor cellular delivery and non-specific stimulation of the immune system. Small molecules are preferred as lead drugs or probes, but cannot be designed from sequence. Herein, we describe an approach termed Inforna that designs lead small molecules for RNA from solely sequence. Inforna was applied to all human microRNA precursors and identified bioactive small molecules that inhibit biogenesis by binding to nuclease processing sites (41% hit rate). Amongst 29 lead interactions, the most avid interaction is between a benzimidazole (1) and precursor microRNA-96. Compound 1 selectively inhibits biogenesis of microRNA-96, upregulating a protein target (FOXO1) and inducing apoptosis in cancer cells. Apoptosis is ablated when FOXO1 mRNA expression is knocked down by an siRNA, validating compound selectivity. Importantly, microRNA profiling shows that 1 only significantly effects microRNA-96 biogenesis and is more selective than an oligonucleotide. PMID:24509821

  3. Sequence-based design of bioactive small molecules that target precursor microRNAs.

    PubMed

    Velagapudi, Sai Pradeep; Gallo, Steven M; Disney, Matthew D

    2014-04-01

    Oligonucleotides are designed to target RNA using base pairing rules, but they can be hampered by poor cellular delivery and nonspecific stimulation of the immune system. Small molecules are preferred as lead drugs or probes but cannot be designed from sequence. Herein, we describe an approach termed Inforna that designs lead small molecules for RNA from solely sequence. Inforna was applied to all human microRNA hairpin precursors, and it identified bioactive small molecules that inhibit biogenesis by binding nuclease-processing sites (44% hit rate). Among 27 lead interactions, the most avid interaction is between a benzimidazole (1) and precursor microRNA-96. Compound 1 selectively inhibits biogenesis of microRNA-96, upregulating a protein target (FOXO1) and inducing apoptosis in cancer cells. Apoptosis is ablated when FOXO1 mRNA expression is knocked down by an siRNA, validating compound selectivity. Markedly, microRNA profiling shows that 1 only affects microRNA-96 biogenesis and is at least as selective as an oligonucleotide. PMID:24509821

  4. Functional traits determine formation of mutualism and predation interactions in seed-rodent dispersal system of a subtropical forest

    NASA Astrophysics Data System (ADS)

    Chang, Gang; Zhang, Zhibin

    2014-02-01

    Network structure in plant-animal systems has been widely investigated but the roles of functional traits of plants and animals in formation of mutualism and predation interactions and community structure are still not fully understood. In this study, we quantitatively assessed interaction strength of mutualism and predation between 5 tree species and 7 rodent species by using semi-natural enclosures in a subtropical forest in southwest China. Seeds with high handling-time and nutrition traits (for both rat and mouse species) or high tannin trait (for mouse species) show high mutualism but low predation with rodents; while seeds with low handling-time and low nutrition traits show high predation but low mutualism with rodents. Large-sized rat species are more linked to seeds with high handling-time and high nutrition traits, while small-sized mouse species are more connected with seeds with low handling-time, low nutrition value and high tannin traits. Anti-predation seed traits tend to increase chance of mutualism instead of reducing predation by rodents, suggesting formation of mutualism may be connected with that of predation. Our study demonstrates that seed and animal traits play significant roles in the formation of mutualism and predation and network structure of the seed-rodent dispersal system.

  5. Graph embedded nonparametric mutual information for supervised dimensionality reduction.

    PubMed

    Bouzas, Dimitrios; Arvanitopoulos, Nikolaos; Tefas, Anastasios

    2015-05-01

    In this paper, we propose a novel algorithm for dimensionality reduction that uses as a criterion the mutual information (MI) between the transformed data and their corresponding class labels. The MI is a powerful criterion that can be used as a proxy to the Bayes error rate. Furthermore, recent quadratic nonparametric implementations of MI are computationally efficient and do not require any prior assumptions about the class densities. We show that the quadratic nonparametric MI can be formulated as a kernel objective in the graph embedding framework. Moreover, we propose its linear equivalent as a novel linear dimensionality reduction algorithm. The derived methods are compared against the state-of-the-art dimensionality reduction algorithms with various classifiers and on various benchmark and real-life datasets. The experimental results show that nonparametric MI as an optimization objective for dimensionality reduction gives comparable and in most of the cases better results compared with other dimensionality reduction methods. PMID:25881367

  6. Genome-wide analysis implicates microRNAs and their target genes in the development of bipolar disorder.

    PubMed

    Forstner, A J; Hofmann, A; Maaser, A; Sumer, S; Khudayberdiev, S; Mühleisen, T W; Leber, M; Schulze, T G; Strohmaier, J; Degenhardt, F; Treutlein, J; Mattheisen, M; Schumacher, J; Breuer, R; Meier, S; Herms, S; Hoffmann, P; Lacour, A; Witt, S H; Reif, A; Müller-Myhsok, B; Lucae, S; Maier, W; Schwarz, M; Vedder, H; Kammerer-Ciernioch, J; Pfennig, A; Bauer, M; Hautzinger, M; Moebus, S; Priebe, L; Sivalingam, S; Verhaert, A; Schulz, H; Czerski, P M; Hauser, J; Lissowska, J; Szeszenia-Dabrowska, N; Brennan, P; McKay, J D; Wright, A; Mitchell, P B; Fullerton, J M; Schofield, P R; Montgomery, G W; Medland, S E; Gordon, S D; Martin, N G; Krasnov, V; Chuchalin, A; Babadjanova, G; Pantelejeva, G; Abramova, L I; Tiganov, A S; Polonikov, A; Khusnutdinova, E; Alda, M; Cruceanu, C; Rouleau, G A; Turecki, G; Laprise, C; Rivas, F; Mayoral, F; Kogevinas, M; Grigoroiu-Serbanescu, M; Propping, P; Becker, T; Rietschel, M; Cichon, S; Schratt, G; Nöthen, M M

    2015-01-01

    Bipolar disorder (BD) is a severe and highly heritable neuropsychiatric disorder with a lifetime prevalence of 1%. Molecular genetic studies have identified the first BD susceptibility genes. However, the disease pathways remain largely unknown. Accumulating evidence suggests that microRNAs, a class of small noncoding RNAs, contribute to basic mechanisms underlying brain development and plasticity, suggesting their possible involvement in the pathogenesis of several psychiatric disorders, including BD. In the present study, gene-based analyses were performed for all known autosomal microRNAs using the largest genome-wide association data set of BD to date (9747 patients and 14 278 controls). Associated and brain-expressed microRNAs were then investigated in target gene and pathway analyses. Functional analyses of miR-499 and miR-708 were performed in rat hippocampal neurons. Ninety-eight of the six hundred nine investigated microRNAs showed nominally significant P-values, suggesting that BD-associated microRNAs might be enriched within known microRNA loci. After correction for multiple testing, nine microRNAs showed a significant association with BD. The most promising were miR-499, miR-708 and miR-1908. Target gene and pathway analyses revealed 18 significant canonical pathways, including brain development and neuron projection. For miR-499, four Bonferroni-corrected significant target genes were identified, including the genome-wide risk gene for psychiatric disorder CACNB2. First results of functional analyses in rat hippocampal neurons neither revealed nor excluded a major contribution of miR-499 or miR-708 to dendritic spine morphogenesis. The present results suggest that research is warranted to elucidate the precise involvement of microRNAs and their downstream pathways in BD. PMID:26556287

  7. Biogenesis of Y RNA-derived small RNAs is independent of the microRNA pathway.

    PubMed

    Nicolas, Francisco Esteban; Hall, Adam E; Csorba, Tibor; Turnbull, Carly; Dalmay, Tamas

    2012-04-24

    Y RNAs are approximately 100 nucleotide long conserved cytoplasmic non-coding RNAs, which produce smaller RNA fragments during apoptosis. Here we show that these smaller RNA molecules are also produced in non-stressed cells and in a range of human cancerous and non-cancerous cell types. Recent reports have speculated that the cleavage products of Y RNAs enter the microRNA pathway. We tested this hypothesis and found that Y5 and Y3 RNA fragments are Dicer independent, they are in different complexes than microRNAs and that they are not co-immunoprecipitated with Ago2. Therefore we conclude that Y RNA fragments do not enter the microRNA pathway. PMID:22575660

  8. Nectar bacteria, but not yeast, weaken a plant–pollinator mutualism

    PubMed Central

    Vannette, Rachel L.; Gauthier, Marie-Pierre L.; Fukami, Tadashi

    2013-01-01

    Mutualistic interactions are often subject to exploitation by species that are not directly involved in the mutualism. Understanding which organisms act as such ‘third-party’ species and how they do so is a major challenge in the current study of mutualistic interactions. Here, we show that even species that appear ecologically similar can have contrasting effects as third-party species. We experimentally compared the effects of nectar-inhabiting bacteria and yeasts on the strength of a mutualism between a hummingbird-pollinated shrub, Mimulus aurantiacus, and its pollinators. We found that the common bacterium Gluconobacter sp., but not the common yeast Metschnikowia reukaufii, reduced pollination success, seed set and nectar consumption by pollinators, thereby weakening the plant–pollinator mutualism. We also found that the bacteria reduced nectar pH and total sugar concentration more greatly than the yeasts did and that the bacteria decreased glucose concentration and increased fructose concentration whereas the yeasts affected neither. These distinct changes to nectar chemistry may underlie the microbes' contrasting effects on the mutualism. Our results suggest that it is necessary to understand the determinants of microbial species composition in nectar and their differential modification of floral rewards to explain the mutual benefits that plants and pollinators gain from each other. PMID:23222453

  9. Astrometry of mutual approximations between natural satellites. Application to the Galilean moons

    NASA Astrophysics Data System (ADS)

    Morgado, B.; Assafin, M.; Vieira-Martins, R.; Camargo, J. I. B.; Dias-Oliveira, A.; Gomes-Júnior, A. R.

    2016-08-01

    Typically we can deliver astrometric positions of natural satellites with errors in the 50-150 mas range. Apparent distances from mutual phenomena, have much smaller errors, less than 10 mas. However, this method can only be applied during the equinox of the planets. We developed a method that can provide accurate astrometric data for natural satellites - the mutual approximations. The method can be applied when any two satellites pass close by each other in the apparent sky plane. The fundamental parameter is the central instant t0 of the passage when the distances reach a minimum. We applied the method for the Galilean moons. All observations were made with a 0.6 m telescope with a narrow-band filter centred at 889 nm with width of 15 nm which attenuated Jupiter's scattered light. We obtained central instants for 14 mutual approximations observed in 2014-2015. We determined t0 with an average precision of 3.42 mas (10.43 km). For comparison, we also applied the method for 5 occultations in the 2009 mutual phenomena campaign and for 22 occultations in the 2014-2015 campaign. The comparisons of t0 determined by our method with the results from mutual phenomena show an agreement by less than 1σ error in t0, typically less than 10 mas. This new method is particularly suitable for observations by small telescopes.

  10. Astrometry of mutual approximations between natural satellites. Application to the Galilean moons

    NASA Astrophysics Data System (ADS)

    Morgado, B.; Assafin, M.; Vieira-Martins, R.; Camargo, J. I. B.; Dias-Oliveira, A.; Gomes-Júnior, A. R.

    2016-08-01

    Typically we can deliver astrometric positions of natural satellites with errors in the 50-150 mas range. Apparent distances from mutual phenomena, have much smaller errors, less than 10 mas. However, this method can only be applied during the equinox of the planets. We developed a method that can provide accurate astrometric data for natural satellites -- the mutual approximations. The method can be applied when any two satellites pass close by each other in the apparent sky plane. The fundamental parameter is the central instant $t_0$ of the passage when the distances reach a minimum. We applied the method for the Galilean moons. All observations were made with a 0.6 m telescope with a narrow-band filter centred at 889 nm with width of 15 nm which attenuated Jupiter's scattered light. We obtained central instants for 14 mutual approximations observed in 2014-2015. We determined $t_0$ with an average precision of 3.42 mas (10.43 km). For comparison, we also applied the method for 5 occultations in the 2009 mutual phenomena campaign and for 22 occultations in the 2014-2015 campaign. The comparisons of $t_0$ determined by our method with the results from mutual phenomena show an agreement by less than 1-sigma error in $t_0$, typically less than 10 mas. This new method is particularly suitable for observations by small telescopes.