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Sample records for festuca arundinacea mirnas

  1. Endophyte status of tall fescue (festuca arundinacea) affects seed predation

    USDA-ARS?s Scientific Manuscript database

    In a preliminary study seed of a tall fescue (Festuca arundinacea Schreb.) variety ‘Jesup’ without endophyte were consumed at a slightly higher rate by common cricket (Acheta domesticus L.) in a standard feeding trial than the same fescue variety with the endophyte. Although, the preference for the...

  2. Effect of endophytic fungi on cadmium tolerance and bioaccumulation by Festuca arundinacea and Festuca pratensis.

    PubMed

    Soleimani, Mohsen; Hajabbasi, Mohammad A; Afyuni, Majid; Mirlohi, Aghafakhr; Borggaard, Ole K; Holm, Peter E

    2010-08-01

    Endophytic fungi are a group of fungi that live asymptomatically inside plant tissue. These fungi may increase host plant tolerance to biotic and abiotic stresses. The effect of Neotyphodium endophytes in two grass species (Festuca arundinacea and Festuca pratensis) on cadmium (Cd) tolerance, accumulation and translocation has been our main objective. The plants were grown in a hydroponic system under different Cd concentrations (0, 5, 10, and 20 mg L(-1)) for 6 weeks. They were also grown in soil spiked with different concentrations of Cd (0, 10, 20, and 40 mg kg(-1)) for 2 months. The results from all Cd treatments showed higher biomass production (12-24%) and higher potential to accumulate Cd in roots (6-16%) and shoots (6-20%) of endophyte-infected plants than endophyte-free plants. Cadmium accumulation by plants indicated that the grasses were capable of Cd hyperaccumulation, a property that was augmented after endophyte infection. Maximum photochemical efficiency of photosystem II (Fv/Fm) revealed that Cd stress was significantly reduced in endophyte-infected plants compared to non-infected ones.

  3. Host suitability of tall fescue (Festuca arundinacea) cultivars to Meloidogyne ethiopica and M. graminicola.

    USDA-ARS?s Scientific Manuscript database

    Considering the importance of the perennial grass tall fescue (Festuca arundinacea) having as forage potential and its resistance to many pests, including some phytoparasitic nematodes, the host reaction of three tall fescue cultivars (cvs. Bulldogs 51, Georgia 5 and Jesup AR542 ) were evaluated for...

  4. [Cu and Pb absorption and tolerance of Agrostis stolonifera and Festuca arundinacea].

    PubMed

    Wang, Yan; Xin, Shi-Gang; Ma, Lian-Ju; Dai, Bao-Qing; Yu, Long; Wang, Lan-Lan

    2007-03-01

    This paper studied the seed germination rate, chlorophyll content, net photosynthetic rate, SOD activity, and Cu and Pb absorption of Agrostis stolonifera and Festuca arundinacea under Cu and Pb pollution. The results showed that Cu and Pb pollution had a significant effect on the seed germination rate of F. arundinacea. The chlorophyll content of F. arundinacea decreased dramatically under Pb and Cu-Pb pollution, while decreased slightly under Cu pollution. No significant effect of Cu and Pb was observed on the chlorophyll content of A. stolonifera. The SOD activity of A. stolonifera increased under 350 mg Cu x kg(-1) and all test concentrations of Pb, while that of F. arundinacea only increased under 700 mg Pb x kg(-1) and 350 mg Cu x kg(-1) + 1100 mg Pb x kg(-1). The net photosynthetic rate of F. arundinacea decreased more under Pb pollution than under Cu pollution, but that of A. stolonifera all decreased under Cu or Pb pollution. It was suggested that A. stolonifera was more tolerant in physiological characteristics to Cu and Pb pollution than F. arundinacea, while F. arundinacea was more tolerant to Cu than to Pb. The Cu absorption amount of F. arundinacea was relatively large, but did not increase with increasing Cu pollution. A. stolonifera had a high absorption ability of Pb, and the absorbed Pb amount was increased with increasing Pb pollution. A. stolonifera and F. arundinace could be the potential phytoremediation plants for Pb and Cu-polluted soil, respectively.

  5. Phytoparasitic Nematode Populations in Festuca arundinacea Field Plots in Southwestern Missouri

    PubMed Central

    O'Day, M. H.; Niblack, T. L.; Bailey, W. C.

    1993-01-01

    Field plots of tall rescue (Festuca arundinacea) at two locations on the same experimental farm in southwestern Missouri were sampled (one in 1987-88, the other in 1988-89) to inventory root-parasitic nematodes and to determine whether cultivars or endophyte (Acremonium coenophialum) infection frequencies (EIF) affected nematode population densities within single growing seasons. Plots were planted with seven tall rescue cultivars: Kentucky-31, Kenhy, Johnstone, Martin, Mozark, Missouri-96, and Forager. Kentucky-31 seed with high and low EIF were planted in separate plots. Plant-parasitic nematodes were extracted from soil samples, identified to genus, and enumerated four and three times per year for the 1987-1988 and 1988-1989 studies, respectively. Several plant-parasitic genera were identified from both fields, including Helicotylenchus, Heterodera, Hoplolaimus, Paratylenchus, Pratylenchus, Tylenchorhynchus, and members of genera grouped in the family Tylenchidae. Densities of five of these seven groups of nematodes differed among tall fescue cultivars in the 1987-88 study, but only two out of eight groups did so in the 1988-89 study. Irrespective of tall rescue cultivar, EIF had no consistent impact on nematode densities. The putative suppressive effect of endophyte infection on infection by plant-parasitic nematodes is not detectable within single growing seasons and deserves long-term study in field situations. PMID:19279861

  6. An SSR- and AFLP-based genetic linkage map of tall fescue (Festuca arundinacea Schreb.).

    PubMed

    Saha, Malay C; Mian, Rouf; Zwonitzer, John C; Chekhovskiy, Konstantin; Hopkins, Andrew A

    2005-01-01

    Tall fescue (Festuca arundinacea Schreb.) is commonly grown as forage and turf grass in the temperate regions of the world. Here, we report the first genetic map of tall fescue constructed with PCR-based markers. A combination of amplified fragment length polymorphisms (AFLPs) and expressed sequence tag-simple sequence repeats (EST-SSRs) of both tall fescue and those conserved in grass species was used for map construction. Genomic SSRs developed from Festuca x Lolium hybrids were also mapped. Two parental maps were initially constructed using a two-way pseudo-testcross mapping strategy. The female (HD28-56) map included 558 loci placed in 22 linkage groups (LGs) and covered 2,013 cM of the genome. In the male (R43-64) map, 579 loci were grouped in 22 LGs with a total map length of 1,722 cM. The marker density in the two maps varied from 3.61 cM (female parent) to 2.97 (male parent) cM per marker. These differences in map length indicated a reduced level of recombination in the male parent. Markers that revealed polymorphism within both parents and showed 3:1 segregation ratios were used as bridging loci to integrate the two parental maps as a bi-parental consensus. The integrated map covers 1,841 cM on 17 LGs, with an average of 54 loci per LG, and has an average marker density of 2.0 cM per marker. Homoeologous relationships among linkage groups of six of the seven predicted homeologous groups were identified. Three small groups from the HD28-56 map and four from the R43-64 map are yet to be integrated. Homoeologues of four of those groups were detected. Except for a few gaps, markers are well distributed throughout the genome. Clustering of those markers showing significant segregation distortion (23% of total) was observed in four of the LGs of the integrated map.

  7. Festuca arundinacea, glutathione S-transferase and herbicide safeners: a preliminary case study to reduce herbicidal pollution.

    PubMed

    Scarponi, Luciano; Del Buono, Daniele

    2009-11-01

    The expression of glutathione S-transferase (GST) activity in Festuca arundinacea was investigated in response to the following herbicide safeners: benoxacor, cloquintocet-mexyl, fenchlorazol-ethyl, fenclorim, fluxofenim and oxabetrinil. All the above compounds enhanced the GST activity tested towards the "model" substrate 1-chloro-2,4-dinitrobenzene (CDNB). Assays of GST activity towards the herbicides terbuthylazine (N(2)-tert-butyl-6-chloro-N(4)-ethyl-1,3,5-triazine-2,4-diamine) and butachlor (N-butoxymethyl-2-chloro-2',6'-diethylacetanilide) as substrates also showed the ability of the safeners to enhance the enzyme activity towards both these herbicides, with the exception of cloquintocet-mexyl for the enzyme activity towards butachlor. As a consequence of the above effects at a macro-scale level, decreased herbicide accumulation and persistence were ascertained in response to the addition of the safener benoxacor to both terbuthylazine and butachlor treatments. These results are discussed in terms of capacity of benoxacor to induce herbicide detoxification in Festuca arundinacea with a view to utilizing them in reducing herbicide pollution.

  8. Lead Accumulation by Tall Fescue (Festuca arundinacea Schreb.) Grown on a Lead-Contaminated Soil

    PubMed Central

    Begonia, M. T.; Begonia, G. B.; Ighoavodha, M.; Gilliard, D.

    2005-01-01

    Phytoextraction is gaining acceptance as a cost-effective and environmentally friendly phytoremediation strategy for reducing toxic metal levels from contaminated soils. Cognizant of the potential of this phytoremediation technique as an alternative to expensive engineering-based remediation technologies, experiments were conducted to evaluate the suitability of some plants as phytoextraction species. From one of our preliminary studies, we found that tall fescue (Festuca arundinacea Schreb. cv. Spirit) can tolerate and accumulate significant amounts of lead (Pb) in its shoots when grown in Pb-amended sand. To further evaluate the suitability of tall fescue as one of the potential crop rotation species for phytoextraction, a study was conducted to determine whether the addition of ethylenediaminetetraacetic acid (EDTA) alone or in combination with acetic acid can further enhance the shoot uptake of Pb. Seeds were planted in 3.8 L plastic pots containing top soil, peat, and sand (4:2:1, v:v:v) spiked with various levels (0,1000, 2000 mg Pb/kg dry soil) of lead. At six weeks after planting, aqueous solutions (0, 5 mmol/kg dry soil) of EDTA and acetic acid (5 mmol/kg dry soil) were applied to the root zone, and all plants were harvested a week later. Results revealed that tall fescue was relatively tolerant to moderate levels of Pb as shown by non-significant differences in root and shoot biomass among treatments. An exception to this trend however, was the slight reduction in root and shoot biomass of plants exposed to the highest Pb level in combination with the two chelates. Root Pb concentration increased with increasing level of soil-applied Pb. Further increases in root Pb concentrations were attributed to chelate amendments. Translocation index, which is a measure of the partitioning of the metal to the shoots, was significantly enhanced with chelate addition especially when both EDTA and acetic acid were used. Chelate-induced increases in translocation indices

  9. How planting configuration influences plant secondary metabolites and total N in tall fescue (Festuca arundinacea Schreb.), alfalfa (Medicago sativa L.) and birdsfoot trefoil (Lotus corniculatus L.)

    USDA-ARS?s Scientific Manuscript database

    Theories suggest that incorporating alfalfa (Medicago sativa L.; Alf) or birdsfoot trefoil (Lotus corniculatus L.; BFT) into endophyte-infected tall fescue (Festuca arundinaceas Schreb.; E+TF) pasturelands may improve livestock production. We investigated how planting configuration might influence p...

  10. Effect of simulated acid rain on the mutualism between tall fescue (Festuca arundinacea) and an endophytic fungus (Acremonium coenophialum)

    SciTech Connect

    Cheplick, G.P. )

    1993-03-01

    Biotic interactions between plants and microorganisms have the potential to be affected by acidic precipitation. I examined the effect of simulated sulfuric acid rain on the mutualism between a perennial forage grass (Festuca arundinacea) and a fungal endophyte (Acremonium coenophialum). Acid water was supplied as mists sprayed onto leaf surfaces or as water added to the soil for two groups in a greenhouse: one group had high levels of endophyte infection, while the other was predominantly noninfected. Control plants received distilled water (pH 6), while others received sulfuric acid water at pH 4.5 or pH 3. Plants were harvested after 4, 6, 8, and 23 wk. Leaf endophyte infection intensity as measured by hyphal counts was not affected by acid water treatment. Root mass and root: shoot ratios generally decreased with increasing acidity of both foliar sprays and soil water, but shoot mass was mostly not affected. There was a significant pH x infection interaction for plants exposed to acidic foliar sprays for 4 wk; root and shoot mass decreased with acidity, but only for infected plants. It was found that acid rain may be deleterious to tall fescue growth at specific stages of development, but biomass production in response to acid rain is not likely to be influenced by fungal endophytes within mature plants. 55 refs., 2 figs., 3 tabs.

  11. Ascorbic Acid Enhances the Accumulation of Polycyclic Aromatic Hydrocarbons (PAHs) in Roots of Tall Fescue (Festuca arundinacea Schreb.)

    PubMed Central

    Gao, Yanzheng; Li, Hui; Gong, Shuaishuai

    2012-01-01

    Plant contamination by polycyclic aromatic hydrocarbons (PAHs) is crucial to food safety and human health. Enzyme inhibitors are commonly utilized in agriculture to control plant metabolism of organic components. This study revealed that the enzyme inhibitor ascorbic acid (AA) significantly reduced the activities of peroxidase (POD) and polyphenol oxidase (PPO), thus enhancing the potential risks of PAH contamination in tall fescue (Festuca arundinacea Schreb.). POD and PPO enzymes in vitro effectively decomposed naphthalene (NAP), phenanthrene (PHE) and anthracene (ANT). The presence of AA reduced POD and PPO activities in plants, and thus was likely responsible for enhanced PAH accumulation in tall fescue. This conclusion is supported by the significantly enhanced uptake of PHE in plants in the presence of AA, and the positive correlation between enzyme inhibition efficiencies and the rates of metabolism of PHE in tall fescue roots. This study provides a new perspective, that the common application of enzyme inhibitors in agricultural production could increase the accumulation of organic contaminants in plants, hence enhancing risks to food safety and quality. PMID:23185628

  12. Ascorbic acid enhances the accumulation of polycyclic aromatic hydrocarbons (PAHs) in roots of tall fescue (Festuca arundinacea Schreb.).

    PubMed

    Gao, Yanzheng; Li, Hui; Gong, Shuaishuai

    2012-01-01

    Plant contamination by polycyclic aromatic hydrocarbons (PAHs) is crucial to food safety and human health. Enzyme inhibitors are commonly utilized in agriculture to control plant metabolism of organic components. This study revealed that the enzyme inhibitor ascorbic acid (AA) significantly reduced the activities of peroxidase (POD) and polyphenol oxidase (PPO), thus enhancing the potential risks of PAH contamination in tall fescue (Festuca arundinacea Schreb.). POD and PPO enzymes in vitro effectively decomposed naphthalene (NAP), phenanthrene (PHE) and anthracene (ANT). The presence of AA reduced POD and PPO activities in plants, and thus was likely responsible for enhanced PAH accumulation in tall fescue. This conclusion is supported by the significantly enhanced uptake of PHE in plants in the presence of AA, and the positive correlation between enzyme inhibition efficiencies and the rates of metabolism of PHE in tall fescue roots. This study provides a new perspective, that the common application of enzyme inhibitors in agricultural production could increase the accumulation of organic contaminants in plants, hence enhancing risks to food safety and quality.

  13. Changes in the chloroplast proteome following water deficit and subsequent watering in a high- and a low-drought-tolerant genotype of Festuca arundinacea.

    PubMed

    Kosmala, Arkadiusz; Perlikowski, Dawid; Pawłowicz, Izabela; Rapacz, Marcin

    2012-10-01

    Festuca arundinacea is one of the most drought-tolerant species within the Lolium-Festuca complex and was used as a model for research aimed at identifying the chloroplast components involved in the proteomic response for drought stress in forage grasses. Individual F. arundinacea genotypes with contrasting levels of drought tolerance, the high-drought-tolerant (HDT) and the low-drought-tolerant (LDT) genotypes, were selected for comparative physiological and proteomic work. Measurements of water uptake, chlorophyll fluorescence, relative water content, electrolyte leakage, and gas exchange during drought and rewatering periods were followed by investigations on accumulation levels of chloroplast proteins before drought conditions, on d 3 and 11 of drought treatment, and after 10 d of subsequent watering, using two-dimensional gel electrophoresis. The proteins that were accumulated differentially between the selected plants were then identified by mass spectrometry. The LDT genotype revealed lower levels of water uptake and relative water content as drought progressed, and this was accompanied by lower levels of transpiration and net photosynthesis, and a higher level of electrolyte leakage observed in this genotype. Eighty-two protein accumulation profiles were compared between the HDT and LDT genotypes and ten proteins were shown to be differentially accumulated between them. The functions of the selected proteins in plant cells and their probable influence on the process of recovery after drought treatment in F. arundinacea are discussed.

  14. Arbuscular mycorrhiza affects nickel translocation and expression of ABC transporter and metallothionein genes in Festuca arundinacea.

    PubMed

    Shabani, Leila; Sabzalian, Mohammad R; Mostafavi pour, Sodabeh

    2016-01-01

    Mycorrhizal fungi are key microorganisms for enhancing phytoremediation of soils contaminated with heavy metals. In this study, the effects of the arbuscular mycorrhizal fungus (AMF) Funneliformis mosseae (=Glomus mosseae) on physiological and molecular mechanisms involved in the nickel (Ni) tolerance of tall fescue (Festuca arundinacea = Schedonorus arundinaceus) were investigated. Nickel addition had a pronounced negative effect on tall fescue growth and photosynthetic pigment contents, as well as on AMF colonization. Phosphorus content increased markedly in mycorrhizal plants (M) compared to non-inoculated (NM) ones. However, no significant difference was observed in root carbohydrate content between AMF-inoculated and non-inoculated plants. For both M and NM plants, Ni concentrations in shoots and roots increased according to the addition of the metal into soil, but inoculation with F. mosseae led to significantly lower Ni translocation from roots to the aboveground parts compared to non-inoculated plants. ABC transporter and metallothionein transcripts accumulated to considerably higher levels in tall fescue plants colonized by F. mosseae than in the corresponding non-mycorrhizal plants. These results highlight the importance of mycorrhizal colonization in alleviating Ni-induced stress by reducing Ni transport from roots to shoots of tall fescue plants.

  15. Response to elevated CO2 in the temperate C3 grass Festuca arundinaceae across a wide range of soils.

    PubMed

    Nord, Eric A; Jaramillo, Raúl E; Lynch, Jonathan P

    2015-01-01

    Soils vary widely in mineral nutrient availability and physical characteristics, but the influence of this variability on plant responses to elevated CO2 remains poorly understood. As a first approximation of the effect of global soil variability on plant growth response to CO2, we evaluated the effect of CO2 on tall fescue (Festuca arundinacea) grown in soils representing 10 of the 12 global soil orders plus a high-fertility control. Plants were grown in small pots in continuously stirred reactor tanks in a greenhouse. Elevated CO2 (800 ppm) increased plant biomass in the high-fertility control and in two of the more fertile soils. Elevated CO2 had variable effects on foliar mineral concentration-nitrogen was not altered by elevated CO2, and phosphorus and potassium were only affected by CO2 in a small number of soils. While leaf photosynthesis was stimulated by elevated CO2 in six soils, canopy photosynthesis was not stimulated. Four principle components were identified; the first was associated with foliar minerals and soil clay, and the second with soil acidity and foliar manganese concentration. The third principle component was associated with gas exchange, and the fourth with plant biomass and soil minerals. Soils in which tall fescue did not respond to elevated CO2 account for 83% of global land area. These results show that variation in soil physical and chemical properties have important implications for plant responses to global change, and highlight the need to consider soil variability in models of vegetation response to global change.

  16. Response to elevated CO2 in the temperate C3 grass Festuca arundinaceae across a wide range of soils

    PubMed Central

    Nord, Eric A.; Jaramillo, Raúl E.; Lynch, Jonathan P.

    2015-01-01

    Soils vary widely in mineral nutrient availability and physical characteristics, but the influence of this variability on plant responses to elevated CO2 remains poorly understood. As a first approximation of the effect of global soil variability on plant growth response to CO2, we evaluated the effect of CO2 on tall fescue (Festuca arundinacea) grown in soils representing 10 of the 12 global soil orders plus a high-fertility control. Plants were grown in small pots in continuously stirred reactor tanks in a greenhouse. Elevated CO2 (800 ppm) increased plant biomass in the high-fertility control and in two of the more fertile soils. Elevated CO2 had variable effects on foliar mineral concentration—nitrogen was not altered by elevated CO2, and phosphorus and potassium were only affected by CO2 in a small number of soils. While leaf photosynthesis was stimulated by elevated CO2 in six soils, canopy photosynthesis was not stimulated. Four principle components were identified; the first was associated with foliar minerals and soil clay, and the second with soil acidity and foliar manganese concentration. The third principle component was associated with gas exchange, and the fourth with plant biomass and soil minerals. Soils in which tall fescue did not respond to elevated CO2 account for 83% of global land area. These results show that variation in soil physical and chemical properties have important implications for plant responses to global change, and highlight the need to consider soil variability in models of vegetation response to global change. PMID:25774160

  17. Hormone regulation of rhizome development in tall fescue (Festuca arundinacea) associated with proteomic changes controlling respiratory and amino acid metabolism

    PubMed Central

    Ma, Xiqing; Xu, Qian; Meyer, William A.; Huang, Bingru

    2016-01-01

    Background and Aims Rhizomes are underground stems with meristematic tissues capable of generating shoots and roots. However, mechanisms controlling rhizome formation and growth are yet to be completely understood. The objectives of this study were to investigate whether rhizome development could be regulated by cytokinins (CKs) and gibberellic acids (GAs), and determine underlying mechanisms of regulation of rhizome formation and growth of tall fescue (Festuca arundinacea) by a CK or GA through proteomic and transcript analysis. Methods A rhizomatous genotype of tall fescue (‘BR’) plants were treated with 6-benzylaminopurine (BAP, a synthetic cytokinin) or GA3 in hydroponic culture in growth chambers. Furthermore, comparative proteomic analysis of two-dimensional electrophoresis and mass spectrometry were performed to investigate proteins and associated metabolic pathways imparting increased rhizome number by BAP and rhizome elongation by GA3. Key Results BAP stimulated rhizome formation while GA3 promoted rhizome elongation. Proteomic analysis identified 76 differentially expressed proteins (DEPs) due to BAP treatment and 37 DEPs due to GA3 treatment. Cytokinin-related genes and cell division-related genes were upregulated in the rhizome node by BAP and gibberellin-related and cell growth-related genes in the rhizome by GA3. Conclusions Most of the BAP- or GA-responsive DEPs were involved in respiratory metabolism and amino acid metabolism. Transcription analysis demonstrated that genes involved in hormone metabolism, signalling pathways, cell division and cell-wall loosening were upregulated by BAP or GA3. The CK and GA promoted rhizome formation and growth, respectively, by activating metabolic pathways that supply energy and amino acids to support cell division and expansion during rhizome initiation and elongation in tall fescue. PMID:27443301

  18. Screening the wetland plant species Alisma plantago-aquatica, Carex rostrata and Phalaris arundinacea for innate tolerance to zinc and comparison with Eriophorum angustifolium and Festuca rubra Merlin.

    PubMed

    Matthews, David J; Moran, Bridget M; Otte, Marinus L

    2005-03-01

    Several wetland plant species appear to have constitutive metal tolerance. In previous studies, populations from contaminated and non-contaminated sites of the wetland plants Typha latifolia, Phragmites australis, Glyceria fluitans and Eriophorum angustifolium were found to be tolerant to high concentrations of metals. This study screened three other species of wetland plants: Alisma plantago-aquatica, Carex rostrata and Phalaris arundinacea for innate tolerance to zinc. The degree of tolerance was compared to known zinc-tolerant E. angustifolium and Festuca rubra Merlin. It was found that A. plantago-aquatica and P. arundinacea did not posses innate tolerance to zinc, but that C. rostrata was able to tolerate elevated levels of zinc, at levels comparable to those tolerated by E. angustifolium and F. rubra Merlin. The findings support the theory that some wetland angiosperm species tend to be tolerant to exposure to high levels of metals, regardless of their origin.

  19. Germination, Physiological Responses and Gene Expression of Tall Fescue (Festuca arundinacea Schreb.) Growing under Pb and Cd

    PubMed Central

    Lou, Yanhong; Zhao, Peng; Wang, Deling; Amombo, Erick; Sun, Xin; Wang, Hui; Zhuge, Yuping

    2017-01-01

    Cadmium (Cd) and lead (Pb) are recognized as the most toxic metal ions due to their detrimental effects not only to plants, but also to humans. The objective of this study was to investigate the effects of Cd and Pb treatments on seed germination, plant growth, and physiological response in tall fescue (Festuca arundinacea Schreb.). We employed six treatments: CK (nutrient solution as control), T1 (1000 mg L-1 Pb), T2 (50 mg L-1 Cd), T3 (150 mg L-1 Cd), T4 (1000 mg L-1 Pb+50 mg L-1 Cd), T5 (1000 mg L-1 Pb+150 mg L-1 Cd). Antagonistic and synergistic actions were observed in tall fescue under Pb and Cd combined treatments. Under low Cd, plants exhibited higher relative germination rate, germ length, VSGR, catalase (CAT) and peroxidase (POD) activities. Additionally, in the shoots, the gene expression level of Cu/Zn SOD, FeSOD, POD, GPX, translocation factors, MDA, EL, and soluble protein contents were reduced under Pb stress. Conversely, under high Cd level, there was a decline in NRT, Pb content in shoots, Pb translocation factors, CAT activity; and an increase in VSGR, Pb content in roots, gene expression level of Cu/ZnSOD and POD in tall fescue exposed to Pb2+ regimes. On the other hand, tall fescue plants treated with low Cd exhibited lower relative germination rate, germination index, germ length, NRT, Cd content in roots. On the other hand there was higher Cd content, Cd translocation factor, CAT and POD activities, and gene expression level of Cu/Zn SOD, FeSOD, POD, GPX under Pb treatment compared with single Cd2+ treatment in the shoots. However, after high Cd exposure, plants displayed lower NRT, Cd content, CAT activity, and exhibited higher Cd contents, Cd translocation factor, MDA content, gene expression level of Cu/ZnSOD and GPX with the presence of Pb2+ relative to single Cd2+ treatment. These findings lead to a conclusion that the presence of low Cd level impacted positively towards tall fescue growth under Pb stress, while high level of Cd impacted

  20. Germination, Physiological Responses and Gene Expression of Tall Fescue (Festuca arundinacea Schreb.) Growing under Pb and Cd.

    PubMed

    Lou, Yanhong; Zhao, Peng; Wang, Deling; Amombo, Erick; Sun, Xin; Wang, Hui; Zhuge, Yuping

    2017-01-01

    Cadmium (Cd) and lead (Pb) are recognized as the most toxic metal ions due to their detrimental effects not only to plants, but also to humans. The objective of this study was to investigate the effects of Cd and Pb treatments on seed germination, plant growth, and physiological response in tall fescue (Festuca arundinacea Schreb.). We employed six treatments: CK (nutrient solution as control), T1 (1000 mg L-1 Pb), T2 (50 mg L-1 Cd), T3 (150 mg L-1 Cd), T4 (1000 mg L-1 Pb+50 mg L-1 Cd), T5 (1000 mg L-1 Pb+150 mg L-1 Cd). Antagonistic and synergistic actions were observed in tall fescue under Pb and Cd combined treatments. Under low Cd, plants exhibited higher relative germination rate, germ length, VSGR, catalase (CAT) and peroxidase (POD) activities. Additionally, in the shoots, the gene expression level of Cu/Zn SOD, FeSOD, POD, GPX, translocation factors, MDA, EL, and soluble protein contents were reduced under Pb stress. Conversely, under high Cd level, there was a decline in NRT, Pb content in shoots, Pb translocation factors, CAT activity; and an increase in VSGR, Pb content in roots, gene expression level of Cu/ZnSOD and POD in tall fescue exposed to Pb2+ regimes. On the other hand, tall fescue plants treated with low Cd exhibited lower relative germination rate, germination index, germ length, NRT, Cd content in roots. On the other hand there was higher Cd content, Cd translocation factor, CAT and POD activities, and gene expression level of Cu/Zn SOD, FeSOD, POD, GPX under Pb treatment compared with single Cd2+ treatment in the shoots. However, after high Cd exposure, plants displayed lower NRT, Cd content, CAT activity, and exhibited higher Cd contents, Cd translocation factor, MDA content, gene expression level of Cu/ZnSOD and GPX with the presence of Pb2+ relative to single Cd2+ treatment. These findings lead to a conclusion that the presence of low Cd level impacted positively towards tall fescue growth under Pb stress, while high level of Cd impacted

  1. The use of a biodegradable chelator for enhanced phytoextraction of heavy metals by Festuca arundinacea from municipal solid waste compost and associated heavy metal leaching.

    PubMed

    Zhao, Shulan; Jia, Lina; Duo, Lian

    2013-02-01

    In a column experiment with horizontal permeable barriers, the effects of a biodegradable chelator-nitrilotriacetic acid (NTA) on the uptake of heavy metals from municipal solid waste (MSW) compost by Festuca arundinacea and metal leaching were investigated. The use of NTA was effective in increasing Cu, Pb, and Zn uptakes in shoots of two crops of F. arundinacea. In columns with barriers and treated with 20 mmol NTA per kg MSW compost, metal uptakes by the first and second crop of F. arundinacea were, respectively, 3.8 and 4.0 times for Pb, and 1.8 and 1.7 times for Zn greater with the added NTA than without it. Though NTA application mobilized metals, it caused only slight leaching of metals from MSW compost. Permeable barriers positioned between compost and soil effectively reduced metal leaching. NTA-assisted phytoextraction by turfgrass with permeable barriers to cleanup heavy metal contaminated MSW compost should be environmentally safe. Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. Selenium accumulation and selenium-salt co-tolerance in five grass species. [Festuca arundinaceae; Agropyron deserorum; Buchloe dactyloides; Agrostis stolonifera; Cynodon dactylon

    SciTech Connect

    Wu, L.; Huang, Z.; Burau, R.G.

    1987-04-01

    Five grass species including Tall fescue (Festuca arundinaceae Schred), Crested wheatgrass (Agropyron deserorum Fisch), Buffalo grass (Buchlor dactyloides (Nutt.) Engelm.), Seaside bentgrass (Agrostis stolonifera L.) and Bermuda grass (Cynodon dactylon (L.) Pers., Syn.) were examined for selenium and salt tolerance and selenium accumulation under solution culture conditions. Distinct differences in both selenium and salt tolerance were detected among the five species, but no direct association between selenium and salt resistance was found. Tall fescue displayed considerable tolerance under 1 ppm selenium and 100 mM salt treatment. Combined selenium and salt treatment revealed that selenium uptake was increased by the incorporation of salt in the culture solution. However, salt uptake was not significantly affected by the presence of selenium in the culture solution. At moderate toxic levels of selenium, the species with greater tolerance accumulated less selenium than did the less tolerant species.

  3. Frequency, type, and distribution of EST-SSRs from three genotypes of Lolium perenne, and their conservation across orthologous sequences of Festuca arundinacea, Brachypodium distachyon, and Oryza sativa

    PubMed Central

    Asp, Torben; Frei, Ursula K; Didion, Thomas; Nielsen, Klaus K; Lübberstedt, Thomas

    2007-01-01

    Background Simple sequence repeat (SSR) markers are highly informative and widely used for genetic and breeding studies in several plant species. They are used for cultivar identification, variety protection, as anchor markers in genetic mapping, and in marker-assisted breeding. Currently, a limited number of SSR markers are publicly available for perennial ryegrass (Lolium perenne). We report on the exploitation of a comprehensive EST collection in L. perenne for SSR identification. The objectives of this study were 1) to analyse the frequency, type, and distribution of SSR motifs in ESTs derived from three genotypes of L. perenne, 2) to perform a comparative analysis of SSR motif polymorphisms between allelic sequences, 3) to conduct a comparative analysis of SSR motif polymorphisms between orthologous sequences of L. perenne, Festuca arundinacea, Brachypodium distachyon, and O. sativa, 4) to identify functionally associated EST-SSR markers for application in comparative genomics and breeding. Results From 25,744 ESTs, representing 8.53 megabases of nucleotide information from three genotypes of L. perenne, 1,458 ESTs (5.7%) contained one or more SSRs. Of these SSRs, 955 (3.7%) were non-redundant. Tri-nucleotide repeats were the most abundant type of repeats followed by di- and tetra-nucleotide repeats. The EST-SSRs from the three genotypes were analysed for allelic- and/or genotypic SSR motif polymorphisms. Most of the SSR motifs (97.7%) showed no polymorphisms, whereas 22 EST-SSRs showed allelic- and/or genotypic polymorphisms. All polymorphisms identified were changes in the number of repeat units. Comparative analysis of the L. perenne EST-SSRs with sequences of Festuca arundinacea, Brachypodium distachyon, and Oryza sativa identified 19 clusters of orthologous sequences between these four species. Analysis of the clusters showed that the SSR motif generally is conserved in the closely related species F. arundinacea, but often differs in length of the SSR

  4. Effects of elevated ultraviolet radiation and endophytic fungi on plant growth and insect feeding in Lolium perenne, Festuca rubra, F. arundinacea and F. pratensis.

    PubMed

    McLeod, A R; Rey, A; Newsham, K K; Lewis, G C; Wolferstam, P

    2001-09-01

    Plants of perennial ryegrass (Lolium perenne L.), red fescue (Festuca rubra L.), tall fescue (F. arundinacea Schreb.) and meadow fescue (F. pratensis Huds) were exposed at an outdoor facility located in Edinburgh, UK to modulated levels of UV-B radiation (280-315 nm) using banks of cellulose diacetate filtered UV-B fluorescent lamps that also produce UV-A radiation (315-400 nm). The plants were derived from a single clone of each species and were grown both with and without colonization by naturally-occurring fungal endophytes. The UV-B treatment was a 30% elevation above the ambient erythemally-weighted level of UV-B during July to October. Growth of treated plants was compared with plants grown under elevated UV-A radiation alone produced by banks of polyester filtered lamps and with plants grown at ambient levels of solar radiation under banks of unenergized lamps. At the end of the treatment period, sample leaves were collected for feeding trials with the desert locust Schistocerca gregaria (Forsk). The UV-B treatment produced no effects on the aboveground biomass of any of the four grasses. The UV-B treatment and the UV-A control exposure both increased plant height and the number of daughter plants formed by rhizome growth in F. rubra. There were significant effects of endophyte presence on the total fresh and dry weights of F. arundinacea and F. rubra, on fresh weight only in F. pratensis, and on the fresh and dry weights of inflorescence in F. arundinacea and L. perenne. There were no effects of UV treatments on the absolute amounts of leaf consumed or on the feeding preferences of locusts for leaves with or without endophyte in three species: F. rubra, F. arundinacea and L. perenne. In F. pratensis there was no effect of UV treatment on the weight of leaves consumed but a significant UV x endophyte interaction caused by a marked change in feeding preference between leaves with and without endophyte that differed between the UV-B treatment and UV-A control

  5. Water use efficiency and shoot biomass production under water limitation is negatively correlated to the discrimination against (13)C in the C3 grasses Dactylis glomerata, Festuca arundinacea and Phalaris arundinacea.

    PubMed

    Mårtensson, Linda-Maria; Carlsson, Georg; Prade, Thomas; Kørup, Kirsten; Lærke, Poul Erik; Jensen, Erik Steen

    2017-04-01

    Climate change impacts rainfall patterns which may lead to drought stress in rain-fed agricultural systems. Crops with higher drought tolerance are required on marginal land with low precipitation or on soils with low water retention used for biomass production. It is essential to obtain plant breeding tools, which can identify genotypes with improved drought tolerance and water use efficiency (WUE). In C3 plant species, the variation in discrimination against (13)C (Δ(13)C) during photosynthesis has been shown to be a potential indicator for WUE, where discrimination against (13)C and WUE were negatively correlated. The aim of this study was to determine the variation in the discrimination against (13)C between species and cultivars of three perennial C3 grasses (Dactylis glomerata (cocksfoot), Festuca arundinacea (tall fescue) and Phalaris arundinacea (reed canary grass)) and test the relationships between discrimination against (13)C, season-long water use WUEB, shoot and root biomass production in plants grown under well-watered and water-limited conditions. The grasses were grown in the greenhouse and exposed to two irrigation regimes, which corresponded to 25% and 60% water holding capacity, respectively. We found negative relationships between discrimination against (13)C and WUEB and between discrimination against (13)C and shoot biomass production, under both the well-watered and water-limited growth conditions (p < 0.001). Discrimination against (13)C decreased in response to water limitation (p < 0.001). We found interspecific differences in the discrimination against (13)C, WUEB, and shoot biomass production, where the cocksfoot cultivars showed lowest and the reed canary grass cultivars highest values of discrimination against (13)C. Cocksfoot cultivars also showed highest WUEB, shoot biomass production and potential tolerance to water limitation. We conclude that discrimination against (13)C appears to be a useful indicator, when selecting C3

  6. Expression of a fungal ferulic acid esterase in suspension cultures of tall fescue (Festuca arundinacea) decreases cell wall feruloylation and increases rates of cell wall digestion.

    PubMed

    Morris, Phillip; Dalton, Sue; Langdon, Tim; Hauck, Barbara; de Buanafina, Marcia M O

    2017-01-01

    In the cell walls of grasses ferulic acid is esterified to arabinosyl residues in arabinoxylans that can then undergo oxidative coupling reactions to form ferulate dehydrodimers, trimers and oligomers which function to cross-link cell-wall polysaccharides, limiting cell wall degradability. Fungal ferulic acid esterase can release both esterified monomeric and dimeric ferulic acids from these cell wall arabinoxylans making the cell wall more susceptible to further enzymatic attack and increasing cell wall degradability. Non-embryogenic cell suspension cultures of Festuca arundinacea expressing a Aspergillus niger ferulic acid esterase (faeA) targeted to either the apoplast, or endoplasmic reticulum under the control of a constitutive actin promoter, or to the vacuole under the control of a soybean heat shock promoter, were established and FAE activity determined in the cells and medium during a growth cycle. Analysis of the ester-linked ferulates of the cell walls showed that all three transformed cell lines had both reduced ferulate levels and increased levels of xylanase mediated release of wall phenolics on autodigestion as well as increased rates of cell wall digestion in a simulated rumen environment, when compared to control non-transformed cells.

  7. Enhanced salt tolerance of transgenic progeny of tall fescue (Festuca arundinacea) expressing a vacuolar Na+/H+ antiporter gene from Arabidopsis.

    PubMed

    Zhao, Junsheng; Zhi, Daying; Xue, Zheyong; Liu, Heng; Xia, Guangmin

    2007-10-01

    Salinity is a major abiotic stress factor limiting crop production. To generate salt-tolerant turf and forage, we had transformed tall fescue (Festuca arundinacea) with AtNHX1, a vacuolar Na(+)/H(+) antiporter gene from Arabidopsis thaliana. In this paper, we report that overexpression of the AtNHX1 gene confers enhanced salt tolerance to the transformed tall fescue progenies. DNA gel blot analysis and reverse transcription (RT) polymerase chain reaction (PCR) were carried out to confirm the inheritance and expression of the AtNHX1 gene in transgenic T(1) and T(2) lines. These transgenic lines showed no phenotypic changes or yield reduction. Plants carrying the AtNHX1 gene were more resistant to a 20 mM NaCl solution than control plants. The roots of the transgenic lines had a higher sodium content than controls, due to an increased Na(+)/H(+) antiporter activity in tonoplast vesicles. Our results suggest that this accumulation of sodium in vacuoles of root cells, mediated by vacuolar Na(+)/H(+) antiporters, reduced the toxic effects of salinity to tall fescue and thus enhanced its salt tolerance.

  8. A simple thin-layer chromatographic method for the detection of ergovaline in leaf sheaths of tall fescue (Festuca arundinacea) infected with Neotyphodium coenophialum.

    PubMed

    Salvat, A E; Godoy, H M

    2001-09-01

    A relatively simple and inexpensive thin-layer chromatographic (TLC) method is described for the detection and semiquantitative measurement of ergovaline in leaf sheaths of tall fescue (Festuca arundinacea). Samples were finely ground and extracted with methanol. The extracts were filtered and the methanol was evaporated. The aqueous residue was extracted with hexane, followed by chloroform at pH 9. The chloroform extract was concentrated and further purified on a preparative silica gel TLC plate, developed with toluene/ethyl acetate/acetonitrile (50:10:40). The ergovaline band was scraped and eluted with methanol. The eluant was concentrated and an aliquot was applied to a silica gel TLC plate. The plate was developed successively with chloroform/acetone/acetic acid (90:10:5) and chloroform/ethanol (9:1). Ergovaline was visualized with p-dimethylaminobenzaldehyde and sulfuric acid. Semiquantitation of ergovaline was achieved by comparison with a known standard of ergotamine, which was shown to have the same Rf as ergovaline in this system. Spike recovery of ergotamine averaged 60%, with a limit of detection of 200 microg/kg of dry tall fescue leaf sheaths. The method was applied to 15 tall fescue samples with varying degrees of fungal infection, and ergovaline was identified in all contaminated samples with endophyte infection above 15%. Thin-layer chromatography may be also applicable for tall fescue seed, where the ergovaline content is usually higher and the amount of interfering pigments is much lower.

  9. Water Deficit Affects Primary Metabolism Differently in Two Lolium multiflorum/Festuca arundinacea Introgression Forms with a Distinct Capacity for Photosynthesis and Membrane Regeneration.

    PubMed

    Perlikowski, Dawid; Czyżniejewski, Mariusz; Marczak, Łukasz; Augustyniak, Adam; Kosmala, Arkadiusz

    2016-01-01

    Understanding how plants respond to drought at different levels of cell metabolism is an important aspect of research on the mechanisms involved in stress tolerance. Furthermore, a dissection of drought tolerance into its crucial components by the use of plant introgression forms facilitates to analyze this trait more deeply. The important components of plant drought tolerance are the capacity for photosynthesis under drought conditions, and the ability of cellular membrane regeneration after stress cessation. Two closely related introgression forms of Lolium multiflorum/Festuca arundinacea, differing in the level of photosynthetic capacity during stress, and in the ability to regenerate their cellular membranes after stress cessation, were used as forage grass models in a primary metabolome profiling and in an evaluation of chloroplast 1,6-bisphosphate aldolase accumulation level and activity, during 11 days of water deficit, followed by 10 days of rehydration. It was revealed here that the introgression form, characterized by the ability to regenerate membranes after rehydration, contained higher amounts of proline, melibiose, galactaric acid, myo-inositol and myo-inositol-1-phosphate involved in osmoprotection and stress signaling under drought. Moreover, during the rehydration period, this form also maintained elevated accumulation levels of most the primary metabolites, analyzed here. The other introgression form, characterized by the higher capacity for photosynthesis, revealed a higher accumulation level and activity of chloroplast aldolase under drought conditions, and higher accumulation levels of most photosynthetic products during control and drought periods. The potential impact of the observed metabolic alterations on cellular membrane recovery after stress cessation, and on a photosynthetic capacity under drought conditions in grasses, are discussed.

  10. Water Deficit Affects Primary Metabolism Differently in Two Lolium multiflorum/Festuca arundinacea Introgression Forms with a Distinct Capacity for Photosynthesis and Membrane Regeneration

    PubMed Central

    Perlikowski, Dawid; Czyżniejewski, Mariusz; Marczak, Łukasz; Augustyniak, Adam; Kosmala, Arkadiusz

    2016-01-01

    Understanding how plants respond to drought at different levels of cell metabolism is an important aspect of research on the mechanisms involved in stress tolerance. Furthermore, a dissection of drought tolerance into its crucial components by the use of plant introgression forms facilitates to analyze this trait more deeply. The important components of plant drought tolerance are the capacity for photosynthesis under drought conditions, and the ability of cellular membrane regeneration after stress cessation. Two closely related introgression forms of Lolium multiflorum/Festuca arundinacea, differing in the level of photosynthetic capacity during stress, and in the ability to regenerate their cellular membranes after stress cessation, were used as forage grass models in a primary metabolome profiling and in an evaluation of chloroplast 1,6-bisphosphate aldolase accumulation level and activity, during 11 days of water deficit, followed by 10 days of rehydration. It was revealed here that the introgression form, characterized by the ability to regenerate membranes after rehydration, contained higher amounts of proline, melibiose, galactaric acid, myo-inositol and myo-inositol-1-phosphate involved in osmoprotection and stress signaling under drought. Moreover, during the rehydration period, this form also maintained elevated accumulation levels of most the primary metabolites, analyzed here. The other introgression form, characterized by the higher capacity for photosynthesis, revealed a higher accumulation level and activity of chloroplast aldolase under drought conditions, and higher accumulation levels of most photosynthetic products during control and drought periods. The potential impact of the observed metabolic alterations on cellular membrane recovery after stress cessation, and on a photosynthetic capacity under drought conditions in grasses, are discussed. PMID:27504113

  11. Influence of short-term drought conditions and subsequent re-watering on the physiology and proteome of Lolium multiflorum/Festuca arundinacea introgression forms, with contrasting levels of tolerance to long-term drought.

    PubMed

    Perlikowski, D; Kosmala, A; Rapacz, M; Kościelniak, J; Pawłowicz, I; Zwierzykowski, Z

    2014-03-01

    Festuca arundinacea is a drought tolerant species. Lolium multiflorum has better forage quality but lower tolerance to abiotic stresses. Their hybrids offer an opportunity to perform research on the molecular basis of tolerance to drought. The aim of this work was to recognise the mechanisms of response to short-term drought (11 days) in a glasshouse in two L. multiflorum/F. arundinacea introgression forms with distinct levels of tolerance to long-term drought (14 weeks) in the field. Measurements of physiological parameters, analyses of protein accumulation profiles using two-dimensional gel electrophoresis, and mass spectrometry identification of proteins, which were accumulated differentially between the selected genotypes during short-term drought, were performed. Genotype 7/6, with lower yield potential during 14 weeks of drought, and lower ability to re-grow after watering, had a higher capacity for photosynthesis during 11 days of drought. Genotype 4/10, more tolerant to long-term drought, was able to repair damaged cell membranes after watering and was also characterised by lower transpiration during short-term drought. A total of 455 proteins were analysed, and the 17 that were differentially accumulated between the two genotypes were identified. The results of physiological and proteomic research led to a hypothesis that the higher photosynthetic capacity of genotype 7/6 could be due to a more efficient Calvin cycle, supported by higher accumulation of crucial proteins involving chloroplast aldolase. © 2013 German Botanical Society and The Royal Botanical Society of the Netherlands.

  12. Detection of kestoses and kestose-related oligosaccharides in extracts of Festuca arundinacea, Dactylis glomerate L. , and Asparagus officinalis L. root cultures and invertase by sup 13 C and sup 1 H nuclear magnetic resonance spectroscopy

    SciTech Connect

    Forsythe, K.L.; Feather, M.S.; Gracz, H.; Wong, T.C. )

    1990-04-01

    Previous studies show that {sup 13}C nuclear magnetic resonance spectroscopy can be used to detect and identify mixtures of 1-kestose and neokestose after conversion to the acetate derivatives. In this study, unequivocal assignments are made for the anomeric carbon and proton signals for the above two trisaccharide acetates as well as for 6-kestose hendecaacetate and for nystose tetradecaacetate (a 1-kestose-derived tetrasaccharide). A number of oligosaccharide fractions were isolated from several plant species, converted to the acetates, and nuclear magnetic resonance spectra obtained. Using the above reference data, the following information was obtained. The trisaccharide fraction from Dactylis gomerata L. stem tissue and Asparagus officinalis L. roots contain both 1-kestose and neokestose, and the tetrasaccharide fractions contain three components, one of which is nystose. Penta- and hexasaccharide acetates were also isolated from A. officinalis L. roots and were found to contain, respectively, four and at least five components. All components of both of the above species appear to contain a kestose residue and to be produced by the sequential addition of fructofuranosyl units to these. The trisaccharide fraction from Festuca arundinacea is complex, and contains at least five different components, two of which appear to be 1-kestose and neokestose.

  13. Effects of untreated and treated wastewater at the morphological, physiological and biochemical levels on seed germination and development of sorghum (Sorghum bicolor (L.) Moench), alfalfa (Medicago sativa L.) and fescue (Festuca arundinacea Schreb.).

    PubMed

    Rekik, Imen; Chaabane, Zayneb; Missaoui, Amara; Bouket, Ali Chenari; Luptakova, Lenka; Elleuch, Amine; Belbahri, Lassaad

    2017-03-15

    Wastewater reuse in agriculture may help mitigate water scarcity. This may be reached if high quality treatments removing harmful pollutants are applied. The aim of the present study was to compare the effect of untreated (UTW) and treated wastewater (TW) on germination and seedlings development of alfalfa (Medicago sativa L.), fescue (Festuca arundinacea Schreb.) and sorghum (Sorghum bicolor (L.) Moench). UTW presented high turbidity (130 NTU), chemical and biological oxygen demand (COD, 719mgL(-1), BOD5, 291mgL(-1)) and metal concentrations. These levels caused mortality (18% for fescue), decreased germination speed in seeds (37.5% for alfalfa) and reductions of root and stem length in seedlings (80% and 22% respectively for alfalfa). Adverse effects on seeds germination were reflected at the biochemical level by increased H2O2 levels (6 times for sorghum after 5days) and by increased Malondialdehyde (MDA) levels (more than 600 times for sorghum roots) during seedlings development. When TW was used, these parameters were close to control seeds ones. They were also dependent on plant species and developmental stage. Therefore, for efficient reclaimed wastewater reuse in irrigation, suitable crops, displaying wide tolerance to toxic contents during germination and later seedling development stages have to be selected.

  14. Baculovirus infection of the armyworm (Lepidoptera:Noctuidae) feeding on spiny- or smooth-edged grass (Festuca spp.) leaf blades

    USDA-ARS?s Scientific Manuscript database

    Susceptibility of the armyworm, Mythimna unipuncta (Haworth), to infection by a baculovirus isolated from a Kentucky armyworm population was compared on two suspected progenitors of tall fescue, Festuca mairei and Festuca arundinacea subsp. fenas, with spiny leaf margins intact or removed to test wh...

  15. Interaction of heavy metals and pyrene on their fates in soil and tall fescue (Festuca arundinacea).

    PubMed

    Lu, Mang; Zhang, Zhong-Zhi; Wang, Jing-Xiu; Zhang, Min; Xu, Yu-Xin; Wu, Xue-Jiao

    2014-01-21

    90-Day growth chamber experiments were performed to investigate the interactive effect of pyrene and heavy metals (Cu, Cd, and Pb) on the growth of tall fescue and its uptake, accumulation, and dissipation of heavy metals and pyrene. Results show that plant growth and phytomass production were impacted by the interaction of heavy metals and pyrene. They were significantly decreased with heavy metal additions (100-2000 mg/kg), but they were only slightly declined with pyrene spiked up to 100 mg/kg. The addition of a moderate dosage of pyrene (100 mg/kg) lessened heavy metal toxicity to plants, resulting in enhanced plant growth and increased metal accumulation in plant tissues, thus improving heavy metal removal by plants. In contrast, heavy metals always reduced both plant growth and pyrene dissipation in soils. The chemical forms of Cu, Cd, and Pb in plant organs varied with metal species and pyrene addition. The dissipation and mineralization of pyrene tended to decline in both planted soil and unplanted soils with the presence of heavy metals, whereas they were enhanced with planting. The results demonstrate the complex interactive effects of organic pollutants and heavy metals on phytoremediation in soils. It can be concluded that, to a certain extent, tall fescue may be useful for phytoremediation of pyrene-heavy metal-contaminated sites. Further work is needed to enhance methods for phytoremediation of heavy metal-organics co-contaminated soil.

  16. Tiller production in cocksfoot (Dactylis glomerata) and tall fescue (Festuca arundinacea) growing along a light gradient

    USDA-ARS?s Scientific Manuscript database

    Pasture managers seek to balance leaf appearance with leaf utilization to meet livestock nutritional needs and sustain sward productivity. Achieving this balance when managing forages in silvopasture, requires techniques that account for the influence of light and defoliation on tiller appearance a...

  17. Transcriptomes of Lolium/Schedonorus/Festuca species

    USDA-ARS?s Scientific Manuscript database

    ESTs from normalized cDNA libraries of tall fescue with Neotyphodium coenophialum and meadow fescue with Epichloë festucae have been sequenced. The meadow fescue libraries were from RNA isolated from immature tillers of meadow fescue symbiotic with E. festucae, displaying normal inflorescences and ...

  18. Transcriptomes of Lolium/Schedonorus/Festuca Species

    USDA-ARS?s Scientific Manuscript database

    ESTs from normalized cDNA libraries of tall fescue with Neotyphodium coenophialum and meadow fescue with Epichloë festucae have been sequenced. The meadow fescue libraries were from RNA isolated from immature tillers of meadow fescue symbiotic with E. festucae, displaying normal inflorescences and ...

  19. Transcriptomes of Lolium/Schedonorus/Festuca species

    USDA-ARS?s Scientific Manuscript database

    Molecular tools for forage grasses are presently sparse. In order to make available these tools for the community, a large scale sequencing effort has been conducted. Roughly 140,000 cDNA clones from normalized libraries obtained from meadow fescue/Epichloe festucae inflorescences and stromata and t...

  20. The Effects of Temperature on Germination of Eleven Festuca Cultivars.

    DTIC Science & Technology

    1997-08-01

    Schreb.) had the greatest germination percentage, and "Arctared" red fescue ( Festuca rubra L.) had the least when averaged across the five temperatures...Many studies have shown that water potential at planting affects the germination rate and final germination of Festuca cultivars. Limited information...is available about the extent of variability in temperature-dependence of germination among different Festuca cultivars. Our objective was to study

  1. Association Analysis of Simple Sequence Repeat (SSR) Markers with Agronomic Traits in Tall Fescue (Festuca arundinacea Schreb.)

    PubMed Central

    Chen, Liang; Sun, Xiaoyan; Yang, Yong; Liu, Hongmei; Xu, Qingguo

    2015-01-01

    Tall fescue is widely used in temperate regions throughout the world as a dominant forage grass as well as a turfgrass, in pastoral and turf industry. However, the utilization of tall fescue was limited because of its leaf roughness, poor regeneration ability and poor stress resistance. New cultivars were desirable in modern pastoral industries exceed the potential of existing cultivars. Therefore, well understanding the agronomic traits and describing germplasms would help to overcome these constraints, and morphological evaluation of tall fescue germplasm is the key component in selecting rational parents for hybridization breeding. However, describing the morphological traits of tall fescue germplasm is costly and time-consuming. Fortunately, biotechnology approaches can supplement conventional breeding efforts for tall fescue improvement. Association mapping, as a powerful approach to identify association between agronomic traits and molecular markers has been widely used for enhancing the utilization, conservation and management of the tall fescue germplasms. Therefore, in the present research, 115 tall fescue accessions from different origins (25 accessions are cultivars; 31 accessions from America; 32 accessions from European; 7 accessions from Africa; 20 accessions from Asia), were evaluated for agronomic traits and genetic diversity with 90 simple sequence repeat (SSR) markers. The panel displayed significant variation in spike count per plant (SCP) and spike weight (SW). However, BCS performed the lowest CV among all the observed agronomic traits. Three subpopulations were identified within the collections but no obvious relative kinship (K) was found. The GLM model was used to describe the association between SSR and agronomic traits. Fifty-one SSR markers associated with agronomic traits were observed. Twelve single-associated markers were associated with PH; six single-associated markers were associated with BCS; eight single-associated markers were associated with SW; five single-associated markers were associated with SC; seven single-associated markers were associated with SCP; three single-associated markers were associated with SL. Especially, we observed that the genetic variation of SW was explained 11.6 % by M37 marker. It is interesting to observe that nine markers (M1, M2, M35, M54 marker was associated with both BCS and SC; M3, M4 markers were associated with BCS, SW, and SC; M19 marker was associated with both pH and PD, M40 marker was associated with both SCP and SW; and M193 marker was associated with both PH and SL) were associated with more than two agronomic traits. Notably, Branch count per spike (BCS) was explained by four markers (M1, M2, M3, and M4) exceeding 10 %. These identified marker alleles associated with agronomic traits could provide important information and markers for molecular-assisted breeding that facilitate the breeding process in tall fescue. PMID:26186338

  2. He-Ne laser preillumination improves the resistance of tall fescue (Festuca arundinacea Schreb.) seedlings to high saline conditions.

    PubMed

    Gao, Li-Mei; Li, Yong-Feng; Han, Rong

    2015-07-01

    In this paper, we explored the protective effect and physiochemical mechanism of He-Ne laser preillumination in enhancement of tall fescue seedlings tolerance to high salt stress. The results showed that salt stress greatly reduced plant growth, plant height, biomass, leaf development, ascorbate acid (AsA) and glutathione (GSH) concentration, the enzymatic activities, and gene expression levels of antioxidant enzymes such as catalase (CAT) and glutathione reductase (GR) and enhanced hydrogen peroxide (H2O2) content, superoxide radical (O2 (·-)) generation rates, membrane lipid peroxidation, relative electrolyte leakage, the enzymatic activities, and gene expression levels of superoxide dismutase (SOD), ascorbate peroxidase (APX), and peroxidase (POD), compared with controls. However, He-Ne laser preillumination significantly reversed plant growth retardation, biomass loss, and leaves development decay induced by salt stress. And the values of the physiochemical parameters observed in salt-stressed plants were partially reverted or further increased by He-Ne laser. Salt stress had no obvious effect on the transcriptional activity of phytochromeB, whereas He-Ne laser markedly enhanced its transcriptional level. Preillumination with white fluorescent lamps (W), red light (RL) of the same wavelength, or RL, then far-red light (FRL) had not alleviated the inhibitory effect of salt stress on plant growth and antioxidant enzymes activities, suggesting that the effect of He-Ne laser on improved salt tolerance was most likely attributed to the induction of phytochromeB transcription activities by the laser preillumination, but not RL, FRL or other light sources. In addition, we also utilized sodium nitroprusside (SNP) as NO donor to pre-treat tall fescue seedlings at the same conditions, and further evaluated the differences of physiological effects between He-Ne laser and NO in increasing salt resistance of tall fescue. Taken together, our data illustrated that He-Ne laser preillumination contributed to conferring an increased tolerance to salt stress in tall fescue seedlings due to alleviating oxidative damage through scavenging free radicals and inducing transcriptional activities of some genes involved in plant antioxidant system, and the induction of phytochromeB transcriptional level by He-Ne laser was probably correlated with these processes. Moreover, this positive physiochemical effect seemed more effective with He-Ne laser than NO molecule.

  3. Effects of pseudo-microgravity on symbiosis between endophyte, Neotyphodium, and its host plant, tall fescue (Festuca arundinacea)

    NASA Astrophysics Data System (ADS)

    Tomita-Yokotani, K.; Wakabayashi, K.; Hiraishi, K.; Yoshida, S.; Hashimoto, H.; Shinozaki, S.; Yamashita, M.

    Endophyte is a group of microbes that symbiotically live in plant body Endophyte provides host plant its metabolites that protect the plant from insect pests In addition to this host plants are resistive against environmental stress In general endophyte lives in seeds to seeds of the infected plants through multiple generations The infection of fungi has never been observed and their original pathway is still unknown in nature The aim of this study is to examine whether this stable symbiosis between endophytes and its host plant would be modified under pseudo-microgravity or not We also aim to observe the infection under an exotic environment in terms of gravity We found that the internal hyphae of both the incubated plant under pseudo-microgravity and the ground control became indistinct with the number of incubation days A part of the endophyte in the seed under its autolysis was suggested because the amount of fungi in the base of the shoot that was observed with the incubated plant under the ground control was far less than that in the seed before sowing Hyphae began to grow in the germinating seed after a 3-day incubation period However a lot of aggregated fungi still existed in the 3-day incubated seed under pseudo-microgravity Moreover hyphae in the 3-day incubated seed under pseudo-microgravity were more indistinctly than that under the ground control The fungi were observed in the boundary of the seed and the shoot of the 5-day incubated seed under the ground control but not under pseudo-microgravity By this observation it was suggested that

  4. Evolutionary history of tall fescue morphotypes inferred from molecular phylogenetics of the Lolium-Festuca species complex

    PubMed Central

    2010-01-01

    Background The agriculturally important pasture grass tall fescue (Festuca arundinacea Schreb. syn. Lolium arundinaceum (Schreb.) Darbysh.) is an outbreeding allohexaploid, that may be more accurately described as a species complex consisting of three major (Continental, Mediterranean and rhizomatous) morphotypes. Observation of hybrid infertility in some crossing combinations between morphotypes suggests the possibility of independent origins from different diploid progenitors. This study aims to clarify the evolutionary relationships between each tall fescue morphotype through phylogenetic analysis using two low-copy nuclear genes (encoding plastid acetyl-CoA carboxylase [Acc1] and centroradialis [CEN]), the nuclear ribosomal DNA internal transcribed spacer (rDNA ITS) and the chloroplast DNA (cpDNA) genome-located matK gene. Other taxa within the closely related Lolium-Festuca species complex were also included in the study, to increase understanding of evolutionary processes in a taxonomic group characterised by multiple inter-specific hybridisation events. Results Putative homoeologous sequences from both nuclear genes were obtained from each polyploid species and compared to counterparts from 15 diploid taxa. Phylogenetic reconstruction confirmed F. pratensis and F. arundinacea var. glaucescens as probable progenitors to Continental tall fescue, and these species are also likely to be ancestral to the rhizomatous morphotype. However, these two morphotypes are sufficiently distinct to be located in separate clades based on the ITS-derived data set. All four of the generated data sets suggest independent evolution of the Mediterranean and Continental morphotypes, with minimal affinity between cognate sequence haplotypes. No obvious candidate progenitor species for Mediterranean tall fescues were identified, and only two putative sub-genome-specific haplotypes were identified for this morphotype. Conclusions This study describes the first phylogenetic analysis of

  5. Green synthesis of silver nanoparticle using Bambusa arundinacea leaves

    NASA Astrophysics Data System (ADS)

    Kataria, Bharat; Shyam, Vasvani; Kaushik, Babiya; Vasoya, Jaydeep; Joseph, Joyce; Savaliya, Chirag; Kumar, Sumit; Parikh, Sachin P.; Thakar, C. M.; Pandya, D. D.; Ravalia, A. B.; Markna, J. H.; Shah, N. A.

    2017-05-01

    The synthesis of nanoparticles using ecofriendly way is an interesting area in advance nanotechnology. Silver (Ag) nanoparticles are usually synthesized by chemicals route, which are quite flammable and toxic in nature. This study deals with a biosynthesis process (environment friendly) of silver nanoparticles using Bambusa arundinacea leaves for its antibacterial activity. The formation and characterization of AgNPs was confirmed by UV-Vis spectroscopy. Silver nanoparticles were successfully synthesized from AgNO3 through a simple green route using the latex of Bambusa arundinacea leaves as reducing as well as capping agent. Scanning Electron Microscopy (SEM) study indicates the formation of grains (particles) with different size and shape.

  6. Intrapopulation Genome Size Dynamics in Festuca pallens

    PubMed Central

    Šmarda, Petr; Bureš, Petr; Horová, Lucie; Rotreklová, Olga

    2008-01-01

    Background and Aims It is well known that genome size differs among species. However, information on the variation and dynamics of genome size in wild populations and on the early phase of genome size divergence between taxa is currently lacking. Genome size dynamics, heritability and phenotype effects are analysed here in a wild population of Festuca pallens (Poaceae). Methods Genome size was measured using flow cytometry with DAPI dye in 562 seedlings from 17 maternal plants varying in genome size. The repeatability of genome size measurements was verified at different seasons through the use of different standards and with propidium iodide dye; the range of variation observed was tested via analysis of double-peaks. Additionally, chromosome counts were made in selected seedlings. Key Results and Conclusions Analysis of double-peaks showed that genome size varied up to 1·188-fold within all 562 seedlings, 1·119-fold within the progeny of a single maternal plant and 1·117-fold in seedlings from grains of a single inflorescence. Generally, genome sizes of seedlings and their mothers were highly correlated. However, in maternal plants with both larger and smaller genomes, genome sizes of seedlings were shifted towards the population median. This was probably due to the frequency of available paternal genomes (pollen grains) in the population. There was a stabilizing selection on genome size during the development of seedlings into adults, which may be important for stabilizing genome size within species. Furthermore, a positive correlation was found between genome size and the development rate of seedlings. A larger genome may therefore provide a competitive advantage, perhaps explaining the higher proportion of plants with larger genomes in the population studied. The reason for the observed variation may be the recent induction of genome size variation, e.g. by activity of retrotransposons, which may be preserved in the long term by the segregation of

  7. Metal cotolerance to copper, lead, and zinc in Festuca rubra

    SciTech Connect

    Wong, M.H.

    1982-10-01

    Tillers of red fescue (Festuca rubra) were collected from three copper-contaminated sites: Prescot (Lancashire, near the copper refinery factory), Great Orme (Clwyd, copper mine), and Ecton (Staffordshire, copper mine), as well as from an uncontaminated area (Festuca rubra S59). By comparing their indexes of tolerance, it was discovered that tillers from Ecton which contained a rather high level of copper, lead, and zinc were tolerant to all three metals. This variety of F. rubra would be useful for reclaiming nonferrous mine spoils which contain a high level of the three commonly occurring heavy metals, i.e., copper, lead and zinc.

  8. Models Analyses for Allelopathic Effects of Chicory at Equivalent Coupling of Nitrogen Supply and pH Level on F. arundinacea, T. repens and M. sativa

    PubMed Central

    Wang, Quanzhen; Xie, Bao; Wu, Chunhui; Chen, Guo; Wang, Zhengwei; Cui, Jian; Hu, Tianming; Wiatrak, Pawel

    2012-01-01

    Alllelopathic potential of chicory was investigated by evaluating its effect on seed germination, soluble sugar, malondialdehyde (MDA) and the chlorophyll content of three target plants species (Festuca arundinacea, Trifolium repens and Medicago sativa). The secretion of allelochemicals was regulated by keeping the donor plant (chicory) separate from the three target plant species and using different pH and nitrogen levels. Leachates from donor pots with different pH levels and nitrogen concentrations continuously irrigated the target pots containing the seedlings. The allelopathic effects of the chicory at equivalent coupling of nitrogen supply and pH level on the three target plants species were explored via models analyses. The results suggested a positive effect of nitrogen supply and pH level on allelochemical secretion from chicory plants. The nitrogen supply and pH level were located at a rectangular area defined by 149 to 168 mg/l nitrogen supply combining 4.95 to 7.0 pH value and point located at nitrogen supply 177 mg/l, pH 6.33 when they were in equivalent coupling effects; whereas the inhibitory effects of equivalent coupling nitrogen supply and pH level were located at rectangular area defined by 125 to 131 mg/l nitrogen supply combining 6.71 to 6.88 pH value and two points respectively located at nitrogen supply 180 mg/l with pH 6.38 and nitrogen supply 166 mg/l with pH 7.59. Aqueous extracts of chicory fleshy roots and leaves accompanied by treatment at different sand pH values and nitrogen concentrations influenced germination, seedling growth, soluble sugar, MDA and chlorophyll of F. arundinacea, T. repens and M. sativa. Additionally, we determined the phenolics contents of root and leaf aqueous extracts, which were 0.104% and 0.044% on average, respectively. PMID:22384054

  9. Models analyses for allelopathic effects of chicory at equivalent coupling of nitrogen supply and pH level on F. arundinacea, T. repens and M. sativa.

    PubMed

    Wang, Quanzhen; Xie, Bao; Wu, Chunhui; Chen, Guo; Wang, Zhengwei; Cui, Jian; Hu, Tianming; Wiatrak, Pawel

    2012-01-01

    Alllelopathic potential of chicory was investigated by evaluating its effect on seed germination, soluble sugar, malondialdehyde (MDA) and the chlorophyll content of three target plants species (Festuca arundinacea, Trifolium repens and Medicago sativa). The secretion of allelochemicals was regulated by keeping the donor plant (chicory) separate from the three target plant species and using different pH and nitrogen levels. Leachates from donor pots with different pH levels and nitrogen concentrations continuously irrigated the target pots containing the seedlings. The allelopathic effects of the chicory at equivalent coupling of nitrogen supply and pH level on the three target plants species were explored via models analyses. The results suggested a positive effect of nitrogen supply and pH level on allelochemical secretion from chicory plants. The nitrogen supply and pH level were located at a rectangular area defined by 149 to 168 mg/l nitrogen supply combining 4.95 to 7.0 pH value and point located at nitrogen supply 177 mg/l, pH 6.33 when they were in equivalent coupling effects; whereas the inhibitory effects of equivalent coupling nitrogen supply and pH level were located at rectangular area defined by 125 to 131 mg/l nitrogen supply combining 6.71 to 6.88 pH value and two points respectively located at nitrogen supply 180 mg/l with pH 6.38 and nitrogen supply 166 mg/l with pH 7.59. Aqueous extracts of chicory fleshy roots and leaves accompanied by treatment at different sand pH values and nitrogen concentrations influenced germination, seedling growth, soluble sugar, MDA and chlorophyll of F. arundinacea, T. repens and M. sativa. Additionally, we determined the phenolics contents of root and leaf aqueous extracts, which were 0.104% and 0.044% on average, respectively.

  10. Phalaris arundinacea (reed canarygrass) grass staggers in beef cattle.

    PubMed

    Binder, Ellen M; Blodgett, Dennis J; Currin, John F; Caudell, David; Cherney, Jerry H; LeRoith, Tanya

    2010-09-01

    Four adult mixed-breed beef cows from a cow-calf operation in West Virginia were referred to the Virginia-Maryland Regional College of Veterinary Medicine in March 2009 with weakness, ataxia, hind limb paresis progressing to lateral recumbency, and death within 2-3 days. Histologically, there was accumulation of light brown, granular pigment in neurons of the ventral gray horns of the spinal cord (more severe in thoracic and lumbar sections), brain stem, and pons, resulting in distortion and bulging of the cell body and displacement of the Nissl substance, suggestive of Phalaris sp. grass toxicosis. The most severely affected cow had accumulation of dark green-brown pigment in renal tubular epithelial cells. Reed canarygrass (Phalaris arundinacea) was identified in pastures, and the concentration of tryptamine alkaloids in new leaf blades was approximately 0.2% on a wet weight basis. These alkaloids are serotonergic receptor agonists, resulting in neurologic "staggers" in ruminants. Delayed onset times of up to 4-5 months have been reported in sheep after removal from Phalaris sp. pastures. Distribution of pigment in serotonergic tracts of the midbrain, brain stem, and spinal cord with Phalaris sp. toxicoses is distinct and differs from lipofuscin. Electron microscopy confirmed that the pigment was not lipofuscin. From these findings, a diagnosis of delayed P. arundinacea toxicosis was made. Over a 2-month period, 18 cows died with similar clinical signs.

  11. Marker-trait association of rangeland and turf traits in hybrids of Festuca idahoensis and Festuca ovina

    USDA-ARS?s Scientific Manuscript database

    The fine fescue species Festuca idahoensis Elmer is native to the Intermountain West and has potential for low-input turf and rangeland applications. The poor seed production and weak seedling vigor of this species may be overcome by identification and improvement of interspecific hybrids between F...

  12. Comparative interpretation of the development of species Phalaris arundinacea

    NASA Astrophysics Data System (ADS)

    Ionel, Samfira; Andreea, Ghica; Marius, Boldea; Monica, Butnariu; Marius, Sendroni; Andrei, M.-Kiss

    2013-10-01

    The development of the morpho-productive features of species Phalaris arundinacea was studied from 2011 to 2012. The study dwelt on a collection of 1000 of the Romanian Premier cultivar and a Polycross field, set in Banat Plain. We assessed the dynamics of the following morpho-productive features: plant height, number of shoots, number of leaves, leaf width, leaf length, and foliar area of a shoot, in accordance with the BBCH code. The growth dynamics of the previously mentioned mean morpho-productive features were measured every 7 days in 20 clones of the Premier. Our findings revealed that the growth dynamics under the conditions provided on the plain area involve the height growth of 0.96 cm/day. In addition, height growth presents significantly positive correlation with the increase of the foliar area of a shoot, as well as of the entire plant.

  13. Stress memory induced rearrangements of HSP transcription, photosystem II photochemistry and metabolism of tall fescue (Festuca arundinacea Schreb.) in response to high-temperature stress

    PubMed Central

    Hu, Tao; Liu, Shu-Qian; Amombo, Erick; Fu, Jin-Min

    2015-01-01

    When plants are pre-exposed to stress, they can produce some stable signals and physiological reactions that may be carried forward as “stress memory”. However, there is insufficient information about plants' stress memory responses mechanisms. Here, two tall fescue genotypes, heat-tolerant PI 574522 and heat-sensitive PI 512315, were subjected to recurring high-temperature pre-acclimation treatment. Two heat shock protein (HSP) genes, LMW-HSP and HMW-HSP, exhibited transcriptional memory for their higher transcript abundance during one or more subsequent stresses (S2, S3, S4) relative to the first stress (S1), and basal transcript levels during the recovery states (R1, R2, and R3). Activated transcriptional memory from two trainable genes could persist up to 4 days, and induce higher thermotolerance in tall fescue. This was confirmed by greater turf quality and lower electrolyte leakage. Pre-acclimation treatment inhibited the decline at steps of O-J-I-P and energy transport fluxes in active Photosystem II reaction center (PSII RC) for both tall fescue genotypes. The heat stress memory was associated with major shifts in leaf metabolite profiles. Furthermore, there was an exclusive increase in leaf organic acids (citric acid, malic acid, tris phosphoric acid, threonic acid), sugars (sucrose, glucose, idose, allose, talose, glucoheptose, tagatose, psicose), amino acids (serine, proline, pyroglutamic acid, glycine, alanine), and one fatty acid (butanoic acid) in pre-acclimated plants. These observations involved in transcriptional memory, PSII RC energy transport and metabolite profiles could provide new insights into the plant high–temperature response process. PMID:26136755

  14. Efficient targeted mutagenesis in Epichloë festucae using a split marker system.

    PubMed

    Rahnama, M; Forester, N; Ariyawansa, K G S U; Voisey, C R; Johnson, L J; Johnson, R D; Fleetwood, D J

    2017-03-01

    A split-marker system for targeted gene deletion was developed for the model grass endophytic fungus Epichloë festucae. Compared to the conventional system that yields up to 25% homologous recombinants, the method resulted in 33-74% targeted deletions in E. festucae using as little as 1.5kb of targeting sequence.

  15. Interactions between Metopolophium festucae cerealium (Hemiptera: Aphididae) and Barley yellow dwarf virus (BYDV-PAV)

    PubMed Central

    Sadeghi, S. E.; Bjur, J.; Ingwell, L.; Unger, L.; Bosque-Pérez, N. A.; Eigenbrode, S. D.

    2016-01-01

    Interactions between an invasive aphid, Metopolophium festucae (Theobald) subsp. cerealium, and Barley yellow dwarf virus (BYDV-PAV) were studied under laboratory conditions. M. festucae cerealium is an economic pest of wheat and barley that has recently been found in high population densities in wheat in the Pacific Northwest of the United States. BYDV-PAV is the most prevalent and injurious species of BYDV worldwide and in the Pacific Northwest. Although M. festucae sensu stricto (Theobald 1917) has been reported previously as a vector of some BYDV isolates, there is no confirmed transmission of BYDV by M. festucae cerealium. Two experiments examined the ability of M. festucae cerealium to transmit BYDV-PAV. The first used single aphids caged to indicator plants of a BYDV-susceptible winter wheat cultivar and the second used multiple aphids on each test plant. M. festucae cerealium did not transmit BYDV-PAV in either experiment, whereas transmission by a known BYDV vector, Rhopalosiphum padi L., was consistently high (≥93%). A third experiment compared the intrinsic growth rate, days until first reproduction and daily reproduction by M. festucae cerealium on sham-inoculated and BYDV-PAV-infected wheat, but detected no differences. The findings are reviewed in light published data on M. festucae species, BYDV transmission, and the potential pest status of this new invading aphid. PMID:26896673

  16. Development of fine-leaved Festuca grass for forage and wildfire control in the Great Basin

    USDA-ARS?s Scientific Manuscript database

    Drought and heat tolerant fine-leaved fescue (Festuca ssp.) grasses have potential as components in rangeland greenstrips for wildfire control in semi-arid climates, although such grasses have not been evaluated under rangeland conditions. Therefore, 64 geographically diverse Festuca accessions of ...

  17. Exploiting repetitive sequences and BAC clones in Festuca pratensis karyotyping.

    PubMed

    Majka, Joanna; Książczyk, Tomasz; Kiełbowicz-Matuk, Agnieszka; Kopecký, David; Kosmala, Arkadiusz

    2017-01-01

    The Festuca genus is thought to be the most numerous genus of the Poaceae family. One of the most agronomically important forage grasses, Festuca pratensis Huds. is treated as a model plant to study the molecular mechanisms associated with tolerance to winter stresses, including frost. However, the precise mapping of the genes governing stress tolerance in this species is difficult as its karyotype remains unrecognized. Only two F. pratensis chromosomes with 35S and 5S rDNA sequences can be easily identified, but its remaining chromosomes have not been distinguished to date. Here, two libraries derived from F. pratensis nuclear DNA with various contents of repetitive DNA sequences were used as sources of molecular probes for fluorescent in situ hybridisation (FISH), a BAC library and a library representing sequences most frequently present in the F. pratensis genome. Using FISH, six groups of DNA sequences were revealed in chromosomes on the basis of their signal position, including dispersed-like sequences, chromosome painting-like sequences, centromeric-like sequences, knob-like sequences, a group without hybridization signals, and single locus-like sequences. The last group was exploited to develop cytogenetic maps of diploid and tetraploid F. pratensis, which are presented here for the first time and provide a remarkable progress in karyotype characterization.

  18. Landscape composition and configuration predict the abundance of Phalaris arundinacea L. in Wisconsin wetlands

    USDA-ARS?s Scientific Manuscript database

    Reed canary grass (Phalaris arundinacea L.) is one of the most dominant wetland invaders in North America over the past century. The expansion of urbanization and intensification of agriculture have caused increased sedimentation and eutrophication of wetlands, which have been shown to encourage re...

  19. Leaf Senescence in a Nonyellowing Mutant of Festuca pratensis1

    PubMed Central

    Davies, T. G. Emyr; Thomas, Howard; Thomas, Barry J.; Rogers, Lyndon J.

    1990-01-01

    In a mutant genotype of Festuca pratensis Huds., net degradation of a number of thylakoid membrane proteins during senescence is impaired. Previous studies have suggested that the highly hydrophobic intrinsic chlorophyll-binding proteins were the definitive subjects of the metabolic lesion. In the present study we find that cytochrome f, as determined by haem-staining, Western blotting, enzyme-linked immunosorbent assay, and immunogold electron microscopy, is also abnormally stable in the mutant. The structural feature common to all the proteins in the mutant so far recognized to be abnormally stable is possession of a tetrapyrrole prosthetic group. It is suggested that degradation of chlorophyll and haem may regulate degradation of the associated apoproteins, and hence has an important role to play in membrane protein turnover and in mobilisation of amino acids during chloroplast disassembly. Images Figure 1 Figure 3 Figure 4 Figure 5 PMID:16667508

  20. Fungal Endophyte (Epichloë festucae) Alters the Nutrient Content of Festuca rubra Regardless of Water Availability

    PubMed Central

    Vázquez-de-Aldana, Beatriz R.; García-Ciudad, Antonia; García-Criado, Balbino; Vicente-Tavera, Santiago; Zabalgogeazcoa, Iñigo

    2013-01-01

    Festuca rubra plants maintain associations with the vertically transmitted fungal endophyte Epichloë festucae. A high prevalence of infected host plants in semiarid grasslands suggests that this association could be mutualistic. We investigated if the Epichloë-endophyte affects the growth and nutrient content of F. rubra plants subjected to drought. Endophyte-infected (E+) and non-infected (E−) plants of two half-sib lines (PEN and RAB) were subjected to three water availability treatments. Shoot and root biomass, nutrient content, proline, phenolic compounds and fungal alkaloids were measured after the treatments. The effect of the endophyte on shoot and root biomass and dead leaves depended on the plant line. In the PEN line, E+ plants had a greater S:R ratio than E-, but the opposite occurred in RAB. In both plant lines and all water treatments, endophyte-infected plants had greater concentrations of N, P and Zn in shoots and Ca, Mg and Zn in roots than E- plants. On average, E+ plants contained in their shoots more P (62%), Zn (58%) and N (19%) than E- plants. While the proline in shoots increased in response to water stress, the endophyte did not affect this response. A multivariate analysis showed that endophyte status and plant line impose stronger differences in the performance of the plants than the water stress treatments. Furthermore, differences between PEN and RAB lines seemed to be greater in E- than in E+ plants, suggesting that E+ plants of both lines are more similar than those of their non-infected version. This is probably due to the endophyte producing a similar effect in both plant lines, such as the increase in N, P and Zn in shoots. The remarkable effect of the endophyte in the nutrient balance of the plants could help to explain the high prevalence of infected plants in natural grasslands. PMID:24367672

  1. Fungal endophyte (Epichloë festucae) alters the nutrient content of Festuca rubra regardless of water availability.

    PubMed

    Vázquez-de-Aldana, Beatriz R; García-Ciudad, Antonia; García-Criado, Balbino; Vicente-Tavera, Santiago; Zabalgogeazcoa, Iñigo

    2013-01-01

    Festuca rubra plants maintain associations with the vertically transmitted fungal endophyte Epichloë festucae. A high prevalence of infected host plants in semiarid grasslands suggests that this association could be mutualistic. We investigated if the Epichloë-endophyte affects the growth and nutrient content of F. rubra plants subjected to drought. Endophyte-infected (E+) and non-infected (E-) plants of two half-sib lines (PEN and RAB) were subjected to three water availability treatments. Shoot and root biomass, nutrient content, proline, phenolic compounds and fungal alkaloids were measured after the treatments. The effect of the endophyte on shoot and root biomass and dead leaves depended on the plant line. In the PEN line, E+ plants had a greater S:R ratio than E-, but the opposite occurred in RAB. In both plant lines and all water treatments, endophyte-infected plants had greater concentrations of N, P and Zn in shoots and Ca, Mg and Zn in roots than E- plants. On average, E+ plants contained in their shoots more P (62%), Zn (58%) and N (19%) than E- plants. While the proline in shoots increased in response to water stress, the endophyte did not affect this response. A multivariate analysis showed that endophyte status and plant line impose stronger differences in the performance of the plants than the water stress treatments. Furthermore, differences between PEN and RAB lines seemed to be greater in E- than in E+ plants, suggesting that E+ plants of both lines are more similar than those of their non-infected version. This is probably due to the endophyte producing a similar effect in both plant lines, such as the increase in N, P and Zn in shoots. The remarkable effect of the endophyte in the nutrient balance of the plants could help to explain the high prevalence of infected plants in natural grasslands.

  2. Remodeling of Leaf Cellular Glycerolipid Composition under Drought and Re-hydration Conditions in Grasses from the Lolium-Festuca Complex.

    PubMed

    Perlikowski, Dawid; Kierszniowska, Sylwia; Sawikowska, Aneta; Krajewski, Paweł; Rapacz, Marcin; Eckhardt, Änne; Kosmala, Arkadiusz

    2016-01-01

    Drought tolerant plant genotypes are able to maintain stability and integrity of cellular membranes in unfavorable conditions, and to regenerate damaged membranes after stress cessation. The profiling of cellular glycerolipids during drought stress performed on model species such as Arabidopsis thaliana does not fully cover the picture of lipidome in monocots, including grasses. Herein, two closely related introgression genotypes of Lolium multiflorum (Italian ryegrass) × Festuca arundinacea (tall fescue) were used as a model for other grass species to describe lipid rearrangements during drought and re-hydration. The genotypes differed in their level of photosynthetic capacity during drought, and in their capacity for membrane regeneration after stress cessation. A total of 120 lipids, comprising the classes of monogalactosyldiacyloglycerol, digalactosyldiacyloglycerol, sulfoquinovosyldiacylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, diacylglicerol, and triacylglicerol, were analyzed. The results clearly showed that water deficit had a significant impact on lipid metabolism in studied forage grasses. It was revealed that structural and metabolic lipid species changed their abundance during drought and re-watering periods and some crucial genotype-dependent differences were also observed. The introgression genotype characterized by an ability to regenerate membranes after re-hydration demonstrated a higher accumulation level of most chloroplast and numerous extra-chloroplast membrane lipid species at the beginning of drought. Furthermore, this genotype also revealed a significant reduction in the accumulation of most chloroplast lipids after re-hydration, compared with the other introgression genotype without the capacity for membrane regeneration. The potential influence of observed lipidomic alterations on a cellular membrane stability and photosynthetic capacity, are discussed

  3. Remodeling of Leaf Cellular Glycerolipid Composition under Drought and Re-hydration Conditions in Grasses from the Lolium-Festuca Complex

    PubMed Central

    Perlikowski, Dawid; Kierszniowska, Sylwia; Sawikowska, Aneta; Krajewski, Paweł; Rapacz, Marcin; Eckhardt, Änne; Kosmala, Arkadiusz

    2016-01-01

    Drought tolerant plant genotypes are able to maintain stability and integrity of cellular membranes in unfavorable conditions, and to regenerate damaged membranes after stress cessation. The profiling of cellular glycerolipids during drought stress performed on model species such as Arabidopsis thaliana does not fully cover the picture of lipidome in monocots, including grasses. Herein, two closely related introgression genotypes of Lolium multiflorum (Italian ryegrass) × Festuca arundinacea (tall fescue) were used as a model for other grass species to describe lipid rearrangements during drought and re-hydration. The genotypes differed in their level of photosynthetic capacity during drought, and in their capacity for membrane regeneration after stress cessation. A total of 120 lipids, comprising the classes of monogalactosyldiacyloglycerol, digalactosyldiacyloglycerol, sulfoquinovosyldiacylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, diacylglicerol, and triacylglicerol, were analyzed. The results clearly showed that water deficit had a significant impact on lipid metabolism in studied forage grasses. It was revealed that structural and metabolic lipid species changed their abundance during drought and re-watering periods and some crucial genotype-dependent differences were also observed. The introgression genotype characterized by an ability to regenerate membranes after re-hydration demonstrated a higher accumulation level of most chloroplast and numerous extra-chloroplast membrane lipid species at the beginning of drought. Furthermore, this genotype also revealed a significant reduction in the accumulation of most chloroplast lipids after re-hydration, compared with the other introgression genotype without the capacity for membrane regeneration. The potential influence of observed lipidomic alterations on a cellular membrane stability and photosynthetic capacity, are discussed

  4. Variation in sequences containing microsatellite motifs in the perennial biomass and forage grass, Phalaris arundinacea (Poaceae).

    PubMed

    Barth, Susanne; Jankowska, Marta Jolanta; Hodkinson, Trevor Roland; Vellani, Tia; Klaas, Manfred

    2016-03-22

    Forty three microsatellite markers were developed for further genetic characterisation of a forage and biomass grass crop, for which genomic resources are currently scarce. The microsatellite markers were developed from a normalized EST-SSR library. All of the 43 markers gave a clear banding pattern on 3% Metaphor agarose gels. Eight selected SSR markers were tested in detail for polymorphism across eleven DNA samples of large geographic distribution across Europe. The new set of 43 SSR markers will help future research to characterise the genetic structure and diversity of Phalaris arundinacea, with a potential to further understand its invasive character in North American wetlands, as well as aid in breeding work for desired biomass and forage traits. P. arundinacea is particularly valued in the northern latitude as a crop with high biomass potential, even more so on marginal lands.

  5. A totivirus infecting the mutualistic fungal endophyte Epichloë festucae.

    PubMed

    Romo, María; Leuchtmann, Adrian; García, Balbino; Zabalgogeazcoa, Iñigo

    2007-03-01

    Epichloë festucae (Ascomycota) infects the grass Festuca rubra. Infected plants may be more resistant to herbivores and obtain other benefits. The 5109bp dsRNA genome of a virus which infects E. festucae was sequenced, and its incidence in natural populations and transmission were studied. The viral genome has characteristics of the family Totiviridae. Its two ORFs are overlapped by four nucleotides; ORF1 codes a 765 amino acid putative coat protein (CP); ORF2 is in a -1 frameshift with respect to ORF1, and codes a 826 amino acid RNA dependent RNA polymerase (RdRp). This virus, denominated Epichloë festucae virus 1 (EfV1), is closely related to members of the genus Totivirus which infect filamentous fungi, as deduced from phylogenetic analyses of CPs and RdRps. In two natural populations of Epichloë festucae, 36.4% of the isolates were infected by EfV1. The virus was efficiently transmitted to asexual fungal spores. However, when ascospore progeny of matings between virus-free and infected strains was analyzed, it was found that the virus was not transmitted to progeny of sexual spores.

  6. Reduced atmospheric CO2 inhibits nitrogen mobilization in Festuca rubra.

    PubMed

    Thornton, Barry; Paterson, Eric; Kingston-Smith, Alison H; Bollard, Andrea L; Pratt, Shona M; Sim, Allan

    2002-09-01

    In defoliated grasses, where photosynthesis is reduced due to removal of leaf material, it is well established that remobilization of nitrogen occurs from both older remaining leaves and roots towards the younger growing leaves. In contrast, little is known about the movement of nitrogen within intact grass plants experiencing prolonged inhibition of photosynthesis. We tested the following hypotheses in Festuca rubra L. ssp. rubra cv. Boreal: that both reduction of the atmospheric CO2 concentration and defoliation (1) induce mobilization of nitrogen from roots and older leaves towards growing leaves and (2) elicit similar directional change in the abundance of proteins in roots and older leaves relevant to the process of nitrogen mobilization including, glutamine synthetase (GS), EC 6.3.1.2; papain, EC 3.4.22.2; chymopapain, EC 3.4.22.6; ribulose bisphosphate carboxylase/oxygenase (Rubisco), EC 4.1.1.39; and the light harvesting complex of photosystem II (LHCPII). After growth at ambient atmospheric CO2 concentration, plants of F. rubra were subject to atmospheres containing either ambient (350 micro l l-1) or deplete (< 20 micro l l-1) CO2. Concurrently, plants were either left intact or defoliated on one occasion. Steady state 15N labelling coupled with a series of destructive harvests over a 7-day period enabled changes in the nitrogen dynamics of the plants to be established. Proteins pertinent to the process of nitrogen mobilization were quantified by immunoblotting. Irrespective of defoliation, plants in ambient CO2 mobilized nitrogen from older to growing leaves. This mobilization was inhibited by deplete CO2. Greater concentration of Rubisco and reduced chymopapain abundance in older remaining leaves of intact plants, in deplete compared with ambient CO2, suggested the inhibition of mobilization was due to inhibition of protein degradation, rather than to the export of degradation products. Both deplete CO2 and defoliation induced nitrogen mobilization from

  7. Seed transfer zones for a native grass Festuca roemeri: genecological evidence

    Treesearch

    Barbara L. Wilson; Dale C. Darris; Rob Fiegener; Randy Johnson; Matthew E. Horning; Keli Kuykendall

    2008-01-01

    A common-garden study of Festuca roemeri (Pavlick) E. B. Alexeev (Poaceae) revealed substantial genetic variation within and among 47 populations from throughout its range in the Pacific Northwest, USA, for growth, fitness, phenological, and morphological traits. Using climatic and physiographic variables, genetic patterns over the landscape were...

  8. Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex

    PubMed Central

    Hand, Melanie L.; Spangenberg, German C.; Forster, John W.; Cogan, Noel O. I.

    2013-01-01

    Chloroplast genome sequences are of broad significance in plant biology, due to frequent use in molecular phylogenetics, comparative genomics, population genetics, and genetic modification studies. The present study used a second-generation sequencing approach to determine and assemble the plastid genomes (plastomes) of four representatives from the agriculturally important Lolium-Festuca species complex of pasture grasses (Lolium multiflorum, Festuca pratensis, Festuca altissima, and Festuca ovina). Total cellular DNA was extracted from either roots or leaves, was sequenced, and the output was filtered for plastome-related reads. A comparison between sources revealed fewer plastome-related reads from root-derived template but an increase in incidental bacterium-derived sequences. Plastome assembly and annotation indicated high levels of sequence identity and a conserved organization and gene content between species. However, frequent deletions within the F. ovina plastome appeared to contribute to a smaller plastid genome size. Comparative analysis with complete plastome sequences from other members of the Poaceae confirmed conservation of most grass-specific features. Detailed analysis of the rbcL–psaI intergenic region, however, revealed a “hot-spot” of variation characterized by independent deletion events. The evolutionary implications of this observation are discussed. The complete plastome sequences are anticipated to provide the basis for potential organelle-specific genetic modification of pasture grasses. PMID:23550121

  9. The potential value of Festuca valesiaca for use on Great Basin Rangelands

    USDA-ARS?s Scientific Manuscript database

    Fine-leaved Festuca valesiaca possesses varied abiotic tolerances and is widely distributed on Asian rangelands. However, its performance in the western United States has not been investigated. Therefore, F. valesiaca accessions were evaluated for performance and their relatedness to species in th...

  10. Shade Tolerance of Festuca paradoxa Desv., a Cool-Season Grass Native to North America

    Treesearch

    Nadia Navarrete-Tindall; Larry Mechlin; J. W. Van Sambeek

    2003-01-01

    Paradox grass (Festuca paradoxa Desv.) is a native cool-season grass found in prairies and forest openings. Paradox grass has not been included in tree plantings. To determine paradox grass adaptation to shaded environmmts, we established a pot experiment in the shade laboratory at the University of Missouri Horticulture and Agroforestry Research...

  11. Genome-Wide Analysis of Codon Usage Bias in Epichloë festucae

    PubMed Central

    Li, Xiuzhang; Song, Hui; Kuang, Yu; Chen, Shuihong; Tian, Pei; Li, Chunjie; Nan, Zhibiao

    2016-01-01

    Analysis of codon usage data has both practical and theoretical applications in understanding the basics of molecular biology. Differences in codon usage patterns among genes reflect variations in local base compositional biases and the intensity of natural selection. Recently, there have been several reports related to codon usage in fungi, but little is known about codon usage bias in Epichloë endophytes. The present study aimed to assess codon usage patterns and biases in 4870 sequences from Epichloë festucae, which may be helpful in revealing the constraint factors such as mutation or selection pressure and improving the bioreactor on the cloning, expression, and characterization of some special genes. The GC content with 56.41% is higher than the AT content (43.59%) in E. festucae. The results of neutrality and effective number of codons plot analyses showed that both mutational bias and natural selection play roles in shaping codon usage in this species. We found that gene length is strongly correlated with codon usage and may contribute to the codon usage patterns observed in genes. Nucleotide composition and gene expression levels also shape codon usage bias in E. festucae. E. festucae exhibits codon usage bias based on the relative synonymous codon usage (RSCU) values of 61 sense codons, with 25 codons showing an RSCU larger than 1. In addition, we identified 27 optimal codons that end in a G or C. PMID:27428961

  12. Cluster fescue (Festuca paradoxa Desv.): A multipurpose native cool-season grass

    Treesearch

    Nadia E. Navarrete-Tindall; J.W. Van Sambeek; R.A. Pierce

    2005-01-01

    Native cool-season grasses (NCSG) are adapted to a wide range of habitats and environmental conditions, and cluster fescue (Festuca paradoxa Desv.) is no exception. Cluster fescue can be found in unplowed upland prairies, prairie draws, savannas, forest openings, and glades (Aiken et al. 1996). Although its range includes 23 states in the continental...

  13. The combined effects of sediment accretion (burial) and nutrient enrichment on the growth and propagation of Phalaris arundinacea

    PubMed Central

    Chen, Xinsheng; Liao, Yulin; Xie, Yonghong; Wu, Chao; Li, Feng; Deng, Zhengmiao; Li, Xu

    2017-01-01

    Sediment accretion (burial) and nutrient enrichment occur concurrently in lacustrine wetlands, but the role of these two aspects of sedimentation on macrophyte performance has rarely been examined. Here, we investigated the concurrent effects of sediment accretion and nutrient enrichment on the growth and propagation of Phalaris arundinacea L. using a factorial sediment burial by nutrient addition experimental design. Regardless of burial depth, nutrient addition increased biomass accumulation, shoot mass ratio, the number of rhizomes, and the length of ramets and rhizomes. While burial had little effect on plant growth and propagation, it had an interactive effect with nutrient addition on belowground growth and ramet production. These results indicate that P. arundinacea is tolerant to burial, which allows it to grow in habitats with high sedimentation rates. However, the enhanced growth and propagation of P. arundinacea following sedimentation were primarily related to nutrient enrichment. This suggests that nutrient enrichment of sediments, which occurs in many lacustrine wetlands, increases the risk of invasion by P. arundinacea. PMID:28054590

  14. The combined effects of sediment accretion (burial) and nutrient enrichment on the growth and propagation of Phalaris arundinacea.

    PubMed

    Chen, Xinsheng; Liao, Yulin; Xie, Yonghong; Wu, Chao; Li, Feng; Deng, Zhengmiao; Li, Xu

    2017-01-05

    Sediment accretion (burial) and nutrient enrichment occur concurrently in lacustrine wetlands, but the role of these two aspects of sedimentation on macrophyte performance has rarely been examined. Here, we investigated the concurrent effects of sediment accretion and nutrient enrichment on the growth and propagation of Phalaris arundinacea L. using a factorial sediment burial by nutrient addition experimental design. Regardless of burial depth, nutrient addition increased biomass accumulation, shoot mass ratio, the number of rhizomes, and the length of ramets and rhizomes. While burial had little effect on plant growth and propagation, it had an interactive effect with nutrient addition on belowground growth and ramet production. These results indicate that P. arundinacea is tolerant to burial, which allows it to grow in habitats with high sedimentation rates. However, the enhanced growth and propagation of P. arundinacea following sedimentation were primarily related to nutrient enrichment. This suggests that nutrient enrichment of sediments, which occurs in many lacustrine wetlands, increases the risk of invasion by P. arundinacea.

  15. Changes in carbohydrate content and membrane stability of two ecotypes of Calamagrostis arundinacea growing at different elevations in the drawdown zone of the Three Gorges Reservoir.

    PubMed

    Lei, Shutong; Zeng, Bo; Yuan, Zhi; Su, Xiaolei

    2014-01-01

    The Three Gorges project has caused many ecosystem problems. Ecological restoration using readily-available plants is an effective way of mitigating environmental impacts. Two perennial submergence-tolerant ecotypes of Calamagrostis arundinacea were planted in an experimental field in the drawdown zone. Responses of the two plant ecotypes to flooding stress in the drawdown zone were unknown. Carbohydrate content and membrane stability, two key factors for survival of plants under flooding stress, of two ecotypes (designated "dwarf" and "green") of C. arundinacea growing at different elevations of the drawdown zone were investigated. Live stems (LS) and dead stems (DS) of the two plant ecotypes at eight elevations (175, 170, 162, 160, 158, 155, 152 m and 149 m) were sampled. Contents of soluble sugar, starch and malondialdehyde (MDA), as well as plasma membrane permeability of live stems were measured. The lowest elevations for survival of dwarf and green C. arundinacea were 160 m and 158 m, respectively. Soluble sugar content of live stems of both ecotypes decreased with elevation, with amounts from an elevation of 170 m being lower than from an elevation of 175 m. MDA content and plasma membrane permeability in live stems of green C. arundinacea did not increase with the decrease in elevation, while these measures in dwarf C. arundinacea from an elevation of 162 m were significantly higher than from an elevation of 175 m. Carbohydrate content, especially soluble sugar content, in both ecotypes was more sensitive to flooding stress than membrane stability. Green C. arundinacea had a higher tolerance to submergence than dwarf C. arundinacea, and thus green C. arundinacea can be planted at lower elevations than dwarf C. arundinacea.

  16. Comparative physico-chemical profiles of Tugaksheeree (Curcuma angustifolia Roxb. and Maranta arundinacea Linn.)

    PubMed Central

    Rajashekhara, N.; Shukla, Vinay J.; Ravishankar, B.; Sharma, Parameshwar P.

    2013-01-01

    Tugaksheeree is as an ingredient in many Ayurvedic formulations. The starch obtained from the rhizomes of two plants, is used as Tugaksheeree, Curcuma angustifolia (CA) Roxb. (Family: Zingiberaceae) and Maranta arundinacea (MA) Linn. (Family Marantaceae). In the present study, a comparative physico-analysis of both the drugs has been carried out. The results suggest that the starch from CA and MA has similar organoleptic characters. The percentage of starch content is higher in the rhizome of CA when compared with that of MA and the starch of MA is packed more densely than the starch in CA. The chemical constituents of both the starch and rhizomes are partially similar to each other. Hence, the therapeutic activities may be similar. PMID:24696578

  17. Comparative physico-chemical profiles of Tugaksheeree (Curcuma angustifolia Roxb. and Maranta arundinacea Linn.).

    PubMed

    Rajashekhara, N; Shukla, Vinay J; Ravishankar, B; Sharma, Parameshwar P

    2013-10-01

    Tugaksheeree is as an ingredient in many Ayurvedic formulations. The starch obtained from the rhizomes of two plants, is used as Tugaksheeree, Curcuma angustifolia (CA) Roxb. (Family: Zingiberaceae) and Maranta arundinacea (MA) Linn. (Family Marantaceae). In the present study, a comparative physico-analysis of both the drugs has been carried out. The results suggest that the starch from CA and MA has similar organoleptic characters. The percentage of starch content is higher in the rhizome of CA when compared with that of MA and the starch of MA is packed more densely than the starch in CA. The chemical constituents of both the starch and rhizomes are partially similar to each other. Hence, the therapeutic activities may be similar.

  18. Evaluation of Antidiarrheal Activity of Methanolic Extract of Maranta arundinacea Linn. Leaves

    PubMed Central

    Rahman, Md. Khalilur; Chowdhury, Md. Ashraf Uddin; Islam, Mohammed Taufiqual; Chowdhury, Md. Anisuzzaman; Uddin, Muhammad Erfan; Sumi, Chandra Datta

    2015-01-01

    Diarrhea is one of the most common causes for thousands of deaths every year. Therefore, identification of new source of antidiarrheal drugs becomes one of the most prominent focuses in modern research. Our aim was to investigate the antidiarrheal and cytotoxic activities of methanolic extract of Maranta arundinacea linn. (MEMA) leaves in rats and brine shrimp, respectively. Antidiarrheal effect was evaluated by using castor oil-induced diarrhea, enteropooling, and gastrointestinal motility tests at 200 mg/kg and 400 mg/kg body weight in rats where the cytotoxic activity was justified using brine shrimp lethality bioassay at different concentrations of MEMA. The extract showed considerable antidiarrheal effect by inhibiting 42.67% and 57.75% of diarrheal episode at the doses of 200 and 400 mg/kg, respectively. MEMA also significantly (p < 0.01) reduced the castor oil-induced intestinal volume (2.14 ± 0.16 to 1.61 ± 0.12 mL) in enteropooling test as well as intestinal transit (33.00 to 43.36%) in GI motility test, compared to their respective control. These observed effects are comparable to that of standard drug loperamide (5 mg/kg). On the other hand, in brine shrimp lethality test after 24 h, surviving brine shrimp larvae were counted and LD50 was assessed. Result showed that MEMA was potent against brine shrimp with LD50 value of 420 µg/mL. So the highest dose of 400 µg/mL of MEMA was not toxic to mice. So these results indicate that bioactive compounds are present in methanolic extract of Maranta arundinacea leaves including significant antidiarrheal activity and could be accounted for pharmacological effects. PMID:26346095

  19. Functional characterization of salicylate hydroxylase from the fungal endophyte Epichloë festucae.

    PubMed

    Ambrose, Karen V; Tian, Zipeng; Wang, Yifei; Smith, Jordan; Zylstra, Gerben; Huang, Bingru; Belanger, Faith C

    2015-06-09

    Epichloë spp. are symbiotic fungal endophytes of many cool season grasses. The presence of the fungal endophytes often confers insect, drought, and disease tolerance to the host grasses. The presence of the fungal endophytes within the host plants does not elicit host defense responses. The molecular basis for this phenomenon is not known. Epichloë festucae, the endophyte of Festuca rubra, expresses a salicylate hydroxylase similar to NahG from the bacterium Pseudomonas putida. Few fungal salicylate hydroxylase enzymes have been reported. The in planta expression of an endophyte salicylate hydroxylase raised the possibility that degradation of plant-produced salicylic acid is a factor in the mechanism of how the endophyte avoids eliciting host plant defenses. Here we report the characterization of the E. festucae salicylate hydroxylase, designated Efe-shyA. Although the fungal enzyme has the expected activity, based on salicylic acid levels in endophyte-free and endophyte-infected plants it is unlikely that expression of the endophyte salicylate hydroxylase is a factor in the lack of a host defense response to the presence of the fungal endophyte.

  20. Functional characterization of salicylate hydroxylase from the fungal endophyte Epichloë festucae

    PubMed Central

    Ambrose, Karen V.; Tian, Zipeng; Wang, Yifei; Smith, Jordan; Zylstra, Gerben; Huang, Bingru; Belanger, Faith C.

    2015-01-01

    Epichloë spp. are symbiotic fungal endophytes of many cool season grasses. The presence of the fungal endophytes often confers insect, drought, and disease tolerance to the host grasses. The presence of the fungal endophytes within the host plants does not elicit host defense responses. The molecular basis for this phenomenon is not known. Epichloë festucae, the endophyte of Festuca rubra, expresses a salicylate hydroxylase similar to NahG from the bacterium Pseudomonas putida. Few fungal salicylate hydroxylase enzymes have been reported. The in planta expression of an endophyte salicylate hydroxylase raised the possibility that degradation of plant-produced salicylic acid is a factor in the mechanism of how the endophyte avoids eliciting host plant defenses. Here we report the characterization of the E. festucae salicylate hydroxylase, designated Efe-shyA. Although the fungal enzyme has the expected activity, based on salicylic acid levels in endophyte-free and endophyte-infected plants it is unlikely that expression of the endophyte salicylate hydroxylase is a factor in the lack of a host defense response to the presence of the fungal endophyte. PMID:26055188

  1. Plasticity of nitrogen allocation in the leaves of the invasive wetland grass, Phalaris arundinacea and co-occurring Carex species determines the photosynthetic sensitivity to nitrogen availability.

    PubMed

    Holaday, A Scott; Schwilk, Dylan W; Waring, Elizabeth F; Guvvala, Hasitha; Griffin, Chelsea M; Lewis, O Milo

    2015-04-01

    Phalaris arundinacea displaces the slower-growing, native sedge, Carex stricta, where nitrogen availability is high. Our aim was to address whether morphological and physiological traits associated with carbon gain for P. arundinacea and C. stricta responded to nitrogen supply differently and if the species exhibited different degrees of plasticity in these traits. The plants were grown in gravel and provided modified Hoagland's solution containing four nitrogen concentrations from 0.15 to 15 mM for 6 to 7 weeks. Supplied nitrogen affected the leaf nitrogen content to the same degree for both species. Increasing supplied nitrogen strongly increased CO2 assimilation (A), photosynthetic nitrogen use efficiency (PNUE), and respiration for P. arundinacea but had only a small effect on these parameters for C. stricta. Relative to growth at 15 mM nitrogen, growth at 0.15 mM for young leaves decreased carboxylation capacity and efficiency and the capacity for electron transport for P. arundinacea and a larger, stouter Carex species, Carex lacustris, by 53 to 70% but only 20 to 24% for C. stricta. Leaf nitrogen decreased approximately 50% for all species, but vacuolar nitrate did not decrease for P. arundinacea and C. stricta, suggesting that it does not serve as a nitrogen reserve for use during nitrogen deprivation in these species. After 4 months of nitrogen deprivation, P. arundinacea doubled A in 12 days after being supplied 15 mM nitrogen, whereas A for C. stricta increased only 22%. We propose that one factor linking P. arundinacea abundance to nitrogen availability involves this species' plastic response of carbon gain to nitrogen supply. C. stricta appears to be adapted to tolerate low nitrogen availability but cannot respond as rapidly and extensively as P. arundinacea when nitrogen supply is high.

  2. Platelet miRNAs and cardiovascular diseases.

    PubMed

    Fuentes, Eduardo; Palomo, Iván; Alarcón, Marcelo

    2015-07-15

    Activated platelets play a critical role in the acute complications of atherosclerosis that cause life-threatening ischemic events at late stages of the disease. The miRNAs are a novel class of small, non-coding RNAs that play a significant role in both inflammatory and cardiovascular diseases. The miRNAs are known to be present in platelets and exert important regulatory functions. Here we systematically examine the genes that are regulated by platelet miRNAs (miRNA-223,miRNA-126,miRNA-21, miRNA-24 and miRNA-197) and the association with cardiovascular disease risks. Platelet-secreted miRNAs could be novel biomarkers associated with cardiovascular diseases.

  3. Prevalence of an intraspecific Neotyphodium hybrid in natural populations of stout wood reed (Cinna arundinacea L.) from eastern North America.

    PubMed

    Ghimire, Sita R; Rudgers, Jennifer A; Charlton, Nikki D; Young, Carolyn; Craven, Kelly D

    2011-01-01

    Members of genus Neotyphodium are asexual derivatives of sexual Epichloë species and maintain endophytic relationships with many cool-season grasses. Most Neotyphodium species analyzed so far are interspecific hybrids with combined or partial genomes of two or three ancestral species. In this study we characterized Neotyphodium isolates from Cinna arundinacea, a perennial cool-season grass from eastern North America. A total of 23 isolates grouping into two distinct morphotypes were obtained from five local populations of C. arundinacea. PCR amplification and cloning of translation-elongation factor 1-α (tefA) and β-tubulin (tubB) genes of 10 isolates comprising both morphotypes (two isolates per location) revealed that all 10 contain two copies of tefA and tubB genes. Surprisingly phylogenetic analysis of mainly non-coding sequence from these genes revealed that both copies in each isolate were inherited from Epichloë typhina ancestors, indicating that the C. arundinacea endophytes arose through intraspecific hybridization between two E. typhina progenitors with extant relatives infecting hosts Poa nemoralis and Poa pratensis. Furthermore the tefA sequences were identical between isolates, as were tubB sequences, despite obvious morphological differences. Profiling of alkaloid biosynthetic genes from these isolates indicated the presence of the peramine biosynthetic gene (perA) and the absence of genes required for biosynthesis of lolines, indole-diterpenes and ergot alkaloids. Thus this endophyte is potentially capable of producing peramine in planta and providing protection to its host from insect pests. The absence of genes for indole-diterpenes and ergot alkaloid biosynthesis makes this endophyte a candidate for agricultural applications. Based on our phylogenetic analysis, alkaloid profiling and description of morphological characteristics, we propose the name Neotyphodium schardlii for these isolates from C. arundinacea, a new member of genus

  4. A comparative study of efficacy of Tugaksheeree [Curcuma angustifolia Roxb. and Maranta arundinacea Linn.] in management of Amlapitta.

    PubMed

    Rajashekhara, N; Sharma, P P

    2010-10-01

    Amlapitta is a disease caused by increase of Amla Guna of Pitta. Starch obtained from the rhizomes of two plants viz., Curcuma angustifolia Roxb. (Fam. Zingiberaceae) and Maranta arundinacea Linn. (Fam. Marantaceae) are used as Tugaksheeree. In the present clinical study, the efficacy of Tugaksheeree was studied on 67 patients of Amlapitta. A 0 total of 84 patients suffering from Amlapitta were selected from the O.P.D. and I.P.D. sections in the department of Dravyaguna, I.P.G.T. and R.A., Hospital, Jamnagar, and were randomly divided into two groups. Thirty four patients completed the treatment course in Group I, and 33 patients completed the treatment course in Group II. The efficacy of drug Tugaksheeree was studied through internal administration of the starches of C. angustifolia Roxb. (Fam. Zingiberaceae) in Group I and M. arundinacea Linn. (Fam. Marantaceae) in Group II with the dose of 4 g TID with water for 30 days. Both the drugs were found highly effective in treating Amlapitta. They significantly relieved the cardinal symptoms viz., Avipaka, Tikta-amlodgara, Daha, Shoola, Chhardi and the associated symptoms viz., Aruchi, Gaurava, Udaradhmana, Antrakujana, Vit bheda, Shiroruja, Angasada, and Trit. Statistically significant increase in body weight was noticed in both the groups. This may be because the drugs corrected the Agni and acted as Brihmana and Dhatupushtikara. Both the drugs did not produce any side effects. Therefore, both these drugs (C. angustifolia Roxb. and M. arundinacea Linn.) can be used as substitutes for each other.

  5. Rathayibacter caricis sp. nov. and Rathayibacter festucae sp. nov., isolated from the phyllosphere of Carex sp. and the leaf gall induced by the nematode Anguina graminis on Festuca rubra L., respectively.

    PubMed

    Dorofeeva, Lubov V; Evtushenko, Lyudmila I; Krausova, Valentina I; Karpov, Alexander V; Subbotin, Sergey A; Tiedje, James M

    2002-11-01

    Two novel species, Rathayibacter caricis sp. nov. (type strain VKM Ac-1799T = UCM Ac-618T) and Rathayibacter festucae sp. nov. (type strain VKM Ac-1390T UCM Ac-619T), are proposed for two coryneform actinomycetes found in the phyllosphere of Carex sp. and in the leaf gall induced by the plant-parasitic nematode Anguina graminis on Festuca rubra L., respectively. The strains of the novel species are typical of the genus Rathayibacter in their chemotaxonomic characteristics and fall into the Rathayibacter 16S rDNA phylogenetic cluster. They belong to two separate genomic species and differ markedly from current validly described species of Rathayibacter at the phenotypic level. The most striking feature differentiating Rathayibacter caricis sp. nov. from other species of the genus is the presence of fucose in its cell wall and Rathayibacter festucae sp. nov. can be easily recognized among other yellow-pigmented rathayibacters because of its rose-orange-coloured colonies.

  6. Genetic characterization of Kyrgyzstan fine-leaved Festuca valesiaca germplasm for use in semi-arid low-maintenance turf applications

    USDA-ARS?s Scientific Manuscript database

    Fine-leaved Festuca valesiaca Shleidcher ex. Gaudin (2n = 2x-4x) is native to heavily grazed, cold, semi-arid, Asian rangelands. However, its potential for low-maintenance turf applications in the semi-arid western United States and its relatedness to other agriculturally important Festuca species ...

  7. Identifying miRNAs, targets and functions

    PubMed Central

    Liu, Bing; Li, Jiuyong

    2014-01-01

    microRNAs (miRNAs) are small endogenous non-coding RNAs that function as the universal specificity factors in post-transcriptional gene silencing. Discovering miRNAs, identifying their targets and further inferring miRNA functions have been a critical strategy for understanding normal biological processes of miRNAs and their roles in the development of disease. In this review, we focus on computational methods of inferring miRNA functions, including miRNA functional annotation and inferring miRNA regulatory modules, by integrating heterogeneous data sources. We also briefly introduce the research in miRNA discovery and miRNA-target identification with an emphasis on the challenges to computational biology. PMID:23175680

  8. Gangrenous ergotism in cattle grazing fescue (Festuca elatior L.) in South Africa.

    PubMed

    Botha, C J; Naudé, T W; Moroe, M L; Rottinghaus, G E

    2004-03-01

    The 1st outbreak of fescue toxicosis in South Africa was recently confirmed in a Brahman herd at Perdekop, near Standerton, in Mpumalanga province, South Africa. Within 3 weeks of being placed on a fescue pasture in mid-winter, 50 of 385 cattle developed lameness and/or necrosis of the tail. The farmer had established Festuca elatior L. (tall fescue, Iewag variety) on c. 140 ha for winter grazing. Fescue may be infected by an endophyte, Neotyphodium coenophialum, which produces ergot alkaloids, in particular ergovaline. Ergovaline concentrations in basal leaf sheaths and grass stems collected during the outbreak ranged from 1720-8170 ppb on a dry-matter basis.

  9. Characterization of microsatellites in Bambusa arundinacea and cross species amplification in other bamboos.

    PubMed

    Nayak, Sumitra; Rout, Gyana Ranjan

    2005-01-01

    Microsatellites, tandem repeats of short nucleotide (1-6 bp) sequences, are the DNA marker of choice because of their highly polymorphic, ubiquitous distribution within genome, ease of genotyping through polymerase chain reaction (PCR), selectively neutral, co-dominant and multi allelic nature. Six microsatellites, three polymorphic and three monomorphic, have been characterized for the first time in a bamboo species, Bambusa arudinacea belonging to the family Poaceae. The number of alleles per locus ranges form 2 to 13. Allelic diversity ranges from 0.041 to 0.870. Polymorphic information content (PIC) values for two loci were > 0.3, an indicator of polymorphic allele. Cross species amplification has been tested in other 18 bamboo species. Monomorphic simple sequence repeats (SSRs) have been found to be cross amplified in most of the tested species while polymorphic ones in only three to four species. The utility of the SSR loci in genetic diversity study of B. arundinacea and other cross amplified bamboo species have been discussed.

  10. Mine wastewater treatment using Phalaris arundinacea plant material hydrolyzate as substrate for sulfate-reducing bioreactor.

    PubMed

    Lakaniemi, Aino-Maija; Nevatalo, Laura M; Kaksonen, Anna H; Puhakka, Jaakko A

    2010-06-01

    A low-cost substrate, Phalaris arundinacea was acid hydrolyzed (Reed Canary Grass hydrolyzate, RCGH) and used to support sulfate reduction. The experiments included batch bottle assays (35 degrees C) and a fluidized-bed bioreactor (FBR) experiment (35 degrees C) treating synthetic mine wastewater. Dry plant material was also tested as substrate in batch bottle assays. The batch assays showed sulfate reduction with the studied substrates, producing 540 and 350mgL(-1) dissolved sulfide with RCGH and dry plant material, respectively. The soluble sugars of the RCGH presumably fermented into volatile fatty acids and hydrogen, which served as electron donors for sulfate reducing bacteria. A sulfate reduction rate of 2.2-3.3gL(-1)d(-1) was obtained in the FBR experiment. The acidic influent was neutralized and the highest metal precipitation rates were 0.84g FeL(-1)d(-1) and 15mg ZnL(-1)d(-1). The sulfate reduction rate in the FBR was limited by the acetate oxidation rate of the sulfate-reducing bacteria. Copyright 2010 Elsevier Ltd. All rights reserved.

  11. Multiple disturbances accelerate invasion of reed canary grass (Phalaris arundinaceaL.) in a mesocosm study.

    PubMed

    Kercher, Suzanne M; Zedler, Joy B

    2004-02-01

    Disturbances that intensify with agriculture and/or urban development are thought to promote the spread of invasive plants, such as the clonal perennial reed canary grass (Phalaris arundinaceaL). To test this relationship and interactions among disturbances, we subjected wet prairie assemblages within 1.1 m(2) mesocosms to invasion by Phalaris and addition of nutrients, sediments, and flooding. Species richness decreased with the application of sediments and/or flooding of 4 consecutive weeks or longer. Losses of up to six dominant and subdominant species in these treatments increased light transmission through the plant canopy by as much as 400% over the control. Light availability in July and September was a strong predictor of end-of-season aboveground biomass of Phalaris. Phalaris was also 35% and 195% more productive when nutrients were added at low and high levels, respectively. Multiple factors in combination were usually additive in their effects on invasion, but sediments and nutrients interacted with flood regime to synergistically increase invasion in some cases. A separate experiment likewise revealed a synergistic interaction between added nutrients and simulated grazing. We suggest that multiple factors be mitigated simultaneously to reduce invasion of Phalaris.

  12. Evaluation of immunostimulatory effect of the arrowroot (Maranta arundinacea. L) in vitro and in vivo.

    PubMed

    Kumalasari, Ika Dyah; Harmayani, Eni; Lestari, Lily Arsanti; Raharjo, Sri; Asmara, Widya; Nishi, Kosuke; Sugahara, Takuya

    2012-03-01

    Arrowroot (Maranta arundinacea. L) is an underutilized local crop potentially to be developed as carbohydrate source and functional food in Indonesia. The objectives of this research are to evaluate the immunostimulatory effects of arrowroot extracts in vitro by using animal cell culture techniques, and in vivo by using BALB/c mice. The arrowroot tuber extracts were prepared by heat-treatment at 121 °C for 20 min in distilled water. The IgM production stimulatory activity of arrowroot tuber extracts against human hybridoma HB4C5 cells and mouse splenocytes was assessed. The result indicated that the arrowroot tuber extract stimulated IgM production by HB4C5 cells and immunoglobulin (IgG, IgA and IgM) production by splenocytes in vitro. In addition, the arrowroot tuber extracts strongly enhanced interferon γ production by splenocytes. In vivo study indicated that the diet containing arrowroot extracts increased the serum IgG, IgA and IgM levels in mice. These results revealed that the arrowroot tuber extracts have immunostimulatory effects in vivo as well as in vitro.

  13. miRNAs in brain development

    SciTech Connect

    Petri, Rebecca; Malmevik, Josephine; Fasching, Liana; Åkerblom, Malin; Jakobsson, Johan

    2014-02-01

    MicroRNAs (miRNAs) are small, non-coding RNAs that negatively regulate gene expression at the post-transcriptional level. In the brain, a large number of miRNAs are expressed and there is a growing body of evidence demonstrating that miRNAs are essential for brain development and neuronal function. Conditional knockout studies of the core components in the miRNA biogenesis pathway, such as Dicer and DGCR8, have demonstrated a crucial role for miRNAs during the development of the central nervous system. Furthermore, mice deleted for specific miRNAs and miRNA-clusters demonstrate diverse functional roles for different miRNAs during the development of different brain structures. miRNAs have been proposed to regulate cellular functions such as differentiation, proliferation and fate-determination of neural progenitors. In this review we summarise the findings from recent studies that highlight the importance of miRNAs in brain development with a focus on the mouse model. We also discuss the technical limitations of current miRNA studies that still limit our understanding of this family of non-coding RNAs and propose the use of novel and refined technologies that are needed in order to fully determine the impact of specific miRNAs in brain development. - Highlights: • miRNAs are essential for brain development and neuronal function. • KO of Dicer is embryonically lethal. • Conditional Dicer KO results in defective proliferation or increased apoptosis. • KO of individual miRNAs or miRNA families is necessary to determine function.

  14. Polycross populations of the native grass Festuca roemeri as pre-varietal germplasm: their derivation, release, increase, and use

    Treesearch

    Dale C. Darris; Barbara L. Wilson; Rob Fiegener; Randy Johnson; Matthew E. Horning

    2008-01-01

    Results of a recent common-garden study provide evidence needed to delineate appropriate seed transfer zones for the native grass Festuca roemeri (Pavlick) E. B. Alexeev (Poaceae). That information has been used to develop pre-variety germplasm releases to provide ecologically and genetically appropriate seeds for habitat restoration, erosion...

  15. A spectroscopy approach to the study of virus infection in the endophytic fungus Epichloë festucae

    PubMed Central

    2011-01-01

    Background In this work we propose a rapid method based on visible and near-infrared (Vis-NIR) spectroscopy to determine the occurrence of double-stranded RNA (dsRNA) viruses in Epichloë festucae strains isolated from Festuca rubra plants. In addition, we examined the incidence of infections by E. festucae in populations of F. rubra collected in natural grasslands of Western Spain. Methods Vis-NIR spectra (400-2498 nm) from 124 virus-infected and virus-free E. festucae isolates were recorded directly from ground and freeze-dried mycelium. To estimate how well the spectra for uninfected and infected fungal samples could be differentiated, we used partial least-squares discriminant analysis (PLS1-DA) and several data pre-treatments to develop calibration models. Results Applying the best regression model, obtained with two sampling years and using standard normal variate (SNV) combined with first derivative transformation to a new validating data set (42 samples), we obtained a correct classification for 75% of the uninfected isolates and up to 86% of the infected isolates. Conclusions The results obtained suggest that Vis-NIR spectroscopy is a promising technology for detection of viral infections in fungal samples when an alternative faster approach is desirable. It provides a tool adequately exact and more time- and cost-saving than the conventional reference analysis. PMID:21651818

  16. Draft Genome Sequence of Pseudomonas putida Strain GM4FR, an Endophytic Bacterium Isolated from Festuca rubra L.

    PubMed Central

    Hollensteiner, Jacqueline; Granzow, Sandra; Daniel, Rolf; Vidal, Stefan; Wemheuer, Bernd

    2017-01-01

    ABSTRACT Pseudomonas putida GM4FR is an endophytic bacterium isolated from aerial plant tissues of Festuca rubra L. Functional annotation of the draft genome (7.1 Mb) revealed 6,272 predicted protein-encoding genes. The genome provides insights into the biocontrol and plant growth-promoting potential of P. putida GM4FR. PMID:28360162

  17. A comparative study of efficacy of Tugaksheeree [Curcuma angustifolia Roxb. and Maranta arundinacea Linn.] in management of Amlapitta

    PubMed Central

    Rajashekhara, N.; Sharma, P. P.

    2010-01-01

    Amlapitta is a disease caused by increase of Amla Guna of Pitta. Starch obtained from the rhizomes of two plants viz., Curcuma angustifolia Roxb. (Fam. Zingiberaceae) and Maranta arundinacea Linn. (Fam. Marantaceae) are used as Tugaksheeree. In the present clinical study, the efficacy of Tugaksheeree was studied on 67 patients of Amlapitta. A 0 total of 84 patients suffering from Amlapitta were selected from the O.P.D. and I.P.D. sections in the department of Dravyaguna, I.P.G.T. and R.A., Hospital, Jamnagar, and were randomly divided into two groups. Thirty four patients completed the treatment course in Group I, and 33 patients completed the treatment course in Group II. The efficacy of drug Tugaksheeree was studied through internal administration of the starches of C. angustifolia Roxb. (Fam. Zingiberaceae) in Group I and M. arundinacea Linn. (Fam. Marantaceae) in Group II with the dose of 4 g TID with water for 30 days. Both the drugs were found highly effective in treating Amlapitta. They significantly relieved the cardinal symptoms viz., Avipaka, Tikta-amlodgara, Daha, Shoola, Chhardi and the associated symptoms viz., Aruchi, Gaurava, Udaradhmana, Antrakujana, Vit bheda, Shiroruja, Angasada, and Trit. Statistically significant increase in body weight was noticed in both the groups. This may be because the drugs corrected the Agni and acted as Brihmana and Dhatupushtikara. Both the drugs did not produce any side effects. Therefore, both these drugs (C. angustifolia Roxb. and M. arundinacea Linn.) can be used as substitutes for each other. PMID:22048544

  18. miRNA Digger: a comprehensive pipeline for genome-wide novel miRNA mining.

    PubMed

    Yu, Lan; Shao, Chaogang; Ye, Xinghuo; Meng, Yijun; Zhou, Yincong; Chen, Ming

    2016-01-06

    MicroRNAs (miRNAs) are important regulators of gene expression. The recent advances in high-throughput sequencing (HTS) technique have greatly facilitated large-scale detection of the miRNAs. However, thoroughly discovery of novel miRNAs from the available HTS data sets remains a major challenge. In this study, we observed that Dicer-mediated cleavage sites for the processing of the miRNA precursors could be mapped by using degradome sequencing data in both animals and plants. In this regard, a novel tool, miRNA Digger, was developed for systematical discovery of miRNA candidates through genome-wide screening of cleavage signals based on degradome sequencing data. To test its sensitivity and reliability, miRNA Digger was applied to discover miRNAs from four organs of Arabidopsis. The results revealed that a majority of already known mature miRNAs along with their miRNA*s expressed in these four organs were successfully recovered. Notably, a total of 30 novel miRNA-miRNA* pairs that have not been registered in miRBase were discovered by miRNA Digger. After target prediction and degradome sequencing data-based validation, eleven miRNA-target interactions involving six of the novel miRNAs were identified. Taken together, miRNA Digger could be applied for sensitive detection of novel miRNAs and it could be freely downloaded from http://www.bioinfolab.cn/miRNA_Digger/index.html.

  19. The evaluation of anti-ulcerogenic effect of rhizome starch of two source plants of Tugaksheeree (Curcuma angustifolia Roxb. and Maranta arundinacea Linn.) on pyloric ligated rats

    PubMed Central

    Rajashekhara, N.; Ashok, B. K.; Sharma, Parmeshwar P.; Ravishankar, B.

    2014-01-01

    Background: In the present era, because of the life-style, the disorders such as hyperacidity and gastric ulcers are found very frequently. Satwa (starch) obtained from the rhizomes of two plants namely Curcuma angustifolia Roxb. and Maranta arundinacea Linn. are used in folklore practice for the treatment of above complaints under the name Tugaksheeree. Aim: To compare the anti-ulcerogenic activity of the above two drugs in pyloric ligation induced gastric ulcer in albino rats. Materials and Methods: A total of 18 Wistar strain albino rats of both sexes grouped into three groups. Group C served as pyloric ligated control group, Group I received starch of C. angustifolia suspension and Group II received starch of M. arundinacea for seven days. On 8th day pylorus was ligated. After ligation the animals were deprived of food and water and sacrificed at the end of 14 h. The collected gastric contents were used for biochemical estimation and ulcer index was calculated from excised stomach. Results: Both the test drugs showed statistically significant decrease in the volume, increase in the pH, reduced the free acidity of gastric juice and decreased the peptic activity. The starch of C. angustifolia reduced a total acidity non-significantly while M. arundinacea reduced it significantly. Among the two drugs the M. arundinacea has effectively reduced the peptic activity, which is statistically significant. M. arundinacea shown statistically significant increase of total carbohydrates. Conclusion: Both the test drugs proved anti-ulcer activity and prevents the chance of gastric ulcer. Among these two M. arundinacea is more effective. PMID:25558167

  20. Bioinformatics of cardiovascular miRNA biology.

    PubMed

    Kunz, Meik; Xiao, Ke; Liang, Chunguang; Viereck, Janika; Pachel, Christina; Frantz, Stefan; Thum, Thomas; Dandekar, Thomas

    2015-12-01

    MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs and are highly conserved among species. Moreover, miRNAs regulate gene expression of a large number of genes associated with important biological functions and signaling pathways. Recently, several miRNAs have been found to be associated with cardiovascular diseases. Thus, investigating the complex regulatory effect of miRNAs may lead to a better understanding of their functional role in the heart. To achieve this, bioinformatics approaches have to be coupled with validation and screening experiments to understand the complex interactions of miRNAs with the genome. This will boost the subsequent development of diagnostic markers and our understanding of the physiological and therapeutic role of miRNAs in cardiac remodeling. In this review, we focus on and explain different bioinformatics strategies and algorithms for the identification and analysis of miRNAs and their regulatory elements to better understand cardiac miRNA biology. Starting with the biogenesis of miRNAs, we present approaches such as LocARNA and miRBase for combining sequence and structure analysis including phylogenetic comparisons as well as detailed analysis of RNA folding patterns, functional target prediction, signaling pathway as well as functional analysis. We also show how far bioinformatics helps to tackle the unprecedented level of complexity and systemic effects by miRNA, underlining the strong therapeutic potential of miRNA and miRNA target structures in cardiovascular disease. In addition, we discuss drawbacks and limitations of bioinformatics algorithms and the necessity of experimental approaches for miRNA target identification. This article is part of a Special Issue entitled 'Non-coding RNAs'.

  1. Genome Size and GC Content Evolution of Festuca: Ancestral Expansion and Subsequent Reduction

    PubMed Central

    Šmarda, Petr; Bureš, Petr; Horová, Lucie; Foggi, Bruno; Rossi, Graziano

    2008-01-01

    Background and Aims Plant evolution is well known to be frequently associated with remarkable changes in genome size and composition; however, the knowledge of long-term evolutionary dynamics of these processes still remains very limited. Here a study is made of the fine dynamics of quantitative genome evolution in Festuca (fescue), the largest genus in Poaceae (grasses). Methods Using flow cytometry (PI, DAPI), measurements were made of DNA content (2C-value), monoploid genome size (Cx-value), average chromosome size (C/n-value) and cytosine + guanine (GC) content of 101 Festuca taxa and 14 of their close relatives. The results were compared with the existing phylogeny based on ITS and trnL-F sequences. Key Results The divergence of the fescue lineage from related Poeae was predated by about a 2-fold monoploid genome and chromosome size enlargement, and apparent GC content enrichment. The backward reduction of these parameters, running parallel in both main evolutionary lineages of fine-leaved and broad-leaved fescues, appears to diverge among the existing species groups. The most dramatic reductions are associated with the most recently and rapidly evolving groups which, in combination with recent intraspecific genome size variability, indicate that the reduction process is probably ongoing and evolutionarily young. This dynamics may be a consequence of GC-rich retrotransposon proliferation and removal. Polyploids derived from parents with a large genome size and high GC content (mostly allopolyploids) had smaller Cx- and C/n-values and only slightly deviated from parental GC content, whereas polyploids derived from parents with small genome and low GC content (mostly autopolyploids) generally had a markedly increased GC content and slightly higher Cx- and C/n-values. Conclusions The present study indicates the high potential of general quantitative characters of the genome for understanding the long-term processes of genome evolution, testing evolutionary

  2. meta-Tyrosine in Festuca rubra ssp. commutata (Chewings fescue) is synthesized by hydroxylation of phenylalanine.

    PubMed

    Huang, Tengfang; Rehak, Ludmila; Jander, Georg

    2012-03-01

    m-Tyrosine is a non-protein amino acid that is structurally similar to the common protein amino acids p-tyrosine and phenylalanine. Copious amounts of m-tyrosine can be found in root exudates of the fine fescue cultivar, Festuca rubra L. ssp. commutata (Chewings fescue). The phytotoxicity of m-tyrosine may contribute to the allelopathic potential of F. rubra. m-Tyrosine in Euphorbia myrsinites (donkey-tail spurge), was previously shown to be synthesized via transamination of m-hydroxyphenylpyruvate. Here we show that m-tyrosine biosynthesis in F. rubra occurs through direct hydroxylation of phenylalanine in the root tips, perhaps through the activity of a cytochrome P450 enzyme. Hence, E. myrsinites and F. rubra, the only two plant species known to produce m-tyrosine, use distinct biosynthetic pathways that likely arose independently in evolutionary history.

  3. miRNAs in human cancer

    PubMed Central

    Farazi, Thalia A.; Spitzer, Jessica I.; Morozov, Pavel; Tuschl, Thomas

    2010-01-01

    Mature microRNAs (miRNAs) are single-stranded RNA molecules of 20- to 23-nucleotide (nt) length that control gene expression in many cellular processes. These molecules typically reduce the stability of mRNAs, including those of genes that mediate processes in tumorigenesis, such as inflammation, cell cycle regulation, stress response, differentiation, apoptosis, and invasion. miRNA targeting is mostly achieved through specific base-pairing interactions between the 5′ end (“seed” region) of the miRNA and sites within coding and untranslated regions (UTRs) of mRNAs; target sites in the 3′ UTR lead to more effective mRNA destabilization. Since miRNAs frequently target hundreds of mRNAs, miRNA regulatory pathways are complex. To provide a critical overview of miRNA dysregulation in cancer we first discuss the methods currently available for studying the role of miRNAs in cancer and then review miRNA genomic organization, biogenesis, and mechanism of target recognition examining how these processes are altered in tumorigenesis. Given the critical role miRNAs play in tumorigenesis processes and their disease specific expression, they hold potential as therapeutic targets and novel biomarkers. PMID:21125669

  4. Evaluation of acute toxicity and anti-ulcerogenic study of rhizome starch of two source plants of Tugaksheeree (Curcuma angustifolia Roxb. and Maranta arundinacea Linn.).

    PubMed

    Rajashekhara, N; Ashok, B K; Sharma, Parmeshwar P; Ravishankar, B

    2014-01-01

    Disorders like hyperacidity and gastric ulcers are found very frequently now days because of a faulty lifestyle. Starches (Satwa) obtained from the rhizomes of two plants namely, Curcuma angustifolia Roxb. (Fam. Zingiberaceae) and Maranta arundinacea Linn. (Fam. Marantaceae) are used in folklore practice, as Tugaksheeree, for the treatment of the above-mentioned complaints. To assess the acute toxicity potential of the C. angustifolia and M. arundinacea along with their assessment for adaptogenic activity, by noting their effect on forced swimming-induced hypothermia and gastric ulceration in rats. For acute toxicity study, the effect of test drugs C. angustifolia and M. arundinacea rhizome starch were studied after a single administration of up to three dose levels, with 4400 mg/kg as the maximum dose. The animals were observed for 72 hours periodically and mortality was recorded up to seven days. The adaptogenic and anti-ulcer activities were assessed by determining and comparing the changes in rectal temperature, ponderal changes, ulcer index and histopathological parameters in the test drug group with that of stress control group. Both the drugs did not produce any toxic symptoms or mortality even up to the maximum dose level of 4400 mg/kg. Both the test drugs significantly reversed the stress-induced gastric ulceration in comparison to stress-control rats. Starch from rhizome of C. angustifolia reversed forced swimming-induced hypothermia apparently, but not to a significant extent. However, the reversal of hypothermia found statistically significant in the rhizome starch of the M. arundinacea treated group. M. arundinacea had better anti-stress activity in comparision to C. angustifolia.

  5. Evaluation of acute toxicity and anti-ulcerogenic study of rhizome starch of two source plants of Tugaksheeree (Curcuma angustifolia Roxb. and Maranta arundinacea Linn.)

    PubMed Central

    Rajashekhara, N.; Ashok, B.K.; Sharma, Parmeshwar P.; Ravishankar, B.

    2014-01-01

    Background: Disorders like hyperacidity and gastric ulcers are found very frequently now days because of a faulty lifestyle. Starches (Satwa) obtained from the rhizomes of two plants namely, Curcuma angustifolia Roxb. (Fam. Zingiberaceae) and Maranta arundinacea Linn. (Fam. Marantaceae) are used in folklore practice, as Tugaksheeree, for the treatment of the above-mentioned complaints. Aim: To assess the acute toxicity potential of the C. angustifolia and M. arundinacea along with their assessment for adaptogenic activity, by noting their effect on forced swimming-induced hypothermia and gastric ulceration in rats. Materials and Methods: For acute toxicity study, the effect of test drugs C. angustifolia and M. arundinacea rhizome starch were studied after a single administration of up to three dose levels, with 4400 mg/kg as the maximum dose. The animals were observed for 72 hours periodically and mortality was recorded up to seven days. The adaptogenic and anti-ulcer activities were assessed by determining and comparing the changes in rectal temperature, ponderal changes, ulcer index and histopathological parameters in the test drug group with that of stress control group. Results: Both the drugs did not produce any toxic symptoms or mortality even up to the maximum dose level of 4400 mg/kg. Both the test drugs significantly reversed the stress-induced gastric ulceration in comparison to stress-control rats. Starch from rhizome of C. angustifolia reversed forced swimming-induced hypothermia apparently, but not to a significant extent. However, the reversal of hypothermia found statistically significant in the rhizome starch of the M. arundinacea treated group. Conclusion: M. arundinacea had better anti-stress activity in comparision to C. angustifolia. PMID:26195908

  6. Regulation of miRNA Processing and miRNA Mediated Gene Repression in Cancer

    PubMed Central

    Bajan, Sarah; Hutvagner, Gyorgy

    2014-01-01

    The majority of human protein-coding genes are predicted to be targets of miRNA-mediated post-transcriptional regulation. The widespread influence of miRNAs is illustrated by their essential roles in all biological processes. Regulated miRNA expression is essential for maintaining cellular differentiation; therefore alterations in miRNA expression patterns are associated with several diseases, including various cancers. High-throughput sequencing technologies revealed low level expressing miRNA isoforms, termed isomiRs. IsomiRs may differ in sequence, length, target preference and expression patterns from their parental miRNA and can arise from differences in miRNA biosynthesis, RNA editing, or SNPs inherent to the miRNA gene. The association between isomiR expression and disease progression is largely unknown. Misregulated miRNA expression is thought to contribute to the formation and/or progression of cancer. However, due to the diversity of targeted transcripts, miRNAs can function as both tumor-suppressor genes and oncogenes as defined by cellular context. Despite this, miRNA profiling studies concluded that the differential expression of particular miRNAs in diseased tissue could aid the diagnosis and treatment of some cancers. PMID:25069508

  7. MiRNAs in bone diseases.

    PubMed

    Moore, Benjamin T; Xiao, Peng

    2013-01-01

    MicroRNAs (miRNAs), which mainly inhibit protein expression by targeting the 3'UTR (untranslated region) of mRNAs, are known to play various roles in the pathogenesis of many different types of diseases. Specifically, in bone diseases, recent emphasis has been placed on the involvement of miRNAs in the differentiation and proliferation of bone and cartilage cells, particularly with regards to how these mechanisms contribute to bone homeostasis. In this review, we summarize miRNAs that are important in the differentiation and proliferation of bone cells, and specific miRNAs associated with bone diseases, such as osteoporosis, osteoarthritis and rheumatoid arthritis. This review also provides the perspective that miRNA studies will identify not only new mechanisms in basic bone research, but also potential novel diagnostic biomarkers and drug targets for bone diseases.

  8. A leachate a day keeps the seedlings away: mowing and the inhibitory effects of Festuca paniculata in subalpine grasslands

    PubMed Central

    Viard-Crétat, Flore; Gallet, Christiane; Lefebvre, Marianne; Lavorel, Sandra

    2009-01-01

    Background and Aims Is the release of allelochemicals by the dominant tussock grass Festuca paniculata responsible for its dominance by inhibiting growth of neighbour grasses in subalpine grasslands? As such a community is also structured by mowing practices, what could be the impact of mowing on allelopathy? Methods A design was used that isolated allelopathy from resource competition by separating donor plants (Festuca paniculata) from target plants (F. paniculata, Dactylis glomerata and Bromus erectus). Leachates from donor pots containing bare soil, unmown F. paniculata or mown F. paniculata continuously irrigated target pots containing seedlings. Activated carbon was added in half of the target pots to adsorb potential allelochemicals. C and N analyses of target potting soil were used to test for any effect of treatments on resources. Total phenol concentration was measured in the solutions flowing from donor to target pots. Results Festuca paniculata leachates inhibited seedling growth of D. glomerata and B. erectus. Inhibition was correlated with polyphenol concentration, and was not due to resource competition for nitrogen. Mowing the leaves of the donor plants did not significantly increase this inhibition. The activated carbon treatment was not conclusive as it inhibited the seedling growing under control pots with only bare soil. Conclusions The results suggest that allelopathy may be at least partly responsible for F. paniculata dominance in subalpine meadows by inhibition of colonization by neighbouring species. PMID:19324898

  9. Interface design and reinforced features of arrowroot (Maranta arundinacea) starch/polyester-based membranes: Preparation, antioxidant activity, and cytocompatibility.

    PubMed

    Wu, Chin-San; Liao, Hsin-Tzu

    2017-01-01

    The structural, mechanical, antioxidant, and cytocompatibility properties of membranes prepared from the polyhydroxyalkanoate (PHA) and arrowroot (Maranta arundinacea) starch powder (ASP) blend (PHA/ASP) were studied. The acrylic acid-grafted PHA (PHA-g-AA) and the coupling agent treated ASP (TASP) were used to enhance the desired characteristics of these membranes. The PHA-g-AA/TASP membranes had better mechanical properties than the PHA/ASP membrane. This effect was attributed to greater compatibility between the grafted PHA and TASP. The water resistance of the PHA-g-AA/TASP membranes was greater than that of the PHA/ASP membranes, and a cytocompatibility evaluation with human foreskin fibroblasts (FBs) indicated that both materials were nontoxic. Moreover, both ASP and TASP enhanced the polyphenol content and antioxidant properties of the membranes. PHA-g-AA/TASP and PHA/ASP membranes had better antioxidant activity than the control group.

  10. Redox Regulation of an AP-1-Like Transcription Factor, YapA, in the Fungal Symbiont Epichloë festucae

    PubMed Central

    Cartwright, Gemma M.

    2013-01-01

    One of the central regulators of oxidative stress in Saccharomyces cerevisiae is Yap1, a bZIP transcription factor of the AP-1 family. In unstressed cells, Yap1 is reduced and cytoplasmic, but in response to oxidative stress, it becomes oxidized and accumulates in the nucleus. To date, there have been no reports on the role of AP-1-like transcription factors in symbiotic fungi. An ortholog of Yap1, named YapA, was identified in the genome of the grass symbiont Epichloë festucae and shown to complement an S. cerevisiae Δyap1 mutant. Hyphae of the E. festucae ΔyapA strain were sensitive to menadione and diamide but resistant to H2O2, KO2, and tert-butyl hydroperoxide (t-BOOH). In contrast, conidia of the ΔyapA strain were very sensitive to H2O2 and failed to germinate. Using a PcatA-eGFP degron-tagged reporter, YapA was shown to be required for expression of a spore-specific catalase gene, catA. Although YapA-EGFP localized to the nucleus in response to host reactive oxygen species during seedling infection, there was no difference in whole-plant and cellular phenotypes of plants infected with the ΔyapA strain compared to the wild-type strain. Homologs of the S. cerevisiae and Schizosaccharomyces pombe redox-sensing proteins (Gpx3 and Tpx1, respectively) did not act as redox sensors for YapA in E. festucae. In response to oxidative stress, YapA-EGFP localized to the nuclei of E. festucae ΔgpxC, ΔtpxA, and ΔgpxC ΔtpxA cells to the same degree as that in wild-type cells. These results show that E. festucae has a robust system for countering oxidative stress in culture and in planta but that Gpx3- or Tpx1-like thiol peroxidases are dispensable for activation of YapA. PMID:23893078

  11. Redox regulation of an AP-1-like transcription factor, YapA, in the fungal symbiont Epichloe festucae.

    PubMed

    Cartwright, Gemma M; Scott, Barry

    2013-10-01

    One of the central regulators of oxidative stress in Saccharomyces cerevisiae is Yap1, a bZIP transcription factor of the AP-1 family. In unstressed cells, Yap1 is reduced and cytoplasmic, but in response to oxidative stress, it becomes oxidized and accumulates in the nucleus. To date, there have been no reports on the role of AP-1-like transcription factors in symbiotic fungi. An ortholog of Yap1, named YapA, was identified in the genome of the grass symbiont Epichloë festucae and shown to complement an S. cerevisiae Δyap1 mutant. Hyphae of the E. festucae ΔyapA strain were sensitive to menadione and diamide but resistant to H2O2, KO2, and tert-butyl hydroperoxide (t-BOOH). In contrast, conidia of the ΔyapA strain were very sensitive to H2O2 and failed to germinate. Using a PcatA-eGFP degron-tagged reporter, YapA was shown to be required for expression of a spore-specific catalase gene, catA. Although YapA-EGFP localized to the nucleus in response to host reactive oxygen species during seedling infection, there was no difference in whole-plant and cellular phenotypes of plants infected with the ΔyapA strain compared to the wild-type strain. Homologs of the S. cerevisiae and Schizosaccharomyces pombe redox-sensing proteins (Gpx3 and Tpx1, respectively) did not act as redox sensors for YapA in E. festucae. In response to oxidative stress, YapA-EGFP localized to the nuclei of E. festucae ΔgpxC, ΔtpxA, and ΔgpxC ΔtpxA cells to the same degree as that in wild-type cells. These results show that E. festucae has a robust system for countering oxidative stress in culture and in planta but that Gpx3- or Tpx1-like thiol peroxidases are dispensable for activation of YapA.

  12. Repetitive DNA: A Versatile Tool for Karyotyping in Festuca pratensis Huds.

    PubMed

    Křivánková, Anna; Kopecký, David; Stočes, Štěpán; Doležel, Jaroslav; Hřibová, Eva

    2017-01-01

    FISH is a useful method to identify individual chromosomes in a karyotype and to discover their structural changes accompanying genome evolution and speciation. DNA probes for FISH should be chromosome specific and/or exhibit specific patterns of distribution along each chromosome. Such probes are not available in many plants including meadow fescue (Festuca pratensis Huds.), an important forage grass species. In the present study, various DNA repeats identified in Illumina shotgun sequences specific to chromosome 4F of F. pratensis were used as probes for FISH to develop the molecular karyotype of meadow fescue and to reveal a long-range molecular organization of its chromosomes. Five tandem repeats produced specific patterns on individual chromosomes. Their use in combination with probes for rRNA genes enabled the establishment of the molecular karyotype of meadow fescue. Most of the mobile genetic elements were dispersed along all the chromosomes except for the DNA transposon CACTA, which was localized preferentially to telomeric and subtelomeric regions, and a putative LTR element, which was localized to (peri)centromeric regions. Cytogenetic mapping of the 5 tandem repeats in other accessions of meadow fescue showed a highly similar distribution and confirmed the versatility and robustness of these probes. © 2017 S. Karger AG, Basel.

  13. Physical and genetic mapping in the grasses Lolium perenne and Festuca pratensis.

    PubMed Central

    King, J; Armstead, I P; Donnison, I S; Thomas, H M; Jones, R N; Kearsey, M J; Roberts, L A; Thomas, A; Morgan, W G; King, I P

    2002-01-01

    A single chromosome of the grass species Festuca pratensis has been introgressed into Lolium perenne to produce a diploid monosomic substitution line 2n = 2x = 14. In this line recombination occurs throughout the length of the F. pratensis/L. perenne bivalent. The F. pratensis chromosome and recombinants between it and its L. perenne homeologue can be visualized using genomic in situ hybridization (GISH). GISH junctions represent the physical locations of sites of recombination, enabling a range of recombinant chromosomes to be used for physical mapping of the introgressed F. pratensis chromosome. The physical map, in conjunction with a genetic map composed of 104 F. pratensis-specific amplified fragment length polymorphisms (AFLPs), demonstrated: (1) the first large-scale analysis of the physical distribution of AFLPs; (2) variation in the relationship between genetic and physical distance from one part of the F. pratensis chromosome to another (e.g., variation was observed between and within chromosome arms); (3) that nucleolar organizer regions (NORs) and centromeres greatly reduce recombination; (4) that coding sequences are present close to the centromere and NORs in areas of low recombination in plant species with large genomes; and (5) apparent complete synteny between the F. pratensis chromosome and rice chromosome 1. PMID:12019245

  14. Isolation and culture of protoplasts from embryogenic suspension cultures of red fescue (Festuca rubva L.).

    PubMed

    Zaghmout, O M; Torello, W A

    1990-10-01

    Protoplasts were isolated from fast-growing embryogenic suspension cultures of red fescue cv. Dawson (Festuca rubra L.) without agitation. The enzyme isolation solution was highly efficient at releasing protoplasts of greater than 95% viability (5×10(6)-10(7) protoplasts per ml of packed cell volume). A three step procedure was followed for washing and transferring protoplasts from a solution high in inorganic salts to a medium containing glucose and sucrose. The addition of 30 mM sodium thiosulfate to the wash and culture media was found to be helpful in reducing the number of lysed protoplasts. Isolated protoplasts began to divide within 48-72 h when protoplasts were plated in agarose squares and surrounded by nurse cells (mixed nurse plating technique). Maximum colony formation (plating efficiency) was approximately 1%. Many of the colonies continued to grow and produced embryos when transferred to a medium consisting of half-strength MS salts, 4 mg/l 2,4-D, 3 g/l casein hydrolysate and 30 g/l sucrose. Upon transfer to hormone-free medium and exposure to light 16 h/day, many of the embryos germinated to produce green leaves and roots.

  15. Germination responses to GA3 and stratification of threatened Festuca L. species from Eastern Mediterranean.

    PubMed

    Celikler, Serap; Güleryüz, Gürcan; Bilaloğlu, Rahmi

    2006-01-01

    The seed germination characteristics of three threatened Festuca sp. [F. punctoria Sm., F. cyllenica Boiss. et Heldr. subsp. uluana Markgr.-Dannenb., F. paphlagonica (St.-Yves) Markgr.-Dannenb. subsp. paphlagonica] were investigated. These species are endemic and spread on alpine belt. The study was carried out with wet-cold and dry-cold stratification throughout 15 days, different doses of GA3 (50, 100 and 150 ppm) and hormone-stratification combined treatments, and non-treatment series. We found that the germination rates of three fescue seeds for various treatment series were different. The mean germination percentage of F. cyllenica was higher (80%) than that of F. punctoria and F. paphlagonica which were fairly low (50-60%). Germination rates increased by wet-stratification treatment in F. punctoria and also increased with 100 ppm GA3 application to the seeds of F. paphlagonica. When taken into consideration the germination percentages of all fescue species, the seeds of F. punctoria and F. paphlagonica can be dormant, but the seeds of F. cyllenica are non-dormant.

  16. Past climate changes facilitated homoploid speciation in three mountain spiny fescues (Festuca, Poaceae)

    PubMed Central

    Marques, I.; Draper, D.; López-Herranz, M. L.; Garnatje, T.; Segarra-Moragues, J. G.; Catalán, P.

    2016-01-01

    Apart from the overwhelming cases of allopolyploidization, the impact of speciation through homoploid hybridization is becoming more relevant than previously thought. Much less is known, however, about the impact of climate changes as a driven factor of speciation. To investigate these issues, we selected Festuca picoeuropeana, an hypothetical natural hybrid between the diploid species F. eskia and F. gautieri that occurs in two different mountain ranges (Cantabrian Mountains and Pyrenees) separated by more than 400 km. To unravel the outcomes of this mode of speciation and the impact of climate during speciation we used a multidisciplinary approach combining genome size and chromosome counts, data from an extensive nuclear genotypic analysis, plastid sequences and ecological niche models (ENM). Our results show that the same homoploid hybrid was originated independently in the two mountain ranges, being currently isolated from both parents and producing viable seeds. Parental species had the opportunity to contact as early as 21000 years ago although niche divergence occurs nowadays as result of a climate-driven shift. A high degree of niche divergence was observed between the hybrid and its parents and no recent introgression or backcrossed hybrids were detected, supporting the current presence of reproductive isolation barriers between these species. PMID:27808118

  17. Past climate changes facilitated homoploid speciation in three mountain spiny fescues (Festuca, Poaceae).

    PubMed

    Marques, I; Draper, D; López-Herranz, M L; Garnatje, T; Segarra-Moragues, J G; Catalán, P

    2016-11-03

    Apart from the overwhelming cases of allopolyploidization, the impact of speciation through homoploid hybridization is becoming more relevant than previously thought. Much less is known, however, about the impact of climate changes as a driven factor of speciation. To investigate these issues, we selected Festuca picoeuropeana, an hypothetical natural hybrid between the diploid species F. eskia and F. gautieri that occurs in two different mountain ranges (Cantabrian Mountains and Pyrenees) separated by more than 400 km. To unravel the outcomes of this mode of speciation and the impact of climate during speciation we used a multidisciplinary approach combining genome size and chromosome counts, data from an extensive nuclear genotypic analysis, plastid sequences and ecological niche models (ENM). Our results show that the same homoploid hybrid was originated independently in the two mountain ranges, being currently isolated from both parents and producing viable seeds. Parental species had the opportunity to contact as early as 21000 years ago although niche divergence occurs nowadays as result of a climate-driven shift. A high degree of niche divergence was observed between the hybrid and its parents and no recent introgression or backcrossed hybrids were detected, supporting the current presence of reproductive isolation barriers between these species.

  18. MiRNAs and miRNA Polymorphisms Modify Drug Response

    PubMed Central

    Li, Mu-Peng; Hu, Yao-Dong; Hu, Xiao-Lei; Zhang, Yan-Jiao; Yang, Yong-Long; Jiang, Chun; Tang, Jie; Chen, Xiao-Ping

    2016-01-01

    Differences in expression of drug response-related genes contribute to inter-individual variation in drugs’ biological effects. MicroRNAs (miRNAs) are small noncoding RNAs emerging as new players in epigenetic regulation of gene expression at post-transcriptional level. MiRNAs regulate the expression of genes involved in drug metabolism, drug transportation, drug targets and downstream signal molecules directly or indirectly. MiRNA polymorphisms, the genetic variations affecting miRNA expression and/or miRNA-mRNA interaction, provide a new insight into the understanding of inter-individual difference in drug response. Here, we provide an overview of the recent progress in miRNAs mediated regulation of biotransformation enzymes, drug transporters, and nuclear receptors. We also describe the implications of miRNA polymorphisms in cancer chemotherapy response. PMID:27834829

  19. Analysis of miRNA Modifications

    PubMed Central

    Yu, Bin; Chen, Xuemei

    2016-01-01

    After transcription, a large number of cellular RNAs employ modifications to increase their diversity and functional potential. Modifications can occur on the base, ribose, or both, and are important steps in the maturation of many RNAs. Our lab recently showed that plant microRNAs (miRNAs) possess a 2′-O-methyl group on the ribose of the 3′ terminal nucleotide, and that this methyl group is added after miRNA/miRNA* formation. One function of this modification is to protect miRNAs from 3′ terminal uridylation by an unknown enzymatic activity. It is possible that uridylation of miRNAs triggers their degradation. Here we describe a protocol to purify a specific miRNA in order to determine its molecular mass so that the presence of a modification can be inferred, an in vivo method to detect 3′ terminal modification of miRNAs, and an (α-32P) dATP incorporation assay to study 3′ terminal uridylation of miRNAs. PMID:19802594

  20. miRNAs associated with immune response in teleost fish.

    PubMed

    Andreassen, Rune; Høyheim, Bjørn

    2017-02-28

    MicroRNAs (miRNAs) have been identified as important post transcriptional regulators of gene expression. In higher vertebrates, a subset of miRNAs has been identified as important regulators of a number of key genes in immune system gene networks, and this paper review recent studies on miRNAs associated with immune response in teleost fish. Challenge studies conducted in several species have identified differently expressed miRNAs associated with viral or bacterial infection. The results from these studies point out several miRNAs that are likely to have evolutionary conserved functions that are related to immune response in teleost fish. Changed expression levels of mature miRNAs from the five miRNA genes miRNA-462, miRNA-731, miRNA-146, miRNA-181 and miRNA-223 are observed following viral as well as bacterial infection in several teleost fish. Furthermore, significant changes in expression of mature miRNAs from the five genes miRNA-21, miRNA-155, miRNA-1388, miRNA-99 and miRNA-100 are observed in multiple studies of virus infected fish while changes in expression of mature miRNA from the three genes miRNA-122, miRNA-192 and miRNA-451 are observed in several studies of fish with bacterial infections. Interestingly, some of these genes are not present in higher vertebrates. The function of the evolutionary conserved miRNAs responding to infection depends on the target gene(s) they regulate. A few target genes have been identified while a large number of target genes have been predicted by in silico analysis. The results suggest that many of the targets are genes from the host's immune response gene networks. We propose a model with expected temporal changes in miRNA expression if they target immune response activators/effector genes or immune response inhibitors, respectively. The best way to understand the function of a miRNA is to identify its target gene(s), but as the amount of genome resources for teleost fish is limited, with less well characterized genomes

  1. Geographic Variation in Festuca rubra L. Ploidy Levels and Systemic Fungal Endophyte Frequencies.

    PubMed

    Dirihan, Serdar; Helander, Marjo; Väre, Henry; Gundel, Pedro E; Garibaldi, Lucas A; Irisarri, J Gonzalo N; Saloniemi, Irma; Saikkonen, Kari

    2016-01-01

    Polyploidy and symbiotic Epichloë fungal endophytes are common and heritable characteristics that can facilitate environmental range expansion in grasses. Here we examined geographic patterns of polyploidy and the frequency of fungal endophyte colonized plants in 29 Festuca rubra L. populations from eight geographic sites across latitudes from Spain to northernmost Finland and Greenland. Ploidy seemed to be positively and negatively correlated with latitude and productivity, respectively. However, the correlations were nonlinear; 84% of the plants were hexaploids (2n = 6x = 42), and the positive correlation between ploidy level and latitude is the result of only four populations skewing the data. In the southernmost end of the gradient 86% of the plants were tetraploids (2n = 4x = 28), whereas in the northernmost end of the gradient one population had only octoploid plants (2n = 8x = 56). Endophytes were detected in 22 out of the 29 populations. Endophyte frequencies varied among geographic sites, and populations and habitats within geographic sites irrespective of ploidy, latitude or productivity. The highest overall endophyte frequencies were found in the southernmost end of the gradient, Spain, where 69% of plants harbored endophytes. In northern Finland, endophytes were detected in 30% of grasses but endophyte frequencies varied among populations from 0% to 75%, being higher in meadows compared to riverbanks. The endophytes were detected in 36%, 30% and 27% of the plants in Faroe Islands, Iceland and Switzerland, respectively. Practically all examined plants collected from southern Finland and Greenland were endophyte-free, whereas in other geographic sites endophyte frequencies were highly variable among populations. Common to all populations with high endophyte frequencies is heavy vertebrate grazing. We propose that the detected endophyte frequencies and ploidy levels mirror past distribution history of F. rubra after the last glaciation period, and local

  2. Effect of nitrogen supply and defoliation on loss of organic compounds from roots of Festuca rubra.

    PubMed

    Paterson, E; Sim, A

    2000-08-01

    The aim of this study was to determine the effects of N-supply and defoliation on rhizodeposition from Festuca rubra, in the context of whole-plant C- partitioning and root morphology. Plants were grown for 36 d in axenic sand microcosms continuously percolated with nutrient solutions of either high or low N concentration (2 mM or 0.01 mM NH(4)NO(3), respectively). The effects of partial defoliation at weekly intervals were determined at high and low N. At low N, dry matter accumulation in roots and shoots was reduced significantly (P<0.001), with proportionately increased partitioning to roots, in comparison with the high N treatment. Root morphology was also affected by N-treatment; at low N, lower biomass production was offset by increased specific root length (P<0.001), reducing the magnitude of the significant (P=0.002) increase in total root length at high N. Cumulative release of organic C from roots of F: rubra over the experimental period was not altered significantly by N-treatment. However, as a proportion of net C-assimilation, rhizodeposition was significantly (P<0.001) greater at low N than at high N. Defoliation transiently (3-5 d) increased the release of soluble organic compounds from roots at each N-supply rate, and increased significantly (P<0.001) cumulative rhizodeposition over the experimental period. These effects of N-supply and defoliation on rhizodeposition are of importance in understanding interactions between plant and microbial productivity in grazed grasslands, and in interpretation of concurrent effects on microbially driven nutrient cycling processes in these systems.

  3. The potential of Festuca rubra and Calamagrostis epigejos for the revegetation of fly ash deposits.

    PubMed

    Mitrović, Miroslava; Pavlović, Pavle; Lakusić, Dmitar; Djurdjević, Lola; Stevanović, Branka; Kostić, Olga; Gajić, Gordana

    2008-12-15

    Two grass species, Festuca rubra (sown) and Calamagrostis epigejos (naturally recolonised), were studied at two fly ash deposit lagoons, weathered 5 (L1) and 13 years (L2). Both species were assessed in terms of their invasive ability, photosynthetic efficiency, trace elements accumulation, and damage symptoms, while the characteristics of the habitat were assessed in terms of trace element content, and the pH and EC of the ash. In the ash weathered for 5 and 13 years, B and Mn concentrations fell within the normal range for soils, while there was an As, Mo and Cu excess, and Se and Zn deficit. There was no difference in the photosynthetic efficiency (ns) of the C. epigejos populations at the different-aged ash lagoons, but differences were found between the populations of F. rubra (P<0.001). F. rubra displayed damage symptoms, in the form of leaf tip chlorosis and necrosis, and wilting seedlings--a result of B accumulation in toxic concentrations and a Cu and Mn deficit. After 13 years the sown F. rubra remained over 9.5% of the ash lagoon's area (L2), while over the same period the naturally recolonised C. epigejos had overgrown 87.5% of the area. The greater colonisation and survival potential of C. epigejos is a result of multiple tolerance to the conditions at ash deposits and of the competitive ability of this species to dominate the colonised habitat. Therefore, characteristics of naturally colonised species can be used for modelling future actions of biological restoration of fly ash deposits aimed at binding the ash with minimal investment (the short-term aim), and for providing conditions for revegetation, and shortening the successive phases in the revegetation of ash deposits after the closure of thermal plants (the long-term aim).

  4. Geographic Variation in Festuca rubra L. Ploidy Levels and Systemic Fungal Endophyte Frequencies

    PubMed Central

    Dirihan, Serdar; Helander, Marjo; Väre, Henry; Gundel, Pedro E.; Garibaldi, Lucas A.; Irisarri, J. Gonzalo N.; Saloniemi, Irma; Saikkonen, Kari

    2016-01-01

    Polyploidy and symbiotic Epichloë fungal endophytes are common and heritable characteristics that can facilitate environmental range expansion in grasses. Here we examined geographic patterns of polyploidy and the frequency of fungal endophyte colonized plants in 29 Festuca rubra L. populations from eight geographic sites across latitudes from Spain to northernmost Finland and Greenland. Ploidy seemed to be positively and negatively correlated with latitude and productivity, respectively. However, the correlations were nonlinear; 84% of the plants were hexaploids (2n = 6x = 42), and the positive correlation between ploidy level and latitude is the result of only four populations skewing the data. In the southernmost end of the gradient 86% of the plants were tetraploids (2n = 4x = 28), whereas in the northernmost end of the gradient one population had only octoploid plants (2n = 8x = 56). Endophytes were detected in 22 out of the 29 populations. Endophyte frequencies varied among geographic sites, and populations and habitats within geographic sites irrespective of ploidy, latitude or productivity. The highest overall endophyte frequencies were found in the southernmost end of the gradient, Spain, where 69% of plants harbored endophytes. In northern Finland, endophytes were detected in 30% of grasses but endophyte frequencies varied among populations from 0% to 75%, being higher in meadows compared to riverbanks. The endophytes were detected in 36%, 30% and 27% of the plants in Faroe Islands, Iceland and Switzerland, respectively. Practically all examined plants collected from southern Finland and Greenland were endophyte-free, whereas in other geographic sites endophyte frequencies were highly variable among populations. Common to all populations with high endophyte frequencies is heavy vertebrate grazing. We propose that the detected endophyte frequencies and ploidy levels mirror past distribution history of F. rubra after the last glaciation period, and local

  5. Effect of fertiliser application and abandonment on plant species composition of Festuca rubra grassland

    NASA Astrophysics Data System (ADS)

    Pavlů, Vilém; Gaisler, Jan; Pavlů, Lenka; Hejcman, Michal; Ludvíková, Vendula

    2012-11-01

    Little is known about the effects of nitrogen (N), phosphorus (P) and potassium (K) application on soil chemical properties and plant species composition of mountain Festuca rubra grasslands. In this study, we aimed to determine whether fertiliser application affects plant species composition and soil properties during periods of management, and whether residual after-effects of fertiliser application can be detected eight years after its use is abandoned. The experiment with unfertilised control, PK treatment and treatments with low and higher level of NPK application under three (intensive management from 1993 to 1997) and two cut management (moderate management from 1997 to 1999) was established in the Jizera Mts. (Czech Republic) on F. rubra meadow and then the experiment was eight years abandoned. Immediately after the introduction of intensive management, a decrease in species richness and diversification of plant species composition occurred. Plant communities which had diversified in different fertiliser treatments persisted under moderately intensive management. The cover of Alopecurus pratensis increased to >50% while the cover of Agrostis capillaris decreased to <5% in NPK treatments during the period of intensive management. Trifolium repens became the dominant species in the PK treatment. Within eight years, under no management, the differences in plant species composition disappeared, species richness decreased and F. rubra, followed by Hypericum maculatum, became dominant in all treatments. The differences in biomass P concentration and plant available P and K concentrations in the soil were still detectable eight years after the last fertiliser application. As shown in this study, moderate application of NPK and consequent abandonment need not generate irreversible changes in species composition of mountain grassland.

  6. Levels of Organic Compounds, Number of Microorganisms and Cadmium Accumulation in Festuca ovina Hydroponic Culture.

    PubMed

    Majewska, Małgorzata; Słomka, Anna

    2016-01-01

    Understanding the microbiological, biochemical and physiological aspects of phytoremediation of soil and water environments polluted to different degrees with heavy metals has very important theoretical and practical implications. In this study, a comparison was made between total cadmium concentration in root and shoot tissues as well as concentrations of particular fractions of Cd immobilized by roots of Festuca ovina (Sheep’s fescue) hydroponically cultivated in nutrient solutions supplemented with 1 μg Cd ml(–1) and those cultivated at 10 μg Cd ml(–1). After three weeks of F. ovina cultivation, the number of bacterial CFU and the amounts of organic chelators, siderophores, proteins and reducing sugars in the growth medium and on the root surface were higher at 10 than at 1 μg Cd ml(–1). The grass also reacted to the high Cd concentration by a decrease in plant growth and dehydrogenase activity in root tissues. The concentration of Cd determined in fractions bound with different strength in roots was significantly dependent on Cd concentration in the growth medium. When the plants were grown at 1 μg Cd ml(–1), 9% of the immobilized cadmium was loosely bound to the root surface, 20% was exchangeable adsorbed, and 28% was bound by chelation; at 10 μg Cd ml(–1), the respective values were 12%, 25%, and 20%. About 43% of the immobilized cadmium remained in roots after sequential extraction, and bioaccumulation factors in shoots had the same values independently of Cd concentration. At both Cd concentrations, the cadmium translocation index for F. ovina was low (< 1), which is why this grass can be recommended for phytostabilization of the metal under study.

  7. Endophyte-mediated resistance to herbivores depends on herbivore identity in the wild grass Festuca subverticillata.

    PubMed

    Afkhami, Michelle E; Rudgers, Jennifer A

    2009-08-01

    Understanding factors that affect the context dependency of species interactions has been identified as a critical research area in ecology. The presence of symbionts in host plants can be an important factor influencing the outcome of plant-insect interactions. Similarly, herbivore identity can alter the outcome of plant-symbiont interactions. Symbiotic foliar fungal endophytes confer resistance to herbivores in economically important agronomic grasses, in part through the production of alkaloids. Although endophytes are common in nature, relatively little is known about their effects on herbivores of native, wild grass species, and a recent meta-analysis suggested that endophytes are only beneficial in agronomic settings. In this study, we performed choice trials for five insect species and a greenhouse experiment with one species to assess effects of the fungal endophyte Neotyphodium sp. on herbivores of the wild grass Festuca subverticillata. In feeding trials, endophyte presence altered the preference of all five insect species tested. However, the magnitude and direction of preference varied among species, with Pterophylla camellifolia (F.), Spodoptera frugiperda (J. E. Smith), and Rhopalosiphum padi L. preferring endophyte-disinfected plants and Encoptolophus costalis (Scudder) and Romalea guttata (Houttuyn) preferring endophyte-symbiotic plants. Despite reducing insect preference, the endophyte had no significant effect on S. frugiperda performance in a no-choice greenhouse experiment and did not increase plant growth in response to this herbivore. Our results show that endophyte-mediated resistance to herbivory depends strongly on herbivore identity and suggest that the fitness consequences of endophyte symbiosis for host plants will be context dependent on the local composition of insect herbivores.

  8. Random Distribution Pattern and Non-adaptivity of Genome Size in a Highly Variable Population of Festuca pallens

    PubMed Central

    Šmarda, Petr; Bureš, Petr; Horová, Lucie

    2007-01-01

    Background and Aims The spatial and statistical distribution of genome sizes and the adaptivity of genome size to some types of habitat, vegetation or microclimatic conditions were investigated in a tetraploid population of Festuca pallens. The population was previously documented to vary highly in genome size and is assumed as a model for the study of the initial stages of genome size differentiation. Methods Using DAPI flow cytometry, samples were measured repeatedly with diploid Festuca pallens as the internal standard. Altogether 172 plants from 57 plots (2·25 m2), distributed in contrasting habitats over the whole locality in South Moravia, Czech Republic, were sampled. The differences in DNA content were confirmed by the double peaks of simultaneously measured samples. Key Results At maximum, a 1·115-fold difference in genome size was observed. The statistical distribution of genome sizes was found to be continuous and best fits the extreme (Gumbel) distribution with rare occurrences of extremely large genomes (positive-skewed), as it is similar for the log-normal distribution of the whole Angiosperms. Even plants from the same plot frequently varied considerably in genome size and the spatial distribution of genome sizes was generally random and unautocorrelated (P > 0·05). The observed spatial pattern and the overall lack of correlations of genome size with recognized vegetation types or microclimatic conditions indicate the absence of ecological adaptivity of genome size in the studied population. Conclusions These experimental data on intraspecific genome size variability in Festuca pallens argue for the absence of natural selection and the selective non-significance of genome size in the initial stages of genome size differentiation, and corroborate the current hypothetical model of genome size evolution in Angiosperms (Bennetzen et al., 2005, Annals of Botany 95: 127–132). PMID:17565968

  9. Random distribution pattern and non-adaptivity of genome size in a highly variable population of Festuca pallens.

    PubMed

    Smarda, Petr; Bures, Petr; Horová, Lucie

    2007-07-01

    The spatial and statistical distribution of genome sizes and the adaptivity of genome size to some types of habitat, vegetation or microclimatic conditions were investigated in a tetraploid population of Festuca pallens. The population was previously documented to vary highly in genome size and is assumed as a model for the study of the initial stages of genome size differentiation. Using DAPI flow cytometry, samples were measured repeatedly with diploid Festuca pallens as the internal standard. Altogether 172 plants from 57 plots (2.25 m(2)), distributed in contrasting habitats over the whole locality in South Moravia, Czech Republic, were sampled. The differences in DNA content were confirmed by the double peaks of simultaneously measured samples. At maximum, a 1.115-fold difference in genome size was observed. The statistical distribution of genome sizes was found to be continuous and best fits the extreme (Gumbel) distribution with rare occurrences of extremely large genomes (positive-skewed), as it is similar for the log-normal distribution of the whole Angiosperms. Even plants from the same plot frequently varied considerably in genome size and the spatial distribution of genome sizes was generally random and unautocorrelated (P > 0.05). The observed spatial pattern and the overall lack of correlations of genome size with recognized vegetation types or microclimatic conditions indicate the absence of ecological adaptivity of genome size in the studied population. These experimental data on intraspecific genome size variability in Festuca pallens argue for the absence of natural selection and the selective non-significance of genome size in the initial stages of genome size differentiation, and corroborate the current hypothetical model of genome size evolution in Angiosperms (Bennetzen et al., 2005, Annals of Botany 95: 127-132).

  10. Occurrence and genetic structure of the systemic grass endophyte Epichloë festucae in fine fescue populations.

    PubMed

    Wäli, Piippa R; Ahlholm, Jouni U; Helander, Marjo; Saikkonen, Kari

    2007-01-01

    Epichloë species are systemic fungal endophytes that usually specialize in a certain group of related grass species. We examined the infection frequency of Epichloë festucae in populations of two fine fescue species (Festuca rubra and F. ovina) in natural and seminatural habitats at 86 study sites (total=2514 plants) across Finland and northern Norway. Infection incidence varied significantly among grass species and populations. A substantial number of the F. rubra and F. ovina populations (53 out of 77 and 25 out of 30, respectively) were either endophyte-free or had very low (<20%) infection frequencies. The highest infection frequencies were found in subarctic areas. Moreover, infection incidence differed between habitats. In the area with the highest infection frequencies, we used microsatellite markers to study genetic diversity and the rates of gene flow of E. festucae among 12 F. rubra populations. Twenty out of the 25 fungal genotypes detected with four microsatellite markers were carrying multiple alleles in at least one locus, indicating multiple infections or vegetative hybridization of the fungus. One dominant genotype occurred in all 12 populations, representing 63.5% of all isolates. We found a moderate level of average genotypic variation and a low level of genetic differentiation (Fst=0.0814). There was no correlation between infection frequency and genotypic diversity. Although the existence of a dominant genotype and the detected linkage disequilibrium suggest that the fungus is mainly asexual and vertically transmitted, the multiallelic loci and variation of genetic diversity among populations indicate occasional contagious spread and sexual or parasexual recombination of the fungus in some populations. Furthermore, the genotypes carrying multiallelic loci suggest the possibility of multiple infections or hybridization of the endophyte.

  11. Telomere Length, TERT, and miRNA Expression

    PubMed Central

    Slattery, Martha L.; Herrick, Jennifer S.; Pellatt, Andrew J.; Wolff, Roger K.; Mullany, Lila E.

    2016-01-01

    It has been proposed that miRNAs are involved in the control of telomeres. We test that hypothesis by examining the association between miRNAs and telomere length (TL). Additionally, we evaluate if genetic variation in telomerase reverse transcriptase (TERT) is associated with miRNA expression levels. We use data from a population-based study of colorectal cancer (CRC), where we have previously shown associations between TL and TERT and CRC, to test associations between TL and miRNA expression and TERT and miRNA expression. To gain insight into functions of miRNAs associated with TERT we tested linear associations between miRNAs and their targeted gene mRNAs. An Agilent platform that contained information on over 2000 miRNAs was used. TL was measured using a multiplexed quantitative PCR (qPCR). RNAseq was used to assess gene expression. Our sample consisted of 1152 individuals with SNP data and miRNA expression data; 363 individuals with both TL and miRNA; and 148 individuals with miRNA and mRNA data. Thirty-three miRNAs were directly associated with TL after adjusting for age and sex (false discovery rate (FDR) of 0.05). TERT rs2736118 was associated with differences in miRNA expression between carcinoma and normal colonic mucosa for 75 miRNAs (FDR <0.05). Genes regulated by these miRNAs, as indicated by mRNA/miRNA associations, were associated with major signaling pathways beyond their TL-related functions, including PTEN, and PI3K/AKT signaling. Our data support a direct association between miRNAs and TL; differences in miRNA expression levels by TERT genotype were observed. Based on miRNA and targeted mRNA associations our data suggest that TERT is involved in non-TL-related functions by acting through altered miRNA expression. PMID:27627813

  12. Effects of polycystic ovary syndrome (PCOS), sex hormones, and obesity on circulating miRNA-21, miRNA-27b, miRNA-103, and miRNA-155 expression.

    PubMed

    Murri, Mora; Insenser, María; Fernández-Durán, Elena; San-Millán, José L; Escobar-Morreale, Héctor F

    2013-11-01

    MicroRNAs (miRNAs) are small, noncoding RNA sequences that negatively regulate gene expression at the post-transcriptional level. miRNA-21, miRNA-27b, miRNA-103, and miRNA-155 have been associated with metabolic disorders such as obesity and diabetes, which are also associated with polycystic ovary syndrome (PCOS). We aimed to evaluate the effects of sex, sex hormones, and PCOS and their interactions with obesity on the expression in the circulation of these miRNAs. This was a case-control study. The setting was an academic hospital. We included 12 control women, 12 patients with PCOS, and 12 men selected as to have similar body mass index (BMI) and age. Six subjects per group had normal weight (BMI < 25 kg/m(2)), and six subjects per group were obese (BMI ≥ 30 kg/m(2)). Blood samples were collected early in the morning after a 12-hour fast. We measured whole blood expression of miRNA-21, miRNA-27b, miRNA-103, and miRNA-155. Obesity significantly reduced the expression of miRNA-21, miRNA-27b, and miRNA-103. However, there was a significant interaction between obesity and the group of subjects in the expression of miRNA-21, miRNA-27b, miRNA-103, and miRNA-155 consisting of obesity reducing the expression of these miRNAs in control woman and men, but tending to increase their expression in women with PCOS. These differences paralleled those observed in serum T concentrations. The present results suggest that miRNAs that play an important role in metabolic and immune system processes are influenced by obesity and circulating androgen concentrations.

  13. Transcriptional regulation of mammalian miRNA genes

    PubMed Central

    Schanen, Brian C.; Li, Xiaoman

    2010-01-01

    MicroRNAs (miRNAs) are members of a growing family of non-coding transcripts, 21-23 nucleotides long, which regulate a diverse collection of biological processes and various diseases by RNA-mediated gene-silencing mechanisms. While currently many studies focus on defining the regulatory functions of miRNAs, few are directed towards how miRNA genes are themselves transcriptionally regulated. Recent studies of miRNA transcription have elucidated RNA polymerase II as the major polymerase of miRNAs, however, little is known of the structural features of miRNA promoters, especially those of mammalian miRNAs. Here, we review the current literature regarding features conserved among miRNA promoters useful for their detection and the current novel methodologies available to enable researchers to advance our understanding of the transcriptional regulation of miRNA genes. PMID:20977933

  14. Mechanosensitive miRNAs and Bone Formation

    PubMed Central

    Chen, Zhihao; Zhang, Yan; Liang, Chao; Chen, Lei

    2017-01-01

    Mechanical stimuli are required for the maintenance of skeletal integrity and bone mass. An increasing amount of evidence indicates that multiple regulators (e.g., hormone, cytoskeleton proteins and signaling pathways) are involved in the mechanical stimuli modulating the activities of osteogenic cells and the process of bone formation. Significantly, recent studies have showed that several microRNAs (miRNAs) were sensitive to various mechanical stimuli and played a crucial role in osteogenic differentiation and bone formation. However, the functional roles and further mechanisms of mechanosensitive miRNAs in bone formation are not yet completely understood. This review highlights the roles of mechanosensitive miRNAs in osteogenic differentiation and bone formation and underlines their potential therapeutic application for bone loss induced by the altering of mechanical stimuli. PMID:28767056

  15. Use of Mature miRNA Strand Selection in miRNAs Families in Cervical Cancer Development.

    PubMed

    Granados-López, Angelica Judith; Ruiz-Carrillo, José Luis; Servín-González, Luis Steven; Martínez-Rodríguez, José Luis; Reyes-Estrada, Claudia Araceli; Gutiérrez-Hernández, Rosalinda; López, Jesús Adrián

    2017-02-14

    Aberrant miRNA expression is well recognized as a cancer hallmark, nevertheless miRNA function and expression does not always correlate in patients tissues and cell lines studies. In addition to this issue, miRNA strand usage conduces to increased cell signaling pathways modulation diversifying cellular processes regulation. In cervical cancer, 20 miRNA families are involved in carcinogenesis induction and development to this moment. These families have 5p and 3p strands with different nucleotide (nt) chain sizes. In general, mature 5p strands are larger: two miRNAs of 24 nt, 24 miRNAs of 23 nt, 35 miRNAs of 22 nt and three miRNAs of 21 nt. On the other hand, the 3p strands lengths observed are: seven miRNAs of 23 nt, 50 miRNAs of 22 nt, six miRNAs of 21 nt and four miRNAs of 20 nt. Based on the analysis of the 20 miRNA families associated with cervical cancer, 67 3p strands and 65 5p strands are selected suggesting selectivity and specificity mechanisms regulating cell processes like proliferation, apoptosis, migration, invasion, metabolism and Warburg effect. The insight reviewed here could be used in the miRNA based therapy, diagnosis and prognosis approaches.

  16. Use of Mature miRNA Strand Selection in miRNAs Families in Cervical Cancer Development

    PubMed Central

    Granados-López, Angelica Judith; Ruiz-Carrillo, José Luis; Servín-González, Luis Steven; Martínez-Rodríguez, José Luis; Reyes-Estrada, Claudia Araceli; Gutiérrez-Hernández, Rosalinda; López, Jesús Adrián

    2017-01-01

    Aberrant miRNA expression is well recognized as a cancer hallmark, nevertheless miRNA function and expression does not always correlate in patients tissues and cell lines studies. In addition to this issue, miRNA strand usage conduces to increased cell signaling pathways modulation diversifying cellular processes regulation. In cervical cancer, 20 miRNA families are involved in carcinogenesis induction and development to this moment. These families have 5p and 3p strands with different nucleotide (nt) chain sizes. In general, mature 5p strands are larger: two miRNAs of 24 nt, 24 miRNAs of 23 nt, 35 miRNAs of 22 nt and three miRNAs of 21 nt. On the other hand, the 3p strands lengths observed are: seven miRNAs of 23 nt, 50 miRNAs of 22 nt, six miRNAs of 21 nt and four miRNAs of 20 nt. Based on the analysis of the 20 miRNA families associated with cervical cancer, 67 3p strands and 65 5p strands are selected suggesting selectivity and specificity mechanisms regulating cell processes like proliferation, apoptosis, migration, invasion, metabolism and Warburg effect. The insight reviewed here could be used in the miRNA based therapy, diagnosis and prognosis approaches. PMID:28216603

  17. Intensity and importance of competition for a grass (Festuca rubra) and a legume (Trifolium pratense) vary with environmental changes.

    PubMed

    Zhang, Junyan; Cheng, Genwei; Yu, Feihai; Kräuchi, Norbert; Li, Mai-He

    2008-12-01

    How plant competition varies across environmental gradients has been a long debate among ecologists. We conducted a growth chamber experiment to determine the intensity and importance of competition for plants grown in changed environmental conditions. Festuca rubra and Trifolium pratense were grown in monoculture and in two- and/or three-species mixtures under three environmental treatments. The measured competitive variations in terms of growth (height and biomass) were species-dependent. Competition intensity for Festuca increased with decreased productivity, whilst competition importance displayed a humpback response. However, significant response was detected in neither competition intensity nor importance for Trifolium. Intensity and importance of competition followed different response patterns, suggesting that they may not be correlated along an environmental gradient. The biological and physiological variables of plants play an important role to determine the interspecific competition associated with competition intensity and importance. However, the competitive feature can be modified by multiple environmental changes which may increase or hinder how competitive a plant is.

  18. Intraspecific DNA Content Variability in Festuca pallens on Different Geographical Scales and Ploidy Levels

    PubMed Central

    ŠMARDA, PETR; BUREŠ, PETR

    2006-01-01

    • Background and Aims Intraspecific genome size variability of Festuca pallens occurring on relict rocky steppes in Central Europe was studied on two ploidy levels and three geographical scales: (1) local scale of 24 populations, (2) landscape scale of three transects in river canyons or hill systems, and (3) global scale of 160 samples covering the whole distribution area. • Methods DAPI flow cytometry of homogeneously cultivated samples (≥1 year), measured randomly with two internal standards, Lycopersicon esculentum and Pisum sativum. Differences in DNA content were confirmed (1) by the double peaks of simultaneously measured samples, (2) based on measurements carried out in different seasons, and (3) by additional measurements with propidium iodide. • Key Results On a global scale, the relative DNA content ranged between 1·170-fold in diploids and 1·164-fold in tetraploids. A maximum difference of 1·088-fold between the mean relative DNA content of nearby populations was found. In 16 of 24 populations significant variability was shown (P < 0·001, 1·121-fold as maximum). For both ploidy levels, the relative genome size had the same range and geographical pattern, correlated with geographical coordinates (P < 0·01). Diploids with larger genomes occur on relict habitats (P < 0·01), and in areas of periglacial steppes (20 000 years ago; P < 0·02). In tetraploids, the relative DNA content differs among the three previously recognized geographical types (Alpine, Pannonian and Scabrifolia, P < 0·001). Tetraploids have a relative DNA content smaller than twice that of the diploids (P < 0·001). An influence of microhabitat on DNA content variation was not confirmed. • Conclusions Genome size variability occurs over all spatial scales: intrapopulation, landscape and global. Correlation between geographical coordinates and palaeovegetation type, concomitant with diploids and tetraploids, and no influence of microhabitat were found. Genome size

  19. RNA Binding Proteins in the miRNA Pathway.

    PubMed

    Connerty, Patrick; Ahadi, Alireza; Hutvagner, Gyorgy

    2015-12-26

    microRNAs (miRNAs) are short ~22 nucleotides (nt) ribonucleic acids which post-transcriptionally regulate gene expression. miRNAs are key regulators of all cellular processes, and the correct expression of miRNAs in an organism is crucial for proper development and cellular function. As a result, the miRNA biogenesis pathway is highly regulated. In this review, we outline the basic steps of miRNA biogenesis and miRNA mediated gene regulation focusing on the role of RNA binding proteins (RBPs). We also describe multiple mechanisms that regulate the canonical miRNA pathway, which depends on a wide range of RBPs. Moreover, we hypothesise that the interaction between miRNA regulation and RBPs is potentially more widespread based on the analysis of available high-throughput datasets.

  20. Virus-Mediated Alterations in miRNA Factors and Degradation of Viral miRNAs by MCPIP1

    PubMed Central

    Happel, Christine; Ramalingam, Dhivya; Ziegelbauer, Joseph M.

    2016-01-01

    Kaposi’s sarcoma-associated herpesvirus (KSHV), the causative agent of Kaposi’s sarcoma, encodes 25 mature viral miRNAs. MCP-1-induced protein-1 (MCPIP1), a critical regulator of immune homeostasis, has been shown to suppress miRNA biosynthesis via cleavage of precursor miRNAs through its RNase domain. We demonstrate that MCPIP1 can directly cleave KSHV and EBV precursor miRNAs and that MCPIP1 expression is repressed following de novo KSHV infection. In addition, repression with siRNAs to MCPIP1 in KSHV-infected cells increased IL-6 and KSHV miRNA expression, supporting a role for MCPIP1 in IL-6 and KSHV miRNA regulation. We also provide evidence that KSHV miRNAs repress MCPIP1 expression by targeting the 3’UTR of MCPIP1. Conversely, expression of essential miRNA biogenesis components Dicer and TRBP is increased following latent KSHV infection. We propose that KSHV infection inhibits a negative regulator of miRNA biogenesis (MCPIP1) and up-regulates critical miRNA processing components to evade host mechanisms that inhibit expression of viral miRNAs. KSHV-mediated alterations in miRNA biogenesis represent a novel mechanism by which KSHV interacts with its host and a new mechanism for the regulation of viral miRNA expression. PMID:27893764

  1. An Epichloë festucae homologue of MOB3, a component of the STRIPAK complex, is required for the establishment of a mutualistic symbiotic interaction with Lolium perenne

    PubMed Central

    Green, Kimberly A.; Becker, Yvonne; Fitzsimons, Helen L.

    2016-01-01

    Summary In both Sordaria macrospora and Neurospora crassa, components of the conserved STRIPAK (striatin‐interacting phosphatase and kinase) complex regulate cell–cell fusion, hyphal network development and fruiting body formation. Interestingly, a number of Epichloë festucae genes that are required for hyphal cell–cell fusion, such as noxA, noxR, proA, mpkA and mkkA, are also required for the establishment of a mutualistic symbiotic interaction with Lolium perenne. To determine whether MobC, a homologue of the STRIPAK complex component MOB3 in S. macrospora and N. crassa, is required for E. festucae hyphal fusion and symbiosis, a mobC deletion strain was generated. The ΔmobC mutant showed reduced rates of hyphal cell–cell fusion, formed intrahyphal hyphae and exhibited enhanced conidiation. Plants infected with ΔmobC were severely stunted. Hyphae of ΔmobC showed a proliferative pattern of growth within the leaves of Lolium perenne with increased colonization of the intercellular spaces and vascular bundles. Although hyphae were still able to form expressoria, structures allowing the colonization of the leaf surface, the frequency of formation was significantly reduced. Collectively, these results show that the STRIPAK component MobC is required for the establishment of a mutualistic symbiotic association between E. festucae and L. perenne, and plays an accessory role in the regulation of hyphal cell–cell fusion and expressorium development in E. festucae. PMID:27277141

  2. Assessment of Grazing Effect on Sheep Fescue (Festuca valesiaca)Dominated Steppe Rangelands in the semi-arid Central Anatolian Region of Turkey

    USDA-ARS?s Scientific Manuscript database

    Because of increased grazing pressure over the last fifty years, vegetation of the steppe rangelands in the semi-arid Central Anatolian Region of Turkey has been severely degraded. In these pastures, Festuca valesiaca (a sod forming short-grass) and Thymus sipyleus ssp rosulans (a prostrate shrub) a...

  3. Development of fine-leaved Festuca grass populations identified genetic resources having potential for improved forage production and wildfire control in the western United States

    USDA-ARS?s Scientific Manuscript database

    Drought and heat tolerant fine-leaved fescue (Festuca ssp.) grasses have potential as components in rangeland greenstrips for wildfire control in semi-arid climates. However, such fine-leaved grasses have been difficult to identify because of specific adaptations, lack of late maturity, and often p...

  4. Draft Genome Sequence of Bacillus pumilus Strain GM3FR, an Endophyte Isolated from Aerial Plant Tissues of Festuca rubra L.

    PubMed Central

    Hollensteiner, Jacqueline; Daniel, Rolf; Liesegang, Heiko; Vidal, Stefan

    2017-01-01

    ABSTRACT Here, we report the draft genome sequence of Bacillus pumilus GM3FR, an endophytic bacterium isolated from aerial plant tissues of Festuca rubra L. The draft genome consists of 3.5 Mb and harbors 3,551 predicted protein-encoding genes. The genome provides insights into the biocontrol potential of B. pumilus GM3FR. PMID:28360161

  5. Phenotypic and genotypic analysis of a U.S. native fine-leaved Festuca population portends its potential use for low-input urban landscapes

    USDA-ARS?s Scientific Manuscript database

    Continued reduction in limited natural resources worldwide increasingly necessitates the incorporation of low maintenance and input plant materials into urban landscapes. Although some fine-leaved Festuca grass species have been utilized in formal gardens and native urban landscapes because of thei...

  6. Discovery of miRNAs and Their Corresponding miRNA Genes in Atlantic Cod (Gadus morhua): Use of Stable miRNAs as Reference Genes Reveals Subgroups of miRNAs That Are Highly Expressed in Particular Organs.

    PubMed

    Andreassen, Rune; Rangnes, Fredrik; Sivertsen, Maria; Chiang, Michelle; Tran, Michelle; Worren, Merete Molton

    2016-01-01

    Atlantic cod (Gadus morhua) is among the economically most important species in the northern Atlantic Ocean and a model species for studying development of the immune system in vertebrates. MicroRNAs (miRNAs) are an abundant class of small RNA molecules that regulate fundamental biological processes at the post-transcriptional level. Detailed knowledge about a species miRNA repertoire is necessary to study how the miRNA transcriptome modulate gene expression. We have therefore discovered and characterized mature miRNAs and their corresponding miRNA genes in Atlantic cod. We have also performed a validation study to identify suitable reference genes for RT-qPCR analysis of miRNA expression in Atlantic cod. Finally, we utilized the newly characterized miRNA repertoire and the dedicated RT-qPCR method to reveal miRNAs that are highly expressed in certain organs. The discovery analysis revealed 490 mature miRNAs (401 unique sequences) along with precursor sequences and genomic location of the miRNA genes. Twenty six of these were novel miRNA genes. Validation studies ranked gmo-miR-17-1-5p or the two-gene combination gmo-miR25-3p and gmo-miR210-5p as most suitable qPCR reference genes. Analysis by RT-qPCR revealed 45 miRNAs with significantly higher expression in tissues from one or a few organs. Comparisons to other vertebrates indicate that some of these miRNAs may regulate processes like growth, lipid metabolism, immune response to microbial infections and scar damage repair. Three teleost-specific and three novel Atlantic cod miRNAs were among the differentially expressed miRNAs. The number of known mature miRNAs was considerably increased by our identification of miRNAs and miRNA genes in Atlantic cod. This will benefit further functional studies of miRNA expression using deep sequencing methods. The validation study showed that stable miRNAs are suitable reference genes for RT-qPCR analysis of miRNA expression. Applying RT-qPCR we have identified several miRNAs

  7. Discovery of miRNAs and Their Corresponding miRNA Genes in Atlantic Cod (Gadus morhua): Use of Stable miRNAs as Reference Genes Reveals Subgroups of miRNAs That Are Highly Expressed in Particular Organs

    PubMed Central

    Andreassen, Rune; Rangnes, Fredrik; Sivertsen, Maria; Chiang, Michelle; Tran, Michelle; Worren, Merete Molton

    2016-01-01

    Background Atlantic cod (Gadus morhua) is among the economically most important species in the northern Atlantic Ocean and a model species for studying development of the immune system in vertebrates. MicroRNAs (miRNAs) are an abundant class of small RNA molecules that regulate fundamental biological processes at the post-transcriptional level. Detailed knowledge about a species miRNA repertoire is necessary to study how the miRNA transcriptome modulate gene expression. We have therefore discovered and characterized mature miRNAs and their corresponding miRNA genes in Atlantic cod. We have also performed a validation study to identify suitable reference genes for RT-qPCR analysis of miRNA expression in Atlantic cod. Finally, we utilized the newly characterized miRNA repertoire and the dedicated RT-qPCR method to reveal miRNAs that are highly expressed in certain organs. Results The discovery analysis revealed 490 mature miRNAs (401 unique sequences) along with precursor sequences and genomic location of the miRNA genes. Twenty six of these were novel miRNA genes. Validation studies ranked gmo-miR-17-1—5p or the two-gene combination gmo-miR25-3p and gmo-miR210-5p as most suitable qPCR reference genes. Analysis by RT-qPCR revealed 45 miRNAs with significantly higher expression in tissues from one or a few organs. Comparisons to other vertebrates indicate that some of these miRNAs may regulate processes like growth, lipid metabolism, immune response to microbial infections and scar damage repair. Three teleost-specific and three novel Atlantic cod miRNAs were among the differentially expressed miRNAs. Conclusions The number of known mature miRNAs was considerably increased by our identification of miRNAs and miRNA genes in Atlantic cod. This will benefit further functional studies of miRNA expression using deep sequencing methods. The validation study showed that stable miRNAs are suitable reference genes for RT-qPCR analysis of miRNA expression. Applying RT-qPCR we

  8. Exosomes as miRNA Carriers: Formation-Function-Future.

    PubMed

    Yu, Xiaojie; Odenthal, Margarete; Fries, Jochen W U

    2016-12-02

    Exosomes, which are one of the smallest extracellular vesicles released from cells, have been shown to carry different nucleic acids, including microRNAs (miRNAs). miRNAs significantly regulate cell growth and metabolism by posttranscriptional inhibition of gene expression. The rapidly changing understanding of exosomes' formation and function in delivering miRNAs from cell to cell has prompted us to review current knowledge in exosomal miRNA secretion mechanisms as well as possible therapeutic applications for personalized medicine.

  9. Improved targeting of miRNA with antisense oligonucleotides.

    PubMed

    Davis, Scott; Lollo, Bridget; Freier, Susan; Esau, Christine

    2006-01-01

    MicroRNAs (miRNAs) are a class of 20-24 nt noncoding RNAs that regulate target mRNAs post-transcriptionally by binding with imperfect complementarity in the 3'-untranslated region (3'-UTR) and inhibiting translation or RNA stability. Current understanding of miRNA biology is limited, and antisense oligonucleotide (ASO) inhibition is a powerful technique for miRNA functionalization in vitro and in vivo, and for therapeutic targeting of miRNAs. Identification of optimal ASO chemistries for targeting miRNAs is therefore of great interest. We evaluated a number of 2'-sugar and backbone ASO modifications for their ability to inhibit miR-21 activity on a luciferase reporter mRNA. ASO modifications that improved target affinity improved miRNA ASO activity, yet the positioning of high-affinity modifications also had dramatically different effects on miRNA activity, suggesting that more than affinity determined the effectiveness of the miRNA ASOs. We present data in which the activity of a modified miRNA ASO was inversely correlated to its tolerability as an siRNA passenger strand, suggesting that a similar mechanism could be involved in the dissociation of miRNA ASOs and siRNA passenger strands. These studies begin to define the factors important for designing improved miRNA ASOs, enabling more effective miRNA functionalization and therapeutic targeting.

  10. Improved targeting of miRNA with antisense oligonucleotides

    PubMed Central

    Davis, Scott; Lollo, Bridget; Freier, Susan; Esau, Christine

    2006-01-01

    MicroRNAs (miRNAs) are a class of 20–24 nt noncoding RNAs that regulate target mRNAs post-transcriptionally by binding with imperfect complementarity in the 3′-untranslated region (3′-UTR) and inhibiting translation or RNA stability. Current understanding of miRNA biology is limited, and antisense oligonucleotide (ASO) inhibition is a powerful technique for miRNA functionalization in vitro and in vivo, and for therapeutic targeting of miRNAs. Identification of optimal ASO chemistries for targeting miRNAs is therefore of great interest. We evaluated a number of 2′-sugar and backbone ASO modifications for their ability to inhibit miR-21 activity on a luciferase reporter mRNA. ASO modifications that improved target affinity improved miRNA ASO activity, yet the positioning of high-affinity modifications also had dramatically different effects on miRNA activity, suggesting that more than affinity determined the effectiveness of the miRNA ASOs. We present data in which the activity of a modified miRNA ASO was inversely correlated to its tolerability as an siRNA passenger strand, suggesting that a similar mechanism could be involved in the dissociation of miRNA ASOs and siRNA passenger strands. These studies begin to define the factors important for designing improved miRNA ASOs, enabling more effective miRNA functionalization and therapeutic targeting. PMID:16690972

  11. Are miRNA-103, miRNA-107 and miRNA-122 Involved in the Prevention of Liver Steatosis Induced by Resveratrol?

    PubMed

    Gracia, Ana; Fernández-Quintela, Alfredo; Miranda, Jonatan; Eseberri, Itziar; González, Marcela; Portillo, María P

    2017-04-04

    The aim of the present study was to determine whether the reduction in liver fat previously observed in our laboratory in a cohort of rats which had been fed an obesogenic diet was mediated by changes in the expression of microRNA (miRNA)-103-3p, miRNA-107-3p and miRNA-122-5p, which represent 70% of total miRNAs in the liver, as well as in their target genes. The expression of the three analysed miRNAs was reduced in rats treated with resveratrol. A reduction in sterol-regulatory element binding protein 1 (SREBP1) and an increase in carnitine palmitoyltransferase 1a (CPT1a) were observed in resveratrol-treated rats. No changes were found in fatty acid synthase (FAS). In cultured hepatocytes, SREBP1 protein was increased after the transfection of each miRNA. FAS protein expression was decreased after the transfection of miRNA-122-5p, and CPT1a protein was down-regulated by the over-expression of miRNA-107-3p. This study provides new evidences which show that srebf1 is a target gene for miRNA-103-3p and miRNA-107-3p, fasn a target gene for miRNA-122-5p and cpt1a a target gene for miRNA-107-3p. Moreover, the reduction in liver steatosis induced by resveratrol in rats fed an obesegenic diet is mediated, at least in part, by the increase in CPT1a protein expression and activity, via a decrease in miRNA-107-3p expression.

  12. Breeding bird territory placement in riparian wet meadows in relation to invasive reed canary grass, Phalaris arundinacea

    USGS Publications Warehouse

    Kirsch, E.M.; Gray, B.R.; Fox, T.J.; Thogmartin, W.E.

    2007-01-01

    Invasive plants are a growing concern worldwide for conservation of native habitats. In endangered wet meadow habitat in the Upper Midwestern United States, reed canary grass (Phalaris arundinacea) is a recognized problem and its prevalence is more widespread than the better-known invasive wetland plant purple loosestrife (Lythrum salicaria). Although resource managers are concerned about the effect of reed canary grass on birds, this is the first study to report how common wet meadow birds use habitat in relation to reed canary grass cover and dominance. We examined three response variables: territory placement, size of territories, and numbers of territories per plot in relation to cover of reed canary grass. Territory locations for Sedge Wren (Cistothorus platensis) and Song Sparrow (Melospiza melodia) were positively associated with reed canary grass cover, while those for Common Yellowthroat (Geothlypis trichas) were not. Only Swamp Sparrow (M. georgiana) territory locations were negatively associated with reed canary grass cover and dominance (which indicated a tendency to place territories where there was no reed canary grass or where many plant species occurred with reed canary grass). Swamp Sparrow territories were positively associated with vegetation height density and litter depth. Common Yellowthroat territories were positively associated with vegetation height density and shrub cover. Song Sparrow territories were negatively associated with litter depth. Reed canary grass cover within territories was not associated with territory size for any of these four bird species. Territory density per plot was not associated with average reed canary grass cover of plots for all four species. Sedge Wrens and Song Sparrows may not respond negatively to reed canary grass because this grass is native to wet meadows of North America, and in the study area it merely replaces other tall lush plants. Avoidance of reed canary grass by Swamp Sparrows may be mediated

  13. The expression of miRNA-221 and miRNA-222 in gliomas patients and their prognosis.

    PubMed

    Xue, Liang; Wang, Yi; Yue, Shuyuan; Zhang, Jianning

    2017-01-01

    The aim of this study is to explore the expression of microRNA (miRNA)-221 and miRNA-222 in human glioma cells and tissues. The expression of miRNA-221 and miRNA-222 in human glioma cell line U87, U251, A172, LN229 and surgery resected glioma tissues were measured. The survival rate of X-ray (2 Gy) irradiated glioma cells were calculated. 165 cases of glioma patients were recruited successfully; the expression of miRNA-221 and miRNA-222 in their resected tissues were measured. The expression of miRNA-221 and miRNA-222 in cancer tissues were obviously higher than control tissues (normal brain tissue) and control cell (gastric mucosal epithelial cell, GES) (p < 0.05). The highly malignant glioma tissues expressed significantly higher miRNA-221 and miRNA-222 than low malignant glioma tissues. Patients with highly expressed miRNA-221 and miRNA-222 have shorter survival time. Survival rate of glioma cells was significantly higher than GES cell after irradiation (p < 0.05); miRNA-221 in glioma cells. The expressions of miRNA-221 and miRNA-222 in irritated glioma cells were positively correlated with the survival rate of glioma cells (r = 0.629, 0.712, both p < 0.01). For the 165 glioma patients, the expressions of miRNA-221 and miRNA-222 increased with the increasing of pathological grades (χ (2) = 42.85, p < 0.01); and their survival time decreased when miRNA-221 expression elevated (χ (2) = 57.12, p < 0.01). MiRNA-221 and miRNA-222 express highly in human glioma cells and tissues. Expression of miRNA-221 and miRNA-222 are closely related to pathological grading and prognosis of glioma; they could be used as independent prognostic factor for glioma.

  14. Stabilization of metals in acidic mine spoil with amendments and red fescue (Festuca rubra L.) growth.

    PubMed

    Simon, László

    2005-12-01

    Stabilization of metals with amendments and red fescue (Festuca rubra, cv. Keszthelyi 2) growth was studied on an acidic and phytotoxic mine spoil (pH(KCl) 3.20-3.26; Cd 7.1 mg kg(-1), Cu 120 mg kg(-1), Pb 2154 mg kg(-1) and Zn 605 mg kg(-1)) from Gyöngyösoroszi, Hungary in a pot experiment. Raising the pH above 5.0 by lime (CaCO(3)), and supplementing with 40 mg kg(-1)nitrogen (NH(4)NO(3)) made this material suitable for plant growth. All cultures were limed with 0.5% (m/m) CaCO(3) (treatment 1), which was combined with 5% (m/m) municipal sewage sludge compost (treatment 2), 5% (m/m) peat (treatment 3), 7.5% (m/m) natural zeolite (clinoptilolite) (treatment 4), and 0.5 (m/m) KH(2)PO(4) (treatment 5). Treatments 1-5 were combined with each other (treatment 6). After 60 days of red fescue growth, pH of the limed mine spoil decreased in all cultures units. Application of peat caused the highest pH decrease (1.15), while decrease of pH was less than 0.23 in treatments 2, 5 or 6. Application of lime significantly reduced concentrations of metals in the 'plant available' fraction of mine spoil compared to non-limed mine spoil. Amendments added to limed mine spoil changed variously the ratio of Cd, Cu, Pb and Zn in exchangeable or 'plant available' fractions, differently influencing the phytoavailability of these metals. Most of the metals were captured in the roots of test plants. Treatment 2 caused the appearance of less Cd in shoots (<0.1 microg g(-1)) or roots (3.11 microg g(-1)), while treatment 5 resulted in the highest Cd concentration (2.13 microg g(-1)) in shoots. Treatments did not influence significantly the Cu accumulation in shoots. The Pb accumulation of roots (44.7 microg g(-1)) was most effectively inhibited by combined treatment, while the highest value (136 microg g(-1)) was found in the culture treated with potassium phosphate. Pb concentration in shoots was below the detection limit, except for treatments 5 and 6. Peat application resulted in higher

  15. Variability of ribosomal DNA sites in Festuca pratensis, Lolium perenne, and their intergeneric hybrids, revealed by FISH and GISH.

    PubMed

    Ksiazczyk, T; Taciak, M; Zwierzykowski, Z

    2010-01-01

    This study focuses on the variability of chromosomal location and number of ribosomal DNA (rDNA) sites in some diploid and autotetraploid Festuca pratensis and Lolium perenne cultivars, as well as on identification of rDNA-bearing chromosomes in their triploid and tetraploid F. pratensis × L. perenne hybrids. The rDNA loci were mapped using fluorescence in situ hybridization (FISH) with 5S and 25S rDNA probes, and the origin of parental genomes was verified by genomic in situ hybridization (GISH) with L. perenne genomic DNA as a probe, and F. pratensis genomic DNA as a block. FISH detected variation in the number and chromosomal location of both 5S and 45S rDNA sites. In F. pratensis mostly additional signals of 5S rDNA loci occurred, as compared with standard F. pratensis karyotypes. Losses of 45S rDNA loci were more frequent in L. perenne cultivars and intergeneric hybrids. Comparison of the F. pratensis and L. perenne genomes approved a higher number of rDNA sites as well as variation in chromosomal rDNA location in L. perenne. A greater instability of F. pratensis-genome-like and L. perenne-genome-like chromosomes in tetraploid hybrids was revealed, indicating gains and losses of rDNA loci, respectively. Our data indicate that the rDNA loci physically mapped on chromosomes 2 and 3 in F. pratensis and on chromosome 3 in L. perenne are useful markers for these chromosomes in intergeneric Festuca × Lolium hybrids.

  16. MicroRNAs, macrocontrol: regulation of miRNA processing.

    PubMed

    Slezak-Prochazka, Izabella; Durmus, Selvi; Kroesen, Bart-Jan; van den Berg, Anke

    2010-06-01

    MicroRNAs (miRNAs) are a set of small, non-protein-coding RNAs that regulate gene expression at the post-transcriptional level. Maturation of miRNAs comprises several regulated steps resulting in approximately 22-nucleotide single-stranded mature miRNAs. Regulation of miRNA expression can occur both at the transcriptional level and at the post-transcriptional level during miRNA processing. Recent studies have elucidated specific aspects of the well-regulated nature of miRNA processing involving various regulatory proteins, editing of miRNA transcripts, and cellular location. In addition, single nucleotide polymorphisms in miRNA genes can also affect the processing efficiency of primary miRNA transcripts. In this review we present an overview of the currently known regulatory pathways of miRNA processing and provide a basis to understand how aberrant miRNA processing may arise and may be involved in pathophysiological conditions such as cancer.

  17. miRConnect: Identifying Effector Genes of miRNAs and miRNA Families in Cancer Cells

    PubMed Central

    Larsen, Niels; Kjems, Jørgen; Lund, Anders H.; Peter, Marcus E.

    2011-01-01

    micro(mi)RNAs are small non-coding RNAs that negatively regulate expression of most mRNAs. They are powerful regulators of various differentiation stages, and the expression of genes that either negatively or positively correlate with expressed miRNAs is expected to hold information on the biological state of the cell and, hence, of the function of the expressed miRNAs. We have compared the large amount of available gene array data on the steady state system of the NCI60 cell lines to two different data sets containing information on the expression of 583 individual miRNAs. In addition, we have generated custom data sets containing expression information of 54 miRNA families sharing the same seed match. We have developed a novel strategy for correlating miRNAs with individual genes based on a summed Pearson Correlation Coefficient (sPCC) that mimics an in silico titration experiment. By focusing on the genes that correlate with the expression of miRNAs without necessarily being direct targets of miRNAs, we have clustered miRNAs into different functional groups. This has resulted in the identification of three novel miRNAs that are linked to the epithelial-to-mesenchymal transition (EMT) in addition to the known EMT regulators of the miR-200 miRNA family. In addition, an analysis of gene signatures associated with EMT, c-MYC activity, and ribosomal protein gene expression allowed us to assign different activities to each of the functional clusters of miRNAs. All correlation data are available via a web interface that allows investigators to identify genes whose expression correlates with the expression of single miRNAs or entire miRNA families. miRConnect.org will aid in identifying pathways regulated by miRNAs without requiring specific knowledge of miRNA targets. PMID:22046300

  18. Mitochondria: one of the destinations of miRNAs.

    PubMed

    Sripada, Lakshmi; Tomar, Dhanendra; Singh, Rajesh

    2012-11-01

    The cellular processes are controlled by a narrow range of mRNA and proteins levels, where small RNAs (sRNAs) known as miRNAs play a critical role. The spatial and temporal regulation of miRNA processing components and mature miRNA is emerging. The recent studies suggest that mitochondria are one of the destinations of pre as well as mature miRNAs. The role of mitochondria extends beyond energy metabolism to many other cellular processes like metabolism, cell death and inflammation. The new found destination of miRNAs suggest the role of mitochondria in monitoring site specific regulations of proteins as well as the function of mitochondria. The studies in this direction will decipher the novel role of mitochondria-associated miRNAs in different cellular processes. This review is focussed on the recent studies demonstrating the presence of miRNAs in mitochondria and its possible significance in different cellular and physiological conditions.

  19. Evolutionary relationships between miRNA genes and their activity.

    PubMed

    Zhu, Yan; Skogerbø, Geir; Ning, Qianqian; Wang, Zhen; Li, Biqing; Yang, Shuang; Sun, Hong; Li, Yixue

    2012-12-22

    The emergence of vertebrates is characterized by a strong increase in miRNA families. MicroRNAs interact broadly with many transcripts, and the evolution of such a system is intriguing. However, evolutionary questions concerning the origin of miRNA genes and their subsequent evolution remain unexplained. In order to systematically understand the evolutionary relationship between miRNAs gene and their function, we classified human known miRNAs into eight groups based on their evolutionary ages estimated by maximum parsimony method. New miRNA genes with new functional sequences accumulated more dynamically in vertebrates than that observed in Drosophila. Different levels of evolutionary selection were observed over miRNA gene sequences with different time of origin. Most genic miRNAs differ from their host genes in time of origin, there is no particular relationship between the age of a miRNA and the age of its host genes, genic miRNAs are mostly younger than the corresponding host genes. MicroRNAs originated over different time-scales are often predicted/verified to target the same or overlapping sets of genes, opening the possibility of substantial functional redundancy among miRNAs of different ages. Higher degree of tissue specificity and lower expression level was found in young miRNAs. Our data showed that compared with protein coding genes, miRNA genes are more dynamic in terms of emergence and decay. Evolution patterns are quite different between miRNAs of different ages. MicroRNAs activity is under tight control with well-regulated expression increased and targeting decreased over time. Our work calls attention to the study of miRNA activity with a consideration of their origin time.

  20. Improving miRNA Delivery by Optimizing miRNA Expression Cassettes in Diverse Virus Vectors

    PubMed Central

    Herrera-Carrillo, Elena; Liu, Ying Poi; Berkhout, Ben

    2017-01-01

    The RNA interference pathway is an evolutionary conserved post-transcriptional gene regulation mechanism that is exclusively triggered by double-stranded RNA inducers. RNAi-based methods and technologies have facilitated the discovery of many basic science findings and spurred the development of novel RNA therapeutics. Transient induction of RNAi via transfection of synthetic small interfering RNAs can trigger the selective knockdown of a target mRNA. For durable silencing of gene expression, either artificial short hairpin RNA or microRNA encoding transgene constructs were developed. These miRNAs are based on the molecules that induce the natural RNAi pathway in mammals and humans: the endogenously expressed miRNAs. Significant efforts focused on the construction and delivery of miRNA cassettes in order to solve basic biology questions or to design new therapy strategies. Several viral vectors have been developed, which are particularly useful for the delivery of miRNA expression cassettes to specific target cells. Each vector system has its own unique set of distinct properties. Thus, depending on the specific application, a particular vector may be most suitable. This field was previously reviewed for different viral vector systems, and now the recent progress in the field of miRNA-based gene-silencing approaches using lentiviral vectors is reported. The focus is on the unique properties and respective limitations of the available vector systems for miRNA delivery. PMID:28712309

  1. Effects of citric acid and the siderophore desferrioxamine B (DFO-B) on the mobility of germanium and rare earth elements in soil and uptake in Phalaris arundinacea.

    PubMed

    Wiche, Oliver; Tischler, Dirk; Fauser, Carla; Lodemann, Jana; Heilmeier, Hermann

    2017-02-03

    Effects of citric acid and desferrioxamine B (DFO-B) on the availability of Ge and selected REEs (La, Nd, Gd, Er) to P. arundinacea were investigated. A soil dissolution experiment was conducted to elucidate the effect of citric acid and DFO-B at different concentrations (1 and 10 mmol l(-1) citric acid) on the release of Ge and REEs from soil. In a greenhouse plants of P. arundinacea were cultivated on soil and on sand cultures to investigate the effects of citric acid and DFO-B on the uptake of Ge and REEs by the plants. Addition of 10 mmol l(-1) citric acid significantly enhanced desorption of Ge and REEs from soil and uptake into soil-grown plants. Applying DFO-B enhanced the dissolution and the uptake of REEs, while no effect on Ge was observed. In sand cultures, presence of citric acid and DFO-B significantly decreased the uptake of Ge and REEs, indicating a discrimination of the formed complexes during uptake. This study clearly indicates that citric acid and the microbial siderophore DFO-B may enhance phytoextraction of Ge and REEs due to the formation of soluble complexes that increase the migration of elements in the rhizosphere.

  2. miRNA Isolation from FFPET Specimen: A Technical Comparison of miRNA and Total RNA Isolation Methods.

    PubMed

    Nagy, Zsófia Brigitta; Wichmann, Barnabás; Kalmár, Alexandra; Barták, Barbara Kinga; Tulassay, Zsolt; Molnár, Béla

    2016-07-01

    MiRNA remain stable for detection and PCR-based amplification in FFPE tissue samples. Several miRNA extraction kits are available, however miRNA fraction, as part of total RNA can be isolated using total RNA purification methods, as well. Our primary aim was to compare four different miRNA and total RNA isolation methods from FFPE tissues. Further purposes were to evaluate quantitatively and qualitatively the yield of the isolated miRNA. MiRNAs were isolated from normal colorectal cancer FFPE specimens from the same patients. Two miRNA isolation kits (High Pure miRNA Isolation Kit, miRCURY™ RNA Isolation Kit) and two total RNA isolation kits were compared (High Pure RNA Paraffin Kit, MagNA Pure 96 Cellular RNA LV Kit). Quantity and quality were determined, expression analysis was performed by real-time PCR using qPCR Human Panel I + II (Exiqon) method detecting 742 human miRNAs in parallel. The yield of total RNA was found to be higher than miRNA purification protocols (in CRC: Ex: 0203 ± 0021 μg; HPm: 1,45 ± 0,8 μg; HPp: 21,36 ± 4,98 μg; MP: 8,6 ± 5,1 μg). MiRNAs were detected in lower relative quantity of total RNA compared to the miRNA kits. Higher number of miRNAs could be detected by the miRNA isolation kits in comparison to the total RNA isolation methods. (Ex: 497 ± 16; HPm: 542 ± 11; HPp: 332 ± 36; MP: 295 ± 74). Colon specific miRNAs (miR-21-5p;-34-5p) give satisfying results by miRNA isolation kits. Although miRNA can be detected also after total RNA isolation methods, for reliable and reproducible miRNA expression profiling the use of miRNA isolation kits are more suitable.

  3. MiRNA-155 and miRNA-132 as potential diagnostic biomarkers for pulmonary tuberculosis: A preliminary study.

    PubMed

    Zheng, Meng-Li; Zhou, Nai-Kang; Luo, Cheng-Hua

    2016-11-01

    In our study, we aimed to profile a panel microRNAs (miRNAs) as potential biomarkers for the early diagnosis of pulmonary tuberculosis (PTB) and to illuminate the molecular mechanisms in the development of PTB. Firstly, gene expression profile of E-GEOD-49951 was downloaded from ArrayExpress database, and quantile-adjusted conditional maximum likelihood method was utilized to identify statistical difference between miRNAs of Mycobacterium tuberculosis (MTB)-infected individuals and healthy subjects. Furthermore, in order to assess the performance of our methodology, random forest (RF) classification model was utilized to identify the top 10 miRNAs with better Area Under The Curve (AUC) using 10-fold cross-validation method. Additionally, Monte Carlo Cross-Validation was repeated 50 times to explore the best miRNAs. In order to learn more about the differentially-expressed miRNAs, the target genes of differentially-expressed miRNAs were retrieved from TargetScan database and Ingenuity Pathways Analysis (IPA) was used to screen out biological pathways where target genes were involved. After normalization, a total of 478 miRNAs with higher than 0.25-fold quantile average across all samples were required. Based on the differential expression analysis, 38 differentially expressed miRNAs were identified when the significance was set as false discovery rate (FDR) < 0.01. Among the top 10 differentially expressed miRNAs, miRNA-155 obtained a highest AUC value 0.976, showing a good performance between PTB and control groups. Similarly, miRNA-449a, miRNA-212 and miRNA-132 revealed also a good performance with AUC values 0.947, 0.931 and 0.930, respectively. Moreover, miRNA-155, miRNA-449a, miRNA-29b-1* and miRNA-132 appeared in 50, 49, 49 and 48 bootstraps. Thus, miRNA-155 and miRNA-132 might be important in the progression of PTB and thereby, might present potential signatures for diagnosis of PTB.

  4. Neuronal Activity Regulates Hippocampal miRNA Expression

    PubMed Central

    Eacker, Stephen M.; Keuss, Matthew J.; Berezikov, Eugene; Dawson, Valina L.; Dawson, Ted M.

    2011-01-01

    Neuronal activity regulates a broad range of processes in the hippocampus, including the precise regulation of translation. Disruptions in proper translational control in the nervous system are associated with a variety of disorders that fall in the autistic spectrum. MicroRNA (miRNA) represent a relatively recently discovered player in the regulation of translation in the nervous system. We have conducted an in depth analysis of how neuronal activity regulates miRNA expression in the hippocampus. Using deep sequencing we exhaustively identify all miRNAs, including 15 novel miRNAs, expressed in hippocampus of the adult mouse. We identified 119 miRNAs documented in miRBase but less than half of these miRNA were expressed at a level greater than 0.1% of total miRNA. Expression profiling following induction of neuronal activity by electroconvulsive shock demonstrates that most miRNA show a biphasic pattern of expression: rapid induction of specific mature miRNA expression followed by a decline in expression. These results have important implications into how miRNAs influence activity-dependent translational control. PMID:21984899

  5. Semirna: searching for plant miRNAs using target sequences.

    PubMed

    Muñoz-Mérida, Antonio; Perkins, James R; Viguera, Enrique; Thode, Guillermo; Bejarano, Eduardo R; Pérez-Pulido, Antonio J

    2012-04-01

    Many plant genomes are already known, and new ones are being sequenced every year. The next step for researchers is to identify all of the functional elements in these genomes, including the important class of functional elements known as microRNAs (miRNAs), which are involved in posttranscriptional regulatory pathways. However, computational tools for predicting new plant miRNAs are limited, and there is a particular need for tools that can be used easily by laboratory researchers. We present semirna, a new tool for predicting miRNAs in plant genomes, available as a Web server. This tool takes a putative target sequence such as a messenger RNA (mRNA) as input, and allows users to search for miRNAs that target this sequence. It can also be used to determine whether small RNA sequences from massive sequencing analysis represent true miRNAs and to search for miRNAs in new genomes using homology. Semirna has shown a high level of accuracy using various test sets, and gives users the ability to search for miRNAs with several different adjustable parameters. Semirna, a user-friendly and intuitive Web server for predicting miRNA sequences, can be reached at http://www.bioinfocabd.upo.es/semirna/ . It is useful for researchers searching for miRNAs involved in particular pathways, as well as those searching for miRNAs in newly sequenced genomes.

  6. Influence of papermill sludge on growth of Medicago sativa, Festuca rubra and Agropyron trachycaulum in gold mine tailings: a greenhouse study.

    PubMed

    Green, Scott; Renault, Sylvie

    2008-02-01

    A greenhouse study was undertaken to determine the suitability of adding papermill sludge to neutral/alkaline gold mine tailings to improve the establishment of Festuca rubra, Agropyron trachycaulum and Medicago sativa. Festuca rubra root and shoot biomass and A. Trachycaulum shoot biomass were increased with papermill sludge amendment. The addition of papermill sludge and fertilizer drastically increased the shoot and root biomass of M. sativa (20-30 times) while A. trachycaulum and F. rubra showed a more moderate increase in growth. Photosynthetic pigment content of the leaves was higher in papermill sludge treatments than in the treatments without papermill sludge. The organic carbon content, macro-aggregate content and field capacity of the gold mine tailings were increased while the bulk density was decreased by the addition of papermill sludge. This study suggests that addition of papermill sludge and adequate fertilization can alleviate some of the adverse conditions of neutral/alkaline gold mine tailings.

  7. MiRNA inhibition in tissue engineering and regenerative medicine.

    PubMed

    Beavers, Kelsey R; Nelson, Christopher E; Duvall, Craig L

    2015-07-01

    MicroRNAs (miRNAs) are noncoding RNAs that provide an endogenous negative feedback mechanism for translation of messenger RNA (mRNA) into protein. Single miRNAs can regulate hundreds of mRNAs, enabling miRNAs to orchestrate robust biological responses by simultaneously impacting multiple gene networks. MiRNAs can act as master regulators of normal and pathological tissue development, homeostasis, and repair, which has motivated expanding efforts toward the development of technologies for therapeutically modulating miRNA activity for regenerative medicine and tissue engineering applications. This review highlights the tools currently available for miRNA inhibition and their recent therapeutic applications for improving tissue repair.

  8. miRNA Inhibition in Tissue Engineering and Regenerative Medicine

    PubMed Central

    Beavers, Kelsey R.; Nelson, Christopher E.; Duvall, Craig L.

    2014-01-01

    MicroRNA (miRNA) are noncoding RNA that provide an endogenous negative feedback mechanism for translation of messenger RNA (mRNA) into protein. Single miRNAs can regulate hundreds of mRNAs, enabling miRNAs to orchestrate robust biological responses by simultaneously impacting multiple gene networks. MiRNAs can act as master regulators of normal and pathological tissue development, homeostasis, and repair, which has recently motivated expanding efforts toward development of technologies for therapeutically modulating miRNA activity for regenerative medicine and tissue engineering applications. This review highlights the tools currently available for miRNA inhibition and their recent therapeutic applications for improving tissue repair. PMID:25553957

  9. Genome-wide miRNA seeds prediction in Archaea.

    PubMed

    Wang, Shengqin; Xu, Yuming; Lu, Zuhong

    2014-01-01

    Growing evidence indicates that miRNA genes exist in the archaeal genome, though the functional role of such noncoding RNA remains unclear. Here, we integrated the phylogenetic information of available archaeal genomes to predict miRNA seeds (typically defined as the 2-8 nucleotides of mature miRNAs) on the genomic scale. Finally, we found 2649 candidate seeds with significant conservation signal. Eleven of 29 unique seeds from previous study support our result (P value <0.01), which demonstrates that the pipeline is suitable to predict experimentally detectable miRNA seeds. The statistical significance of the overlap between the detected archaeal seeds and known eukaryotic seeds shows that the miRNA may evolve before the divergence of these two domains of cellular life. In addition, miRNA targets are enriched for genes involved in transcriptional regulation, which is consistent with the situation in eukaryote. Our research will enhance the regulatory network analysis in Archaea.

  10. miRNAs in the pathogenesis of oncogenic human viruses

    PubMed Central

    Lin, Zhen; Flemington, Erik K.

    2010-01-01

    Tumor viruses are a class of pathogens with well established roles in the development of malignant diseases. Numerous bodies of work have highlighted miRNAs (microRNAs) as critical regulators of tumor pathways and it is clear that the dysregulation of cellular miRNA expression can promote tumor formation. Tumor viruses encode their own miRNAs and/or manipulate the expression of cellular miRNAs to modulate their host cell environment, thereby facilitating their respective infection cycles. The modulation of these miRNA responsive pathways, however, often influences certain signal transduction cascades in ways that favor tumorigenesis. In this review, we discuss the roles of virally-encoded and virally-regulated cellular miRNAs in the respective viral life-cycles and in virus associated pathogenesis. PMID:20943311

  11. Epigenetic regulation of miRNAs in cancer.

    PubMed

    Fabbri, Muller; Calore, Federica; Paone, Alessio; Galli, Roberta; Calin, George A

    2013-01-01

    MicroRNAs (miRNAs) are short noncoding RNAs with gene regulatory functions. It has been demonstrated that the genes encoding for miRNAs undergo the same regulatory epigenetic processes of protein coding genes. In turn, a specific subgroup of miRNAs, called epi-miRNAs, is able to directly target key enzymatic effectors of the epigenetic machinery (such as DNA methyltransferases, histone deacetylases, and polycomb genes), therefore indirectly affecting the expression of epigenetically regulated oncogenes and tumor suppressor genes. Also, several of the epigenetic drugs currently approved as anticancer agents affect the expression of miRNAs and this might explain part of their mechanism of action. This chapter focuses on the tight relationship between epigenetics and miRNAs and provides some insights on the translational implications of these findings, leading to the upcoming introduction of epigenetically related miRNAs in the treatment of cancer.

  12. Distribution of miRNA expression across human tissues

    PubMed Central

    Ludwig, Nicole; Leidinger, Petra; Becker, Kurt; Backes, Christina; Fehlmann, Tobias; Pallasch, Christian; Rheinheimer, Steffi; Meder, Benjamin; Stähler, Cord; Meese, Eckart; Keller, Andreas

    2016-01-01

    We present a human miRNA tissue atlas by determining the abundance of 1997 miRNAs in 61 tissue biopsies of different organs from two individuals collected post-mortem. One thousand three hundred sixty-four miRNAs were discovered in at least one tissue, 143 were present in each tissue. To define the distribution of miRNAs, we utilized a tissue specificity index (TSI). The majority of miRNAs (82.9%) fell in a middle TSI range i.e. were neither specific for single tissues (TSI > 0.85) nor housekeeping miRNAs (TSI < 0.5). Nonetheless, we observed many different miRNAs and miRNA families that were predominantly expressed in certain tissues. Clustering of miRNA abundances revealed that tissues like several areas of the brain clustered together. Considering -3p and -5p mature forms we observed miR-150 with different tissue specificity. Analysis of additional lung and prostate biopsies indicated that inter-organism variability was significantly lower than inter-organ variability. Tissue-specific differences between the miRNA patterns appeared not to be significantly altered by storage as shown for heart and lung tissue. MiRNAs TSI values of human tissues were significantly (P = 10−8) correlated with those of rats; miRNAs that were highly abundant in certain human tissues were likewise abundant in according rat tissues. We implemented a web-based repository enabling scientists to access and browse the data (https://ccb-web.cs.uni-saarland.de/tissueatlas). PMID:26921406

  13. Reprogramming of miRNA networks in cancer and leukemia

    PubMed Central

    Volinia, Stefano; Galasso, Marco; Costinean, Stefan; Tagliavini, Luca; Gamberoni, Giacomo; Drusco, Alessandra; Marchesini, Jlenia; Mascellani, Nicoletta; Sana, Maria Elena; Abu Jarour, Ramzey; Desponts, Caroline; Teitell, Michael; Baffa, Raffaele; Aqeilan, Rami; Iorio, Marilena V.; Taccioli, Cristian; Garzon, Ramiro; Di Leva, Gianpiero; Fabbri, Muller; Catozzi, Marco; Previati, Maurizio; Ambs, Stefan; Palumbo, Tiziana; Garofalo, Michela; Veronese, Angelo; Bottoni, Arianna; Gasparini, Pierluigi; Harris, Curtis C.; Visone, Rosa; Pekarsky, Yuri; de la Chapelle, Albert; Bloomston, Mark; Dillhoff, Mary; Rassenti, Laura Z.; Kipps, Thomas J.; Huebner, Kay; Pichiorri, Flavia; Lenze, Dido; Cairo, Stefano; Buendia, Marie-Annick; Pineau, Pascal; Dejean, Anne; Zanesi, Nicola; Rossi, Simona; Calin, George A.; Liu, Chang-Gong; Palatini, Jeff; Negrini, Massimo; Vecchione, Andrea; Rosenberg, Anne; Croce, Carlo M.

    2010-01-01

    We studied miRNA profiles in 4419 human samples (3312 neoplastic, 1107 nonmalignant), corresponding to 50 normal tissues and 51 cancer types. The complexity of our database enabled us to perform a detailed analysis of microRNA (miRNA) activities. We inferred genetic networks from miRNA expression in normal tissues and cancer. We also built, for the first time, specialized miRNA networks for solid tumors and leukemias. Nonmalignant tissues and cancer networks displayed a change in hubs, the most connected miRNAs. hsa-miR-103/106 were downgraded in cancer, whereas hsa-miR-30 became most prominent. Cancer networks appeared as built from disjointed subnetworks, as opposed to normal tissues. A comparison of these nets allowed us to identify key miRNA cliques in cancer. We also investigated miRNA copy number alterations in 744 cancer samples, at a resolution of 150 kb. Members of miRNA families should be similarly deleted or amplified, since they repress the same cellular targets and are thus expected to have similar impacts on oncogenesis. We correctly identified hsa-miR-17/92 family as amplified and the hsa-miR-143/145 cluster as deleted. Other miRNAs, such as hsa-miR-30 and hsa-miR-204, were found to be physically altered at the DNA copy number level as well. By combining differential expression, genetic networks, and DNA copy number alterations, we confirmed, or discovered, miRNAs with comprehensive roles in cancer. Finally, we experimentally validated the miRNA network with acute lymphocytic leukemia originated in Mir155 transgenic mice. Most of miRNAs deregulated in these transgenic mice were located close to hsa-miR-155 in the cancer network. PMID:20439436

  14. Reprogramming of miRNA networks in cancer and leukemia.

    PubMed

    Volinia, Stefano; Galasso, Marco; Costinean, Stefan; Tagliavini, Luca; Gamberoni, Giacomo; Drusco, Alessandra; Marchesini, Jlenia; Mascellani, Nicoletta; Sana, Maria Elena; Abu Jarour, Ramzey; Desponts, Caroline; Teitell, Michael; Baffa, Raffaele; Aqeilan, Rami; Iorio, Marilena V; Taccioli, Cristian; Garzon, Ramiro; Di Leva, Gianpiero; Fabbri, Muller; Catozzi, Marco; Previati, Maurizio; Ambs, Stefan; Palumbo, Tiziana; Garofalo, Michela; Veronese, Angelo; Bottoni, Arianna; Gasparini, Pierluigi; Harris, Curtis C; Visone, Rosa; Pekarsky, Yuri; de la Chapelle, Albert; Bloomston, Mark; Dillhoff, Mary; Rassenti, Laura Z; Kipps, Thomas J; Huebner, Kay; Pichiorri, Flavia; Lenze, Dido; Cairo, Stefano; Buendia, Marie-Annick; Pineau, Pascal; Dejean, Anne; Zanesi, Nicola; Rossi, Simona; Calin, George A; Liu, Chang-Gong; Palatini, Jeff; Negrini, Massimo; Vecchione, Andrea; Rosenberg, Anne; Croce, Carlo M

    2010-05-01

    We studied miRNA profiles in 4419 human samples (3312 neoplastic, 1107 nonmalignant), corresponding to 50 normal tissues and 51 cancer types. The complexity of our database enabled us to perform a detailed analysis of microRNA (miRNA) activities. We inferred genetic networks from miRNA expression in normal tissues and cancer. We also built, for the first time, specialized miRNA networks for solid tumors and leukemias. Nonmalignant tissues and cancer networks displayed a change in hubs, the most connected miRNAs. hsa-miR-103/106 were downgraded in cancer, whereas hsa-miR-30 became most prominent. Cancer networks appeared as built from disjointed subnetworks, as opposed to normal tissues. A comparison of these nets allowed us to identify key miRNA cliques in cancer. We also investigated miRNA copy number alterations in 744 cancer samples, at a resolution of 150 kb. Members of miRNA families should be similarly deleted or amplified, since they repress the same cellular targets and are thus expected to have similar impacts on oncogenesis. We correctly identified hsa-miR-17/92 family as amplified and the hsa-miR-143/145 cluster as deleted. Other miRNAs, such as hsa-miR-30 and hsa-miR-204, were found to be physically altered at the DNA copy number level as well. By combining differential expression, genetic networks, and DNA copy number alterations, we confirmed, or discovered, miRNAs with comprehensive roles in cancer. Finally, we experimentally validated the miRNA network with acute lymphocytic leukemia originated in Mir155 transgenic mice. Most of miRNAs deregulated in these transgenic mice were located close to hsa-miR-155 in the cancer network.

  15. Distribution of miRNA expression across human tissues.

    PubMed

    Ludwig, Nicole; Leidinger, Petra; Becker, Kurt; Backes, Christina; Fehlmann, Tobias; Pallasch, Christian; Rheinheimer, Steffi; Meder, Benjamin; Stähler, Cord; Meese, Eckart; Keller, Andreas

    2016-05-05

    We present a human miRNA tissue atlas by determining the abundance of 1997 miRNAs in 61 tissue biopsies of different organs from two individuals collected post-mortem. One thousand three hundred sixty-four miRNAs were discovered in at least one tissue, 143 were present in each tissue. To define the distribution of miRNAs, we utilized a tissue specificity index (TSI). The majority of miRNAs (82.9%) fell in a middle TSI range i.e. were neither specific for single tissues (TSI > 0.85) nor housekeeping miRNAs (TSI < 0.5). Nonetheless, we observed many different miRNAs and miRNA families that were predominantly expressed in certain tissues. Clustering of miRNA abundances revealed that tissues like several areas of the brain clustered together. Considering -3p and -5p mature forms we observed miR-150 with different tissue specificity. Analysis of additional lung and prostate biopsies indicated that inter-organism variability was significantly lower than inter-organ variability. Tissue-specific differences between the miRNA patterns appeared not to be significantly altered by storage as shown for heart and lung tissue. MiRNAs TSI values of human tissues were significantly (P = 10(-8)) correlated with those of rats; miRNAs that were highly abundant in certain human tissues were likewise abundant in according rat tissues. We implemented a web-based repository enabling scientists to access and browse the data (https://ccb-web.cs.uni-saarland.de/tissueatlas).

  16. miRNAs as biomarkers of atrial fibrillation.

    PubMed

    Gomes da Silva, Ananília Medeiros; Silbiger, Vivian Nogueira

    2014-12-01

    Atrial fibrillation (AF) is a highly prevalent arrhythmia with pronounced morbidity and mortality. Genetics analysis has established electrophysiological substrates, which determine individual vulnerability to AF occurrence and maintenance. MicroRNAs (miRNAs) found in virtually all organisms function as negative regulators of protein-coding genes. Several studies have suggested a role for miRNAs in the regulation of cardiac excitability and arrhythmogenesis. This review is based on 18 studies conducted between 2009 and 2013 to investigate the association of miRNAs with AF. miRNAs are discussed here as candidate biomarkers for AF in blood and cardiac tissues and as potential targets for AF therapy.

  17. miRNA expression during prickly pear cactus fruit development.

    PubMed

    Rosas-Cárdenas, Flor de Fátima; Caballero-Pérez, Juan; Gutiérrez-Ramos, Ximena; Marsch-Martínez, Nayelli; Cruz-Hernández, Andrés; de Folter, Stefan

    2015-02-01

    miRNAs are a class of small non-coding RNAs that regulate gene expression. They are involved in the control of many developmental processes, including fruit development. The increasing amount of information on miRNAs, on their expression, abundance, and conservation between various species, provides a new opportunity to study the role of miRNAs in non-model plant species. In this work, we used a combination of Northern blot and tissue print hybridization analysis to identify conserved miRNAs expressed during prickly pear cactus (Opuntia ficus indica) fruit development. Comparative profiling detected the expression of 34 miRNAs, which were clustered in three different groups that were associated with the different phases of fruit development. Variation in the level of miRNA expression was observed. Gradual expression increase of several miRNAs was observed during fruit development, including miR164. miR164 was selected for stem-loop RT-PCR and for a detailed spatial-temporal expression analysis. At early floral stages, miR164 was mainly localized in meristematic tissues, boundaries and fusion zones, while it was more homogenously expressed in fruit tissues. Our results provide the first evidence of miRNA expression in the prickly pear cactus and provide the basis for future research on miRNAs in Opuntia. Moreover, our analyses suggest that miR164 plays different roles during prickly pear cactus fruit development.

  18. miRNAs: roles and clinical applications in vascular disease.

    PubMed

    Jamaluddin, Md Saha; Weakley, Sarah M; Zhang, Lidong; Kougias, Panagiotis; Lin, Peter H; Yao, Qizhi; Chen, Changyi

    2011-01-01

    miRNAs are small, endogenously expressed noncoding RNAs that regulate gene expression, mainly at the post-transcriptional level, via degradation or translational inhibition of their target mRNAs. Functionally, an individual miRNA can regulate the expression of multiple target genes. The study of miRNAs is rapidly growing and recent studies have revealed a significant role of miRNAs in vascular biology and disease. Many miRNAs are highly expressed in the vasculature, and their expression is dysregulated in diseased vessels. Several miRNAs have been found to be critical modulators of vascular pathologies, such as atherosclerosis, lipoprotein metabolism, inflammation, arterial remodeling, angiogenesis, smooth muscle cell regeneration, hypertension, apoptosis, neointimal hyperplasia and signal transduction pathways. Thus, miRNAs may serve as novel biomarkers and/or therapeutic targets for vascular disease. This article summarizes the current studies related to the disease correlations and functional roles of miRNAs in the vascular system and discusses the potential applications of miRNAs in vascular disease.

  19. miRNAs in cancer: approaches, aetiology, diagnostics and therapy.

    PubMed

    Blenkiron, Cherie; Miska, Eric A

    2007-04-15

    MicroRNAs (miRNAs) are causing tremendous excitement in cancer research. MiRNAs are a large class of short non-coding RNAs that are found in many plants, animals and DNA viruses and often act to inhibit gene expression post-transcriptionally. Approximately 500 miRNA genes have been identified in the human genome. Their function is largely unknown, but data from worms, flies, fish and mice suggest that they have important roles in animal growth, development, homeostasis and disease. MiRNA expression profiles demonstrate that many miRNAs are deregulated in human cancers. MiRNAs have been shown to regulate oncogenes, tumour suppressors and a number of cancer-related genes controlling cell cycle, apoptosis, cell migration and angiogenesis. MiRNAs encoded by the mir-17-92 cluster have oncogenic potential and others may act as tumour suppressors. Some miRNAs and their target sites were found to be mutated in cancer. MiRNAs may have great diagnostic potential for human cancer and even miRNA-based cancer therapies may be on the horizon.

  20. Methylation of miRNA genes and oncogenesis.

    PubMed

    Loginov, V I; Rykov, S V; Fridman, M V; Braga, E A

    2015-02-01

    Interaction between microRNA (miRNA) and messenger RNA of target genes at the posttranscriptional level provides fine-tuned dynamic regulation of cell signaling pathways. Each miRNA can be involved in regulating hundreds of protein-coding genes, and, conversely, a number of different miRNAs usually target a structural gene. Epigenetic gene inactivation associated with methylation of promoter CpG-islands is common to both protein-coding genes and miRNA genes. Here, data on functions of miRNAs in development of tumor-cell phenotype are reviewed. Genomic organization of promoter CpG-islands of the miRNA genes located in inter- and intragenic areas is discussed. The literature and our own results on frequency of CpG-island methylation in miRNA genes from tumors are summarized, and data regarding a link between such modification and changed activity of miRNA genes and, consequently, protein-coding target genes are presented. Moreover, the impact of miRNA gene methylation on key oncogenetic processes as well as affected signaling pathways is discussed.

  1. NMDA Mediated Contextual Conditioning Changes miRNA Expression

    PubMed Central

    Kye, Min Jeong; Zhou, Miou; Steen, Judith A.; Sahin, Mustafa; Kosik, Kenneth S.; Silva, Alcino J.

    2011-01-01

    We measured the expression of 187 miRNAs using quantitative real time PCR in the hippocampal CA1 region of contextually conditioned mice and cultured embryonic rat hippocampal neurons after neuronal stimulation with either NMDA or bicuculline. Many of the changes in miRNA expression after these three types of stimulation were similar. Surprisingly, the expression level of half of the 187 measured miRNAs was changed in response to contextual conditioning in an NMDA receptor-dependent manner. Genes that control miRNA biogenesis and components of the RISC also exhibited activity induced expression changes and are likely to contribute to the widespread changes in the miRNA profile. The widespread changes in miRNA expression are consistent with the finding that genes up-regulated by contextual conditioning have longer 3′ UTRs and more predicted binding sites for miRNAs. Among the miRNAs that changed their expression after contextual conditioning, several inhibit inhibitors of the mTOR pathway. These findings point to a role for miRNAs in learning and memory that includes mTOR-dependent modulation of protein synthesis. PMID:21931811

  2. Exosomes as miRNA Carriers: Formation–Function–Future

    PubMed Central

    Yu, Xiaojie; Odenthal, Margarete; Fries, Jochen W. U.

    2016-01-01

    Exosomes, which are one of the smallest extracellular vesicles released from cells, have been shown to carry different nucleic acids, including microRNAs (miRNAs). miRNAs significantly regulate cell growth and metabolism by posttranscriptional inhibition of gene expression. The rapidly changing understanding of exosomes’ formation and function in delivering miRNAs from cell to cell has prompted us to review current knowledge in exosomal miRNA secretion mechanisms as well as possible therapeutic applications for personalized medicine. PMID:27918449

  3. Exploration of miRNA families for hypotheses generation

    NASA Astrophysics Data System (ADS)

    Kamanu, Timothy K. K.; Radovanovic, Aleksandar; Archer, John A. C.; Bajic, Vladimir B.

    2013-10-01

    Technological improvements have resulted in increased discovery of new microRNAs (miRNAs) and refinement and enrichment of existing miRNA families. miRNA families are important because they suggest a common sequence or structure configuration in sets of genes that hint to a shared function. Exploratory tools to enhance investigation of characteristics of miRNA families and the functions of family-specific miRNA genes are lacking. We have developed, miRNAVISA, a user-friendly web-based tool that allows customized interrogation and comparisons of miRNA families for hypotheses generation, and comparison of per-species chromosomal distribution of miRNA genes in different families. This study illustrates hypothesis generation using miRNAVISA in seven species. Our results unveil a subclass of miRNAs that may be regulated by genomic imprinting, and also suggest that some miRNA families may be species-specific, as well as chromosome- and/or strand-specific.

  4. Comparative analysis of known miRNAs across platyhelminths.

    PubMed

    Jin, Xiaoliang; Lu, Lixia; Su, Hailong; Lou, Zhongzi; Wang, Fang; Zheng, Yadong; Xu, Guo-Tong

    2013-08-01

    MicroRNAs (miRNAs) are a subtype of small regulatory RNAs that are involved in numerous biological processes through small RNA-induced silencing networks. In an attempt to explore the phylogeny of miRNAs across five platyhelminths, we integrated annotated miRNAs and their full genomes. We identified conserved miRNA clusters and, in particular, miR-71/2 was conserved from planarian to parasitic flatworms and was expanded in free-living Schmidtea mediterranea. Analysis of 22 miRNA loci provided compelling evidence that most known miRNAs are conserved across platyhelminths. Meanwhile, we also observed alterations of known protein-coding genes flanking miRNA(s), such as transcriptional direction conversion and locus relocation, in around ~ 41% of 22 known miRNA loci. Compared with Echinococcus multilocularis, the majority of these events occurred in evolution-distant Hymenolepis microstoma, Schistosoma japonicum or/and S. mediterranea. These results imply rearrangement events occurred near the known miRNA loci. © 2013 FEBS.

  5. Isolation and Identification of miRNAs in Jatropha curcas

    PubMed Central

    Wang, Chun Ming; Liu, Peng; Sun, Fei; Li, Lei; Liu, Peng; Ye, Jian; Yue, Gen Hua

    2012-01-01

    MicroRNAs (miRNAs) are small noncoding RNAs that play crucial regulatory roles by targeting mRNAs for silencing. To identify miRNAs in Jatropha curcas L, a bioenergy crop, cDNA clones from two small RNA libraries of leaves and seeds were sequenced and analyzed using bioinformatic tools. Fifty-two putative miRNAs were found from the two libraries, among them six were identical to known miRNAs and 46 were novel. Differential expression patterns of 15 miRNAs in root, stem, leave, fruit and seed were detected using quantitative real-time PCR. Ten miRNAs were highly expressed in fruit or seed, implying that they may be involved in seed development or fatty acids synthesis in seed. Moreover, 28 targets of the isolated miRNAs were predicted from a jatropha cDNA library database. The miRNA target genes were predicted to encode a broad range of proteins. Sixteen targets had clear BLASTX hits to the Uniprot database and were associated with genes belonging to the three major gene ontology categories of biological process, cellular component, and molecular function. Four targets were identified for JcumiR004. By silencing JcumiR004 primary miRNA, expressions of the four target genes were up-regulated and oil composition were modulated significantly, indicating diverse functions of JcumiR004. PMID:22419887

  6. Rapid divergence and high diversity of miRNAs and miRNA targets in the Camelineae.

    PubMed

    Smith, Lisa M; Burbano, Hernán A; Wang, Xi; Fitz, Joffrey; Wang, George; Ural-Blimke, Yonca; Weigel, Detlef

    2015-02-01

    MicroRNAs (miRNAs) are short RNAs involved in gene regulation through translational inhibition and transcript cleavage. After processing from imperfect fold-back structures, miRNAs are incorporated into RNA-induced silencing complexes (RISCs) before targeting transcripts with varying degrees of complementarity. Some miRNAs are evolutionarily deep-rooted, and sequence complementarity with their targets is maintained through purifying selection. Both Arabidopsis and Capsella belong to the tribe Camelineae in the Brassicaceae, with Capsella rubella serving as an outgroup to the genus Arabidopsis. The genome sequence of C. rubella has recently been released, which allows characterization of its miRNA complement in comparison with Arabidopsis thaliana and Arabidopsis lyrata. Through next-generation sequencing, we identify high-confidence miRNA candidates specific to the C. rubella lineage. Only a few lineage-specific miRNAs have been studied for evolutionary constraints, and there have been no systematic studies of miRNA target diversity within or divergence between closely related plant species. Therefore we contrast sequence variation in miRNAs and their targets within A. thaliana, and between A. thaliana, A. lyrata and C. rubella. We document a surprising amount of small-scale variation in miRNA-target pairs, where many miRNAs are predicted to have species-specific targets in addition to ones that are shared between species. Our results emphasize that the transitive nature of many miRNA-target pairs can be observed even on a relatively short evolutionary time-scale, with non-random occurrences of differences in miRNAs and their complements in the miRNA precursors, the miRNA* sequences.

  7. Identification of candidate miRNA biomarkers from miRNA regulatory network with application to prostate cancer

    PubMed Central

    2014-01-01

    Background MicroRNAs (miRNAs) are a class of non-coding regulatory RNAs approximately 22 nucleotides in length that play a role in a wide range of biological processes. Abnormal miRNA function has been implicated in various human cancers including prostate cancer (PCa). Altered miRNA expression may serve as a biomarker for cancer diagnosis and treatment. However, limited data are available on the role of cancer-specific miRNAs. Integrative computational bioinformatics approaches are effective for the detection of potential outlier miRNAs in cancer. Methods The human miRNA-mRNA target network was reconstructed by integrating multiple miRNA-mRNA interaction datasets. Paired miRNA and mRNA expression profiling data in PCa versus benign prostate tissue samples were used as another source of information. These datasets were analyzed with an integrated bioinformatics framework to identify potential PCa miRNA signatures. In vitro q-PCR experiments and further systematic analysis were used to validate these prediction results. Results Using this bioinformatics framework, we identified 39 miRNAs as potential PCa miRNA signatures. Among these miRNAs, 20 had previously been identified as PCa aberrant miRNAs by low-throughput methods, and 16 were shown to be deregulated in other cancers. In vitro q-PCR experiments verified the accuracy of these predictions. miR-648 was identified as a novel candidate PCa miRNA biomarker. Further functional and pathway enrichment analysis confirmed the association of the identified miRNAs with PCa progression. Conclusions Our analysis revealed the scale-free features of the human miRNA-mRNA interaction network and showed the distinctive topological features of existing cancer miRNA biomarkers from previously published studies. A novel cancer miRNA biomarker prediction framework was designed based on these observations and applied to prostate cancer study. This method could be applied for miRNA biomarker prediction in other cancers. PMID

  8. Comprehensive expression analysis of miRNA in breast cancer at the miRNA and isomiR levels.

    PubMed

    Wu, Xianjin; Zeng, Rong; Wu, Shaoke; Zhong, Jixin; Yang, Lawei; Xu, Junfa

    2015-02-25

    Breast cancer (BC) is the main factor that leads cause of cancer death in women worldwide. A class of small non-coding RNAs, microRNAs (miRNAs), has been widely studied in human cancers as crucial regulatory molecule. Recent studies indicate that a series of isomiRs can be yielded from a miRNA locus, and these physiological miRNA isoforms have versatile roles in miRNA biogenesis. Herein, we performed a comprehensive analysis of miRNAs at the miRNA and isomiR levels in BC using next-generation sequencing data from The Cancer Genome Atlas (TCGA). Abnormally expressed miRNA (miR-21, miR-221, miR-155, miR-30e and miR-25) and isomiR profiles could be obtained at the miRNA and isomiR levels, and similar biological roles could be detected. IsomiR expression profiles should be further concerned, and especially isomiRs are actual regulatory molecules in the miRNA-mRNA regulatory networks. The study provides a comprehensive expression analysis at the miRNA and isomiR levels in BC, which indicates biological roles of isomiRs.

  9. A Comprehensive Prescription for Plant miRNA Identification

    PubMed Central

    Alptekin, Burcu; Akpinar, Bala A.; Budak, Hikmet

    2017-01-01

    microRNAs (miRNAs) are tiny ribo-regulatory molecules involved in various essential pathways for persistence of cellular life, such as development, environmental adaptation, and stress response. In recent years, miRNAs have become a major focus in molecular biology because of their functional and diagnostic importance. This interest in miRNA research has resulted in the development of many specific software and pipelines for the identification of miRNAs and their specific targets, which is the key for the elucidation of miRNA-modulated gene expression. While the well-recognized importance of miRNAs in clinical research pushed the emergence of many useful computational identification approaches in animals, available software and pipelines are fewer for plants. Additionally, existing approaches suffers from mis-identification and annotation of plant miRNAs since the miRNA mining process for plants is highly prone to false-positives, particularly in cereals which have a highly repetitive genome. Our group developed a homology-based in silico miRNA identification approach for plants, which utilizes two Perl scripts “SUmirFind” and “SUmirFold” and since then, this method helped identify many miRNAs particularly from crop species such as Triticum or Aegliops. Herein, we describe a comprehensive updated guideline by the implementation of two new scripts, “SUmirPredictor” and “SUmirLocator,” and refinements to our previous method in order to identify genuine miRNAs with increased sensitivity in consideration of miRNA identification problems in plants. Recent updates enable our method to provide more reliable and precise results in an automated fashion in addition to solutions for elimination of most false-positive predictions, miRNA naming and miRNA mis-annotation. It also provides a comprehensive view to genome/transcriptome-wide location of miRNA precursors as well as their association with transposable elements. The “SUmirPredictor” and

  10. Expression profiles of miRNAs in Gossypium raimondii *

    PubMed Central

    Ma, Jun; Guo, Teng-long; Wang, Qing-lian; Wang, Kun-bo; Sun, Run-run; Zhang, Bao-hong

    2015-01-01

    miRNAs are a class of conserved, small, endogenous, and non-protein-coding RNA molecules with 20–24 nucleotides (nt) in length that function as post-transcriptional modulators of gene expression in eukaryotic cells. Functional studies have demonstrated that plant miRNAs are involved in the regulation of a wide range of plant developmental processes. To date, however, no research has been carried out to study the expression profiles of miRNAs in Gossypium raimondii, a model cotton species. We selected 16 miRNAs to profile their tissue-specific expression patterns in G. raimondii four different tissues, and these miRNAs are reported to play important roles in plant growth and development. Our results showed that the expression levels of these miRNAs varied significantly from one to another in a tissue-dependent manner. Eight miRNAs, including miR-159, miR-162, miR-164, miR-172, miR-390, miR-395, miR-397, and miR-398, exhibited exclusively high expression levels in flower buds, suggesting that these miRNAs may play significant roles in floral development. The expression level of miR-164 was relatively high in shoots beside flower buds, implying that the function of miR-164 is not only limited to floral development but it may also play an important role in shoot development. Certain miRNAs such as miR-166 and miR-160 were extremely highly expressed in all of the four tissues tested compared with other miRNAs investigated, suggesting that they may play regulatory roles at multiple development stages. This study will contribute to future studies on the functional characterization of miRNAs in cotton. PMID:25845363

  11. Decondensation of chromosomal 45S rDNA sites in Lolium and Festuca genotypes does not result in karyotype instability.

    PubMed

    Rocha, Laiane Corsini; Jankowska, Maja; Fuchs, Joerg; Mittelmann, Andréa; Techio, Vânia Helena; Houben, Andreas

    2017-01-01

    Fragile sites (FSs) in plants have been described for species like Lolium and other grasses. Whereas in humans FSs were shown to be involved in genome instabilities; the consequences of FSs expression in plants are not known yet. To evaluate whether FSs cause karyotype instabilities, we assessed the frequency of micronuclei and lagging chromosomes in meristematic cells, the stability of the DNA content, and the occurrence of neocentromeres in the presumed chromosomal fragments of Lolium perenne, Lolium multiflorum, Festuca arrundinacea, and two Festulolium hybrids. The cell cycle analysis along with flow cytometric genome size measurements showed high stability in all genomes evaluated. Neocentromeric activity was neither observed in the presumed fragments nor in any other chromosomal region, then this is not the mechanism responsible by the stability. However, Fluorescence in situ hybridization (FISH) with a 45S ribosomal DNA (rDNA) probe in combination with YOYO staining of metaphasic chromosomes showed that many extended nucleolus organizing region (NOR) form very thin YOYO-positive chromatin fibers connecting the acentric 'fragment' with the centromere-containing chromosome region. The obtained data indicate that the expression of FSs does not result in genome instabilities or neocentromere formation. The FS-containing 45S rDNA carrying chromatin fibers undergo a cell cycle and gene activity-dependent dynamic decondensation process.

  12. Identifying, cloning and structural analysis of differentially expressed genes upon Puccinia infection of Festuca rubra var. rubra.

    PubMed

    Ergen, Neslihan Z; Dinler, Gizem; Shearman, Robert C; Budak, Hikmet

    2007-05-15

    Differentially expressed genes in response to rust infection (Puccinia sp.) in creeping red fescue (Festuca rubra var. rubra) were identified and quantified using the mRNA differential display technique. The differentially induced genes were identified as homologs of mitogen-activated protein kinase (MAPK) 3 of Arabidopsis thaliana, stem rust resistance protein Rpg1 of barley and Hsp70 of Spinacia oleracea. The change in the steady state expression levels of these genes in response to rust infection was tested by Northern blot analysis and further quantified by real-time PCR. A steady accumulation of transcripts in the course of rust infection was observed. Full-length transcript of a fescue MPK-3 was obtained by RACE PCR. Its corresponding cDNA encodes a protein with a predicted MW of 42.5 kDa which was mapped onto the structural model of homologs MAPK to illustrate the corresponding MAPK signature motifs. This study, for the first time, presents evidence on the rust infection dependent metabolic pathways in creeping red fescue.

  13. Expression and function analysis of the metallothionein-like (MT-like) gene from Festuca rubra in Chlamydomonas reinhardtii chloroplast.

    PubMed

    Han, SiHai; Hu, ZhangLi; Lei, AnPing

    2008-12-01

    The cDNA of the metallothionein-like (MT-like) gene from Festuca rubra cv. Merlin was optimized with bias codon of Chlamydomonas reinhardtii chloroplast genome. The optimized MT-like gene was delivered into C. reinhardtii chloroplast and the transgenic strains expressing MT-like gene was obtained. PCR-Southern blot and RT-PCR-Southern blot analysis demonstrated that the MT-like gene was integrated into chloroplast genome of C. reinhardtii and expressed at the transcriptional level. The cadmium binding capacity of the transgenic C. reinhardtii was determined by hydride generation-atomic fluorescence spectrometry (HG-AFS) and the binding properties were analyzed. Results showed that the transgenic C. reinhardtii expressing the MT-like gene exhibited remarkably higher Cd(2+) binding capacity and grew to higher densities at toxic Cd(2+) concentrations (40-100 micromol/L) than the wild type strain, and that the IC(50) of Cd(2+) (3-d treating) to algal cell growth of transgenic strain was 55.43% higher than that of the wild type strain, indicating that the Cd(2+) binding capacity and Cd(2+) tolerance of C. reinhardtii was enhanced through the expression of the foreign MT-like gene in chloroplast.

  14. Potential for phytoextraction of copper by Sinapis alba and Festuca rubra cv. Merlin grown hydroponically and in vineyard soils.

    PubMed

    Malagoli, Mario; Rossignolo, Virginia; Salvalaggio, Nico; Schiavon, Michela

    2014-03-01

    The extensive use of copper-bearing fungicides in vineyards is responsible for the accumulation of copper (Cu) in soils. Grass species able to accumulate Cu could be cultivated in the vineyard inter-rows for copper phytoextraction. In this study, the capacity of Festuca rubra cv Merlin and Sinapis alba to tolerate and accumulate copper (Cu) was first investigated in a hydroponic system without the interference of soil chemical-physical properties. After the amendment of Cu (5 or 10 mg Cu l-(1)) to nutrient solution, shoot Cu concentration in F. rubra increased up to 108.63 mg Cu kg(-1) DW, more than three times higher than in S. alba (31.56 mg Cu kg(-1) DW). The relationship between Cu concentration in plants and external Cu was dose-dependent and species specific. Results obtained from the hydroponic experiment were confirmed by growing plants in pots containing soil collected from six Italian vineyards. The content of soil organic matter was crucial to enhance Cu tolerance and accumulation in the shoot tissues of both plant species. Although S. alba produced more biomass than F. rubra in most soils, F. rubra accumulated significantly more Cu (up to threefold to fourfold) in the shoots. Given these results, we recommended that F. rubra cv Merlin could be cultivated in the vineyard rows to reduce excess Cu in vineyard soils.

  15. Restoration of regeneration potential of long-term cultures of red fescue (Festuca rubra L.) by elevated sucrose levels.

    PubMed

    Zaghmout, O M; Torello, W A

    1992-04-01

    A tissue culture protocol for restoring embryogenic ability and increasing green plant regeneration from long-term callus (5-year old) and suspension cultures of "Dawson" red fescue (Festuca rubra var trichyoplylla Gaud) was developed. Pretreatment with elevated levels of sucrose over the standard level (60 mM) enhanced regeneration capacity and decreased the number of albino plants. The highest degree of embryogenesis and green shoot number occurred when calli were pre-treated on MS basal medium supplemented with 120 mM sucrose. Mannitol caused callus discoloration and death if added to pre-treatment media at 60, 90, 120, 150 or 180 mM. Cell suspension growth was greatest when 135 mM sucrose was added to the pre-treatment growth media. High concentrations of sucrose (135 and 180 mM) were necessary for plant regeneration from suspension aggregates pretreated with 135 or 180 mM sucrose and then plated on a growth regulator-free regeneration medium composed of half-strength MS salts and B5 vitamins.

  16. miRNA Control of Tissue Repair and Regeneration

    PubMed Central

    Sen, Chandan K.; Ghatak, Subhadip

    2016-01-01

    Tissue repair and regeneration rely on the function of miRNA, molecular silencers that enact post-transcriptional gene silencing of coding genes. Disruption of miRNA homeostasis is developmentally lethal, indicating that fetal tissue development is tightly controlled by miRNAs. Multiple critical facets of adult tissue repair are subject to control by miRNAs, as well. Sources of cell pool for tissue repair and regeneration are diverse and provided by processes including cellular dedifferentiation, transdifferentiation, and reprogramming. Each of these processes is regulated by miRNAs. Furthermore, induced pluripotency may be achieved by miRNA-based strategies independent of transcription factor manipulation. The observation that miRNA does not integrate into the genome makes miRNA-based therapeutic strategies translationally valuable. Tools to manipulate cellular and tissue miRNA levels include mimics and inhibitors that may be specifically targeted to cells of interest at the injury site. Here, we discuss the extraordinary importance of miRNAs in tissue repair and regeneration based on emergent reports and rapid advances in miRNA-based therapeutics. PMID:26056933

  17. Genome-wide characterization of maize miRNA genes

    USDA-ARS?s Scientific Manuscript database

    MicroRNAs (miRNAs) are small non-coding RNAs that play essential roles in plant growth and development. We conducted a genome-wide survey of maize miRNA genes, characterizing their structure, expression, and evolution. Computational approaches based on homology and secondary structure modeling ident...

  18. Co-expressed miRNAs in gastric adenocarcinoma.

    PubMed

    Yepes, Sally; López, Rocío; Andrade, Rafael E; Rodriguez-Urrego, Paula A; López-Kleine, Liliana; Torres, Maria Mercedes

    2016-08-01

    Co-expression networks may provide insights into the patterns of molecular interactions that underlie cellular processes. To obtain a better understanding of miRNA expression patterns in gastric adenocarcinoma and to provide markers that can be associated with histopathological findings, we performed weighted gene correlation network analysis (WGCNA) and compare it with a supervised analysis. Integrative analysis of target predictions and miRNA expression profiles in gastric cancer samples was also performed. WGCNA identified a module of co-expressed miRNAs that were associated with histological traits and tumor condition. Hub genes were identified based on statistical analysis and network centrality. The miRNAs 100, let-7c, 125b and 99a stood out for their association with the diffuse histological subtype. The 181 miRNA family and miRNA 21 highlighted for their association with the tumoral phenotype. The integrated analysis of miRNA and gene expression profiles showed the let-7 miRNA family playing a central role in the regulatory relationships.

  19. Modulation of Host miRNAs by Intracellular Bacterial Pathogens

    PubMed Central

    Das, Kishore; Garnica, Omar; Dhandayuthapani, Subramanian

    2016-01-01

    MicroRNAs (miRNAs) are short non-coding RNAs that regulate the expression of protein coding genes of viruses and eukaryotes at the post-transcriptional level. The eukaryotic genes regulated by miRNAs include those whose products are critical for biological processes such as cell proliferation, metabolic pathways, immune response, and development. It is now increasingly recognized that modulation of miRNAs associated with biological processes is one of the strategies adopted by bacterial pathogens to survive inside host cells. In this review, we present an overview of the recent findings on alterations of miRNAs in the host cells by facultative intracellular bacterial pathogens. In addition, we discuss how the altered miRNAs help in the survival of these pathogens in the intracellular environment. PMID:27536558

  20. miRNA Regulation of Immune Tolerance in Early Pregnancy.

    PubMed

    Schjenken, John E; Zhang, Bihong; Chan, Hon Y; Sharkey, David J; Fullston, Tod; Robertson, Sarah A

    2016-03-01

    To support embryo implantation, the female reproductive tract must provide a tolerogenic immune environment. Seminal fluid contact at conception contributes to activating the endometrial gene expression and immune cell changes required for robust implantation, influencing not only the quality of the ensuing pregnancy but also the health of offspring. miRNAs are small non-coding RNAs that play important regulatory roles in biological processes, including regulation of the immune environment. miRNAs are known to contribute to gene regulation in pregnancy and are altered in pregnancy pathologies. Recent studies indicate that miRNAs participate in establishing immune tolerance at conception, and may contribute to the regulatory effects of seminal fluid in generating tolerogenic dendritic cells and T regulatory cells. This review highlights those miRNAs implicated in programming immune cells that are critical during the peri-conception period and explores how seminal fluid may regulate female tract miRNA expression following coitus.

  1. Differentially expressed miRNAs in trisomy 21 placentas.

    PubMed

    Svobodová, Iveta; Korabečná, Marie; Calda, Pavel; Břešťák, Miroslav; Pazourková, Eva; Pospíšilová, Šárka; Krkavcová, Miroslava; Novotná, Michaela; Hořínek, Aleš

    2016-08-01

    Molecular pathogenesis of Down syndrome (DS) is still incompletely understood. Epigenetic mechanisms, including miRNAs gene expression regulation, belong to potential influencing factors. The aims of this study were to compare miRNAs expressions in placentas with normal and trisomic karyotype and to associate differentially expressed miRNAs with concrete biological pathways. A total of 80 CVS samples - 41 with trisomy 21 and 39 with normal karyotype - were included in our study. Results obtained in the pilot study using real-time PCR technology and TaqMan Human miRNA Array Cards were subsequently validated on different samples using individual TaqMan miRNA Assays. Seven miRNAs were verified as upregulated in DS placentas (miR-99a, miR-542-5p, miR-10b, miR-125b, miR-615, let-7c and miR-654); three of these miRNAs are located on chromosome 21 (miR-99a, miR-125b and let-7c). Many essential biological processes, transcriptional regulation or apoptosis, were identified as being potentially influenced by altered miRNA levels. Moreover, miRNAs overexpressed in DS placenta apparently regulate genes involved in placenta development (GJA1, CDH11, EGF, ERVW-1, ERVFRD-1, LEP or INHA). These findings suggest the possible participation of miRNAs in Down syndrome impaired placentation and connected pregnancy pathologies. © 2016 John Wiley & Sons, Ltd. © 2016 John Wiley & Sons, Ltd.

  2. miRNAs: Miracle or Mirage?

    PubMed Central

    2007-01-01

    The evolution of complex animals such as insects and mammals is achieved with surprisingly few additions in protein coding genes. MicroRNAs (miRNAs), a class of noncoding RNAs, have emerged as important regulators of organogenesis in insects, fish and mammals. The microRNA repertoire of animals has expanded significantly during evolution especially in vertebrates, insects and nematodes, accompanying the appearance of complex body plans. MicroRNAs therefore have gained enormous interest in recent years. They are now regarded as key modulators of gene expression in many tissues during embryogenesis, in adult organisms and in disease processes. Therefore, these small RNA molecules have entered the center stage of molecular biology and are promising candidates not only for the regulation of key biological processes such as proliferation and apoptosis, but also for therapy of human diseases. PMID:19279697

  3. Phytoalexins, miRNAs and breast cancer: a review of phytochemical mediated miRNA regulation in breast cancer

    USDA-ARS?s Scientific Manuscript database

    A specific class of endogenous, non-coding RNAs, classified as microRNAs (miRNAs), has been identified. It has been found that miRNAs are associated with many biological processes and disease states, including all stages of cancer from initiation to tumor promotion and progression. These studies d...

  4. Small RNA zippers lock miRNA molecules and block miRNA function in mammalian cells

    PubMed Central

    Meng, Lingyu; Liu, Cuicui; Lü, Jinhui; Zhao, Qian; Deng, Shengqiong; Wang, Guangxue; Qiao, Jing; Zhang, Chuyi; Zhen, Lixiao; Lu, Ying; Li, Wenshu; Zhang, Yuzhen; Pestell, Richard G.; Fan, Huiming; Chen, Yi-Han; Liu, Zhongmin; Yu, Zuoren

    2017-01-01

    MicroRNAs (miRNAs) loss-of-function phenotypes are mainly induced by chemically modified antisense oligonucleotides. Here we develop an alternative inhibitor for miRNAs, termed ‘small RNA zipper'. It is designed to connect miRNA molecules end to end, forming a DNA–RNA duplex through a complementary interaction with high affinity, high specificity and high stability. Two miRNAs, miR-221 and miR-17, are tested in human breast cancer cell lines, demonstrating the 70∼90% knockdown of miRNA levels by 30–50 nM small RNA zippers. The miR-221 zipper shows capability in rescuing the expression of target genes of miR-221 and reversing the oncogenic function of miR-221 in breast cancer cells. In addition, we demonstrate that the miR-221 zipper attenuates doxorubicin resistance with higher efficiency than anti-miR-221 in human breast cancer cells. Taken together, small RNA zippers are a miRNA inhibitor, which can be used to induce miRNA loss-of-function phenotypes and validate miRNA target genes. PMID:28045030

  5. A Toolbox for Herpesvirus miRNA Research: Construction of a Complete Set of KSHV miRNA Deletion Mutants.

    PubMed

    Jain, Vaibhav; Plaisance-Bonstaff, Karlie; Sangani, Rajnikumar; Lanier, Curtis; Dolce, Alexander; Hu, Jianhong; Brulois, Kevin; Haecker, Irina; Turner, Peter; Renne, Rolf; Krueger, Brian

    2016-02-19

    Kaposi's sarcoma-associated herpesvirus (KSHV) encodes 12 viral microRNAs (miRNAs) that are expressed during latency. Research into KSHV miRNA function has suffered from a lack of genetic systems to study viral miRNA mutations in the context of the viral genome. We used the Escherichia coli Red recombination system together with a new bacmid background, BAC16, to create mutants for all known KSHV miRNAs. The specific miRNA deletions or mutations and the integrity of the bacmids have been strictly quality controlled using PCR, restriction digestion, and sequencing. In addition, stable viral producer cell lines based on iSLK cells have been created for wildtype KSHV, for 12 individual miRNA knock-out mutants (ΔmiR-K12-1 through -12), and for mutants deleted for 10 of 12 (ΔmiR-cluster) or all 12 miRNAs (ΔmiR-all). NGS, in combination with SureSelect technology, was employed to sequence the entire latent genome within all producer cell lines. qPCR assays were used to verify the expression of the remaining viral miRNAs in a subset of mutants. Induction of the lytic cycle leads to efficient production of progeny viruses that have been used to infect endothelial cells. Wt BAC16 and miR mutant iSLK producer cell lines are now available to the research community.

  6. Integrating miRNA and mRNA Expression Profiling Uncovers miRNAs Underlying Fat Deposition in Sheep

    PubMed Central

    Zhou, Guangxian; Wang, Xiaolong; Yuan, Chao; Kang, Danju; Xu, Xiaochun; Zhou, Jiping; Geng, Rongqing; Yang, Yuxin; Yang, Zhaoxia

    2017-01-01

    MicroRNAs (miRNAs) are endogenous, noncoding RNAs that regulate various biological processes including adipogenesis and fat metabolism. Here, we adopted a deep sequencing approach to determine the identity and abundance of miRNAs involved in fat deposition in adipose tissues from fat-tailed (Kazakhstan sheep, KS) and thin-tailed (Tibetan sheep, TS) sheep breeds. By comparing HiSeq data of these two breeds, 539 miRNAs were shared in both breeds, whereas 179 and 97 miRNAs were uniquely expressed in KS and TS, respectively. We also identified 35 miRNAs that are considered to be putative novel miRNAs. The integration of miRNA-mRNA analysis revealed that miRNA-associated targets were mainly involved in the gene ontology (GO) biological processes concerning cellular process and metabolic process, and miRNAs play critical roles in fat deposition through their ability to regulate fundamental pathways. These pathways included the MAPK signaling pathway, FoxO and Wnt signaling pathway, and focal adhesion. Taken together, our results define miRNA expression signatures that may contribute to fat deposition and lipid metabolism in sheep. PMID:28293627

  7. Integrating miRNA and mRNA Expression Profiling Uncovers miRNAs Underlying Fat Deposition in Sheep.

    PubMed

    Zhou, Guangxian; Wang, Xiaolong; Yuan, Chao; Kang, Danju; Xu, Xiaochun; Zhou, Jiping; Geng, Rongqing; Yang, Yuxin; Yang, Zhaoxia; Chen, Yulin

    2017-01-01

    MicroRNAs (miRNAs) are endogenous, noncoding RNAs that regulate various biological processes including adipogenesis and fat metabolism. Here, we adopted a deep sequencing approach to determine the identity and abundance of miRNAs involved in fat deposition in adipose tissues from fat-tailed (Kazakhstan sheep, KS) and thin-tailed (Tibetan sheep, TS) sheep breeds. By comparing HiSeq data of these two breeds, 539 miRNAs were shared in both breeds, whereas 179 and 97 miRNAs were uniquely expressed in KS and TS, respectively. We also identified 35 miRNAs that are considered to be putative novel miRNAs. The integration of miRNA-mRNA analysis revealed that miRNA-associated targets were mainly involved in the gene ontology (GO) biological processes concerning cellular process and metabolic process, and miRNAs play critical roles in fat deposition through their ability to regulate fundamental pathways. These pathways included the MAPK signaling pathway, FoxO and Wnt signaling pathway, and focal adhesion. Taken together, our results define miRNA expression signatures that may contribute to fat deposition and lipid metabolism in sheep.

  8. miRNA and mRNA expression analysis reveals potential sex-biased miRNA expression

    PubMed Central

    Guo, Li; Zhang, Qiang; Ma, Xiao; Wang, Jun; Liang, Tingming

    2017-01-01

    Recent studies suggest that mRNAs may be differentially expressed between males and females. This study aimed to perform expression analysis of mRNA and its main regulatory molecule, microRNA (miRNA), to discuss the potential sex-specific expression patterns using abnormal expression profiles from The Cancer Genome Atlas database. Generally, deregulated miRNAs and mRNAs had consistent expression between males and females, but some miRNAs may be oppositely expressed in specific diseases: up-regulated in one group and down-regulated in another. Studies of miRNA gene families and clusters further confirmed that these sequence or location related miRNAs might have opposing expression between sexes. The specific miRNA might have greater expression divergence across different groups, suggesting flexible expression across different individuals, especially in tumor samples. The typical analysis regardless of the sex will ignore or balance these sex-specific deregulated miRNAs. Compared with flexible miRNAs, their targets of mRNAs showed relative stable expression between males and females. These relevant results provide new insights into miRNA-mRNA interaction and sex difference. PMID:28045090

  9. Five freely circulating miRNAs and bone tissue miRNAs are associated with osteoporotic fractures.

    PubMed

    Seeliger, Claudine; Karpinski, Katrin; Haug, Alexander T; Vester, Helen; Schmitt, Andreas; Bauer, Jan S; van Griensven, Martijn

    2014-08-01

    Osteoporosis as a systemic skeletal disorder is characterized by increased bone fragility and the risk of fractures. According to the World Health Organization, osteoporosis is one of the 10 most common diseases and affects approximately 75 million people in Europe, the United States, and Japan. In this context, the identification of specific microRNA (miRNA) signatures is an important step for new diagnostic and therapeutic approaches. The focus of interest on miRNAs as biomarkers came with new publications identifying free circulating extracellular miRNAs associated with various types of cancer. This study aimed to identify specific miRNAs in patients with osteoporotic fractures compared with nonosteoporotic fractures. For the array analysis, miRNAs were isolated from the serum of 20 patients with hip fractures, transcribed, and the samples were pooled into 10 osteoporotic and 10 nonosteoporotic specimens. With each pool of samples, human serum and plasma miRNA PCR arrays were performed, which are able to identify 83 different miRNAs. Subsequently, a separate validation analysis of each miRNA found to be regulated in the array followed with miRNA samples isolated from the serum of 30 osteoporotic and 30 nonosteoporotic patients and miRNA samples isolated from the bone tissue of 20 osteoporotic and 20 nonosteoporotic patients. With the validation analysis of the regulated miRNAs, we identified 9 miRNAs, namely miR-21, miR-23a, miR-24, miR-93, miR-100, miR-122a, miR-124a, miR-125b, and miR-148a, that were significantly upregulated in the serum of patients with osteoporosis. In the bone tissue of osteoporotic patients, we identified that miR-21, miR-23a, miR-24, miR-25, miR-100, and miR-125b displayed a significantly higher expression. A total of 5 miRNAs display an upregulation both in serum and bone tissue. This study reveals an important role for several miRNAs in osteoporotic patients and suggested that they may be used as biomarkers for diagnostic purposes and

  10. [The role of miRNA in endometrial cancer in the context of miRNA 205].

    PubMed

    Wilczyński, Miłosz; Danielska, Justyna; Dzieniecka, Monika; Malinowski, Andrzej

    2015-11-01

    MiRNAs are small, non-coding molecules of ribonucleic acids of approximately 22 bp length, which serve as regulators of gene expression and protein translation due to interference with messenger RNA (mRNA). MiRNAs, which take part in the regulation of cell cycle and apoptosis, may be associated with carcinogenesis. Aberrant expression of miRNAs in endometrial cancer might contribute to the endometrial cancer initiation or progression, as well as metastasis formation, and may influence cancer invasiveness. Specific-miRNAs expressed in endometrial cancer tissues may serve as diagnostic markers of the disease, prognostic biomarkers, or play an important part in oncological therapy We aimed to describe the role of miRNAs in endometrial cancer with special consideration of miRNA 205.

  11. GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists

    PubMed Central

    Antonov, Alexey V.; Dietmann, Sabine; Wong, Philip; Lutter, Dominik; Mewes, Hans W.

    2009-01-01

    GeneSet2miRNA is the first web-based tool which is able to identify whether or not a gene list has a signature of miRNA-regulatory activity. As input, GeneSet2miRNA accepts a list of genes. As output, a list of miRNA-regulatory models is provided. A miRNA-regulatory model is a group of miRNAs (single, pair, triplet or quadruplet) that is predicted to regulate a significant subset of genes from the submitted list. GeneSet2miRNA provides a user friendly dialog-driven web page submission available for several model organisms. GeneSet2miRNA is freely available at http://mips.helmholtz-muenchen.de/proj/gene2mir/. PMID:19420064

  12. Transcript profiling of the salt-tolerant Festuca rubra ssp. litoralis reveals a regulatory network controlling salt acclimatization.

    PubMed

    Diédhiou, Calliste J; Popova, Olga V; Golldack, Dortje

    2009-05-01

    We report an analysis of salt-stress responses in the monocotyledonous halophyte Festuca rubra ssp. litoralis. Salt-dependent expression of transcripts encoding a PIP2;1 aquaporin, V-ATPase subunit B, and the Na+/H+ antiporter NHX was characterized. Transcription of FrPIP2;1, FrVHA-B, and FrNHX1 was induced in root tissue of F. rubra ssp. litoralis by salt treatment, and during salt-stress F. rubra ssp. litoralis accumulated sodium in leaves and roots. Cell specificity of FrPIP2;1, FrVHA-B, and FrNHX1 transcription was analyzed by in situ PCR in roots of F. rubra ssp. litoralis. Expression of the genes was localized to the root epidermis, cortex cells, endodermis, and the vascular tissue. In plants treated with 500 mM NaCl, transcripts were repressed in the epidermis and the outer cortex cells, whereas endodermis and vasculature showed strong signals. These data demonstrate that transcriptional regulation of the aquaporin PIP2;1, V-ATPase, and the Na+/H+ antiporter NHX is correlated with salt tolerance in F. rubra ssp. litoralis and suggests coordinated control of ion homeostasis and water status at high salinity in plants. Salt-induced transcript accumulation in F. rubra ssp. litoralis was further monitored by cDNA-arrays with expressed sequence tags derived from a cDNA subtraction library. The salt-regulated transcripts included those involved in the control of gene expression and signal transduction elements such as a serine/threonine protein kinase, an SNF1-related protein kinase, and a WRKY-type transcription factor. Other ESTs with salt-dependent regulation included transcripts encoding proteins that function in metabolism, general stress responses, and defense and transport proteins.

  13. miRNA and cancer; computational and experimental approaches.

    PubMed

    Tutar, Yusuf

    2014-01-01

    Human genome sequencing was started to solve four letter algorithm of the genome to understand the complex nature of human metabolism. However, after completion of Human Genome Project many scientists realized that sequence information alone was not sufficient to solve the biochemical mechanism of the organism through classical approaches. Non-coding parts of the genome produce small conserved ribonucleic acids, miRNAs to control cellular and physiological processes [1, 2]. This breakthrough discovery directed researches to examine role of miRNA in cancer since miRNAs are involved in the development, cell differentiation, and regulation of cell cycle [3]. The first paper of the special issue provides general information of miRNA in cancer research. This thematic issue presents two computational approaches for miRNA identification and their role in cancer. The first one comes from Dr. Wang and his presented work predicts cancer-related miRNAs by using expression profiles in tumor tissues. The work relies on R-squared method to investigate miRNA-mRNA regulatory relationship between miRNAs and mRNAs from different tissues and predicts miRNAs associated with colon, prostate, pancreatic, lung, breast, bladder, and kidney cancer. The second paper by Allmer et al. examines miRNA-gene regulatory networks and their implications in cancer. Their work provides complex network of expression regulation and miRNAs' role in personalized medicine. miRNAs regulate tumor progression and metastasis by interacting with target genes in the cells. Exosomal shuttle small RNAs mediate cell to cell communication and regulate cancer metastasis. The regulation via heterotypic signals in the microenvironment was explained by Dr. Liang and Dr. Yu groups. The rest of the issue highlights the roles of miRNAs on multiple myeloma, non-small cell lung cancer, urological malignancies, myeloid leukemia, and laryngeal squamous cell carcinoma. Proliferation of bone marrow of malignant plasma cells

  14. Crosstalk between kinases, phosphatases and miRNAs in cancer.

    PubMed

    Abrantes, Júlia L F; Tornatore, Thaís F; Pelizzaro-Rocha, Karin J; de Jesus, Marcelo B; Cartaxo, Rodrigo T; Milani, Renato; Ferreira-Halder, Carmen V

    2014-12-01

    Reversible phosphorylation of proteins, performed by kinases and phosphatases, is the major post translational protein modification in eukaryotic cells. This intracellular event represents a critical regulatory mechanism of several signaling pathways and can be related to a vast array of diseases, including cancer. Cancer research has produced increasing evidence that kinase and phosphatase activity can be compromised by mutations and also by miRNA silencing, performed by small non-coding and endogenously produced RNA molecules that lead to translational repression. miRNAs are believed to target about one-third of human mRNAs while a single miRNA may target about 200 transcripts simultaneously. Regulation of the phosphorylation balance by miRNAs has been a topic of intense research over the last years, spanning topics going as far as cancer aggressiveness and chemotherapy resistance. By addressing recent studies that have shown miRNA expression patterns as phenotypic signatures of cancers and how miRNA influence cellular processes such as apoptosis, cell cycle control, angiogenesis, inflammation and DNA repair, we discuss how kinases, phosphatases and miRNAs cooperatively act in cancer biology.

  15. Protocol for miRNA isolation from biofluids.

    PubMed

    Lekchnov, Evgeny A; Zaporozhchenko, Ivan A; Morozkin, Evgeny S; Bryzgunova, Olga E; Vlassov, Valentin V; Laktionov, Pavel P

    2016-04-15

    MicroRNAs (miRNAs) have been identified as promising biomarkers in cancer and other diseases. Packaging of miRNAs into vesicles and complexes with proteins ensures their stability in biological fluids but also complicates their isolation. Conventional protocols used to isolate cell-free RNA are generally successful in overcoming these difficulties; however, they are costly, labor-intensive, or heavily reliant on the use of hazardous chemicals. Here we describe a protocol that is suitable for isolating miRNAs from biofluids, including blood plasma and urine. The protocol is based on precipitation of proteins, denaturation of miRNA-containing complexes with octanoic acid and guanidine isothiocyanate, and subsequent purification of miRNA on spin columns. The efficacy of miRNA extraction by phenol-chloroform extraction, miRCURY RNA isolation kit--biofluids (Exiqon), and the proposed protocol was compared by quantitative reverse-transcription PCR of miR-16 and miR-126. The proposed protocol was slightly more effective for isolating miRNA from plasma and significantly superior to the other two methods for miRNA isolation from urine. Spectrophotometry and SDS-PAGE data suggest that the disparity in performance between miRCURY Biofluids and the proposed protocol can be attributed to differences in precipitation mechanisms, as confirmed by the retention of different proteins in the supernatant.

  16. Vasopressin-regulated miRNAs and AQP2-targeting miRNAs in kidney collecting duct cells.

    PubMed

    Kim, Jae-Eun; Jung, Hyun Jun; Lee, Yu-Jung; Kwon, Tae-Hwan

    2015-04-01

    Mature microRNA (miRNA) acts as an important posttranscriptional regulator. We aimed to profile vasopressin-responsive miRNAs in kidney inner medullary collecting duct cells and to identify aquaporin-2 (AQP2)-targeting miRNAs. Microarray chip assay was carried out in inner medullary collecting duct tubule suspensions from rat kidneys in the absence or presence of desmopressin (dDAVP) stimulation (10(-9) M, 2 h). The results demonstrated 19 miRNAs, including both precursor and mature miRNAs, as potential candidates that showed significant changes in expression after dDAVP stimulation (P < 0.05). Nine mature miRNAs exhibiting >1.3-fold changes in expression on the microarray (miR-127, miR-1, miR-873, miR-16, miR-206, miR-678, miR-496, miR-298, and miR-463) were further examined by quantitative real-time PCR, and target genes of the selected miRNAs were predicted. Next, to identify AQP2-targeting miRNAs, in silico analysis was performed. Four miRNAs (miR-32, miR-137, miR-216a, and miR-216b) target the 3'-untranslated region of rat AQP2 mRNA. Target seed regions of miR-32 and miR-137 were also conserved in the 3'-untranslated region of mouse AQP2 mRNA. Quantitative real-time PCR and immunoblot analysis demonstrated that dDAVP-induced AQP2 expression was significantly attenuated in mpkCCDc14 cells when cells were transfected with miRNA mimics of miR-32 or miR-137. Moreover, luciferase reporter assay demonstrated a significant decrease of AQP2 translation in mpkCCDc14 cells transfected with miRNA mimics of miR-32 or miR-137. The present study provides novel insights into the regulation of AQP2 by RNA interference; however, vasopressin-regulated miRNAs did not include miR-32 or miR-137, indicating that the interaction of miRNAs with the AQP2 regulatory pathway requires further analysis. Copyright © 2015 the American Physiological Society.

  17. miRNA and miRNA target genes in copy number variations occurring in individuals with intellectual disability.

    PubMed

    Qiao, Ying; Badduke, Chansonette; Mercier, Eloi; Lewis, Suzanne M E; Pavlidis, Paul; Rajcan-Separovic, Evica

    2013-08-10

    MicroRNAs (miRNAs) are a family of short, non-coding RNAs modulating expression of human protein coding genes (miRNA target genes). Their dysfunction is associated with many human diseases, including neurodevelopmental disorders. It has been recently shown that genomic copy number variations (CNVs) can cause aberrant expression of integral miRNAs and their target genes, and contribute to intellectual disability (ID). To better understand the CNV-miRNA relationship in ID, we investigated the prevalence and function of miRNAs and miRNA target genes in five groups of CNVs. Three groups of CNVs were from 213 probands with ID (24 de novo CNVs, 46 familial and 216 common CNVs), one group of CNVs was from a cohort of 32 cognitively normal subjects (67 CNVs) and one group of CNVs represented 40 ID related syndromic regions listed in DECIPHER (30 CNVs) which served as positive controls for CNVs causing or predisposing to ID. Our results show that 1). The number of miRNAs is significantly higher in de novo or DECIPHER CNVs than in familial or common CNV subgroups (P < 0.01). 2). miRNAs with brain related functions are more prevalent in de novo CNV groups compared to common CNV groups. 3). More miRNA target genes are found in de novo, familial and DECIPHER CNVs than in the common CNV subgroup (P < 0.05). 4). The MAPK signaling cascade is found to be enriched among the miRNA target genes from de novo and DECIPHER CNV subgroups. Our findings reveal an increase in miRNA and miRNA target gene content in de novo versus common CNVs in subjects with ID. Their expression profile and participation in pathways support a possible role of miRNA copy number change in cognition and/or CNV-mediated developmental delay. Systematic analysis of expression/function of miRNAs in addition to coding genes integral to CNVs could uncover new causes of ID.

  18. Investigation of key miRNAs and target genes in bladder cancer using miRNA profiling and bioinformatic tools.

    PubMed

    Canturk, Kemal Murat; Ozdemir, Muhsin; Can, Cavit; Öner, Setenay; Emre, Ramazan; Aslan, Huseyin; Cilingir, Oguz; Ciftci, Evrim; Celayir, Fatih Mehmet; Aldemir, Ozgur; Özen, Mustafa; Artan, Sevilhan

    2014-12-01

    Despite the association of several miRNAs with bladder cancer, little is known about the miRNAs' regulatory networks. In this study, we aimed to construct potential networks of bladder-cancer-related miRNAs and their known target genes using miRNA expression profiling and bioinformatics tools and to investigate potential key molecules that might play roles in bladder cancer regulatory networks. Global miRNA expression profiles were obtained using microarray followed by RT-qPCR validation using two randomly selected miRNAs. Known targets of deregulated miRNAs were utilized using DIANA-TarBase database v6.0. The incorporation of deregulated miRNAs and target genes into KEGG pathways were utilized using DIANA-mirPath software. To construct potential miRNA regulatory networks, the overlapping parts of three selected KEGG pathways were visualized by Cytoscape software. We finally gained 19 deregulated miRNAs, including 5 ups- and 14 down regulated in 27 bladder-cancer tissue samples and 8 normal urothelial tissue samples. The enrichment results of deregulated miRNAs and known target genes showed that most pathways were related to cancer or cell signaling pathways. We determined the hub CDK6, BCL2, E2F3, PTEN, MYC, RB, and ERBB3 target genes and hub hsa-let-7c, hsa-miR-195-5p, hsa-miR-141-3p, hsa-miR-26a-5p, hsa-miR-23b-3p, and hsa-miR-125b-5p miRNAs of the constructed networks. These findings provide new insights into the bladder cancer regulatory networks and give us a hypothesis that hsa-let-7c, hsa-miR-195-5p, and hsa-miR-125b-5p, along with CDK4 and CDK6 genes might exist in the same bladder cancer pathway. Particularly, hub miRNAs and genes might be potential biomarkers for bladder cancer clinics.

  19. Molecular and cellular analysis of the pH response transcription factor PacC in the fungal symbiont Epichloë festucae.

    PubMed

    Lukito, Yonathan; Chujo, Tetsuya; Scott, Barry

    2015-12-01

    In order to survive and adapt to the environment, it is imperative for fungi to be able to sense and respond to changes in extracellular pH conditions. In ascomycetes, sensing of extracellular pH is mediated by the Pal pathway resulting in activation of the PacC transcription factor at alkaline pH. The role of PacC in regulating fungal virulence and pathogenicity has been described in several pathogenic fungi but to date not in a symbiotic fungus. Epichloë festucae is a biotrophic fungal endophyte that forms a stable mutualistic interaction with Lolium perenne. In this study, pacC deletion (ΔpacC) and dominant active (pacC(C)) mutants were generated in order to study the cellular roles of PacC in E. festucae. Deletion of pacC resulted in increased sensitivity of the mutant to salt-stress but surprisingly did not affect the ability of the mutant to grow under alkaline pH conditions. Alkaline pH was observed to induce conidiation in wild-type E. festucae but not in the ΔpacC mutant. On the other hand the pacC(C) mutant had increased conidiation at neutral pH alone. Null pacC mutants had no effect on the symbiotic interaction with ryegrass plants whereas the pacC(C) mutant increased the tiller number. Examination of the growth of the pacC(C) mutant in the plant revealed the formation of aberrant convoluted hyphal structures and an increase in hyphal breakage, which are possible reasons for the altered host interaction phenotype.

  20. Assay Reproducibility in Clinical Studies of Plasma miRNA

    PubMed Central

    Rice, Jonathan; Roberts, Henry; Burton, James; Pan, Jianmin; States, Vanessa; Rai, Shesh N.; Galandiuk, Susan

    2015-01-01

    There are increasing reports of plasma miRNAs as biomarkers of human disease but few standards in methodologic reporting, leading to inconsistent data. We systematically reviewed plasma miRNA studies published between July 2013-June 2014 to assess methodology. Six parameters were investigated: time to plasma extraction, methods of RNA extraction, type of miRNA, quantification, cycle threshold (Ct) setting, and methods of statistical analysis. We compared these data with a proposed standard methodologic technique. Beginning with initial screening for 380 miRNAs using microfluidic array technology and validation in an additional cohort of patients, we compared 11 miRNAs that exhibited differential expression between 16 patients with benign colorectal neoplasms (advanced adenomas) and 16 patients without any neoplasm (controls). Plasma was isolated immediately, 12, 24, 48, or 72 h following phlebotomy. miRNA was extracted using two different techniques (Trizol LS with pre-amplification or modified miRNeasy). We performed Taqman-based RT-PCR assays for the 11 miRNAs with subsequent analyses using a variable Ct setting or a fixed Ct set at 0.01, 0.03, 0.05, or 0.5. Assays were performed in duplicate by two different operators. RNU6 was the internal reference. Systematic review yielded 74 manuscripts meeting inclusion criteria. One manuscript (1.4%) documented all 6 methodological parameters, while < 5% of studies listed Ct setting. In our proposed standard technique, plasma extraction ≤12 h provided consistent ΔCt. miRNeasy extraction yielded higher miRNA concentrations and fewer non-expressed miRNAs compared to Trizol LS (1/704 miRNAs [0.14%] vs 109/704 miRNAs [15%], not expressed, respectively). A fixed Ct bar setting of 0.03 yielded the most reproducible data, provided that <10% miRNA were non-expressed. There was no significant intra-operator variability. There was significant inter-operator variation using Trizol LS extraction, while this was negligible using

  1. Comparison of sensitivity of grasses (Lolium perenne L. and Festuca rubra L.) and lettuce (Lactuca sativa L.) exposed to water contaminated with microcystins.

    PubMed

    Pereira, Silvia; Saker, Martin L; Vale, Micaela; Vasconcelos, Vitor M

    2009-07-01

    The effects of aqueous extracts from Microcysts aeruginosa strains (both microcystin-producers and non-microcystin producers) on germination and root growth were investigated for three economically important plant species: Festuca rubra L., Lolium perenne L., and Lactuca sativa L. There was a clear inhibition of root growth for L. sativa exposed to strains containing microcystins (5.9-56.4 microg L(-1)). The strain that produced the most pronounced effects contained the lowest concentration of microcystin suggesting that other cellular compounds may also affect growth.

  2. Differential expression of microRNA (miRNA) in chordoma reveals a role for miRNA-1 in Met expression.

    PubMed

    Duan, Zhenfeng; Choy, Edwin; Nielsen, G Petur; Rosenberg, Andrew; Iafrate, John; Yang, Cao; Schwab, Joe; Mankin, Henry; Xavier, Ramnik; Hornicek, Francis J

    2010-06-01

    Emerging evidence suggests that microRNA (miRNA) expression signatures in cancer may have important diagnostic, prognostic, and therapeutic value, but there is no data on miRNA expression in chordoma. The purpose of this study was to identify the role of miRNAs in human chordoma. We analyzed miRNA expression in chordoma-derived cell lines and chordoma tissue by using miRNA microarray technology with unsupervised hierarchical clustering analysis. The relative expression levels of these miRNAs were confirmed by real-time quantitative RT-PCR and Northern blot analysis. To characterize the potential role of miRNA-1, miRNA-1 was stably transfected into a chordoma cell line, UCH1. The expression of miRNA-1 targeted gene Met in chordoma tissues was also studied. We observe that human chordoma tissues and cell lines can be distinguished from normal muscle tissue by comparing miRNA expression profiles. Several miRNAs were differentially expressed in chordoma cell lines compared to controls, and similar expression patterns were found in primary chordoma tissues. Importantly, we were able to show for the first time, to our knowledge, that expression of miRNA-1 and miRNA-206, two miRNAs implicated in a number of other cancer types, were markedly decreased in both chordoma tissues and cell lines. When chordoma cell lines were transfected with miRNA-1, downregulation of known miRNA-1 targets was observed. These targets included Met and HDAC4-two genes that were observed to be overexpressed in chordoma. Our results demonstrate that some miRNAs are differentially expressed in chordoma and, in particular, miRNA-1 may have a functional effect on chordoma tumor pathogenesis.

  3. Targeting oncomiRNAs and mimicking tumor suppressor miRNAs: New trends in the development of miRNA therapeutic strategies in oncology (Review)

    PubMed Central

    GAMBARI, ROBERTO; BROGNARA, ELEONORA; SPANDIDOS, DEMETRIOS A.; FABBRI, ENRICA

    2016-01-01

    MicroRNA (miRNA or miR) therapeutics in cancer are based on targeting or mimicking miRNAs involved in cancer onset, progression, angiogenesis, epithelial-mesenchymal transition and metastasis. Several studies conclusively have demonstrated that miRNAs are deeply involved in tumor onset and progression, either behaving as tumor-promoting miRNAs (oncomiRNAs and metastamiRNAs) or as tumor suppressor miRNAs. This review focuses on the most promising examples potentially leading to the development of anticancer, miRNA-based therapeutic protocols. The inhibition of miRNA activity can be readily achieved by the use of miRNA inhibitors and oligomers, including RNA, DNA and DNA analogues (miRNA antisense therapy), small molecule inhibitors, miRNA sponges or through miRNA masking. On the contrary, the enhancement of miRNA function (miRNA replacement therapy) can be achieved by the use of modified miRNA mimetics, such as plasmid or lentiviral vectors carrying miRNA sequences. Combination strategies have been recently developed based on the observation that i) the combined administration of different antagomiR molecules induces greater antitumor effects and ii) some anti-miR molecules can sensitize drug-resistant tumor cell lines to therapeutic drugs. In this review, we discuss two additional issues: i) the combination of miRNA replacement therapy with drug administration and ii) the combination of antagomiR and miRNA replacement therapy. One of the solid results emerging from different independent studies is that miRNA replacement therapy can enhance the antitumor effects of the antitumor drugs. The second important conclusion of the reviewed studies is that the combination of anti-miRNA and miRNA replacement strategies may lead to excellent results, in terms of antitumor effects. PMID:27175518

  4. Identification of targets of miRNA-221 and miRNA-222 in fulvestrant-resistant breast cancer

    PubMed Central

    Liu, Pengfei; Sun, Manna; Jiang, Wenhua; Zhao, Jinkun; Liang, Chunyong; Zhang, Huilai

    2016-01-01

    The present study aimed to identify the differentially expressed genes (DEGs) regulated by microRNA (miRNA)-221 and miRNA-222 that are associated with the resistance of breast cancer to fulvestrant. The GSE19777 transcription profile was downloaded from the Gene Expression Omnibus database, and includes data from three samples of antisense miRNA-221-transfected fulvestrant-resistant MCF7-FR breast cancer cells, three samples of antisense miRNA-222-transfected fulvestrant-resistant MCF7-FR cells and three samples of control inhibitor (green fluorescent protein)-treated fulvestrant-resistant MCF7-FR cells. The linear models for microarray data package in R/Bioconductor was employed to screen for DEGs in the miRNA-transfected cells, and the pheatmap package in R was used to perform two-way clustering. Pathway enrichment was conducted using the Gene Set Enrichment Analysis tool. Furthermore, a miRNA-messenger (m) RNA regulatory network depicting interactions between miRNA-targeted upregulated DEGs was constructed and visualized using Cytoscape. In total, 492 and 404 DEGs were identified for the antisense miRNA-221-transfected MCF7-FR cells and the antisense miRNA-222-transfected MCF7-FR cells, respectively. Genes of the pentose phosphate pathway (PPP) were significantly enriched in the antisense miRNA-221-transfected MCF7-FR cells. In addition, components of the Wnt signaling pathway and cell adhesion molecules (CAMs) were significantly enriched in the antisense miRNA-222-transfected MCF7-FR cells. In the miRNA-mRNA regulatory network, miRNA-222 was demonstrated to target protocadherin 10 (PCDH10). The results of the present study suggested that the PPP and Wnt signaling pathways, as well as CAMs and PCDH10, may be associated with the resistance of breast cancer to fulvestrant. PMID:27895744

  5. Identification of targets of miRNA-221 and miRNA-222 in fulvestrant-resistant breast cancer.

    PubMed

    Liu, Pengfei; Sun, Manna; Jiang, Wenhua; Zhao, Jinkun; Liang, Chunyong; Zhang, Huilai

    2016-11-01

    The present study aimed to identify the differentially expressed genes (DEGs) regulated by microRNA (miRNA)-221 and miRNA-222 that are associated with the resistance of breast cancer to fulvestrant. The GSE19777 transcription profile was downloaded from the Gene Expression Omnibus database, and includes data from three samples of antisense miRNA-221-transfected fulvestrant-resistant MCF7-FR breast cancer cells, three samples of antisense miRNA-222-transfected fulvestrant-resistant MCF7-FR cells and three samples of control inhibitor (green fluorescent protein)-treated fulvestrant-resistant MCF7-FR cells. The linear models for microarray data package in R/Bioconductor was employed to screen for DEGs in the miRNA-transfected cells, and the pheatmap package in R was used to perform two-way clustering. Pathway enrichment was conducted using the Gene Set Enrichment Analysis tool. Furthermore, a miRNA-messenger (m) RNA regulatory network depicting interactions between miRNA-targeted upregulated DEGs was constructed and visualized using Cytoscape. In total, 492 and 404 DEGs were identified for the antisense miRNA-221-transfected MCF7-FR cells and the antisense miRNA-222-transfected MCF7-FR cells, respectively. Genes of the pentose phosphate pathway (PPP) were significantly enriched in the antisense miRNA-221-transfected MCF7-FR cells. In addition, components of the Wnt signaling pathway and cell adhesion molecules (CAMs) were significantly enriched in the antisense miRNA-222-transfected MCF7-FR cells. In the miRNA-mRNA regulatory network, miRNA-222 was demonstrated to target protocadherin 10 (PCDH10). The results of the present study suggested that the PPP and Wnt signaling pathways, as well as CAMs and PCDH10, may be associated with the resistance of breast cancer to fulvestrant.

  6. Identifying miRNA synergistic regulatory networks in heterogeneous human data via network motifs.

    PubMed

    Zhang, Junpeng; Duy Le, Thuc; Liu, Lin; He, Jianfeng; Li, Jiuyong

    2016-02-01

    Understanding the synergism of multiple microRNAs (miRNAs) in gene regulation can provide important insights into the mechanisms of complex human diseases caused by miRNA regulation. Therefore, it is important to identify miRNA synergism and study miRNA characteristics in miRNA synergistic regulatory networks. A number of methods have been proposed to identify miRNA synergism. However, most of the methods only use downstream target genes of miRNAs to infer miRNA synergism when miRNAs can also be regulated by upstream transcription factors (TFs) at the transcriptional level. Additionally, most methods are based on statistical associations identified from data without considering the causal nature of gene regulation. In this paper, we present a causality based framework, called mirSRN (miRNA synergistic regulatory network), to infer miRNA synergism in human molecular systems by considering both downstream miRNA targets and upstream TF regulation. We apply the proposed framework to two real world datasets and discover that almost all the top 10 miRNAs with the largest node degree in the mirSRNs are associated with different human diseases, including cancer, and that the mirSRNs are approximately scale-free and small-world networks. We also find that most miRNAs in the networks are frequently synergistic with other miRNAs, and miRNAs related to the same disease are likely to be synergistic and in a cluster linked to a biological function. Synergistic miRNA pairs show higher co-expression level, and may have potential functional relationships indicating collaboration between the miRNAs. Functional validation of the identified synergistic miRNAs demonstrates that these miRNAs cause different kinds of diseases. These results deepen our understanding of the biological meaning of miRNA synergism.

  7. Circulating miRNAs as biomarkers for endocrine disorders.

    PubMed

    Butz, H; Kinga, N; Racz, K; Patocs, A

    2016-01-01

    Specific, sensitive and non-invasive biomarkers are always needed in endocrine disorders. miRNAs are short, non-coding RNA molecules with well-known role in gene expression regulation. They are frequently dysregulated in metabolic and endocrine diseases. Recently it has been shown that they are secreted into biofluids by nearly all kind of cell types. As they can be taken up by other cells they may have a role in a new kind of paracrine, cell-to-cell communication. Circulating miRNAs are protected by RNA-binding proteins or microvesicles hence they can be attractive candidates as diagnostic or prognostic biomarkers. In this review, we summarize the characteristics of extracellular miRNA's and our knowledge about their origin and potential roles in endocrine and metabolic diseases. Discussions about the technical challenges occurring during identification and measurement of extracellular miRNAs and future perspectives about their roles are also highlighted.

  8. Implications of miRNAs in Colorectal Cancer Chemoresistance.

    PubMed

    Ju, Jingfang

    2011-01-01

    With the exponential growth of research efforts on non-coding microRNAs (miRNAs) in the past decade, miRNAs have been demonstrated to be important in many major human diseases, including diabetes, heart disease, and cancer. Due to the broad regulatory function of miRNAs, alterations of their expression can have profound consequences on multiple critical genes and pathways. One of the major issues related to the success of treating advanced colorectal cancer is chemoresistance. In this review, we will present some of the recent advancements in miRNA research related to chemoresistance mechanisms to 5-FU based chemotherapy in colorectal cancer and cancer stem cells. We believe that this miRNA-mediated resistance mechanism will offer novel strategies to develop future anti-cancer therapies.

  9. Regulation of Bone Formation During Disuse by miRNA

    NASA Technical Reports Server (NTRS)

    Thomas, Nicholas; Choi, Catherine Y.; Alwood, Joshua S.

    2016-01-01

    Astronauts lose bone structure during long-duration spaceflight. These changes are due, in part, to insufficient bone formation by the osteoblast cells. Little is known about the role that small (approximately 22 nucleotide), non-coding micro-RNAs (miRNAs) play in the osteoblast response to microgravity. We hypothesize that osteoblast-lineage cells alter their miRNA status during microgravity exposure, contributing to impaired bone formation during weightlessness. To simulate weightlessness, female mice (C57BL/6, Charles River, 10 weeks of age, n = 6) were hindlimb unloaded for 12 days. Age-matched and normally ambulating mice served as controls (n=6). To assess the expression of miRNAs in skeletal tissue, the right and left tibia of the mice were collected ex vivo and cleaned of soft-tissue and marrow. Total RNA was collected from tibial bone and relative abundance was measured for miRNAs of interest using quantitative real time PCR array looking at 372 unique and well-characterized mature miRNAs using the delta-delta Ct method. Transcripts of interest were normalized to an average of 6 reference RNAs. Preliminary results show that hindlimb unloading decreased the expression of 14 miRNAs to less than 1.4-2.9X control levels and increased the expression of 5 miRNAs relative to the control mice greater than 1-2-1.5X (p less than 0.05, respectively). Using the miRSystem we assessed overlapping target genes predicted to be regulated by multiple members of the 19 differentially expressed miRNAs as well as in silico predicted targets of our individual miRNAs. Our miRSystem results indicated that a number of our differentially expressed miRNAs were regulators of genes related to the Wnt-Beta Catenin pathway-a known regulator of bone health-and, interestingly, the estrogen-mediated cell-cycle regulation pathway, which may indicate that simulated weightlessness induced systemic hormonal changes that contributed to bone loss. We plan to follow up these findings by measuring

  10. Airway Epithelial miRNA Expression Is Altered in Asthma

    PubMed Central

    Solberg, Owen D.; Ostrin, Edwin J.; Love, Michael I.; Peng, Jeffrey C.; Bhakta, Nirav R.; Nguyen, Christine; Solon, Margaret; Nguyen, Cindy; Barczak, Andrea J.; Zlock, Lorna T.; Blagev, Denitza P.; Finkbeiner, Walter E.; Ansel, K. Mark; Arron, Joseph R.; Erle, David J.

    2012-01-01

    Rationale: Changes in airway epithelial cell differentiation, driven in part by IL-13, are important in asthma. Micro-RNAs (miRNAs) regulate cell differentiation in many systems and could contribute to epithelial abnormalities in asthma. Objectives: To determine whether airway epithelial miRNA expression is altered in asthma and identify IL-13–regulated miRNAs. Methods: We used miRNA microarrays to analyze bronchial epithelial brushings from 16 steroid-naive subjects with asthma before and after inhaled corticosteroids, 19 steroid-using subjects with asthma, and 12 healthy control subjects, and the effects of IL-13 and corticosteroids on cultured bronchial epithelial cells. We used quantitative polymerase chain reaction to confirm selected microarray results. Measurements and Main Results: Most (12 of 16) steroid-naive subjects with asthma had a markedly abnormal pattern of bronchial epithelial miRNA expression by microarray analysis. Compared with control subjects, 217 miRNAs were differentially expressed in steroid-naive subjects with asthma and 200 in steroid-using subjects with asthma (false discovery rate < 0.05). Treatment with inhaled corticosteroids had modest effects on miRNA expression in steroid-naive asthma, inducing a statistically significant (false discovery rate < 0.05) change for only nine miRNAs. qPCR analysis confirmed differential expression of 22 miRNAs that were highly differentially expressed by microarrays. IL-13 stimulation recapitulated changes in many differentially expressed miRNAs, including four members of the miR-34/449 family, and these changes in miR-34/449 family members were resistant to corticosteroids. Conclusions: Dramatic alterations of airway epithelial cell miRNA levels are a common feature of asthma. These alterations are only modestly corrected by inhaled corticosteroids. IL-13 effects may account for some of these alterations, including repression of miR-34/449 family members that have established roles in airway

  11. Aberrant miRNA profiles associated with chronic benzene poisoning.

    PubMed

    Bai, Wenlin; Chen, Yujiao; Yang, Jing; Niu, Piye; Tian, Lin; Gao, Ai

    2014-06-01

    Chronic occupational benzene exposure is associated with an increased risk of hematological malignancies. To gain an insight into the new biomarkers and molecular mechanisms of chronic benzene poisoning, miRNA profiles and mRNA expression pattern from the peripheral blood mononuclear cells of chronic benzene poisoning patients and health controls matched age and gender without benzene exposure were performed using the Exiqon miRNA PCR ARRAY and Gene Chip Human Gene 2.0ST Arrays, respectively. Totally, 6 up-regulated miRNAs (miR-34a, miR-205, miR-10b, let-7d, miR-185 and miR-423-5p-2) and 7 down-regulated miRNAs (miR-133a, miR-543, hsa-miR-130a, miR-27b,miR-223, miR-142-5p and miR-320b) were found in chronic benzene poisoning group compared to health controls (P ≤ 0.05). By integrating miRNA and mRNA expression data, these differential miRNAs were mainly involved in regulation of transcription from RNA polymerase II promoter, axon guidance, regulation of transcription, DNA-dependent, nervous system development, and regulation of actin cytoskeleton organization. Further, pathway analysis indicated that SMAD4, PLCB1, NFAT5, GNAI2, PTEN, VEGFA, BCL2, CTNNB1 and CCND1 were key target genes of differential miRNAs which were implicated in Adherens junction, TGF-beta signaling pathway, Wnt signaling pathway, tight junction and Pathways in cancer. In conclusion, the aberrant miRNAs might be a potential biomarker of chronic benzene poisoning.

  12. miRNA in Macrophage Development and Function

    PubMed Central

    2016-01-01

    Abstract Significance: MicroRNAs (miRNAs) control cellular gene expression via primarily binding to 3′ or 5′ untranslated region of the target transcript leading to translational repression or mRNA degradation. In most cases, miRNAs have been observed to fine-tune the cellular responses and, therefore, act as a rheostat rather than an on/off switch. Transcription factor PU.1 is a master switch that controls monocyte/macrophage development from hematopoietic stem cells. Recent Advances: PU.1 induces a specific set of miRNAs while suppressing the miR17-92 cluster to regulate monocyte/macrophage development. In addition to development, miRNAs tightly control the macrophage polarization continuum from proinflammatory M1 or proreparative M2 by regulating expression of key transcription factors involved in the process of polarization. Critical Issues: miRNAs are intricately involved with fine-tuning fundamental macrophage functions such as phagocytosis, efferocytosis, inflammation, tissue repair, and tumor promotion. Macrophages are secretory cells that participate in intercellular communication by releasing regulatory molecules and microvesicles (MVs). MVs are bilayered lipid membranes packaging a hydrophilic cargo, including proteins and nucleic acids. Macrophage-derived MVs carry functionally active miRNAs that suppress gene expression in target cells via post-transcriptional gene silencing, thus regulating cell function. In summary, miRNAs fine-tune several major facets of macrophage development and function. Such fine-tuning is critical in preventing exaggerated macrophage response to endogenous or exogenous stimuli. Future Directions: A critical role of miRNAs in the regulation of innate immune response and macrophage biology, including development, differentiation, and activation, has emerged. A clear understanding of such regulation on macrophage function remains to be elucidated. Antioxid. Redox Signal. 25, 795–804. PMID:27353423

  13. DAB2IP-Coordinated miRNA Biogenesis

    DTIC Science & Technology

    2015-09-01

    work provides a mechanistic insight of miR-363 regulation within the miR-106a-363 cluster by interferon -induced protein with tetratricopeptide...suppressive miRNA within a cluster containing mostly oncogenic miRNAs. 15. SUBJECT TERMS Prostate cancer, microRNA turnover machinery, Interferon ...12,13. In this study, we unveil a new post-transcriptional regulatory mechanism specific to miR-363 turnover by a novel protein complex- Interferon

  14. MicroRNA (miRNA) cloning analysis reveals sex differences in miRNA expression profiles between adult mouse testis and ovary.

    PubMed

    Mishima, Takuya; Takizawa, Takami; Luo, Shan-Shun; Ishibashi, Osamu; Kawahigashi, Yutaka; Mizuguchi, Yoshiaki; Ishikawa, Tomoko; Mori, Miki; Kanda, Tomohiro; Goto, Tadashi; Takizawa, Toshihiro

    2008-12-01

    MicroRNAs (miRNAs) are endogenous non-coding small RNAs that can regulate the expression of complementary mRNA targets. Identifying tissue-specific miRNAs is the first step toward understanding the biological functions of miRNAs, which include the regulation of tissue differentiation and the maintenance of tissue identity. In this study, we performed small RNA library sequencing in adult mouse testis and ovary to reveal their characteristic organ- and gender-specific profiles and to elucidate the characteristics of the miRNAs expressed in the reproductive system. We obtained 10,852 and 11 744 small RNA clones from mouse testis and ovary respectively (greater than 10,000 clones per organ), which included 6630 (159 genes) and 10,192 (154 genes) known miRNAs. A high level of efficiency of miRNA library sequencing was achieved: 61% (6630 miRNA clones/10,852 small RNA clones) and 87% (10,192/11,744) for adult mouse testis and ovary respectively. We obtained characteristic miRNA signatures in testis and ovary; 55 miRNAs were detected highly, exclusively, or predominantly in adult mouse testis and ovary, and discovered two novel miRNAs. Male-biased expression of miRNAs occurred on the X-chromosome. Our data provide important information on sex differences in miRNA expression that should facilitate studies of the reproductive organ-specific roles of miRNAs.

  15. miRNA regulation of nutrient homeostasis in plants

    PubMed Central

    Paul, Soumitra; Datta, Swapan K.; Datta, Karabi

    2015-01-01

    Small RNAs including micro RNAs (miRNA) play an indispensable role in cell signaling mechanisms. Generally, miRNAs that are 20–24 nucleotides long bind to specific complementary transcripts, attenuating gene expression at the post-transcriptional level or via translational inhibition. In plants, miRNAs have emerged as the principal regulator of various stress responses, including low nutrient availability. It has been reported that miRNAs are vital for maintaining nutrient homeostasis in plants by regulating the expression of transporters that are involved in nutrient uptake and mobilization. The present review highlights the role of various miRNAs in several macro- or micronutrient deficiencies in plants. Understanding the regulation of different transporters by miRNAs will aid in elucidating the underlying molecular signal transduction mechanisms during nutritional stress. Recent findings regarding nutrient related-miRNAs and their gene regulation machinery may delineate a novel platform for improving the nutritional status of cereal grains or crop biofortification programs in the future. PMID:25914709

  16. Cell-free Circulating miRNA Biomarkers in Cancer

    PubMed Central

    Mo, Meng-Hsuan; Chen, Liang; Fu, Yebo; Wang, Wendy; Fu, Sidney W.

    2012-01-01

    Considerable attention and an enormous amount of resources have been dedicated to cancer biomarker discovery and validation. However, there are still a limited number of useful biomarkers available for clinical use. An ideal biomarker should be easily assayed with minimally invasive medical procedures but possess high sensitivity and specificity. Commonly used circulating biomarkers are proteins in serum, most of which require labor-intensive analysis hindered by low sensitivity in early tumor detection. Since the deregulation of microRNA (miRNA) is associated with cancer development and progression, profiling of circulating miRNAs has been used in a number of studies to identify novel minimally invasive miRNA biomarkers. In this review, we discuss the origin of the circulating cell-free miRNAs and their carriers in blood. We summarize the clinical use and function of potentially promising miRNA biomarkers in a variety of different cancers, along with their downstream target genes in tumor initiation and development. Additionally, we analyze some technical challenges in applying miRNA biomarkers to clinical practice. PMID:23074383

  17. Lipid Nanoparticles to Deliver miRNA in Cancer.

    PubMed

    Campani, Virginia; De Rosa, Giuseppe; Misso, Gabriella; Zarone, Mayra R; Grimaldi, Anna

    MicroRNAs (miRNAs) are a class of post-transcriptional gene expression modulators. In the past two decades, over 1500 human miRNAs were discovered. These small non-coding RNAs regulate various biological processes, including cell growth, proliferation, differentiation, and cell death. Thus, miRNAs have been proposed as new therapeutical agents in different multifactorial diseases such as cancer. Since miRNAs therapies represent a great promise, many research studies have been focused on the development of delivery strategies to overcome miRNAs biopharmaceutical issues. Lipid delivery systems are undoubtedly the non-viral carriers most largely investigated due to their biocompatibility, biodegradability, easy production, low toxicity and immunogenicity, possibility to easily modify the carriers for targeting strategies. In this mini-review we provide a rapid and updated overview on the lipid delivery system currently used to deliver miRNAs, pointing out the progresses achieved in the optimization of these nanovectors, which led up to the first clinical trial.

  18. miRNA Expression in Pediatric Failing Human Heart

    PubMed Central

    Stauffer, Brian L.; Russell, Gloria; Nunley, Karin; Miyamoto, Shelley D.; Sucharov, Carmen C.

    2013-01-01

    miRNAs are short regulatory RNAs that can regulate gene expression through interacting with the 3'UTR of target mRNAs. Although the role of miRNAs has been extensively studied in adult human and animal models of heart disease, nothing is known about their expression in pediatric heart failure patients. Different than adults with heart failure, pediatric patients respond well to phosphodiesterase inhibitor (PDEi) treatment, which is safe in the outpatient setting, results in fewer heart failure emergency department visits, fewer cardiac hospital admissions and improved NYHA classification. We have recently shown that the pediatric heart failure patients display a unique molecular profile that is different from adults with heart failure. In this study we show for the first time that pediatric heart failure patients display a unique miRNA profile, and that expression of some miRNAs correlate with response to PDEi treatment. Moreover, we show that expression of Smad4, a potential target for PDEi-regulated miRNAs, is normalized in PDEi-treated patients. Since miRNAs may be used as therapy for human heart failure, our results underscore the importance of defining the molecular characteristics of pediatric heart failure patients, so age-appropriate therapy can be designed for this population. PMID:23333438

  19. Susceptibilities of Different Test Systems from Maize (Zea mays), Poa annua, and Festuca rubra to Herbicides That Inhibit the Enzyme Acetyl-Coenzyme A Carboxylase

    PubMed

    Herbert; Cole; Pallett; Harwood

    1996-06-01

    The susceptibilities of maize (Zea mays cv. Champ) and two graminicide-resistant grass species, Poa annua (annual meadow grass) and Festuca rubra (red fescue), to two aryloxyphenoxypropionates (quizalofop and fluazifop) and a cyclohexanedione (sethoxydim) graminicide were evaluated in leaf blades and isolated chloroplasts, and by assaying acetyl-coenzyme A carboxylase (ACCase) in desalted leaf homogenates. The graminicide resistance of P. annua and F. rubra appeared to be at the level of ACCase. Festuca rubra ACCase was highly insensitive and P. annua ACCase was partially insensitive to the graminicides that were tested. Fatty acid synthesis in isolated maize chloroplasts was more susceptible to inhibition than was ACCase activity from whole leaves. There was a smaller difference in graminicide sensitivity between these two test systems in P. annua. The developmental pattern of ACCase specific activity and its inhibition by quizalofop was measured in maize and P. annua leaf blades. There was an age-dependent increase in the sensitivity of maize leaf ACCase activity to inhibition by quizalofop. Together with the greater susceptibility of chloroplasts compared with leaf homogenates this could imply that a graminicide-insensitive (extrachloroplastic) ACCase isoform is less highly expressed in older leaves. Poa annua ACCase did not significantly alter in sensitivity as leaves aged, consistent with the smaller difference in the level of inhibition between chloroplasts and leaf homogenates in this species. A small pyruvate carboxylase activity was detected in maize leaves after 9 days. By 38 days, when leaves were senescing, pyruvate carboxylase activity predominated over ACCase.

  20. Global Expression Patterns of Three Festuca Species Exposed to Different Doses of Glyphosate Using the Affymetrix GeneChip Wheat Genome Array

    PubMed Central

    Cebeci, Ozge; Budak, Hikmet

    2009-01-01

    Glyphosate has been shown to act as an inhibitor of an aromatic amino acid biosynthetic pathway, while other pathways that may be affected by glyphosate are not known. Cross species hybridizations can provide a tool for elucidating biological pathways conserved among organisms. Comparative genome analyses have indicated a high level of colinearity among grass species and Festuca, on which we focus here, and showed rearrangements common to the Pooideae family. Based on sequence conservation among grass species, we selected the Affymetrix GeneChip Wheat Genome Array as a tool for the analysis of expression profiles of three Festuca (fescue) species with distinctly different tolerances to varying levels of glyphosate. Differences in transcript expression were recorded upon foliar glyphosate application at 1.58 mM and 6.32 mM, representing 5% and 20%, respectively, of the recommended rate. Differences highlighted categories of general metabolic processes, such as photosynthesis, protein synthesis, stress responses, and a larger number of transcripts responded to 20% glyphosate application. Differential expression of genes encoding proteins involved in the shikimic acid pathway could not be identified by cross hybridization. Microarray data were confirmed by RT-PCR and qRT-PCR analyses. This is the first report to analyze the potential of cross species hybridization in Fescue species and the data and analyses will help extend our knowledge on the cellular processes affected by glyphosate. PMID:20182642

  1. The impacts of Phalaris arundinacea (reed canary grass) invasion on wetland plant richness in the Oregon Coast Range, USA, depend on beavers

    USGS Publications Warehouse

    Perkins, T.; Wilson, M.

    2005-01-01

    Invasive plants can threaten diversity and ecosystem function. We examined the relationship between the invasive Phalaris arundinacea (reed canarygrass) and species richness in beaver wetlands in Oregon, USA. Four basins (drainages) were chosen and three sites each of beaver impoundments, unimpounded areas and areas upstream of debris jams were randomly chosen in each basin for further study (n = 36). Analysis of covariance (ANCOVA) showed that the relationship between Phalaris and species richness differed significantly (p = 0.01) by site type. Dam sites (beaver impoundments) exhibited a strong inverse relationship between Phalaris and species richness (bD = a??0.15), with one species lost for each 7% increase in Phalaris cover. In contrast, there was essentially no relationship between Phalaris cover and species richness in jam sites (debris jam impoundments formed by flooding; bJ = +0.01) and unimpounded sites (bU = a??0.03). The cycle of beaver impoundment and abandonment both disrupts the native community and provides an ideal environment for Phalaris, which once established tends to exclude development of herbaceous communities and limits species richness. Because beaver wetlands are a dominant wetland type in the Coast Range, Phalaris invasion presents a real threat to landscape heterogeneity and ecosystem function in the region.

  2. Cd, Cu and Zn mobility in contaminated sediments from an infiltration basin colonized by wild plants: the case of Phalaris arundinacea and Typha latifolia.

    PubMed

    Saulais, M; Bedell, J P; Delolme, C

    2011-01-01

    Infiltration basins are shallow reservoirs in which stormwater is temporarily collected in order to reduce water volume in downstream networks. The settling of stormwater particles leads to a contaminated sediment layer. Wild plants can colonize these basins and can also play a role on the fate of heavy metals either directly by their uptake or indirectly by modification of physico-chemical characteristics of the sediment and therefore by modification of the mobility of heavy metals. The aim of this study, carried out in a vegetated infiltration basin, is to assess Cd, Cu and Zn mobility in two zones colonized by different species, Phalaris arundinacea and Typha latifolia. The study was carried out using three single chemical extractions: CaCl2 for the exchangeable phase, acetate buffer for the acido-soluble fraction and diethylenetriamine-pentaacetic acid (DTPA) for the fraction associated to the organic matter. Zn and Cd are mainly associated to carbonated and organic matter phases of the sediment. Moreover, acetate buffer-extractable Zn contents are strongly correlated to carbonates content in the sediment. DTPA-extractable Cu contents are strongly correlated with organic carbon sediment contents. We have also noted that extractable contents were significantly different between both zones whatever the metal.

  3. Novel miRNA-31 and miRNA-200a-Mediated Regulation of Retinoblastoma Proliferation

    PubMed Central

    Montoya, Vanessa; Fan, Hanli; Bryar, Paul J.; Weinstein, Joanna L.; Mets, Marilyn B.; Feng, Gang; Martin, Joshua; Martin, Alissa; Jiang, Hongmei; Laurie, Nikia A.

    2015-01-01

    Retinoblastoma is the most common intraocular tumor in children. Current management includes broad-based treatments such as chemotherapy, enucleation, laser therapy, or cryotherapy. However, therapies that target specific pathways important for retinoblastoma progression could provide valuable alternatives for treatment. MicroRNAs are short, noncoding RNA transcripts that can regulate the expression of target genes, and their aberrant expression often facilitates disease. The identification of post-transcriptional events that occur after the initiating genetic lesions could further define the rapidly aggressive growth displayed by retinoblastoma tumors. In this study, we used two phenotypically different retinoblastoma cell lines to elucidate the roles of miRNA-31 and miRNA-200a in tumor proliferation. Our approach confirmed that miRNAs-31 and -200a expression is significantly reduced in human retinoblastomas. Moreover, overexpression of these two miRNAs restricts the expansion of a highly proliferative cell line (Y79), but does not restrict the growth rate of a less aggressive cell line (Weri1). Gene expression profiling of miRNA-31 and/or miRNA-200a-overexpressing cells identified differentially expressed mRNAs associated with the divergent response of the two cell lines. This work has the potential to enhance the development of targeted therapeutic approaches for retinoblastoma and improve the efficacy of treatment. PMID:26379276

  4. Entangling Relation of Micro RNA-let7, miRNA-200 and miRNA-125 with Various Cancers.

    PubMed

    Masood, Nosheen; Yasmin, Azra

    2017-01-09

    Involvement of micro RNAs (miRNA) is currently the focus for cancer studies as they effect the post transcriptional expression of different genes. Let-7 family is among the firstly discovered miRNAs that play important role in cell proliferation and dysregulation leading to cell based diseases including cancer. Another family, miRNA-200 prevents transformation of cell to malignant form and tumor formation by interacting with epidermal mesenchymal transition (EMT). Similarly miRNA-125 controls apoptosis and proliferation by affecting multiple genes involved in transcription, immunological defense, resistance against viral and bacterial infections that ultimately leads to cell proliferation, metastasis and finally cancer. All of these micro RNAs are known to be either upregulated or downregulated in various cancers. Current review is focused to elaborate the role of these three families of micro RNAs on different genes that ultimately cause cancer. In conclusion we can say that the miRNAs discussed here are mostly downregulated in various cancers with some exceptions when upregulation of miRNA-125 may be attributed to cancer formation.

  5. Computational identification of miRNAs and their targets in Phaseolus vulgaris.

    PubMed

    Han, J; Xie, H; Kong, M L; Sun, Q P; Li, R Z; Pan, J B

    2014-01-21

    MicroRNAs (miRNAs) are a class of non-coding small RNAs that negatively regulate gene expression at the post-transcriptional level. Although thousands of miRNAs have been identified in plants, limited information is available about miRNAs in Phaseolus vulgaris, despite it being an important food legume worldwide. The high conservation of plant miRNAs enables the identification of new miRNAs in P. vulgaris by homology analysis. Here, 1804 known and unique plant miRNAs from 37 plant species were blast-searched against expressed sequence tag and genomic survey sequence databases to identify novel miRNAs in P. vulgaris. All candidate sequences were screened by a series of miRNA filtering criteria. Finally, we identified 27 conserved miRNAs, belonging to 24 miRNA families. When compared against known miRNAs in P. vulgaris, we found that 24 of the 27 miRNAs were newly discovered. Further, we identified 92 potential target genes with known functions for these novel miRNAs. Most of these target genes were predicted to be involved in plant development, signal transduction, metabolic pathways, disease resistance, and environmental stress response. The identification of the novel miRNAs in P. vulgaris is anticipated to provide baseline information for further research about the biological functions and evolution of miRNAs in P. vulgaris.

  6. Forensic miRNA: potential biomarker for body fluids?

    PubMed

    Silva, Sarah S; Lopes, Cátia; Teixeira, A L; Carneiro de Sousa, M J; Medeiros, R

    2015-01-01

    In forensic investigation, body fluids represent an important support to professionals when detected, collected and correctly identified. Through many years, various approaches were used, namely serology-based methodologies however, their lack of sensitivity and specificity became difficult to set aside. In order to sidetrack the problem, miRNA profiling surged with a real potential to be used to identify evidences like urine, blood, menstrual blood, saliva, semen and vaginal secretions. MiRNAs are small RNA structures with 20-25 nt whose proprieties makes them less prone to degradation processes when compared to mRNA which is extremely important once, in a crime scene, biological evidences might be exposed to several unfavorable environmental factors. Recently, published studies were able to identify some specific miRNAs, however their results were not always reproducible by others which can possibly be the reflection of different workflow strategies for their profiling studies. Given the current blast of interest in miRNAs, it is important to acknowledge potential limitations of miRNA profiling, yet, the lack of such studies are evident. This review pretends to gather all the information to date and assessed a multitude of factors that have a potential aptitude to discrediting miRNA profiling, such as: methodological approaches, environmental factors, physiological conditions, gender, pathologies and samples storage. It can be asserted that much has yet to be made, but we pretend to highlight a potential answer for the ultimate question: Can miRNA profiling be used as the forensic biomarker for body fluids identification?

  7. Classification of various muscular tissues using miRNA profiling.

    PubMed

    Endo, Kosuke; Weng, Huachun; Naito, Yukiko; Sasaoka, Toshikuni; Takahashi, Akio; Fukushima, Yasue; Iwai, Naoharu

    2013-01-01

    MicroRNAs (miRNAs) are endogenous small RNAs of 18-23 nucleotides that regulate gene expression. Recently, plasma miRNAs have been investigated as biomarkers for various diseases. In the present study, we explored whether miRNA expression profiling of various muscle cells may be useful for the diagnosis of various diseases involving muscle necrosis. miRNA expression profiling was assessed by miRNA array and real-time reverse-transcriptase polymerase chain reaction by using a reverse primer of a stem loop structure. Profiling of various muscle cells of mouse, including cardiac muscles, skeletal muscles, and vascular and visceral smooth muscles, indicated that profiling of miR-1, miR-133a, miR-133b, miR-145, miR-206, miR-208a, miR-208b, and miR499 were adequate to discriminate muscle cells. miR-145 was remarkably highly expressed in smooth muscles. miR-208a and miR-499 were highly expressed in cardiomyocytes. miR-133a was highly expressed in fast-twitch skeletal muscles. miR-206 and miR-208b were expressed in the slow-twitch skeletal muscles, and they can likely discriminate fast- and slow-twitch types of skeletal muscle cells. We observed that brown fat adipose cells had an miRNA expression profile very similar to those of skeletal muscle cells in the mouse. Plasma concentrations of miR-133a and miR-145 were extremely useful in diagnosing skeletal muscle necrosis in a mouse model of Duchenne muscular dystrophy and colon smooth muscle necrosis in a rat ischemic colitis model, respectively. In the present study, we investigated the miRNA expression profiles of various muscular tissues. Our results suggest that expression profiling would be useful for the diagnosis of various diseases such as muscular necrosis.

  8. SymB and SymC, two membrane associated proteins, are required for Epichloë festucae hyphal cell-cell fusion and maintenance of a mutualistic interaction with Lolium perenne.

    PubMed

    Green, Kimberly A; Becker, Yvonne; Tanaka, Aiko; Takemoto, Daigo; Fitzsimons, Helen L; Seiler, Stephan; Lalucque, Hervé; Silar, Philippe; Scott, Barry

    2017-02-01

    Cell-cell fusion in fungi is required for colony formation, nutrient transfer and signal transduction. Disruption of genes required for hyphal fusion in Epichloë festucae, a mutualistic symbiont of Lolium grasses, severely disrupts the host interaction phenotype. They examined whether symB and symC, the E. festucae homologs of Podospora anserina self-signaling genes IDC2 and IDC3, are required for E. festucae hyphal fusion and host symbiosis. Deletion mutants of these genes were defective in hyphal cell fusion, formed intra-hyphal hyphae, and had enhanced conidiation. SymB-GFP and SymC-mRFP1 localize to plasma membrane, septa and points of hyphal cell fusion. Plants infected with ΔsymB and ΔsymC strains were severely stunted. Hyphae of the mutants colonized vascular bundles, were more abundant than wild type in the intercellular spaces and formed intra-hyphal hyphae. Although these phenotypes are identical to those previously observed for cell wall integrity MAP kinase mutants no difference was observed in the basal level of MpkA phosphorylation or its cellular localization in the mutant backgrounds. Both genes contain binding sites for the transcription factor ProA. Collectively these results show that SymB and SymC are key components of a conserved signaling network for E. festucae to maintain a mutualistic symbiotic interaction within L. perenne. © 2016 The Authors. Molecular Microbiology Published by John Wiley & Sons Ltd.

  9. miRNAs of two medically important mosquito species: Aedes aegypti and Anopheles stephensi

    PubMed Central

    Hu, Wanqi; Crisione, Frank; Liang, Shaohui; Tu, Zhijian

    2014-01-01

    MicroRNAs (miRNAs) are endogenous, single-stranded small RNAs that have important regulatory functions at the post-transcriptional level. Here, we characterize miRNAs in two divergent mosquito species, Aedes aegypti and Anopheles stephensi, through deep sequencing of small RNAs spanning all developmental stages. We discovered eight novel miRNAs in Ae. aegypti and 20 novel miRNAs in An. stephensi, which enabled the first systematic analysis of miRNA evolution in mosquitos. We traced the phylogenetic history of all miRNAs in both species and report a rate of 0.055–0.13 miRNA net gain per million years. Most novel miRNAs originate de novo. Duplications that produced miRNA clusters and families are more common in Ae. aegypti than in An. stephensi. We also identified arm-switch as a source of new miRNAs. Expression profile analysis identified mosquito-specific miRNAs that showed strong stage-specific expression in one or both lineages. For example, the aae-miR-2941/2946 family represents the most abundant maternally-deposited and zygotically transcribed miRNAs in Ae. aegypti. miR-2943 is a highly expressed zygotic miRNA in both Ae. aegypti and An. stephensi. Such information provides the basis to study the function of these miRNAs in biology common to all mosquitos or unique to one particular lineage. PMID:25420875

  10. The miRNA biogenesis in marine bivalves

    PubMed Central

    Rosani, Umberto; Pallavicini, Alberto

    2016-01-01

    Small non-coding RNAs include powerful regulators of gene expression, transposon mobility and virus activity. Among the various categories, mature microRNAs (miRNAs) guide the translational repression and decay of several targeted mRNAs. The biogenesis of miRNAs depends on few gene products, essentially conserved from basal to higher metazoans, whose protein domains allow specific interactions with dsRNA. Here, we report the identification of key genes responsible of the miRNA biogenesis in 32 bivalves, with particular attention to the aquaculture species Mytilus galloprovincialis and Crassostrea gigas. In detail, we have identified and phylogenetically compared eight evolutionary conserved proteins: DROSHA, DGCR8, EXP5, RAN, DICER TARBP2, AGO and PIWI. In mussels, we recognized several other proteins participating in the miRNA biogenesis or in the subsequent RNA silencing. According to digital expression analysis, these genes display low and not inducible expression levels in adult mussels and oysters whereas they are considerably expressed during development. As miRNAs play an important role also in the antiviral responses, knowledge on their production and regulative effects can shed light on essential molecular processes and provide new hints for disease prevention in bivalves. PMID:26989613

  11. Use of miRNAs as Biomarkers in Sepsis

    PubMed Central

    Dumache, Raluca; Rogobete, Alexandru Florin; Bedreag, Ovidiu Horea; Sarandan, Mirela; Cradigati, Alina Carmen; Papurica, Marius; Dumbuleu, Corina Maria; Nartita, Radu; Sandesc, Dorel

    2015-01-01

    Sepsis is one of the most common causes of death in critical patients. Severe generalized inflammation, infections, and severe physiological imbalances significantly decrease the survival rate with more than 50%. Moreover, monitoring, evaluation, and therapy management often become extremely difficult for the clinician in this type of patients. Current methods of diagnosing sepsis vary based especially on the determination of biochemical-humoral markers, such as cytokines, components of the complement, and proinflammatory and anti-inflammatory compounds. Recent studies highlight the use of new biomarkers for sepsis, namely, miRNAs. miRNAs belong to a class of small, noncoding RNAs with an approximate content of 19–23 nucleotides. Following biochemical and physiological imbalances, the expression of miRNAs in blood or other body fluids changes significantly. Moreover, its stability, specificity, and selectivity make miRNAs ideal candidates for sepsis biomarkers. In conclusion, we can affirm that stable species of circulating miRNAs represent potential biomarkers for monitoring the evolution of sepsis. PMID:26221578

  12. miRNA analysis in pancreatic cancer: the Dartmouth experience.

    PubMed

    Abreu, Francine B de; Liu, Xiaoying; Tsongalis, Gregory J

    2017-05-01

    Pancreatic cancer is considered one of the most lethal cancers being the fourth leading cause of cancer deaths in adults in the United States because of the lack of early signs and symptoms and the lack of early detection. Pancreatic ductal adenocarcinoma (PDAC) is the most common histological type among pancreatic cancers, representing 80%-90% of all solid tumors of the pancreas. The majority of PDAC develops from three precursor lesions: pancreatic intraepithelial neoplasia, intraductual papillary mucinous neoplasm and mucinous cystic neoplasm. Although histologic tissue evaluation remains the gold standard for diagnosis, endoscopic ultrasound-guided fine needle aspiration has become the preferred modality for obtaining pathologic confirmation. At Dartmouth-Hitchcock Medical Center (DHMC),we have developed and validated a microRNA (miRNA) panel for patients with pancreatic diseases that can be used in association with the gold standard method for diagnosis. miRNAs have an important role in biological processes, such as apoptosis, metabolism, cell growth and differentiation. In cancer, miRNAs can be classified as either oncogenic or tumor suppressor according to their function in the carcinogenic process. In this study, we describe the expression of many miRNA in benign and malignant pancreatic tissues as well as their clinical significance. For this reason, miRNAs have been considered potential biomarkers of pancreatic diseases that could potentially contribute to an early diagnosis, predict disease progression, accurately monitor disease, contribute to better treatment strategies and reduce mortality by improving disease management.

  13. Microprocessor activity controls differential miRNA biogenesis In Vivo.

    PubMed

    Conrad, Thomas; Marsico, Annalisa; Gehre, Maja; Orom, Ulf Andersson

    2014-10-23

    In miRNA biogenesis, pri-miRNA transcripts are converted into pre-miRNA hairpins. The in vivo properties of this process remain enigmatic. Here, we determine in vivo transcriptome-wide pri-miRNA processing using next-generation sequencing of chromatin-associated pri-miRNAs. We identify a distinctive Microprocessor signature in the transcriptome profile from which efficiency of the endogenous processing event can be accurately quantified. This analysis reveals differential susceptibility to Microprocessor cleavage as a key regulatory step in miRNA biogenesis. Processing is highly variable among pri-miRNAs and a better predictor of miRNA abundance than primary transcription itself. Processing is also largely stable across three cell lines, suggesting a major contribution of sequence determinants. On the basis of differential processing efficiencies, we define functionality for short sequence features adjacent to the pre-miRNA hairpin. In conclusion, we identify Microprocessor as the main hub for diversified miRNA output and suggest a role for uncoupling miRNA biogenesis from host gene expression.

  14. miRNA expression profile in multicellular breast cancer spheroids.

    PubMed

    Mandujano-Tinoco, Edna Ayerim; Garcia-Venzor, Alfredo; Muñoz-Galindo, Laura; Lizarraga-Sanchez, Floria; Favela-Orozco, Andrei; Chavez-Gutierrez, Edwin; Krötzsch, Edgar; Salgado, Rosa M; Melendez-Zajgla, Jorge; Maldonado, Vilma

    2017-10-01

    Multicellular Tumor Spheroids develop a heterogeneous micromilieu and different cell populations, thereby constituting a cancer model with intermediate characteristics between in vitro bi-dimensional cultures and in vivo tumors. Multicellular Tumor Spheroids also acquire tumor aggressiveness features due to transcription modulation of coding and non-coding RNA. Utilizing microarray analyses, we evaluated the microRNAs expression profile in MCF-7 breast cancer cells cultured as Multicellular Tumor Spheroids. The expression data was used to predict associated cellular and molecular functions using different software tools. The biological importance of two dysregulated miRNAs (miR-221-3p and miR-187) was studied by functional assays. Finally, the clinical relevance of these dysregulated miRNAs was explored using previously reported data. Thirty-three dysregulated microRNAs were found in MCF-7 Multicellular Tumor Spheroids. miRNA expression changes were closely linked with growth, proliferation, and cell development. miRNA-221-3p and miR-187 were implicated in the acquisition of migration/invasion capacities, sensitivity to the deprivation of growth factors, cell cycle phase regulation, and cell death. A panel of 5 miRNAs, including miR-187, showed a good predictive value in discriminating between low and high-risk groups of breast cancer. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Serum profiling identifies novel muscle miRNA and cardiomyopathy-related miRNA biomarkers in Golden Retriever muscular dystrophy dogs and Duchenne muscular dystrophy patients.

    PubMed

    Jeanson-Leh, Laurence; Lameth, Julie; Krimi, Soraya; Buisset, Julien; Amor, Fatima; Le Guiner, Caroline; Barthélémy, Inès; Servais, Laurent; Blot, Stéphane; Voit, Thomas; Israeli, David

    2014-11-01

    Duchenne muscular dystrophy (DMD) is a fatal, X-linked neuromuscular disease that affects 1 boy in 3500 to 5000 boys. The golden retriever muscular dystrophy dog is the best clinically relevant DMD animal model. Here, we used a high-thoughput miRNA sequencing screening for identification of candidate serum miRNA biomarkers in golden retriever muscular dystrophy dogs. We confirmed the dysregulation of the previously described muscle miRNAs, miR-1, miR-133, miR-206, and miR-378, and identified a new candidate muscle miRNA, miR-95. We identified two other classes of dysregulated serum miRNAs in muscular dystrophy: miRNAs belonging to the largest known miRNA cluster that resides in the imprinting DLK1-DIO3 genomic region and miRNAs associated with cardiac disease, including miR-208a, miR-208b, and miR-499. No simple correlation was identified between serum levels of cardiac miRNAs and cardiac functional parameters in golden retriever muscular dystrophy dogs. Finally, we confirmed a dysregulation of miR-95, miR-208a, miR-208b, miR-499, and miR-539 in a small cohort of DMD patients. Given the interspecies conservation of miRNAs and preliminary data in DMD patients, these newly identified dysregulated miRNAs are strong candidate biomarkers for DMD patients.

  16. Human milk miRNAs primarily originate from the mammary gland resulting in unique miRNA profiles of fractionated milk

    PubMed Central

    Alsaweed, Mohammed; Lai, Ching Tat; Hartmann, Peter E.; Geddes, Donna T.; Kakulas, Foteini

    2016-01-01

    Human milk (HM) contains regulatory biomolecules including miRNAs, the origin and functional significance of which are still undetermined. We used TaqMan OpenArrays to profile 681 mature miRNAs in HM cells and fat, and compared them with maternal peripheral blood mononuclear cells (PBMCs) and plasma, and bovine and soy infant formulae. HM cells and PBMCs (292 and 345 miRNAs, respectively) had higher miRNA content than HM fat and plasma (242 and 219 miRNAs, respectively) (p < 0.05). A strong association in miRNA profiles was found between HM cells and fat, whilst PBMCs and plasma were distinctly different to HM, displaying marked inter-individual variation. Considering the dominance of epithelial cells in mature milk of healthy women, these results suggest that HM miRNAs primarily originate from the mammary epithelium, whilst the maternal circulation may have a smaller contribution. Our findings demonstrate that unlike infant formulae, which contained very few human miRNA, HM is a rich source of lactation-specific miRNA, which could be used as biomarkers of the performance and health status of the lactating mammary gland. Given the recently identified stability, uptake and functionality of food- and milk-derived miRNA in vivo, HM miRNA are likely to contribute to infant protection and development. PMID:26854194

  17. Use of serum-circulating miRNA profiling for the identification of breast cancer biomarkers.

    PubMed

    Mar-Aguilar, Fermín; Rodríguez-Padilla, Cristina; Reséndez-Pérez, Diana

    2014-01-01

    MicroRNAs (miRNAs) are important regulatory molecules involved in disease pathogenesis. miRNAs are very stable in bodily fluids and can be detected in serum, plasma, saliva, and urine, among other fluids. Several studies have demonstrated the usefulness of serum miRNAs as potential biomarkers for detecting and monitoring cancer progression. Here, we describe in detail the experiment protocol we used to profile miRNA expression in the serum of breast cancer patients, including RNA extraction from serum, RT-qPCR quantification, and analysis of the deregulated miRNAs. Detection of circulating miRNAs may be a useful, noninvasive diagnostic tool for breast cancer.

  18. Insights into MiRNA Regulation of the Human Glycome

    PubMed Central

    Kasper, Brian T.; Koppolu, Sujeethraj; Mahal, Lara K.

    2014-01-01

    Glycosylation is an intricate process requiring the coordinated action of multiple proteins, including glycosyltransferases, glycosidases, sugar nucleotide transporters and trafficking proteins. Work by several groups points to a role for microRNA (miRNA) in controlling the levels of specific glycosyltransferases involved in cancer, neural migration and osteoblast formation. Recent work in our laboratory suggests that miRNA are a principal regulator of the glycome, translating genomic information into the glycocode through tuning of enzyme levels. Herein we overlay predicted miRNA regulation of glycosylation related genes (glycogenes) onto maps of the common N-linked and O-linked glycan biosynthetic pathways to identify key regulatory nodes of the glycome. Our analysis provides insights into glycan regulation and suggests that at the regulatory level, glycogenes are non-redundant. PMID:24463102

  19. miRNAs in mtDNA-less cell mitochondria

    PubMed Central

    Dasgupta, N; Peng, Y; Tan, Z; Ciraolo, G; Wang, D; Li, R

    2015-01-01

    The novel regulation mechanism in mtDNA-less cells was investigated. Very low mtDNA copy in mtDNA-less 206 ρ° cells was identified. But no 13 mitochondria-specific proteins were translated in 206 ρ° cells. Their mitochondrial respiration complexes V, III and II were 86.5, 29.4 and 49.6% of 143B cells, respectively. Complexes I and IV completely lack in 206 ρ° cells. Non-mitochondrial respiration to generate ATP in 206 ρ° cells was discovered. The expression levels of some mitochondrial RNAs including 12S rRNA, COX1, COX2, COX3, ND4 and ND5 were low. However, ND1, ND3 and Cyto b were not expressed in 206 ρ° cells. Unequal transcription of mitochondrial RNAs indicated the post-transcriptional cleavage and processing mechanisms in the regulation of mitochondrial gene expression in 206 ρ° cells. MicroRNAs (miRNAs) may modulate these mitochondrial RNA expression in these cells. RNA-induced silencing complex indeed within 206 ρ° cell mitochondria indicated miRNAs in 206 ρ° cell mitochondria. miRNA profile in mtDNA-less 206 ρ° cells was studied by next-generation sequencing of small RNAs. Several mitochondria-enriched miRNAs such as miR-181c-5p and miR-146a-5p were identified in 206 ρ° cell mitochondria. miR-181c-5p and miR-146a-5p had 23 and 19 potential targets on mitochondrial RNAs respectively, and these two miRNAs had multiple targets on mitochondria-associated messenger RNAs encoded by nuclear genes. These data provided the first direct evidence that miRNAs were imported into mitochondria and regulated mitochondrial RNA expressions. PMID:27551440

  20. Down-regulation of miRNA-148a and miRNA-625-3p in colorectal cancer is associated with tumor budding.

    PubMed

    Baltruskeviciene, Edita; Schveigert, Diana; Stankevicius, Vaidotas; Mickys, Ugnius; Zvirblis, Tadas; Bublevic, Jaroslav; Suziedelis, Kestutis; Aleknavicius, Eduardas

    2017-09-01

    MiRNAs are often deregulated in colorectal cancer and might function as tumor suppressors or as oncogenes. They participate in controlling key signaling pathways involved in proliferation, invasion and apoptosis and may serve as prognostic and predictive markers. In this study we aimed to evaluate the role of miRNA-148a and miRNA-625-3p in metastatic colorectal cancer. Fifty-four patients with a first-time diagnosed CRC receiving FOLFOX ± Bevacizumab were involved in the study. Tumor samples underwent routine pathology examination including evaluation for tumor budding and KRAS. MiRNA-148a and miRNA-625-3p expression analysis was done by RT-PCR. Associations between expression of both miRNAs and clinico-pathological factors, treatment outcomes and survival were analyzed. Both miRNA-148a and miRNA-625-3p were down-regulated in the tumors compared to normal colonic mucosa. Significantly lower expression of both miRNAs was noticed in tumors with budding phenomenon compared to tumors without it (median values of miRNA-148a were 0.314 and 0.753 respectively, p = 0.011, and 0.404 and 0.620 respectively for miRNA-625-3p, p = 0.036). Significantly lower expression of miRNA-625-3p was detected in rectal tumors, compared to tumors in the colon (median 0.390 and 0.665 respectively, p = 0.037). Progression free survival was significantly lower in patients with high miRNA-148a expression (6 and 9 months respectively, p = 0.033), but there were no significant differences in PFS for miRNA-625-3p and in overall survival for both miRNAs. There was a significant relationship between low miRNA-148a and miRNA-625-3p expression and tumor budding, which is thought to represent epithelial-mesenchymal transition. Both studied miRNAs may be associated with a more aggressive phenotype and could be the potential prognostic and predictive biomarkers in CRC. Further investigation is needed to confirm miRNAs involvement in EMT, and their prognostic and predictive value.

  1. Tilletia vankyi, a new species of reticulate-spored bunt fungus with non-conjugating basidiospores infecting species of Festuca and Lolium.

    PubMed

    Carris, Lori M; Castlebury, Lisa A; Huang, Guoming; Alderman, Steve C; Luo, Jiafeng; Bao, Xiaodong

    2007-12-01

    A bunt fungus, exhibiting a spore germination pattern unique to known reticulate-spored species of Tilletia was found infecting plants in seed production fields of Festuca rubra ssp. rubra (red fescue) and F. rubra ssp. fallax (Chewing's fescue) in Oregon, and in seed lots of Lolium perenne (perennial ryegrass) from Australia and Germany. Teliospores germinated to form 20-40 uninucleate, non-conjugating basidiospores, and colonies derived from single basidiospores produced teliospores in culture. In inoculation studies using single basidiospore colonies, perennial ryegrass and L. perenne ssp. multiflorum (Italian or annual ryegrass) were infected. A phylogenetic analysis, based on ITS region rDNA, eukaryotic translation elongation factor 1 alpha, and the second largest subunit of RNA polymerase II demonstrated that the fescue and ryegrass bunts are conspecific, and distinct from known species of Tilletia.

  2. Hypothalamic miRNAs: emerging roles in energy balance control.

    PubMed

    Schneeberger, Marc; Gomez-Valadés, Alicia G; Ramirez, Sara; Gomis, Ramon; Claret, Marc

    2015-01-01

    The hypothalamus is a crucial central nervous system area controlling appetite, body weight and metabolism. It consists in multiple neuronal types that sense, integrate and generate appropriate responses to hormonal and nutritional signals partly by fine-tuning the expression of specific batteries of genes. However, the mechanisms regulating these neuronal gene programmes in physiology and pathophysiology are not completely understood. MicroRNAs (miRNAs) are key regulators of gene expression that recently emerged as pivotal modulators of systemic metabolism. In this article we will review current evidence indicating that miRNAs in hypothalamic neurons are also implicated in appetite and whole-body energy balance control.

  3. Dynamics of 45S rDNA sites in the cell cycle: fragile sites and chromosomal stability in Lolium and Festuca.

    PubMed

    Rocha, L C; Silva, G A; Bustamante, F O; Silveira, R A D; Mittlemann, A; Techio, V H

    2017-01-23

    Analyses carried out with fluorescence in situ hybridization (FISH) in C-metaphases of the Lolium-Festuca complex have shown the occurrence of spontaneous fragile sites (FSs) in 45S rDNA regions. FSs are expressed as gaps but they do not result in breaks or chromosomal fragments in these species. These gaps have high DNA condensation observed as thin chromatin fibers that connect the apparent segments of the fragile chromosome, allowing for genomic stability. Assessing the behavior of these regions in the cell cycle of Lolium and Festuca species may lead to a better understanding of the dynamics that preserve stability during cell division. Furthermore, it is interesting to track the dynamics of chromosomes bearing 45S rDNA sites in the cell cycle as well as to observe the expression of FSs with no effect of the mitotic block. We observed variation in both the number and size of 45S FISH signals from the S/G2 phases of interphase and from prophase to anaphase where gaps in 45S rDNA sites also were observed. The change in the degree of condensation of the 45S site begins in the S/G2 phase and appears to be related to the transcriptional demand. Taking into account that the number of 45S rDNA sites tends to be re-established when cells reach telophase, we suggest that the chromatin fiber goes back to the normal condensation level to the anaphase (after segregation), allowing for the approximation of chromosome segments and ensuring dynamics that favor the genomic stability of these species.

  4. Seminal miRNA Relationship with Apoptotic Markers and Oxidative Stress in Infertile Men with Varicocele

    PubMed Central

    Rashed, Laila A.; Nabil, Nashaat I.; Osman, Ihab; Mostafa, Rashad; Farag, Mohamed

    2016-01-01

    Aim. This study aimed to assess seminal miRNA relationship with seminal apoptotic markers and oxidative stress (OS) in infertile men associated with varicocele (Vx). Methods. In all, 220 subjects were divided into the following groups: fertile normozoospermic men, fertile normozoospermic men with Vx, infertile oligoasthenoteratozoospermic (OAT) men without Vx, and infertile OAT men with Vx. They were subjected to history taking, clinical examination, and semen analysis. In their semen, the following were estimated: miRNA-122, miRNA-181a, and miRNA-34c5 using quantitative real-time PCR, apoptotic markers (BAX, BCL2) protein expression, and OS markers [malondialdehyde (MDA) and glutathione peroxidase (GPx)]. Results. The mean levels of seminal miRNA-122, miRNA-181a, and miRNA-34c5 were significantly reduced in infertile OAT men with Vx compared with other groups coupled with Vx grade and Vx bilaterality. Seminal miRNA-122, miRNA-181a, and miRNA-34c5 were positively correlated with sperm concentration, total sperm motility, sperm normal morphology, seminal GPx, and seminal BCL2 and negatively correlated with seminal MDA and seminal BAX. Conclusions. Seminal miRNA-122, miRNA-181a, and miRNA-34c5 are decreased in infertile OAT men with Vx associated with increased Vx grade and Vx bilaterality. In addition, they are positively correlated with sperm parameters and negatively correlated with OS, apoptotic markers. PMID:28105423

  5. Impacts of Whole-Genome Triplication on MIRNA Evolution in Brassica rapa.

    PubMed

    Sun, Chao; Wu, Jian; Liang, Jianli; Schnable, James C; Yang, Wencai; Cheng, Feng; Wang, Xiaowu

    2015-11-01

    MicroRNAs (miRNAs) are a class of short non-coding, endogenous RNAs that play essential roles in eukaryotes. Although the influence of whole-genome triplication (WGT) on protein-coding genes has been well documented in Brassica rapa, little is known about its impacts on MIRNAs. In this study, through generating a comprehensive annotation of 680 MIRNAs for B. rapa, we analyzed the evolutionary characteristics of these MIRNAs from different aspects in B. rapa. First, while MIRNAs and genes show similar patterns of biased distribution among subgenomes of B. rapa, we found that MIRNAs are much more overretained than genes following fractionation after WGT. Second, multiple-copy MIRNAs show significant sequence conservation than that of single-copy MIRNAs, which is opposite to that of genes. This indicates that increased purifying selection is acting upon these highly retained multiple-copy MIRNAs and their functional importance over singleton MIRNAs. Furthermore, we found the extensive divergence between pairs of miRNAs and their target genes following the WGT in B. rapa. In summary, our study provides a valuable resource for exploring MIRNA in B. rapa and highlights the impacts of WGT on the evolution of MIRNA.

  6. Nanoparticle-mediated delivery of therapeutic genes: focus on miRNA therapeutics.

    PubMed

    Muthiah, Muthunarayanan; Park, In-Kyu; Cho, Chong-Su

    2013-09-01

    Micro RNAs (miRNA) are 21 - 23 nucleotides long and regulate the expression of coding genes by binding imperfectly with their 3' UTR region. The miRNA profile is altered in pathological processes, making miRNAs good targets for drug therapy. Restoration of down-regulated miRNA or inhibition of overexpressed miRNA to return miRNA to its normal state is the basis of miRNA-based therapy. This review focuses on nanocarriers used for the delivery of miRNA that confer physical stability to the unstable RNA structure, protect the RNA from nuclease degradation and aid in effective silencing of target genes. The necessity of the nanocarrier for the delivery of the miRNA is emphasized and the recent research on liposome-, metal- and polymer-mediated miRNA delivery for the inhibition or replacement of the disease-related miRNA is summarized. The size, charge and surface properties of nanocarriers have to be tuned to ensure effective and safe delivery of the miRNA in clinical practice. The immune responses related to the nanocarriers and the double-stranded nucleotide delivery remain to be addressed. Also, the binding of miRNAs to non-specific targets has to be studied in more detail because miRNAs have multiple targets due to partial binding unlike siRNA.

  7. Monitoring the Spatiotemporal Activities of miRNAs in Small Animal Models Using Molecular Imaging Modalities

    PubMed Central

    Baril, Patrick; Ezzine, Safia; Pichon, Chantal

    2015-01-01

    MicroRNAs (miRNAs) are a class of small non-coding RNAs that regulate gene expression by binding mRNA targets via sequence complementary inducing translational repression and/or mRNA degradation. A current challenge in the field of miRNA biology is to understand the functionality of miRNAs under physiopathological conditions. Recent evidence indicates that miRNA expression is more complex than simple regulation at the transcriptional level. MiRNAs undergo complex post-transcriptional regulations such miRNA processing, editing, accumulation and re-cycling within P-bodies. They are dynamically regulated and have a well-orchestrated spatiotemporal localization pattern. Real-time and spatio-temporal analyses of miRNA expression are difficult to evaluate and often underestimated. Therefore, important information connecting miRNA expression and function can be lost. Conventional miRNA profiling methods such as Northern blot, real-time PCR, microarray, in situ hybridization and deep sequencing continue to contribute to our knowledge of miRNA biology. However, these methods can seldom shed light on the spatiotemporal organization and function of miRNAs in real-time. Non-invasive molecular imaging methods have the potential to address these issues and are thus attracting increasing attention. This paper reviews the state-of-the-art of methods used to detect miRNAs and discusses their contribution in the emerging field of miRNA biology and therapy. PMID:25749473

  8. PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs

    PubMed Central

    2013-01-01

    The regulation of intragenic miRNAs by their own intronic promoters is one of the open problems of miRNA biogenesis. Here, we describe PROmiRNA, a new approach for miRNA promoter annotation based on a semi-supervised statistical model trained on deepCAGE data and sequence features. We validate our results with existing annotation, PolII occupancy data and read coverage from RNA-seq data. Compared to previous methods PROmiRNA increases the detection rate of intronic promoters by 30%, allowing us to perform a large-scale analysis of their genomic features, as well as elucidate their contribution to tissue-specific regulation. PROmiRNA can be downloaded from http://promirna.molgen.mpg.de. PMID:23958307

  9. The Role of miRNA in Papillary Thyroid Cancer in the Context of miRNA Let-7 Family

    PubMed Central

    Perdas, Ewelina; Stawski, Robert; Nowak, Dariusz; Zubrzycka, Maria

    2016-01-01

    Papillary thyroid carcinoma (PTC) is the most common endocrine malignancy. RET/PTC rearrangement is the most common genetic modification identified in this category of cancer, increasing proliferation and dedifferentiation by the activation of the RET/PTC-RAS-BRAF-MAPK-ERK signaling pathway. Recently, let-7 miRNA was found to reduce RAS levels, acting as a tumor suppressor gene. Circulating miRNA profiles of the let-7 family may be used as novel noninvasive diagnostic, prognostic, treatment and surveillance markers for PTC. PMID:27314338

  10. Identification and Characterization of miRNA Transcriptome in Potato by High-Throughput Sequencing

    PubMed Central

    Zhang, Runxuan; Marshall, David; Bryan, Glenn J.; Hornyik, Csaba

    2013-01-01

    Micro RNAs (miRNAs) represent a class of short, non-coding, endogenous RNAs which play important roles in post-transcriptional regulation of gene expression. While the diverse functions of miRNAs in model plants have been well studied, the impact of miRNAs in crop plant biology is poorly understood. Here we used high-throughput sequencing and bioinformatics analysis to analyze miRNAs in the tuber bearing crop potato (Solanum tuberosum). Small RNAs were analysed from leaf and stolon tissues. 28 conserved miRNA families were found and potato-specific miRNAs were identified and validated by RNA gel blot hybridization. The size, origin and predicted targets of conserved and potato specific miRNAs are described. The large number of miRNAs and complex population of small RNAs in potato suggest important roles for these non-coding RNAs in diverse physiological and metabolic pathways. PMID:23437348

  11. miRNA therapeutics: a new class of drugs with potential therapeutic applications in the heart.

    PubMed

    Bernardo, Bianca C; Ooi, Jenny Y Y; Lin, Ruby C Y; McMullen, Julie R

    2015-01-01

    miRNAs are small non-coding RNAs (ncRNAs), which regulate gene expression. Here, the authors describe the contribution of miRNAs to cardiac biology and disease. They discuss various strategies for manipulating miRNA activity including antisense oligonucleotides (antimiRs, blockmiRs), mimics, miRNA sponges, Tough Decoys and miRNA mowers. They review developments in chemistries (e.g., locked nucleic acid) and modifications (sugar, 'ZEN', peptide nucleic acids) and miRNA delivery tools (viral vectors, liposomes, nanoparticles, pHLIP). They summarize potential miRNA therapeutic targets for heart disease based on preclinical studies. Finally, the authors review current progress of miRNA therapeutics in clinical development for HCV and cancer, and discuss challenges that will need to be overcome for similar therapies to enter the clinic for patients with cardiac disease.

  12. MiRNAs from cotton roots infected with Meloidogyne incognita

    USDA-ARS?s Scientific Manuscript database

    The molecular activities associated with the resistance of Upland cotton (Gossypium hirsutum L.) to the root-knot nematode (RKN) are largely unknown. Small RNAs or microRNAs (miRNA), a well-conserved gene regulatory system, have an important role in plant development, stress responses, and epigeneti...

  13. Scaffolds for Artificial miRNA Expression in Animal Cells.

    PubMed

    Calloni, Raquel; Bonatto, Diego

    2015-10-01

    Artificial miRNAs (amiRNAs) are molecules that have been developed to promote gene silencing in a similar manner to naturally occurring miRNAs. amiRNAs are generally constructed by replacing the mature miRNA sequence in the pre-miRNA stem-loop with a sequence targeting a gene of interest. These molecules offer an interesting alternative to silencing approaches that are based on shRNAs and siRNAs because they present the same efficiency as these options and are less cytotoxic. amiRNAs have mostly been applied to gene knockdown in plants; they have been examined to a lesser extent in animal cells. Therefore, this article reviews the amiRNAs that have been developed for animal cells and focuses on the miRNA scaffolds that can already be applied to construct the artificial counterparts, as well as on the different approaches that have been described to promote amiRNA expression and silencing efficiency. Furthermore, the availability of amiRNA libraries and other tools that can be used to design and construct these molecules is briefly discussed, along with an overview of the therapeutic applications for which amiRNAs have already been evaluated.

  14. Challenges in using circulating miRNAs as cancer biomarkers.

    PubMed

    Tiberio, Paola; Callari, Maurizio; Angeloni, Valentina; Daidone, Maria Grazia; Appierto, Valentina

    2015-01-01

    In the last years, circulating miRNAs have emerged as a new class of promising cancer biomarkers. Independent studies have shown the feasibility of using these small RNAs as tools for the diagnosis and prognosis of different types of malignancies as well as for predicting and possibly monitoring treatment response. However, despite an initial enthusiasm for their possible clinical application, widespread inconsistencies have been observed among the studies, and miRNA-based tools still represent the object of research within clinical diagnostic or treatment protocols. The poor overlap of results could be explained, at least in part, by preanalytical and analytical variables and donor-related factors that could generate artefacts, impairing an accurate quantification of circulating miRNAs. In fact, critical issues are represented by nonuniform sample choice, handling, and processing, as well as by blood cell contamination in sample preparation and lack of consensus for data normalization. In this review, we address the potential technical biases and individual-related parameters that can influence circulating miRNA studies' outcome. The exciting potential of circulating miRNAs as cancer biomarkers could confer an important advance in the disease management, but their clinical significance might not be proven without a global consensus of procedures and standardized protocols for their accurate detection.

  15. miRNA modulation of the cellular stress response.

    PubMed

    Babar, Imran A; Slack, Frank J; Weidhaas, Joanne B

    2008-04-01

    Cellular stress responses are potent and dynamic, allowing cells to effectively counteract diverse stresses. These pathways are crucial not only for maintaining normal cellular homeostasis, but also for protecting cells from what would otherwise lead to their demise. A novel class of genes, termed miRNAs, has recently been implicated in the cellular stress response. For example, it has been demonstrated that a cardiac-specific miRNA that is not required for normal development is requisite for a normal cardiac stress response in mice. In addition, we have found that a miRNA family is able to modulate the cellular response to cytotoxic cancer treatment both in vitro and in vivo. In this review, we will discuss these and other important developments in the field. In particular, we will focus on studies that have linked miRNAs to the genotoxic stress response and will suggest how this connection may be both important for our understanding of biology and pertinent for the development of novel cancer therapies.

  16. Challenges in Using Circulating miRNAs as Cancer Biomarkers

    PubMed Central

    Tiberio, Paola; Callari, Maurizio; Angeloni, Valentina; Daidone, Maria Grazia; Appierto, Valentina

    2015-01-01

    In the last years, circulating miRNAs have emerged as a new class of promising cancer biomarkers. Independent studies have shown the feasibility of using these small RNAs as tools for the diagnosis and prognosis of different types of malignancies as well as for predicting and possibly monitoring treatment response. However, despite an initial enthusiasm for their possible clinical application, widespread inconsistencies have been observed among the studies, and miRNA-based tools still represent the object of research within clinical diagnostic or treatment protocols. The poor overlap of results could be explained, at least in part, by preanalytical and analytical variables and donor-related factors that could generate artefacts, impairing an accurate quantification of circulating miRNAs. In fact, critical issues are represented by nonuniform sample choice, handling, and processing, as well as by blood cell contamination in sample preparation and lack of consensus for data normalization. In this review, we address the potential technical biases and individual-related parameters that can influence circulating miRNA studies' outcome. The exciting potential of circulating miRNAs as cancer biomarkers could confer an important advance in the disease management, but their clinical significance might not be proven without a global consensus of procedures and standardized protocols for their accurate detection. PMID:25874226

  17. Revisiting absorption of dietary plant-based miRNAs

    USDA-ARS?s Scientific Manuscript database

    We are continuing to test the hypothesis that consumption of genetic information in plant-based foods can modulate animal metabolism. Several studies (1,2,3) have failed to replicate the finding (4) that a rice miRNA survives digestion, enters circulation in copy numbers rivaling endogenous RNAs, an...

  18. [Web server for prediction of miRNAs and their precursors and binding sites].

    PubMed

    Vorozheykin, P S; Titov, I I

    2015-01-01

    A microRNA (miRNA) is a small noncoding RNA molecule about 22 nucleotides in length. The paper describes a web server for predicting miRNAs and their precursors and binding sites. The predictions are based on either sequence similarity to known miRNAs of 223 organisms or context-structural hidden Markov models. It has been shown that the proposed methods of prediction of human miRNAs and pre-miRNAs outperform the existing ones in accuracy. The average deviation of predicted 5'-ends of human miRNAs from actual positions is 3.13 nt in the case of predicting one pair of complementary miRNAs (miRNA-miRNA* duplex). A useful option for our application is the prediction of an additional miRNA pair. In this mode, the pairs closest to actual miRNA deviate by 1.61 nt on average. The proposed method also shows good performance in predicting mouse miRNAs. Binding sites for miRNAs are predicted by two known approaches based on complementarity and thermodynamic stability of the miRNA-mRNA duplex and on a new approach, which takes into account miRNAs competition for the site. The role of the secondary structure in miRNA processing is considered. The web server is available at http://wwwmgs.bionet.nsc.ru/mgs/programs/rnaanalys/.

  19. Increased miRNA-22 expression sensitizes esophageal squamous cell carcinoma to irradiation

    PubMed Central

    Wang, Xiao-chun; Zhang, Zhu-Bo; Wang, Yue-Ying; Wu, Hong-Ying; Li, De-Guan; Meng, Ai-Min; Fan, Fei-Yue

    2013-01-01

    miRNA-22 was previously reported to be a tumor suppressor. The aim of this study was to explore the expression and function of miRNA-22 in esophageal squamous cell carcinoma (ESCC). Expression of miRNA-22 in 100 ESCC tissues was examined by q-PCR. The correlation between miRNA-22 level and clinicopathological features was analyzed using SPSS16.0 statistical software. Moreover, the effect of miRNA-22 expression on radiosensitivity of ESCC cells was examined. miRNA-22 expression decreased in ESCC tissues, and statistical analyses showed that the expression of miRNA-22 was associated with the stage of clinical classification. No correlation was found between miRNA-22 expression and the overall survival of ESCC patients. However, significant positive correlation was found between miRNA-22 expression and the survival of patients who received radiotherapy (P < 0.05). Increased expression of miRNA-22 sensitized ESCC cells to γ-ray radiation and promoted the apoptosis of ESCC cells induced by γ-ray radiation. Increased expression level of miRNA-22 had effects on Rad51 expression after irradiation. These results demonstrate for the first time that decreased miRNA-22 expression correlates with increased radiotherapy resistance of ESCC, and that this effect is mediated, at least in part, by the Rad51 pathway. PMID:23188185

  20. Clinical potential of miRNA-221 as a novel prognostic biomarker for hepatocellular carcinoma.

    PubMed

    Chen, Fan; Li, Xin-Feng; Fu, Dong-Sheng; Huang, Jian-Guo; Yang, Shun-E

    2017-01-01

    miRNA-221 is one of the over 700 kinds of currently known microRNAs (miRNAs) and is up-regulated in multiple tumors, suggesting that it may be a potential carcinogenic miRNA. Few studies have explored the relationship between miRNA-221 and hepatocellular carcinoma (HCC). We performed real-time quantitative polymerase chain reaction (qPCR) to detect miRNA-221 expression in HCC and para-carcinoma tissues and to explore the relationship between abnormal expression of miRNA-221 and clinicopathological features of HCC patients. miRNA-221 expression was significantly higher in HCC tissues than in adjacent tissues (P < 0.001). We analyzed the relationship between miRNA-221 expression level and clinicopathological characteristics of HCC patients. Our results suggested that miRNA-221 expression level was closely related to tumor stage (P = 0.012), number of tumor nodes (P = 0.018), and microvascular invasion (P = 0.010) in HCC patients. The results of survival analysis suggested that HCC patients with up-regulated miRNA-221 expression had a shorter survival time. The high miRNA-221 expression indicates the poor prognosis of HCC patients; thus, miRNA-221 can be regarded an important molecular marker for HCC prognosis.

  1. MYCN-targeting miRNAs are predominantly downregulated during MYCN‑driven neuroblastoma tumor formation.

    PubMed

    Beckers, Anneleen; Van Peer, Gert; Carter, Daniel R; Mets, Evelien; Althoff, Kristina; Cheung, Belamy B; Schulte, Johannes H; Mestdagh, Pieter; Vandesompele, Jo; Marshall, Glenn M; De Preter, Katleen; Speleman, Frank

    2015-03-10

    MYCN is a transcription factor that plays key roles in both normal development and cancer. In neuroblastoma, MYCN acts as a major oncogenic driver through pleiotropic effects regulated by multiple protein encoding genes as well as microRNAs (miRNAs). MYCN activity is tightly controlled at the level of transcription and protein stability through various mechanisms. Like most genes, MYCN is further controlled by miRNAs, but the full complement of all miRNAs implicated in this process has not been determined through an unbiased approach. To elucidate the role of miRNAs in regulation of MYCN, we thus explored the MYCN-miRNA interactome to establish miRNAs controlling MYCN expression levels. We combined results from an unbiased and genome-wide high-throughput miRNA target reporter screen with miRNA and mRNA expression data from patients and a murine neuroblastoma progression model. We identified 29 miRNAs targeting MYCN, of which 12 miRNAs are inversely correlated with MYCN expression or activity in neuroblastoma tumor tissue. The majority of MYCN-targeting miRNAs in neuroblastoma showed a decrease in expression during murine MYCN-driven neuroblastoma tumor development. Therefore, we provide evidence that MYCN-targeting miRNAs are preferentially downregulated in MYCN-driven neuroblastoma, suggesting that MYCN negatively controls the expression of these miRNAs, to safeguard its expression.

  2. Deregulation of the miRNAs Expression in Cervical Cancer: Human Papillomavirus Implications

    PubMed Central

    Gómez-Gómez, Yazmín; Organista-Nava, Jorge; Gariglio, Patricio

    2013-01-01

    MicroRNAs (miRNAs) are a class of small non coding RNAs of 18–25 nucleotides in length. The temporal or short-lived expression of the miRNAs modulates gene expression post transcriptionally. Studies have revealed that miRNAs deregulation correlates and is involved with the initiation and progression of human tumors. Cervical cancer (CC) displays notably increased or decreased expression of a large number of cellular oncogenic or tumor suppressive miRNAs, respectively. However, understanding the potential role of miRNAs in CC is still limited. In CC, the high-risk human papillomaviruses (HR-HPVs) infection can affect the miRNAs expression through oncoprotein E6 and E7 that contribute to viral pathogenesis, although other viral proteins might also be involved. This deregulation in the miRNAs expression has an important role in the hallmarks of CC. Interestingly, the miRNA expression profile in CC can discriminate between normal and tumor tissue and the extraordinary stability of miRNAs makes it suitable to serve as diagnostic and prognostic biomarkers of cancer. In this review, we will summarize the role of the HR-HPVs in miRNA expression, the role of miRNAs in the hallmarks of CC, and the use of miRNAs as potential prognostic biomarkers in CC. PMID:24490161

  3. miRNA and Degradome Sequencing Reveal miRNA and Their Target Genes That May Mediate Shoot Growth in Spur Type Mutant “Yanfu 6”

    PubMed Central

    Song, Chunhui; Zhang, Dong; Zheng, Liwei; Zhang, Jie; Zhang, Baojuan; Luo, Wenwen; Li, Youmei; Li, Guangfang; Ma, Juanjuan; Han, Mingyu

    2017-01-01

    The spur-type growth habit in apple trees is characterized by short internodes, increased number of fruiting spurs, and compact growth that promotes flowering and facilitates management practices, such as pruning. The molecular mechanisms responsible for regulating spur-type growth have not been elucidated. In the present study, miRNAs and the expression of their potential target genes were evaluated in shoot tips of “Nagafu 2” (CF) and spur-type bud mutation “Yanfu 6” (YF). A total of 700 mature miRNAs were identified, including 202 known apple miRNAs and 498 potential novel miRNA candidates. A comparison of miRNA expression in CF and YF revealed 135 differentially expressed genes, most of which were downregulated in YF. YF also had lower levels of GA, ZR, IAA, and ABA hormones, relative to CF. Exogenous applications of GA promoted YF shoot growth. Based on the obtained results, a regulatory network involving plant hormones, miRNA, and their potential target genes is proposed for the molecular mechanism regulating the growth of YF. miRNA164, miRNA166, miRNA171, and their potential targets, and associated plant hormones, appear to regulate shoot apical meristem (SAM) growth. miRNA159, miRNA167, miRNA396, and their potential targets, and associated plant hormones appear to regulate cell division and internode length. This study provides a foundation for further studies designed to elucidate the mechanism underlying spur-type apple architecture. PMID:28424721

  4. Multiplexed miRNA Fluorescence In Situ Hybridization for Formalin-Fixed Paraffin-Embedded Tissues

    PubMed Central

    Renwick, Neil; Cekan, Pavol; Bognanni, Claudia; Tuschl, Thomas

    2015-01-01

    Multiplexed miRNA fluorescence in situ hybridization (miRNA FISH) is an advanced method for visualizing differentially expressed miRNAs, together with other reference RNAs, in archival tissues. Some miRNAs are excellent disease biomarkers due to their abundance and cell-type specificity. However, these short RNA molecules are difficult to visualize due to loss by diffusion, probe mishybridization, and signal detection and signal amplification issues. Here, we describe a reliable and adjustable method for visualizing and normalizing miRNA signals in formalin-fixed paraffin-embedded (FFPE) tissue sections. PMID:25218385

  5. Centenarians maintain miRNA biogenesis pathway while it is impaired in octogenarians.

    PubMed

    Borrás, C; Serna, E; Gambini, J; Inglés, M; Vina, J

    2017-07-25

    Centenarians but not octogenarians up regulate the expression of miRNAs, as we previously reported. We have looked into miRNA biogenesis. We show that RNA POL II, DROSHA, EXPORTIN 5 and DICER, are up-regulated in centenarians compared with octogenarians. Furthermore, factors involved in the control of these miRNAs biogenesis genes are also up-regulated in centenarians. Therefore, the up-regulation of miRNA expression in centenarians can be explained in part because miRNA biogenesis pathway is depressed in octogenarians (ordinary aging) while it is maintained in centenarians (extraordinary aging). Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Multiplexed miRNA fluorescence in situ hybridization for formalin-fixed paraffin-embedded tissues.

    PubMed

    Renwick, Neil; Cekan, Pavol; Bognanni, Claudia; Tuschl, Thomas

    2014-01-01

    Multiplexed miRNA fluorescence in situ hybridization (miRNA FISH) is an advanced method for visualizing differentially expressed miRNAs, together with other reference RNAs, in archival tissues. Some miRNAs are excellent disease biomarkers due to their abundance and cell-type specificity. However, these short RNA molecules are difficult to visualize due to loss by diffusion, probe mishybridization, and signal detection and signal amplification issues. Here, we describe a reliable and adjustable method for visualizing and normalizing miRNA signals in formalin-fixed paraffin-embedded (FFPE) tissue sections.

  7. Differential expression of miRNA between the monolayer and three dimensional cells after ionizing radiation

    NASA Astrophysics Data System (ADS)

    Pan, Dong; Ren, Zhenxin; Hu, Burong

    2014-04-01

    We detect the expression of miRNA in 2D and 3D human lung epithelial cells (3KT). And our primary experimental results showed that more miRNA in 3D 3KT down regulated than in 2D 3KT cells after not only X-ray but also C-beam irradiation using the miRNA chip assay. Meanwhile, X-ray induced more significantly differential expression of miRNA when the relative expression value of miRNA in 3D cells were compared to 2D cells after irradiation.

  8. A Burst of miRNA Innovation in the Early Evolution of Butterflies and Moths.

    PubMed

    Quah, Shan; Hui, Jerome H L; Holland, Peter W H

    2015-05-01

    MicroRNAs (miRNAs) are involved in posttranscriptional regulation of gene expression. Because several miRNAs are known to affect the stability or translation of developmental regulatory genes, the origin of novel miRNAs may have contributed to the evolution of developmental processes and morphology. Lepidoptera (butterflies and moths) is a species-rich clade with a well-established phylogeny and abundant genomic resources, thereby representing an ideal system in which to study miRNA evolution. We sequenced small RNA libraries from developmental stages of two divergent lepidopterans, Cameraria ohridella (Horse chestnut Leafminer) and Pararge aegeria (Speckled Wood butterfly), discovering 90 and 81 conserved miRNAs, respectively, and many species-specific miRNA sequences. Mapping miRNAs onto the lepidopteran phylogeny reveals rapid miRNA turnover and an episode of miRNA fixation early in lepidopteran evolution, implying that miRNA acquisition accompanied the early radiation of the Lepidoptera. One lepidopteran-specific miRNA gene, miR-2768, is located within an intron of the homeobox gene invected, involved in insect segmental and wing patterning. We identified cubitus interruptus (ci) as a likely direct target of miR-2768, and validated this suppression using a luciferase assay system. We propose a model by which miR-2768 modulates expression of ci in the segmentation pathway and in patterning of lepidopteran wing primordia.

  9. Identification of miRNAs and miRNA-mediated regulatory pathways in Carica papaya.

    PubMed

    Liang, Gang; Li, Yang; He, Hua; Wang, Fang; Yu, Diqiu

    2013-10-01

    Plant microRNAs (miRNAs) post-transcriptionally regulate target gene expression to modulate growth and development and biotic and abiotic stress responses. By analyzing small RNA deep sequencing data in combination with the genome sequence, we identified 75 conserved miRNAs and 11 novel miRNAs. Their target genes were also predicted. For most conserved miRNAs, the miRNA-target pairs were conserved across plant species. In addition to these conserved miRNA-target pairs, we also identified some papaya-specific miRNA-target regulatory pathways. Both miR168 and miR530 target the Argonaute 1 gene, indicating a second autoregulatory mechanism for miRNA regulation. A non-conserved miRNA was mapped within an intron of Dicer-like 1 (DCL1), suggesting a conserved homeostatic autoregulatory mechanism for DCL1 expression. A 21-nt miRNA triggers secondary siRNA production from its target genes, nucleotide-binding site leucine-rich repeat protein genes. Certain phased-miRNAs were processed from their conserved miRNA precursors, indicating a putative miRNA evolution mechanism. In addition, we identified a Carica papaya-specific miRNA that targets an ethylene receptor gene, implying its function in the ethylene signaling pathway. This work will also advance our understanding of miRNA functions and evolution in plants.

  10. Regulation of the alkaloid biosynthesis by miRNA in opium poppy.

    PubMed

    Boke, Hatice; Ozhuner, Esma; Turktas, Mine; Parmaksiz, Iskender; Ozcan, Sebahattin; Unver, Turgay

    2015-04-01

    Opium poppy (Papaver somniferum) is an important medicinal plant producing benzylisoquinoline alkaloids (BIA). MicroRNAs (miRNAs) are endogenous small RNAs (sRNAs) of approximately 21 nucleotides. They are noncoding, but regulate gene expression in eukaryotes. Although many studies have been conducted on the identification and functions of plant miRNA, scarce researches on miRNA regulation of alkaloid biosynthesis have been reported. In this study, a total of 316 conserved and 11 novel miRNAs were identified in opium poppy using second-generation sequencing and direct cloning. Tissue-specific regulation of miRNA expression was comparatively analysed by miRNA microarray assays. A total of 232 miRNAs were found to be differentially expressed among four tissues. Likewise, 1469 target transcripts were detected using in silico and experimental approaches. The Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that miRNA putatively regulates carbohydrate metabolism and genetic-information processing. Additionally, miRNA target transcripts were mostly involved in response to stress against various factors and secondary-metabolite biosynthesis processes. Target transcript identification analyses revealed that some of the miRNAs might be involved in BIA biosynthesis, such as pso-miR13, pso-miR2161 and pso-miR408. Additionally, three putatively mature miRNA sequences were predicted to be targeting BIA-biosynthesis genes. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  11. Loop nucleotides control primary and mature miRNA function in target recognition and repression

    PubMed Central

    Yue, Si-Biao; Deis Trujillo, Robin; Tang, Yujie; O'Gorman, William E

    2011-01-01

    MicroRNA (miRNA) genes produce three major RNA products; primary (pri-), precursor (pre-), and mature miRNAs. Each product includes sequences complementary to cognate targets, thus they all can in principle interact with the targets. In a recent study we showed that pri-miRNAs play a direct role in target recognition and repression in the absence of functional mature miRNAs. Here we examined the functional contribution of pri-miRNAs in target regulation when full-length functional miRNAs are present. We found that pri-let-7 loop nucleotides control the production of the 5′ end of mature miRNAs and modulate the activity of the miRNA gene. This insight enabled us to modulate biogenesis of functional mature miRNAs and dissect the causal relationships between mature miRNA biogenesis and target repression. We demonstrate that both pri- and mature miRNAs can contribute to target repression and that their contributions can be distinguished by the differences between the pri- and mature miRNAs' sensitivity to bind to the first seed nucleotide. Our results demonstrate that the regulatory information encoded in the pri-/pre-miRNA loop nucleotides controls the activities of pri-miRNAs and mature let-7 by influencing pri-miRNA and target complex formation and the fidelity of mature miRNA seed generation. PMID:22142974

  12. Hydroxytyrosol supplementation modulates the expression of miRNAs in rodents and in humans.

    PubMed

    Tomé-Carneiro, Joao; Crespo, María Carmen; Iglesias-Gutierrez, Eduardo; Martín, Roberto; Gil-Zamorano, Judit; Tomas-Zapico, Cristina; Burgos-Ramos, Emma; Correa, Carlos; Gómez-Coronado, Diego; Lasunción, Miguel A; Herrera, Emilio; Visioli, Francesco; Dávalos, Alberto

    2016-08-01

    Dietary microRNAs (miRNAs) modulation could be important for health and wellbeing. Part of the healthful activities of polyphenols might be due to a modulation of miRNAs' expression. Among the most biologically active polyphenols, hydroxytyrosol (HT) has never been studied for its actions on miRNAs. We investigated whether HT could modulate the expression of miRNAs in vivo. We performed an unbiased intestinal miRNA screening in mice supplemented (for 8 weeks) with nutritionally relevant amounts of HT. HT modulated the expression of several miRNAs. Analysis of other tissues revealed consistent HT-induced modulation of only few miRNAs. Also, HT administration increased triglycerides levels. Acute treatment with HT and in vitro experiments provided mechanistic insights. The HT-induced expression of one miRNA was confirmed in healthy volunteers supplemented with HT in a randomized, double-blind and placebo-controlled trial. HT consumption affects specific miRNAs' expression in rodents and humans. Our findings suggest that the modulation of miRNAs' action through HT consumption might partially explain its healthful activities and might be pharmanutritionally exploited in current therapies targeting endogenous miRNAs. However, the effects of HT on triglycerides warrant further investigations.

  13. Identification of Dirofilaria immitis miRNA using illumina deep sequencing

    PubMed Central

    2013-01-01

    The heartworm Dirofilaria immitis is the causative agent of cardiopulmonary dirofilariosis in dogs and cats, which also infects a wide range of wild mammals and humans. The complex life cycle of D. immitis with several developmental stages in its invertebrate mosquito vectors and its vertebrate hosts indicates the importance of miRNA in growth and development, and their ability to regulate infection of mammalian hosts. This study identified the miRNA profiles of D. immitis of zoonotic significance by deep sequencing. A total of 1063 conserved miRNA candidates, including 68 anti-sense miRNA (miRNA*) sequences, were predicted by computational methods and could be grouped into 808 miRNA families. A significant bias towards family members, family abundance and sequence nucleotides was observed. Thirteen novel miRNA candidates were predicted by alignment with the Brugia malayi genome. Eleven out of 13 predicted miRNA candidates were verified by using a PCR-based method. Target genes of the novel miRNA candidates were predicted by using the heartworm transcriptome dataset. To our knowledge, this is the first report of miRNA profiles in D. immitis, which will contribute to a better understanding of the complex biology of this zoonotic filarial nematode and the molecular regulation roles of miRNA involved. Our findings may also become a useful resource for small RNA studies in other filarial parasitic nematodes. PMID:23331513

  14. General principals of miRNA biogenesis and regulation in the brain.

    PubMed

    O'Carroll, Dónal; Schaefer, Anne

    2013-01-01

    MicroRNAs (miRNAs) are small, noncoding RNAs that mediate posttranscriptional gene suppression in a sequence-specific manner. The ability of a single miRNA species to target multiple messenger RNAs (mRNAs) makes miRNAs exceptionally important regulators of various cellular functions. The regulatory capacity of miRNAs is increased further by the miRNA ability to suppress gene expression using multiple mechanisms that range from translational inhibition to mRNA degradation. The high miRNA diversity multiplied by the large number of individual miRNA targets generates a vast regulatory RNA network than enables flexible control of mRNA expression. The gene-regulatory capacity and diversity of miRNAs is particularly valuable in the brain, where functional specialization of neurons and persistent flow of information requires constant neuronal adaptation to environmental cues. In this review we will summarize the current knowledge about miRNA biogenesis and miRNA expression regulation with a focus on the role of miRNAs in the mammalian nervous system.

  15. A Burst of miRNA Innovation in the Early Evolution of Butterflies and Moths

    PubMed Central

    Quah, Shan; Hui, Jerome H.L.; Holland, Peter W.H.

    2015-01-01

    MicroRNAs (miRNAs) are involved in posttranscriptional regulation of gene expression. Because several miRNAs are known to affect the stability or translation of developmental regulatory genes, the origin of novel miRNAs may have contributed to the evolution of developmental processes and morphology. Lepidoptera (butterflies and moths) is a species-rich clade with a well-established phylogeny and abundant genomic resources, thereby representing an ideal system in which to study miRNA evolution. We sequenced small RNA libraries from developmental stages of two divergent lepidopterans, Cameraria ohridella (Horse chestnut Leafminer) and Pararge aegeria (Speckled Wood butterfly), discovering 90 and 81 conserved miRNAs, respectively, and many species-specific miRNA sequences. Mapping miRNAs onto the lepidopteran phylogeny reveals rapid miRNA turnover and an episode of miRNA fixation early in lepidopteran evolution, implying that miRNA acquisition accompanied the early radiation of the Lepidoptera. One lepidopteran-specific miRNA gene, miR-2768, is located within an intron of the homeobox gene invected, involved in insect segmental and wing patterning. We identified cubitus interruptus (ci) as a likely direct target of miR-2768, and validated this suppression using a luciferase assay system. We propose a model by which miR-2768 modulates expression of ci in the segmentation pathway and in patterning of lepidopteran wing primordia. PMID:25576364

  16. miRNAs Are Involved in Determining the Improved Vigor of Autotetrapoid Chrysanthemum nankingense

    PubMed Central

    Dong, Bin; Wang, Haibin; Song, Aiping; Liu, Tao; Chen, Yun; Fang, Weimin; Chen, Sumei; Chen, Fadi; Guan, Zhiyong; Jiang, Jiafu

    2016-01-01

    Many plant species are autopolyploid, a condition frequently associated with improvements in both vegetative and reproductive vigor. The possible contribution of miRNAs to this improvement was investigated by characterizing the miRNA content of a diploid and an autotetraploid form of Chrysanthemum nankingense. 162 and 161 known miRNA sequences were identified in 2x and 4x library. The length of 22 and 25 nt was predominant in diploid. However, 21 and 24 nt showed dominance in autotetraploid. It seems likely that autopolyploidization have had an immediate effect the distribution of miRNAs. In addition, the abundance of the miRNAs differed markedly between the two ploidy levels and contributed to their targets diversity. A number of target genes associated with miRNAs play important roles in growth and development. The conclusion was that some miRNAs likely make a contribution to the vigor displayed by autotetraploid C. nankingense. PMID:27733854

  17. The potential of miRNAs for diagnosis, treatment and monitoring of breast cancer.

    PubMed

    Bertoli, Gloria; Cava, Claudia; Castiglioni, Isabella

    2016-01-01

    Dysregulation of microRNAs (miRNAs) has a fundamental role in the initiation, development and progression of several human cancers, including breast cancer (BC), since strong evidence has shown that miRNAs can regulate the expression of oncogenes or tumor suppressor genes. A possible role of miRNAs in the diagnosis in BC has been demonstrated. As miRNAs has been found stable in biofluids, extracellular multiple miRNA profiles have been proposed as diagnostic tools, showing better diagnostic performance than individual miRNAs in BC. In this paper, based on the current literature, we present the role of microRNAs in the diagnosis and therapy monitoring of BC. Furthermore, we report new miRNA-based drugs that could be turned into promising therapy for BC, alone or in combination with conventional therapy. We also discuss how extracellular miRNAs could become new, easily accessible, affordable, non-invasive tools for BC patients.

  18. miRNAs Are Involved in Determining the Improved Vigor of Autotetrapoid Chrysanthemum nankingense.

    PubMed

    Dong, Bin; Wang, Haibin; Song, Aiping; Liu, Tao; Chen, Yun; Fang, Weimin; Chen, Sumei; Chen, Fadi; Guan, Zhiyong; Jiang, Jiafu

    2016-01-01

    Many plant species are autopolyploid, a condition frequently associated with improvements in both vegetative and reproductive vigor. The possible contribution of miRNAs to this improvement was investigated by characterizing the miRNA content of a diploid and an autotetraploid form of Chrysanthemum nankingense. 162 and 161 known miRNA sequences were identified in 2x and 4x library. The length of 22 and 25 nt was predominant in diploid. However, 21 and 24 nt showed dominance in autotetraploid. It seems likely that autopolyploidization have had an immediate effect the distribution of miRNAs. In addition, the abundance of the miRNAs differed markedly between the two ploidy levels and contributed to their targets diversity. A number of target genes associated with miRNAs play important roles in growth and development. The conclusion was that some miRNAs likely make a contribution to the vigor displayed by autotetraploid C. nankingense.

  19. miRNA Repertoires of Demosponges Stylissa carteri and Xestospongia testudinaria

    PubMed Central

    Aranda, Manuel; Ravasi, Timothy

    2016-01-01

    MicroRNAs (miRNAs) are small regulatory RNAs that are involved in many biological process in eukaryotes. They play a crucial role in modulating genetic expression of their targets, which makes them integral components of transcriptional regulatory networks. As sponges (phylum Porifera) are commonly considered the most basal metazoan, the in-depth capture of miRNAs from these organisms provides additional clues to the evolution of miRNA families in metazoans. Here, we identified the core proteins involved in the biogenesis of miRNAs, and obtained evidence for bona fide miRNA sequences for two marine sponges Stylissa carteri and Xestospongia testudinaria (11 and 19 respectively). Our analysis identified several miRNAs that are conserved amongst demosponges, and revealed that all of the novel miRNAs identified in these two species are specific to the class Demospongiae. PMID:26871907

  20. Analysis of miRNA market trends reveals hotspots of research activity.

    PubMed

    Oosta, Gary; Razvi, Enal

    2012-04-01

    We have conducted an analysis of the miRNA research marketplace by evaluating the publication trends in the field. In this article, we present the results of our analysis which reveals that hotspots exist in terms of research activities in the miRNA space--these hotspots illustrate the areas in the miRNA research space where specific miRNAs have been extensively studied, and other areas that represent new territory. We frame these data into the context of areas of opportunity for miRNA content harvest versus segments of opportunity for the development of research tools. Also presented in this article are the primary market data from online surveys we have performed with researchers involved in miRNA research around the world. Taken together, these data frame the current state of the miRNA marketplace and provide niches of opportunity for new entrants into this space.

  1. miRClassify: an advanced web server for miRNA family classification and annotation.

    PubMed

    Zou, Quan; Mao, Yaozong; Hu, Lingling; Wu, Yunfeng; Ji, Zhiliang

    2014-02-01

    MicroRNA (miRNA) family is a group of miRNAs that derive from the common ancestor. Normally, members from the same miRNA family have similar physiological functions; however, they are not always conserved in primary sequence or secondary structure. Proper family prediction from primary sequence will be helpful for accurate identification and further functional annotation of novel miRNA. Therefore, we introduced a novel machine learning-based web server, the miRClassify, which can rapidly identify miRNA from the primary sequence and classify it into a miRNA family regardless of similarity in sequence and structure. Additionally, the medical implication of the miRNA family is also provided when it is available in PubMed. The web server is accessible at the link http://datamining.xmu.edu.cn/software/MIR/home.html.

  2. Three new species of eriophyoid mites from grass hosts in Croatia

    USDA-ARS?s Scientific Manuscript database

    Three new species of grass-feeding eriophyid mites are described from Croatia: Acaralox croatiae n. sp., inhabiting purple moorgrass, Molinia coerulea (L.) Moench; Aculodes festucae n. sp., inhabiting tall fescue, Festuca arundinacea Schreb.; and Aculodes sylvatici n. sp., inhabiting false brome, Br...

  3. Effects of Wastewater and Sewage Sludge on the Growth and Chemical Composition of Turfgrass.

    DTIC Science & Technology

    1978-11-01

    of Kentucky bluegrass (Poa pratensis L. var. ’Merion’), red fescue ( Festuca rubra L. var. ’Pennlawn’) and annual ryegrass. The mixtures were grown in...turfgrass mixtures. A mixture of tall fescue ( Festuca arundinacea Scheb var. ’K-31’) and annual ryegrass (Lolium multiflorum Lam.) was compared to a mixture

  4. miRNA genes of an invasive vector mosquito, Aedes albopictus.

    PubMed

    Gu, Jinbao; Hu, Wanqi; Wu, Jinya; Zheng, Peiming; Chen, Maoshan; James, Anthony A; Chen, Xiaoguang; Tu, Zhijian

    2013-01-01

    Aedes albopictus, a vector of Dengue and Chikungunya viruses, is a robust invasive species in both tropical and temperate environments. MicroRNAs (miRNAs) regulate gene expression and biological processes including embryonic development, innate immunity and infection. While a number of miRNAs have been discovered in some mosquitoes, no comprehensive effort has been made to characterize them from different developmental stages from a single species. Systematic analysis of miRNAs in Ae. albopictus will improve our understanding of its basic biology and inform novel strategies to prevent virus transmission. Between 10-14 million Illumina sequencing reads per sample were obtained from embryos, larvae, pupae, adult males, sugar-fed and blood-fed adult females. A total of 119 miRNA genes represented by 215 miRNA or miRNA star (miRNA*) sequences were identified, 15 of which are novel. Eleven, two, and two of the newly-discovered miRNA genes appear specific to Aedes, Culicinae, and Culicidae, respectively. A number of miRNAs accumulate predominantly in one or two developmental stages and the large number that showed differences in abundance following a blood meal likely are important in blood-induced mosquito biology. Gene Ontology (GO) analysis of the targets of all Ae. albopictus miRNAs provides a useful starting point for the study of their functions in mosquitoes. This study is the first systematic analysis of miRNAs based on deep-sequencing of small RNA samples of all developmental stages of a mosquito species. A number of miRNAs are related to specific physiological states, most notably, pre- and post-blood feeding. The distribution of lineage-specific miRNAs is consistent with mosquito phylogeny and the presence of a number of Aedes-specific miRNAs likely reflects the divergence between the Aedes and Culex genera.

  5. Regulation of Gene Expression in Plants through miRNA Inactivation

    PubMed Central

    Zhang, Yuanji; Ziegler, Todd E.; Roberts, James K.; Heck, Gregory R.

    2011-01-01

    Eukaryotic organisms possess a complex RNA-directed gene expression regulatory network allowing the production of unique gene expression patterns. A recent addition to the repertoire of RNA-based gene regulation is miRNA target decoys, endogenous RNA that can negatively regulate miRNA activity. miRNA decoys have been shown to be a valuable tool for understanding the function of several miRNA families in plants and invertebrates. Engineering and precise manipulation of an endogenous RNA regulatory network through modification of miRNA activity also affords a significant opportunity to achieve a desired outcome of enhanced plant development or response to environmental stresses. Here we report that expression of miRNA decoys as single or heteromeric non-cleavable microRNA (miRNA) sites embedded in either non-protein-coding or within the 3′ untranslated region of protein-coding transcripts can regulate the expression of one or more miRNA targets. By altering the sequence of the miRNA decoy sites, we were able to attenuate miRNA inactivation, which allowed for fine regulation of native miRNA targets and the production of a desirable range of plant phenotypes. Thus, our results demonstrate miRNA decoys are a flexible and robust tool, not only for studying miRNA function, but also for targeted engineering of gene expression in plants. Computational analysis of the Arabidopsis transcriptome revealed a number of potential miRNA decoys, suggesting that endogenous decoys may have an important role in natural modulation of expression in plants. PMID:21731706

  6. Evolutionary comparisons of miRNA regulation system in six model organisms.

    PubMed

    Mao, Xiaofan; Li, Li; Cao, Yicheng

    2014-02-01

    miRNAs are a class of endogenous small non-coding regulatory RNAs, that can mediate the transcriptional gene silencing as well as gene expression activation. miRNAs, which are found in a wide range of species, participate in cell differentiation, proliferation, development, apoptosis, tumorigenesis, metabolism, immune system, and signaling pathways. Here, we focused on the relationship between evolution and the miRNA system, with an emphasis on both miRNAs and their target genes. Six species from the evolutionary ladder were selected as a focus of this study. Public data were retrieved and combined to compare miRNAs abundance, miRNA families, molecular functions of target genes, biological processes of target genes, protein families of target gene products, transcription factors regulated by the miRNAs, signaling pathways and tissues across the six species. We found that the expansion rate of miRNAs was significantly higher compared to other genes in human evolution. Newborn miRNA families, which were quantitatively larger than dead miRNA families, seem to be closely related to the species complexity and tissue specificity. Additionally, miRNAs in higher order species were more likely to target genes related to signaling and the immune system, while miRNAs from lower order species preferred to target genes related to the embryonic development process, reproduction and growth. Meanwhile, miRNA systems displayed diversity in regulating transcription factors, signaling pathways and tissues. Our research suggested that the miRNA system might promote evolution, especially in higher species.

  7. Diet and lifestyle factors associated with miRNA expression in colorectal tissue

    PubMed Central

    Slattery, Martha L; Herrick, Jennifer S; Mullany, Lila E; Stevens, John R; Wolff, Roger K

    2017-01-01

    MicroRNAs (miRNAs) are small non-protein-coding RNA molecules that regulate gene expression. Diet and lifestyle factors have been hypothesized to be involved in the regulation of miRNA expression. In this study it was hypothesized that diet and lifestyle factors are associated with miRNA expression. Data from 1,447 cases of colorectal cancer to evaluate 34 diet and lifestyle variables using miRNA expression in normal colorectal mucosa as well as for differential expression between paired carcinoma and normal tissue were used. miRNA data were obtained using an Agilent platform. Multiple comparisons were adjusted for using the false discovery rate q-value. There were 250 miRNAs differentially expressed between carcinoma and normal colonic tissue by level of carbohydrate intake and 198 miRNAs differentially expressed by the level of sucrose intake. Of these miRNAs, 166 miRNAs were differentially expressed for both carbohydrate intake and sucrose intake. Ninety-nine miRNAs were differentially expressed by the level of whole grain intake in normal colonic mucosa. Level of oxidative balance score was associated with 137 differentially expressed miRNAs between carcinoma and paired normal rectal mucosa. Additionally, 135 miRNAs were differentially expressed in colon tissue based on recent NSAID use. Other dietary factors, body mass index, waist and hip circumference, and long-term physical activity levels did not alter miRNA expression after adjustment for multiple comparisons. These results suggest that diet and lifestyle factors regulate miRNA level. They provide additional support for the influence of carbohydrate, sucrose, whole grains, NSAIDs, and oxidative balance score on colorectal cancer risk. PMID:28053552

  8. The Values of Coronary Circulating miRNAs in Patients with Atrial Fibrillation

    PubMed Central

    Xu, Guiyu; Cui, Yuxia; Jia, Zhenghua; Yue, Yunan; Yang, Shuixiang

    2016-01-01

    The mechanism of miRNA regulation in atrial fibrillation (AF) occurrence and development is still unclear, especially, the regulating values of coronary circulating miRNAs has not been reported. Based on our AF radiofrequency ablation clinical practice and previous miRNA study, we proposed a hypothesis that the coronary circulating miRNA might much better reflect the regulating state and metabolic level of myocardial miRNA in AF patient. To investigate the regulating values of coronary circulation miRNA, 90 AF patients were selected and compared with 90 healthy subjects, the changes of coronary circulating miRNA differential expression profile in the whole genome were observed in this study. We found out that compared with autologous peripheral blood (PB), 6 miRNAs were upregulated and 8 miRNA downregulated in AF patients’ coronary sinus blood (CSB) significantly, especially, the expression of miR-1266, miR-4279 and miR-4666a-3p were obviously increased. Compared with normal donors’ peripheral blood, 16 miRNAs were upregulated and 24 miRNAs downregulated dramatically in patients’ peripheral blood, among them, the miR-3171 decreased, but miR-892a and miR-3149 increased significantly from the early to end stages of AF. Our results indicated that the coronary circulating miRNA can really reflect the regulating values of miRNA in AF patient; the level of miRNA change in 3 types of AF may reflect the severity of AF clinical and pathophysiological advance; The miR-892a, miR-3171 and miR-3149 may be used as biomarkers for earlier diagnosis, while miR-1266, miR-4279 and miR-4666a-3p may serve as potential intervening targets for AF patient in future. PMID:27855199

  9. Plasma miRNA-506 as a Prognostic Biomarker for Esophageal Squamous Cell Carcinoma.

    PubMed

    Li, Shu-Ping; Su, Hong-Xin; Zhao, Da; Guan, Quan-Lin

    2016-06-27

    BACKGROUND MicroRNAs (miRNAs) are responsible for regulating proliferation, differentiation, apoptosis, invasion, and metastasis in tumor cells. miRNA-506 is abnormally expressed in multiple tumors, indicating that it might be oncogenic or tumor-suppressive. However, little is known about the association between miRNA-506 expression and esophageal squamous cell carcinoma (ESCC). MATERIAL AND METHODS We examined the expression of miRNA-506 in the plasma of ESCC patients using quantitative real-time polymerase chain reaction (qRT-PCR) to determine the association between miRNA-506 expression and clinicopathological features of ESCC. ROC curves were produced for ESCC diagnosis by plasma miRNA-506 and the area under curve was calculated to explore its diagnostic value. RESULTS Average miRNA-506 expression levels were remarkably higher in the plasma of ESCC patients than in healthy volunteers (P<0.001). The expression of miRNA-506 in the plasma was closely associated with lymph node status (P=0.004), TNM stage (P=0.031), and tumor length (P<0.001). According to ROC curves, the area under the curve for plasma miRNA-506 was 0.835, indicating statistical significance for ESCC diagnosis by plasma miRNA-506 (P<0.001). Kaplan-Meier analysis showed that patients with high miRNA-506 expression had significantly shorter survival time than those with low miRNA-506 expression. Cox regression analysis demonstrated that T stage, N stage, tumor length, and miRNA-506 expression levels were significantly correlated with prognosis in ESCC patients. CONCLUSIONS miRNA-506 can serve as an important molecular marker for diagnosis and prognostic prediction of ESCC.

  10. Combining miRNA and mRNA Expression Profiles in Wilms Tumor Subtypes

    PubMed Central

    Ludwig, Nicole; Werner, Tamara V.; Backes, Christina; Trampert, Patrick; Gessler, Manfred; Keller, Andreas; Lenhof, Hans-Peter; Graf, Norbert; Meese, Eckart

    2016-01-01

    Wilms tumor (WT) is the most common childhood renal cancer. Recent findings of mutations in microRNA (miRNA) processing proteins suggest a pivotal role of miRNAs in WT genesis. We performed miRNA expression profiling of 36 WTs of different subtypes and four normal kidney tissues using microarrays. Additionally, we determined the gene expression profile of 28 of these tumors to identify potentially correlated target genes and affected pathways. We identified 85 miRNAs and 2107 messenger RNAs (mRNA) differentially expressed in blastemal WT, and 266 miRNAs and 1267 mRNAs differentially expressed in regressive subtype. The hierarchical clustering of the samples, using either the miRNA or mRNA profile, showed the clear separation of WT from normal kidney samples, but the miRNA pattern yielded better separation of WT subtypes. A correlation analysis of the deregulated miRNA and mRNAs identified 13,026 miRNA/mRNA pairs with inversely correlated expression, of which 2844 are potential interactions of miRNA and their predicted mRNA targets. We found significant upregulation of miRNAs-183, -301a/b and -335 for the blastemal subtype, and miRNAs-181b, -223 and -630 for the regressive subtype. We found marked deregulation of miRNAs regulating epithelial to mesenchymal transition, especially in the blastemal subtype, and miRNAs influencing chemosensitivity, especially in regressive subtypes. Further research is needed to assess the influence of preoperative chemotherapy and tumor infiltrating lymphocytes on the miRNA and mRNA patterns in WT. PMID:27043538

  11. Exosomes and Exosomal miRNA in Respiratory Diseases

    PubMed Central

    Alipoor, Shamila D.; Garssen, Johan; Movassaghi, Masoud

    2016-01-01

    Exosomes are nanosized vesicles released from every cell in the body including those in the respiratory tract and lungs. They are found in most body fluids and contain a number of different biomolecules including proteins, lipids, and both mRNA and noncoding RNAs. Since they can release their contents, particularly miRNAs, to both neighboring and distal cells, they are considered important in cell-cell communication. Recent evidence has shown their possible importance in the pathogenesis of several pulmonary diseases. The differential expression of exosomes and of exosomal miRNAs in disease has driven their promise as biomarkers of disease enabling noninvasive clinical diagnosis in addition to their use as therapeutic tools. In this review, we summarize recent advances in this area as applicable to pulmonary diseases. PMID:27738390

  12. Viral miRNA targeting of bicistronic and polycistronic transcripts.

    PubMed

    Zhu, Ying; Huang, Yufei; Jung, Jae U; Lu, Chun; Gao, Shou-Jiang

    2014-08-01

    Successful viral infection entails a choreographic regulation of viral gene expression program. Kaposi's sarcoma-associated herpesvirus (KSHV) encodes numerous miRNAs that regulate viral life cycle. However, few viral targets have been identified due to the lack of information on KSHV 3' untranslated regions (3'UTRs). Recent genome-wide mapping of KSHV transcripts and 3'UTRs has revealed abundant bicistronic and polycistronic transcripts. The extended 3'UTRs of the 5' proximal genes of bicistronic and polycistronic transcripts offer additional regulatory targets. Indeed, a genome-wide screening of KSHV 3'UTRs has identified several bicistronic and polycistronic transcripts as the novel targets of viral miRNAs. Together, these works have expanded our knowledge of the unique features of KSHV gene regulation program and provided valuable resources for the research community.

  13. Viral miRNA Targeting of Bicistronic and Polycistronic Transcripts

    PubMed Central

    Zhu, Ying; Huang, Yufei; Jung, Jae U.; Lu, Chun; Gao, Shou-Jiang

    2014-01-01

    Successful viral infection entails a choreographic regulation of viral gene expression program. Kaposi’s sarcoma–associated herpesvirus (KSHV) encodes numerous miRNAs that regulate viral life cycle. However, few viral targets have been identified due to the lack of information on KSHV 3′ untranslated regions (3′UTRs). Recent genome-wide mapping of KSHV transcripts and 3′UTRs has revealed abundant bicistronic and polycistronic transcripts. The extended 3′UTRs of the 5′ proximal genes of bicistronic and polycistronic transcripts offer additional regulatory targets. Indeed, a genome-wide screening of KSHV 3′UTRs has identified several bicistronic and polycistronic transcripts as the novel targets of viral miRNAs. Together, these works have expanded our knowledge of the unique features of KSHV gene regulation program and provided valuable resources for the research community. PMID:24821460

  14. miRNA signature identification of retinoblastoma and the correlations between differentially expressed miRNAs during retinoblastoma progression.

    PubMed

    Yang, Yang; Mei, Qi

    2015-01-01

    Retinoblastoma (RB) is a common pediatric cancer. The study aimed to uncover the mechanisms of RB progression and identify novel therapeutic biomarkers. The miRNA expression profile GSE7072, which includes three RB samples and three healthy retina samples, was used. After data normalization using the preprocessCore package, differentially expressed miRNAs (DE-miRs) were selected by the limma package. The targets of the DE-miRs were predicted based on two databases, followed by construction of the miRNA-target network. Pathway enrichment analysis was conducted for the targets of the DE-miRNAs using DAVID. The CTD database was used to predict RB-related genes, followed by clustering analysis using the pvclust package. The correlation network of DE-miRs was established. MiRNA expression was validated in another data set, GSE41321. In total, 24 DE-miRs were identified whose targets were correlated with the cell cycle pathway. Among them, hsa-miR-373, hsa-miR-125b, and hsa-miR-181a were highlighted in the miRNA-target regulatory network; 14 DE-miRs, including hsa-miR-373, hsa-miR-125b, hsa-miR-18a, hsa-miR-25, hsa-miR-20a, and hsa-let-7 (a, b, c), were shown to distinguish RB from healthy tissue. In addition, hsa-miR-25, hsa-miR-18a, and hsa-miR-20a shared the common target BCL2L11; hsa-let-7b and hsa-miR-125b targeted the genes CDC25A, CDK6, and LIN28A. Expression of three miRNAs in GSE41321 was consistent with that in GSE7072. Several critical miRNAs were identified in RB progression. Hsa-miR-373 might regulate RB invasion and metastasis, hsa-miR-181a might involve in the CDKN1B-mediated cell cycle pathway, and hsa-miR-125b and hsa-let-7b might serve as tumor suppressors by coregulating CDK6, CDC25A, and LIN28A. The miRNAs hsa-miR-25, hsa-miR-18a, and hsa-miR-20a might exert their function by coregulating BCL2L1.

  15. Altered expression of selected microRNAs in melanoma: antiproliferative and proapoptotic activity of miRNA-155.

    PubMed

    Levati, Lauretta; Alvino, Ester; Pagani, Elena; Arcelli, Diego; Caporaso, Patrizia; Bondanza, Sergio; Di Leva, Gianpiero; Ferracin, Manuela; Volinia, Stefano; Bonmassar, Enzo; Croce, Carlo Maria; D'Atri, Stefania

    2009-08-01

    Altered expression of microRNAs (miRNAs) has been detected in cancer, suggesting that these small non-coding RNAs can act as oncogenes or tumor suppressor genes. In the present study, we investigated the expression of miRNA-17-5p, miRNA-18a, miRNA-20a, miRNA-92a, miRNA-146a, miRNA-146b and miRNA-155 by real-time quantitative RT-PCR in a panel of melanocyte cultures and melanoma cell lines and explored the possible role of miRNA-155 in melanoma cell proliferation and survival. The analyzed miRNAs were selected on the basis of previous studies strongly supporting their involvement in cancer development and/or progression. We found that miRNA-17-5p, miRNA-18a, miRNA-20a, and miRNA-92a were overexpressed, whereas miRNA-146a, miRNA-146b and miRNA-155 were down-regulated in the majority of melanoma cell lines with respect to melanocytes. Ectopic expression of miRNA-155 significantly inhibited proliferation in 12 of 13 melanoma cell lines with reduced levels of this miRNA and induced apoptosis in 4 out of 4 cell lines analyzed. In conclusion, our data further support the finding of altered miRNA expression in melanoma cells and establish for the first time that miRNA-155 is a negative regulator of melanoma cell proliferation and survival.

  16. Role of miRNA-9 in Brain Development

    PubMed Central

    Radhakrishnan, Balachandar; Alwin Prem Anand, A.

    2016-01-01

    MicroRNAs (miRNAs) are a class of small regulatory RNAs involved in gene regulation. The regulation is effected by either translational inhibition or transcriptional silencing. In vertebrates, the importance of miRNA in development was discovered from mice and zebrafish dicer knockouts. The miRNA-9 (miR-9) is one of the most highly expressed miRNAs in the early and adult vertebrate brain. It has diverse functions within the developing vertebrate brain. In this article, the role of miR-9 in the developing forebrain (telencephalon and diencephalon), midbrain, hindbrain, and spinal cord of vertebrate species is highlighted. In the forebrain, miR-9 is necessary for the proper development of dorsoventral telencephalon by targeting marker genes expressed in the telencephalon. It regulates proliferation in telencephalon by regulating Foxg1, Pax6, Gsh2, and Meis2 genes. The feedback loop regulation between miR-9 and Nr2e1/Tlx helps in neuronal migration and differentiation. Targeting Foxp1 and Foxp2, and Map1b by miR-9 regulates the radial migration of neurons and axonal development. In the organizers, miR-9 is inversely regulated by hairy1 and Fgf8 to maintain zona limitans interthalamica and midbrain–hindbrain boundary (MHB). It maintains the MHB by inhibiting Fgf signaling genes and is involved in the neurogenesis of the midbrain–hindbrain by regulating Her genes. In the hindbrain, miR-9 modulates progenitor proliferation and differentiation by regulating Her genes and Elav3. In the spinal cord, miR-9 modulates the regulation of Foxp1 and Onecut1 for motor neuron development. In the forebrain, midbrain, and hindbrain, miR-9 is necessary for proper neuronal progenitor maintenance, neurogenesis, and differentiation. In vertebrate brain development, miR-9 is involved in regulating several region-specific genes in a spatiotemporal pattern. PMID:27721656

  17. Characterization of miRNAs in response to short-term waterlogging in three inbred lines of Zea mays

    USDA-ARS?s Scientific Manuscript database

    To characterize the involvement of miRNAs and their targets in response to short-term hypoxia conditions, a quantitative real time PCR (qRT-PCR) assay was used to quantify the expression of the 24 candidate mature miRNA signatures (22 known and 2 novel mature miRNAs, representing 66 miRNA loci) and ...

  18. Fine tuning by miRNAs in development

    NASA Astrophysics Data System (ADS)

    McHale, Peter; Levine, Erel; Levine, Herbert

    2007-03-01

    The unique role played by microRNA in a developing embryo is a topic of much current research interest. One possibility is that microRNA diffuse within a developing tissue, acting as communicators between different cells. Here we pursue this possibility in two different contexts. The first case occurs when the transcription profiles of the microRNA and its target are spatially anticorrelated, as for example is the case in the iab4-Ubx system in fly. Conversely, in the second context the two transcription profiles are correlated in space, as may be the case for the mir10-Hoxb4 system in mouse. In each context we identify a major function for a mobile miRNA. In the first, miRNA serve to induce an all-or-nothing response of the mRNA profile to its morphogen by generating a sharp boundary between domains of high and (ultimately) low target expression. In the second, miRNA amplify polarity in the target expression pattern by removing residual mRNAs. Importantly, our model predicts that these two functions require very different type of diffusion. While our results are highly quantitative, we propose ways of realizing them in experiments, taking into account limitations of standard experimental techniques.

  19. Multiplexed miRNA northern blots via hybridization chain reaction.

    PubMed

    Schwarzkopf, Maayan; Pierce, Niles A

    2016-09-06

    Northern blots enable detection of a target RNA of interest in a biological sample using standard benchtop equipment. miRNAs are the most challenging targets as they must be detected with a single short nucleic acid probe. With existing approaches, it is cumbersome to perform multiplexed blots in which several RNAs are detected simultaneously, impeding the study of interacting regulatory elements. Here, we address this shortcoming by demonstrating multiplexed northern blotting based on the mechanism of hybridization chain reaction (HCR). With this approach, nucleic acid probes complementary to RNA targets trigger chain reactions in which fluorophore-labeled DNA hairpins self-assemble into tethered fluorescent amplification polymers. The programmability of HCR allows multiple amplifiers to operate simultaneously and independently within a blot, enabling straightforward multiplexing. We demonstrate simultaneous detection of three endogenous miRNAs in total RNA extracted from 293T and HeLa cells. For a given target, HCR signal scales linearly with target abundance, enabling relative and absolute quantitation. Using non-radioactive HCR, sensitive and selective miRNA detection is achieved using 2'OMe-RNA probes. The HCR northern blot protocol takes ∼1.5 days independent of the number of target RNAs.

  20. Genome-wide analysis for discovery of new rice miRNA reveals natural antisense miRNA (nat-miRNAs)

    USDA-ARS?s Scientific Manuscript database

    Small RNAs (21-24nt) are involved in gene regulation through translation inhibition, mRNA cleavage, or directing chromatin modifications. In rice, currently ~240 miRNAs have been annotated. We sequenced more than four million small RNAs from rice and identified another 24 miRNA genes. Among these, w...

  1. Differential expression profile of miRNAs in porcine muscle and adipose tissue during development.

    PubMed

    Wang, Qi; Qi, Renli; Wang, Jing; Huang, Wenming; Wu, Yongjiang; Huang, Xiaofeng; Yang, Feiyun; Huang, Jinxiu

    2017-06-30

    MicroRNAs (miRNAs) are a class of non-coding RNAs that play a crucial regulatory role in many biological processes. Previous studies have reported miRNAs that are associated with the growth, differentiation, and proliferation of myocytes and adipocytes in pigs. However, differences in the miRNA expression profiles between muscle and adipose tissues during porcine development are unknown. Muscle and adipose tissues are the two major organs that are crucial for dynamic energy balance in the development and metabolism. Identification of differential expression profile of miRNAs will be useful for understanding the regulatory role of miRNAs in growth, development and evolution of these two tissues, and the research results will provide theoretical basis to improve meat quality. Therefore, we applied Hiseq sequencing to profile miRNAs in muscle and adipose tissues during four development stage at 1, 30, 90 and 240-day-old to explore their regulatory patterns at critical growth stages of pigs. We slaughtered 6 pigs at each developmental stages (24 pigs in total), respectively, RNA of three individual pigs were pooled and duplicate samples at each time point were given to sequence. We obtained a total of 96 million clean reads, and identified 329 known miRNAs and 157 novel miRNAs from all the libraries. We detected 37 miRNAs that were differentially expressed between porcine muscle and adipose tissues; 17 miRNAs which differentially expressed at 30, 90 and 240-day-old were considered as core differentially expressed miRNAs, among them, three miRNAs (ssc-miR-128, -133a-5p, -489) were differentially expressed at all four stages. KEGG analysis revealed the target genes of 17 core differentially expressed miRNAs were involved in 27 significantly enriched pathways (P<0.01), including the MAPK, Wnt, TGF-beta, and Notch signaling pathways, which are known to regulate myogenesis or are related to lipogenesis. 8 and 11 miRNAs were differentially expressed in the muscle and adipose

  2. miRNA Profiles in Plasma from Patients with Sleep Disorders Reveal Dysregulation of miRNAs in Narcolepsy and Other Central Hypersomnias

    PubMed Central

    Holm, Anja; Bang-Berthelsen, Claus Heiner; Knudsen, Stine; Kornum, Birgitte R.; Modvig, Signe; Jennum, Poul; Gammeltoft, Steen

    2014-01-01

    Study Objectives: MicroRNAs (miRNAs) have been implicated in the pathogenesis of human diseases including neurological disorders. The aim is to address the involvement of miRNAs in the pathophysiology of central hypersomnias including autoimmune narcolepsy with cataplexy and hypocretin deficiency (type 1 narcolepsy), narcolepsy without cataplexy (type 2 narcolepsy), and idiopathic hypersomnia. Design: We conducted high-throughput analysis of miRNA in plasma from three groups of patients—with type 1 narcolepsy, type 2 narcolepsy, and idiopathic hypersomnia, respectively—in comparison with healthy controls using quantitative real-time polymerase chain reaction (qPCR) panels. Setting: University hospital based sleep clinic and research laboratories. Patients: Twelve patients with type 1 narcolepsy, 12 patients with type 2 narcolepsy, 12 patients with idiopathic hypersomnia, and 12 healthy controls. Measurements and Results: By analyzing miRNA in plasma with qPCR we identified 50, 24, and 6 miRNAs that were different in patients with type 1 narcolepsy, type 2 narcolepsy, and idiopathic hypersomnia, respectively, compared with healthy controls. Twenty miRNA candidates who fulfilled the criteria of at least two-fold difference and p-value < 0.05 were selected to validate the miRNA changes in an independent cohort of patients. Four miRNAs differed significantly between type 1 narcolepsy patients and healthy controls. Levels of miR-30c, let-7f, and miR-26a were higher, whereas the level of miR-130a was lower in type 1 narcolepsy than healthy controls. The miRNA differences were not specific for type 1 narcolepsy, since the levels of the four miRNAs were also altered in patients with type 2 narcolepsy and idiopathic hypersomnia compared with healthy controls. Conclusion: The levels of four miRNAs differed in plasma from patients with type 1 narcolepsy, type 2 narcolepsy and idiopathic hypersomnia suggesting that alterations of miRNAs may be involved in the

  3. Comparison of metal tolerant and non-tolerant varieties of Festuca rubra for use in the direct hydraulic seeding of metalliferous fluorspar mine tailings

    SciTech Connect

    Morrey, D.R.; Johnson, M.S.; Cooke, J.A.

    1984-09-01

    The germination and growth of metal tolerant and non-tolerant cultivars of Festuca rubra were compared on metalliferous fluorspar tailings in laboratory and field conditions. The effects of wood pulp mulch and alginate stabilizer on germination and establishment were also assessed in the field experiments. Both cultivars germinated satisfactorily, although the laboratory experiment suggested restricted root development in the non-tolerant cultivar. Both experiments, however, showed that the overall shoot growth and cover of the non-tolerant cultivar were not affected. In fact, in the field experiment, contrary to expectation, the non-tolerant cultivar performed better than the metal tolerant cultivar and showed no pathological symptoms of metal toxicity after 12 months. The advantages of using wood pulp as a mulch were clearly demonstrated. However, the application of an alginate stabilizer had no benefit under these particular experimental conditions. The results suggest that the use of carefully selected non-tolerant cultivars in the revegetation of such calcareous metalliferous wastes is possible, even where the zinc content is as high as 1%.

  4. The effects of zinc on cell viability and on mitochondrial structure in contrasting cultivars of Festuca rubra L. - a rapid test for zinc tolerance.

    PubMed

    Davies, K L; Davies, M S; Francis, D

    1995-01-01

    A 20-min exposure to 5.0 microg Zn cm(-3) reduced the percentage of viable root meristematic cells in three cultivars of Festuca rubra L.: Merlin (Zn-tolerant), Hawk (salt-tolerant but with a degree of Zn tolerance) and S59 (Zn-sensitive). The Zn-induced cell mortality in S59 was approximately twice that of the tolerant cultivars. The mean area of mitochondrial profiles in root meristematic cells of Zn-untreated roots was similar in S59 and Merlin but that of Hawk was smaller. A 4-day exposure to 0.2 microg Zn cm(-3) resulted in mitochondrial swelling in the Zn-sensitive cultivar; there was a 25% increase in the mean area of mitochondrial profiles in this cultivar, but no significant increase occurred in Hawk or Merlin. Zn treatment caused a collapse of the cristae and a localized condensation of the mitochondrial matrix in S59, but not in Hawk or Merlin. The marked increase in cell mortality after only a 20-min Zn exposure and the relative simplicity of the technique, indicates that this procedure could be used as a rapid and independent measure of Zn tolerance.

  5. Genome-wide fungal stress responsive miRNA expression in wheat.

    PubMed

    Inal, Behçet; Türktaş, Mine; Eren, Hakan; Ilhan, Emre; Okay, Sezer; Atak, Mehmet; Erayman, Mustafa; Unver, Turgay

    2014-12-01

    MicroRNAs (miRNAs) are small non-coding class of RNAs. They were identified in many plants with their diverse regulatory roles in several cellular and metabolic processes. A number of miRNAs were involved in biotic and abiotic stress responses. Here, fungal stress responsive wheat miRNAs were analyzed by using miRNA-microarray strategy. Two different fungi (Fusarium culmorum and Bipolaris sorokiniana) were inoculated on resistant and sensitive wheat cultivars. A total of 87 differentially regulated miRNAs were detected in the 8 × 15 K array including all of the available plant miRNAs. Using bioinformatics tools, the target transcripts of responsive miRNAs were predicted, and related biological processes and mechanisms were assessed. A number of the miRNAs such as miR2592s, miR869.1, miR169b were highly differentially regulated showing more than 200-fold change upon fungal-inoculation. Some of the miRNAs were identified as fungal-inoculation responsive for the first time. The analyses showed that some of the differentially regulated miRNAs targeted resistance-related genes such as LRR, glucuronosyl transferase, peroxidase and Pto kinase. The comparison of the two miRNA-microarray analyses indicated that fungal-responsive wheat miRNAs were differentially regulated in pathogen- and cultivar-specific manners.

  6. Analysis of miRNAs and Their Targets during Adventitious Shoot Organogenesis of Acacia crassicarpa

    PubMed Central

    Hou, Lingyu; Wang, Xiaoyu; Zheng, Fei; Wang, Weixuan; Liang, Di; Yang, Hailun; Jin, Yi; Xie, Xiangming

    2014-01-01

    Organogenesis is an important process for plant regeneration by tissue or cell mass differentiation to regenerate a complete plant. MicroRNAs (miRNAs) play an essential role in regulating plant development by mediating target genes at transcriptional and post-transcriptional levels, but the diversity of miRNAs and their potential roles in organogenesis of Acacia crassicarpa have rarely been investigated. In this study, approximately 10 million sequence reads were obtained from a small RNA library, from which 189 conserved miRNAs from 57 miRNA families, and 7 novel miRNAs from 5 families, were identified from A. crassicarpa organogenetic tissues. Target prediction for these miRNAs yielded 237 potentially unique genes, of which 207 received target Gene Ontology annotations. On the basis of a bioinformatic analysis, one novel and 13 conserved miRNAs were selected to investigate their possible roles in A. crassicarpa organogenesis by qRT-PCR. The stage-specific expression patterns of the miRNAs provided information on their possible regulatory functions, including shoot bud formation, modulated function after transfer of the culture to light, and regulatory roles during induction of organogenesis. This study is the first to investigate miRNAs associated with A. crassicarpa organogenesis. The results provide a foundation for further characterization of miRNA expression profiles and roles in the regulation of diverse physiological pathways during adventitious shoot organogenesis of A. crassicarpa. PMID:24718555

  7. Grouping miRNAs of similar functions via weighted information content of gene ontology.

    PubMed

    Lan, Chaowang; Chen, Qingfeng; Li, Jinyan

    2016-12-22

    Regulation mechanisms between miRNAs and genes are complicated. To accomplish a biological function, a miRNA may regulate multiple target genes, and similarly a target gene may be regulated by multiple miRNAs. Wet-lab knowledge of co-regulating miRNAs is limited. This work introduces a computational method to group miRNAs of similar functions to identify co-regulating miRNAsfrom a similarity matrix of miRNAs. We define a novel information content of gene ontology (GO) to measure similarity between two sets of GO graphs corresponding to the two sets of target genes of two miRNAs. This between-graph similarity is then transferred as a functional similarity between the two miRNAs. Our definition of the information content is based on the size of a GO term's descendants, but adjusted by a weight derived from its depth level and the GO relationships at its path to the root node or to the most informative common ancestor (MICA). Further, a self-tuning technique and the eigenvalues of the normalized Laplacian matrix are applied to determine the optimal parameters for the spectral clustering of the similarity matrix of the miRNAs. Experimental results demonstrate that our method has better clustering performance than the existing edge-based, node-based or hybrid methods. Our method has also demonstrated a novel usefulness for the function annotation of new miRNAs, as reported in the detailed case studies.

  8. miRNA in situ hybridization in circulating tumor cells--MishCTC.

    PubMed

    Ortega, Francisco G; Lorente, Jose A; Garcia Puche, Jose L; Ruiz, Maria P; Sanchez-Martin, Rosario M; de Miguel-Pérez, Diego; Diaz-Mochon, Juan J; Serrano, Maria J

    2015-03-17

    Circulating tumor cells (CTCs) must be phenotypically and genetically characterized before they can be utilized in clinical applications. Here, we present the first protocol for the detection of miRNAs in CTCs using in situ hybridization (ISH) combined with immunomagnetic selection based on cytokeratin (CK) expression and immunocytochemistry. Locked-Nucleic Acid (LNA) probes associated with an enzyme-labeled fluorescence (ELF) signal amplification approach were used to detect miRNA-21 in CTCs. This protocol was optimized using both epithelial tumor (MDA-MB468) and epithelial non-tumor (MCF-10A) cell lines, and miRNA-21 was selected as the target miRNA because of its known role as an onco-miRNA. Hematopoietic cells do not express miRNA-21; thus, miRNA-21 is an ideal marker for detecting CTCs. Peripheral blood samples were taken from 25 cancer patients and these samples were analyzed using our developed protocol. Of the 25 samples, 11 contained CTCs. For all 11 CTC-positive samples, the isolated CTCs expressed both CK and miRNA-21. Finally, the protocol was applied to monitor miRNA-21 expression in epithelial to mesenchymal transition (EMT)-induced MCF-7 cells, an epithelial tumor cell line. CK expression was lost in these cells, whereas miRNA-21 was still expressed, suggesting that miRNA-21 might be a good marker for detecting CTCs with an EMT phenotype.

  9. miRNAs: small genes with big potential in metazoan phylogenetics.

    PubMed

    Tarver, James E; Sperling, Erik A; Nailor, Audrey; Heimberg, Alysha M; Robinson, Jeffrey M; King, Benjamin L; Pisani, Davide; Donoghue, Philip C J; Peterson, Kevin J

    2013-11-01

    microRNAs (miRNAs) are a key component of gene regulatory networks and have been implicated in the regulation of virtually every biological process found in multicellular eukaryotes. What makes them interesting from a phylogenetic perspective is the high conservation of primary sequence between taxa, their accrual in metazoan genomes through evolutionary time, and the rarity of secondary loss in most metazoan taxa. Despite these properties, the use of miRNAs as phylogenetic markers has not yet been discussed within a clear conceptual framework. Here we highlight five properties of miRNAs that underlie their utility in phylogenetics: 1) The processes of miRNA biogenesis enable the identification of novel miRNAs without prior knowledge of sequence; 2) The continuous addition of miRNA families to metazoan genomes through evolutionary time; 3) The low level of secondary gene loss in most metazoan taxa; 4) The low substitution rate in the mature miRNA sequence; and 5) The small probability of convergent evolution of two miRNAs. Phylogenetic analyses using both Bayesian and parsimony methods on a eumetazoan miRNA data set highlight the potential of miRNAs to become an invaluable new tool, especially when used as an additional line of evidence, to resolve previously intractable nodes within the tree of life.

  10. PmiRExAt: plant miRNA expression atlas database and web applications.

    PubMed

    Gurjar, Anoop Kishor Singh; Panwar, Abhijeet Singh; Gupta, Rajinder; Mantri, Shrikant S

    2016-01-01

    High-throughput small RNA (sRNA) sequencing technology enables an entirely new perspective for plant microRNA (miRNA) research and has immense potential to unravel regulatory networks. Novel insights gained through data mining in publically available rich resource of sRNA data will help in designing biotechnology-based approaches for crop improvement to enhance plant yield and nutritional value. Bioinformatics resources enabling meta-analysis of miRNA expression across multiple plant species are still evolving. Here, we report PmiRExAt, a new online database resource that caters plant miRNA expression atlas. The web-based repository comprises of miRNA expression profile and query tool for 1859 wheat, 2330 rice and 283 maize miRNA. The database interface offers open and easy access to miRNA expression profile and helps in identifying tissue preferential, differential and constitutively expressing miRNAs. A feature enabling expression study of conserved miRNA across multiple species is also implemented. Custom expression analysis feature enables expression analysis of novel miRNA in total 117 datasets. New sRNA dataset can also be uploaded for analysing miRNA expression profiles for 73 plant species. PmiRExAt application program interface, a simple object access protocol web service allows other programmers to remotely invoke the methods written for doing programmatic search operations on PmiRExAt database.Database URL:http://pmirexat.nabi.res.in.

  11. Genome-wide exploration of miRNA function in mammalian muscle cell differentiation.

    PubMed

    Polesskaya, Anna; Degerny, Cindy; Pinna, Guillaume; Maury, Yves; Kratassiouk, Gueorgui; Mouly, Vincent; Morozova, Nadya; Kropp, Jeremie; Frandsen, Niels; Harel-Bellan, Annick

    2013-01-01

    MiRNAs impact on the control of cell fate by regulating gene expression at the post-transcriptional level. Here, using mammalian muscle differentiation as a model and a phenotypic loss-of-function screen, we explored the function of miRNAs at the genome-wide level. We found that the depletion of a high number of miRNAs (63) impacted on differentiation of human muscle precursors, underscoring the importance of this post-transcriptional mechanism of gene regulation. Interestingly, a comparison with miRNA expression profiles revealed that most of the hit miRNAs did not show any significant variations of expression during differentiation. These constitutively expressed miRNAs might be required for basic and/or essential cell function, or else might be regulated at the post-transcriptional level. MiRNA inhibition yielded a variety of phenotypes, reflecting the widespread miRNA involvement in differentiation. Using a functional screen (the STarS--Suppressor Target Screen--approach, i. e. concomitant knockdown of miRNAs and of candidate target proteins), we discovered miRNA protein targets that are previously uncharacterized controllers of muscle-cell terminal differentiation. Our results provide a strategy for functional annotation of the human miRnome.

  12. Maternal chromium restriction modulates miRNA profiles related to lipid metabolism disorder in mice offspring.

    PubMed

    Zhang, Qian; Xiao, Xinhua; Zheng, Jia; Li, Ming; Yu, Miao; Ping, Fan; Wang, Zhixin; Qi, Cuijuan; Wang, Tong; Wang, Xiaojing

    2017-08-01

    Increasing evidence shows that maternal nutrition status has a vital effect on offspring susceptibility to obesity. MicroRNAs are related to lipid metabolism processes. This study aimed to evaluate whether maternal chromium restriction could affect miRNA expression involved in lipid metabolism in offspring. Weaning C57BL/6J mice born from mothers fed with normal control diet or chromium-restricted diet were fed for 13 weeks. The adipose miRNA expression profile was analyzed by miRNA array analysis. At 16 weeks old, pups from dams fed with chromium-restricted diet exhibit higher body weight, fat weight, and serum TC, TG levels. Six miRNAs were identified as upregulated in the RC group compared with the CC group, whereas eight miRNAs were lower than the threshold level set in the RC group. In the validated target genes of these differentially expressed miRNA, the MAPK signaling pathway serves an important role in the influence of early life chromium-restricted diet on lipid metabolism through miRNA. Long-term programming on various specific miRNA and MAPK signaling pathway may be involved in maternal chromium restriction in the adipose of female offspring. Impact statement For the first time, our study demonstrates important miRNA differences in the effect of maternal chromium restriction in offspring. These miRNAs may serve as "bridges" between the mother and the offspring by affecting the MAPK pathway.

  13. miRNA in situ hybridization in circulating tumor cells - MishCTC

    PubMed Central

    Ortega, Francisco G.; Lorente, Jose A.; Garcia Puche, Jose L.; Ruiz, Maria P.; Sanchez-Martin, Rosario M.; de Miguel-Pérez, Diego; Diaz-Mochon, Juan J.; Serrano, Maria J.

    2015-01-01

    Circulating tumor cells (CTCs) must be phenotypically and genetically characterized before they can be utilized in clinical applications. Here, we present the first protocol for the detection of miRNAs in CTCs using in situ hybridization (ISH) combined with immunomagnetic selection based on cytokeratin (CK) expression and immunocytochemistry. Locked-Nucleic Acid (LNA) probes associated with an enzyme-labeled fluorescence (ELF) signal amplification approach were used to detect miRNA-21 in CTCs. This protocol was optimized using both epithelial tumor (MDA-MB468) and epithelial non-tumor (MCF-10A) cell lines, and miRNA-21 was selected as the target miRNA because of its known role as an onco-miRNA. Hematopoietic cells do not express miRNA-21; thus, miRNA-21 is an ideal marker for detecting CTCs. Peripheral blood samples were taken from 25 cancer patients and these samples were analyzed using our developed protocol. Of the 25 samples, 11 contained CTCs. For all 11 CTC-positive samples, the isolated CTCs expressed both CK and miRNA-21. Finally, the protocol was applied to monitor miRNA-21 expression in epithelial to mesenchymal transition (EMT)-induced MCF-7 cells, an epithelial tumor cell line. CK expression was lost in these cells, whereas miRNA-21 was still expressed, suggesting that miRNA-21 might be a good marker for detecting CTCs with an EMT phenotype. PMID:25777797

  14. High-Throughput Sequencing, Characterization and Detection of New and Conserved Cucumber miRNAs

    PubMed Central

    Martínez, Germán; Forment, Javier; Llave, Cesar; Pallás, Vicente; Gómez, Gustavo

    2011-01-01

    Micro RNAS (miRNAs) are a class of endogenous small non coding RNAs involved in the post-transcriptional regulation of gene expression. In plants, a great number of conserved and specific miRNAs, mainly arising from model species, have been identified to date. However less is known about the diversity of these regulatory RNAs in vegetal species with agricultural and/or horticultural importance. Here we report a combined approach of bioinformatics prediction, high-throughput sequencing data and molecular methods to analyze miRNAs populations in cucumber (Cucumis sativus) plants. A set of 19 conserved and 6 known but non-conserved miRNA families were found in our cucumber small RNA dataset. We also identified 7 (3 with their miRNA* strand) not previously described miRNAs, candidates to be cucumber-specific. To validate their description these new C. sativus miRNAs were detected by northern blot hybridization. Additionally, potential targets for most conserved and new miRNAs were identified in cucumber genome. In summary, in this study we have identified, by first time, conserved, known non-conserved and new miRNAs arising from an agronomically important species such as C. sativus. The detection of this complex population of regulatory small RNAs suggests that similarly to that observe in other plant species, cucumber miRNAs may possibly play an important role in diverse biological and metabolic processes. PMID:21603611

  15. DGCR8-mediated disruption of miRNA biogenesis induces cellular senescence in primary fibroblasts.

    PubMed

    Gómez-Cabello, Daniel; Adrados, Isabel; Gamarra, David; Kobayashi, Hikaru; Takatsu, Yoshihiro; Takatsu, Kyoko; Gil, Jesús; Palmero, Ignacio

    2013-10-01

    The regulation of gene expression by microRNAs (miRNAs) is critical for normal development and physiology. Conversely, miRNA function is frequently impaired in cancer, and other pathologies, either by aberrant expression of individual miRNAs or dysregulation of miRNA synthesis. Here, we have investigated the impact of global disruption of miRNA biogenesis in primary fibroblasts of human or murine origin, through the knockdown of DGCR8, an essential mediator of the synthesis of canonical miRNAs. We find that the inactivation of DGCR8 in these cells results in a dramatic antiproliferative response, with the acquisition of a senescent phenotype. Senescence triggered by DGCR8 loss is accompanied by the upregulation of the cell-cycle inhibitor p21CIP1. We further show that a subset of senescence-associated miRNAs with the potential to target p21CIP1 is downregulated during DGCR8-mediated senescence. Interestingly, the antiproliferative response to miRNA biogenesis disruption is retained in human tumor cells, irrespective of p53 status. In summary, our results show that defective synthesis of canonical microRNAs results in cell-cycle arrest and cellular senescence in primary fibroblasts mediated by specific miRNAs, and thus identify global miRNA disruption as a novel senescence trigger. © 2013 The Anatomical Society and John Wiley & Sons Ltd.

  16. Analysis of Chromosome 17 miRNAs and Their Importance in Medulloblastomas

    PubMed Central

    López-Ochoa, Sebastian; Ramírez-García, Marina

    2015-01-01

    MicroRNAs (miRNAs) are small sequences of nucleotides that regulate posttranscriptionally gene expression. In recent years they have been recognized as very important general regulators of proliferation, differentiation, adhesion, cell death, and others. In some cases, the characteristic presence of miRNAs reflects some of the cellular pathways that may be altered. Particularly medulloblastomas (MB) represent entities that undergo almost characteristic alterations of chromosome 17: from loss of discrete fragments and isochromosomes formation to complete loss of one of them. An analysis of the major loci on this chromosome revealed that it contains at least 19 genes encoding miRNAs which may regulate the development and differentiation of the brain and cerebellum. miRNAs are regulators of real complex networks; they can regulate from 100 to over 300 messengers of various proteins. In this review some miRNAs are considered to be important in MB studies. Some of them are miRNA-5047, miRNA-1253, miRNA-2909, and miRNA-634. Everyone can significantly affect the development, growth, and cell invasion of MB, and they have not been explored in this tumor. In this review, we propose some miRNAs that can affect some genes in MB, and hence the importance of its study. PMID:25866804

  17. PmiRExAt: plant miRNA expression atlas database and web applications

    PubMed Central

    Gurjar, Anoop Kishor Singh; Panwar, Abhijeet Singh; Gupta, Rajinder; Mantri, Shrikant S.

    2016-01-01

    High-throughput small RNA (sRNA) sequencing technology enables an entirely new perspective for plant microRNA (miRNA) research and has immense potential to unravel regulatory networks. Novel insights gained through data mining in publically available rich resource of sRNA data will help in designing biotechnology-based approaches for crop improvement to enhance plant yield and nutritional value. Bioinformatics resources enabling meta-analysis of miRNA expression across multiple plant species are still evolving. Here, we report PmiRExAt, a new online database resource that caters plant miRNA expression atlas. The web-based repository comprises of miRNA expression profile and query tool for 1859 wheat, 2330 rice and 283 maize miRNA. The database interface offers open and easy access to miRNA expression profile and helps in identifying tissue preferential, differential and constitutively expressing miRNAs. A feature enabling expression study of conserved miRNA across multiple species is also implemented. Custom expression analysis feature enables expression analysis of novel miRNA in total 117 datasets. New sRNA dataset can also be uploaded for analysing miRNA expression profiles for 73 plant species. PmiRExAt application program interface, a simple object access protocol web service allows other programmers to remotely invoke the methods written for doing programmatic search operations on PmiRExAt database. Database URL: http://pmirexat.nabi.res.in. PMID:27081157

  18. Circulating miRNAs and miRNA shuttles as biomarkers: Perspective trajectories of healthy and unhealthy aging

    PubMed Central

    Olivieri, Fabiola; Capri, Miriam; Bonafè, Massimiliano; Morsiani, Cristina; Jung, Hwa Jin; Spazzafumo, Liana; Viña, Jose; Suh, Yousin

    2017-01-01

    Human aging is a lifelong process characterized by a continuous trade-off between pro-and anti-inflammatory responses, where the best-adapted and/or remodeled genetic/epigenetic profile may develop a longevity phenotype. Centenarians and their offspring represent such a phenotype and their comparison to patients with age-related diseases (ARDs) is expected to maximize the chance to unravel the genetic makeup that better associates with healthy aging trajectories. Seemingly, such comparison is expected to allow the discovery of new biomarkers of longevity together with risk factor for the most common ARDs. MicroRNAs (miRNAs) and their shuttles (extracellular vesicles in particular) are currently conceived as those endowed with the strongest ability to provide information about the trajectories of healthy and unhealthy aging. We review the available data on miRNAs in aging and underpin the evidence suggesting that circulating miRNAs (and cognate shuttles), especially those involved in the regulation of inflammation (inflamma-miRs) may constitute biomarkers capable of reliably depicting healthy and unhealthy aging trajectories. PMID:27986629

  19. Identification of miRNAs involved in fruit ripening in Cavendish bananas by deep sequencing.

    PubMed

    Bi, Fangcheng; Meng, Xiangchun; Ma, Chao; Yi, Ganjun

    2015-10-13

    MicroRNAs (miRNAs) are a family of non-coding small RNAs that play an important regulatory role in various biological processes. Previous studies have reported that miRNAs are closely related to the ripening process in model plants. However, the miRNAs that are closely involved in the banana fruit ripening process remain unknown. Here, we investigated the miRNA populations from banana fruits in response to ethylene or 1-MCP treatment using a deep sequencing approach and bioinformatics analysis combined with quantitative RT-PCR validation. A total of 125 known miRNAs and 26 novel miRNAs were identified from three libraries. MiRNA profiling of bananas in response to ethylene treatment compared with 1-MCP treatment showed differential expression of 82 miRNAs. Furthermore, the differentially expressed miRNAs were predicted to target a total of 815 target genes. Interestingly, some targets were annotated as transcription factors and other functional proteins closely involved in the development and the ripening process in other plant species. Analysis by qRT-PCR validated the contrasting expression patterns between several miRNAs and their target genes. The miRNAome of the banana fruit in response to ethylene or 1-MCP treatment were identified by high-throughput sequencing. A total of 82 differentially expressed miRNAs were found to be closely associated with the ripening process. The miRNA target genes encode transcription factors and other functional proteins, including SPL, APETALA2, EIN3, E3 ubiquitin ligase, β-galactosidase, and β-glucosidase. These findings provide valuable information for further functional research of the miRNAs involved in banana fruit ripening.

  20. Characterization of an extensive rainbow trout miRNA transcriptome by next generation sequencing.

    PubMed

    Juanchich, Amelie; Bardou, Philippe; Rué, Olivier; Gabillard, Jean-Charles; Gaspin, Christine; Bobe, Julien; Guiguen, Yann

    2016-03-01

    MicroRNAs (miRNAs) have emerged as important post-transcriptional regulators of gene expression in a wide variety of physiological processes. They can control both temporal and spatial gene expression and are believed to regulate 30 to 70% of the genes. Data are however limited for fish species, with only 9 out of the 30,000 fish species present in miRBase. The aim of the current study was to discover and characterize rainbow trout (Oncorhynchus mykiss) miRNAs in a large number of tissues using next-generation sequencing in order to provide an extensive repertoire of rainbow trout miRNAs. A total of 38 different samples corresponding to 16 different tissues or organs were individually sequenced and analyzed independently in order to identify a large number of miRNAs with high confidence. This led to the identification of 2946 miRNA loci in the rainbow trout genome, including 445 already known miRNAs. Differential expression analysis was performed in order to identify miRNAs exhibiting specific or preferential expression among the 16 analyzed tissues. In most cases, miRNAs exhibit a specific pattern of expression in only a few tissues. The expression data from sRNA sequencing were confirmed by RT-qPCR. In addition, novel miRNAs are described in rainbow trout that had not been previously reported in other species. This study represents the first characterization of rainbow trout miRNA transcriptome from a wide variety of tissue and sets an extensive repertoire of rainbow trout miRNAs. It provides a starting point for future studies aimed at understanding the roles of miRNAs in major physiological process such as growth, reproduction or adaptation to stress. These rainbow trout miRNAs repertoire provide a novel resource to advance genomic research in salmonid species.

  1. Regulatory networks between neurotrophins and miRNAs in brain diseases and cancers

    PubMed Central

    Shi, Jian

    2015-01-01

    Neurotrophins are involved in many physiological and pathological processes in the nervous system. They regulate and modify signal transduction, transcription and translation in neurons. It is recently demonstrated that the neurotrophin expression is regulated by microRNAs (miRNAs), changing our views on neurotrophins and miRNAs. Generally, miRNAs regulate neurotrophins and their receptors in at least two ways: (1) miRNAs bind directly to the 3′ untranslated region (UTR) of isoform-specific mRNAs and post-transcriptionally regulate their expression; (2) miRNAs bind to the 3′ UTR of the regulatory factors of neurotrophins and regulate their expression. On the other hand, neurotrophins can regulate miRNAs. The results of BNDF research show that neurotrophins regulate miRNAs in at least three ways: (1) ERK stimulation enhances the activation of TRBP (HIV-1 TAR RNA-binding protein) and Dicer, leading to the upregulation of miRNA biogenesis; (2) ERK-dependent upregulation of Lin28a (RNA-binding proteins) blocks select miRNA biogenesis; (3) transcriptional regulation of miRNA expression through activation of transcription factors, including CREB and NF-κB. These regulatory processes integrate positive and negative regulatory loops in neurotrophin and miRNA signaling pathways, and also expand the function of neurotrophins and miRNAs. In this review, we summarize the current knowledge of the regulatory networks between neurotrophins and miRNAs in brain diseases and cancers, for which novel cutting edge therapeutic, delivery and diagnostic approaches are emerging. PMID:25544363

  2. miRNA regulation in the early development of barley seed

    PubMed Central

    2012-01-01

    Background During the early stages of seed development many genes are under dynamic regulation to ensure the proper differentiation and establishment of the tissue that will constitute the mature grain. To investigate how miRNA regulation contributes to this process in barley, a combination of small RNA and mRNA degradome analyses were used to identify miRNAs and their targets. Results Our analysis identified 84 known miRNAs and 7 new miRNAs together with 96 putative miRNA target genes regulated through a slicing mechanism in grain tissues during the first 15 days post anthesis. We also identified many potential miRNAs including several belonging to known miRNA families. Our data gave us evidence for an increase in miRNA-mediated regulation during the transition between pre-storage and storage phases. Potential miRNA targets were found in various signalling pathways including components of four phytohormone pathways (ABA, GA, auxin, ethylene) and the defence response to powdery mildew infection. Among the putative miRNA targets we identified were two essential genes controlling the GA response, a GA3oxidase1 and a homolog of the receptor GID1, and a homolog of the ACC oxidase which catalyses the last step of ethylene biosynthesis. We found that two MLA genes are potentially miRNA regulated, establishing a direct link between miRNAs and the R gene response. Conclusion Our dataset provides a useful source of information on miRNA regulation during the early development of cereal grains and our analysis suggests that miRNAs contribute to the control of development of the cereal grain, notably through the regulation of phytohormone response pathways. PMID:22838835

  3. Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs

    PubMed Central

    2012-01-01

    Background MicroRNAs (miRNAs) have recently emerged as important gene regulators in plants. MiRNAs and their targets have been extensively studied in Arabidopsis and rice. However, relatively little is known about the characterization of miRNAs and their target genes in peach (Prunus persica), which is a complex crop with unique developmental programs. Results We performed small RNA deep sequencing and identified 47 peach-specific and 47 known miRNAs or families with distinct expression patterns. Together, the identified miRNAs targeted 80 genes, many of which have not been reported previously. Like the model plant systems, peach has two of the three conserved trans-acting siRNA biogenesis pathways with similar mechanistic features and target specificity. Unique to peach, three of the miRNAs collectively target 49 MYBs, 19 of which are known to regulate phenylpropanoid metabolism, a key pathway associated with stone hardening and fruit color development, highlighting a critical role of miRNAs in the regulation of peach fruit development and ripening. We also found that the majority of the miRNAs were differentially regulated in different tissues, in part due to differential processing of miRNA precursors. Up to 16% of the peach-specific miRNAs were differentially processed from their precursors in a tissue specific fashion, which has been rarely observed in plant cells. The miRNA precursor processing activity appeared not to be coupled with its transcriptional activity but rather acted independently in peach. Conclusions Collectively, the data characterizes the unique expression pattern and processing regulation of peach miRNAs and demonstrates the presence of a complex, multi-level miRNA regulatory network capable of targeting a wide variety of biological functions, including phenylpropanoid pathways which play a multifaceted spatial-temporal role in peach fruit development. PMID:22909020

  4. Posttranscriptional deregulation of signaling pathways in meningioma subtypes by differential expression of miRNAs

    PubMed Central

    Ludwig, Nicole; Kim, Yoo-Jin; Mueller, Sabine C.; Backes, Christina; Werner, Tamara V.; Galata, Valentina; Sartorius, Elke; Bohle, Rainer M.; Keller, Andreas; Meese, Eckart

    2015-01-01

    Background Micro (mi)RNAs are key regulators of gene expression and offer themselves as biomarkers for cancer development and progression. Meningioma is one of the most frequent primary intracranial tumors. As of yet, there are limited data on the role of miRNAs in meningioma of different histological subtypes and the affected signaling pathways. Methods In this study, we compared expression of 1205 miRNAs in different meningioma grades and histological subtypes using microarrays and independently validated deregulation of selected miRNAs with quantitative real-time PCR. Clinical utility of a subset of miRNAs as biomarkers for World Health Organization (WHO) grade II meningioma based on quantitative real-time data was tested. Potential targets of deregulated miRNAs were discovered with an in silico analysis. Results We identified 13 miRNAs deregulated between different subtypes of benign meningiomas, and 52 miRNAs deregulated in anaplastic meningioma compared with benign meningiomas. Known and putative target genes of deregulated miRNAs include genes involved in epithelial-to-mesenchymal transition for benign meningiomas, and Wnt, transforming growth factor–β, and vascular endothelial growth factor signaling for higher-grade meningiomas. Furthermore, a 4-miRNA signature (miR-222, -34a*, -136, and -497) shows promise as a biomarker differentiating WHO grade II from grade I meningiomas with an area under the curve of 0.75. Conclusions Our data provide novel insights into the contribution of miRNAs to the phenotypic spectrum in benign meningiomas. By deregulating translation of genes belonging to signaling pathways known to be important for meningioma genesis and progression, miRNAs provide a second in line amplification of growth promoting cellular signals. MiRNAs as biomarkers for diagnosis of aggressive meningiomas might prove useful and should be explored further in a prospective manner. PMID:25681310

  5. Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs.

    PubMed

    Zhu, Hong; Xia, Rui; Zhao, Bingyu; An, Yong-qiang; Dardick, Chris D; Callahan, Ann M; Liu, Zongrang

    2012-08-21

    MicroRNAs (miRNAs) have recently emerged as important gene regulators in plants. MiRNAs and their targets have been extensively studied in Arabidopsis and rice. However, relatively little is known about the characterization of miRNAs and their target genes in peach (Prunus persica), which is a complex crop with unique developmental programs. We performed small RNA deep sequencing and identified 47 peach-specific and 47 known miRNAs or families with distinct expression patterns. Together, the identified miRNAs targeted 80 genes, many of which have not been reported previously. Like the model plant systems, peach has two of the three conserved trans-acting siRNA biogenesis pathways with similar mechanistic features and target specificity. Unique to peach, three of the miRNAs collectively target 49 MYBs, 19 of which are known to regulate phenylpropanoid metabolism, a key pathway associated with stone hardening and fruit color development, highlighting a critical role of miRNAs in the regulation of peach fruit development and ripening. We also found that the majority of the miRNAs were differentially regulated in different tissues, in part due to differential processing of miRNA precursors. Up to 16% of the peach-specific miRNAs were differentially processed from their precursors in a tissue specific fashion, which has been rarely observed in plant cells. The miRNA precursor processing activity appeared not to be coupled with its transcriptional activity but rather acted independently in peach. Collectively, the data characterizes the unique expression pattern and processing regulation of peach miRNAs and demonstrates the presence of a complex, multi-level miRNA regulatory network capable of targeting a wide variety of biological functions, including phenylpropanoid pathways which play a multifaceted spatial-temporal role in peach fruit development.

  6. Mapping circulating serum miRNAs to their immune-related target mRNAs

    PubMed Central

    Nosirov, Bakhtiyor; Billaud, Joël; Vandenbon, Alexis; Diez, Diego; Wijaya, Edward; Ishii, Ken J; Teraguchi, Shunsuke; Standley, Daron M

    2017-01-01

    Purpose Evidence suggests that circulating serum microRNAs (miRNAs) might preferentially target immune-related mRNAs. If this were the case, we hypothesized that immune-related mRNAs would have more predicted serum miRNA binding sites than other mRNAs and, reciprocally, that serum miRNAs would have more immune-related mRNA targets than non-serum miRNAs. Materials and methods We developed a consensus target predictor using the random forest framework and calculated the number of predicted miRNA–mRNA interactions in various subsets of miRNAs (serum, non-serum) and mRNAs (immune related, nonimmune related). Results Immune-related mRNAs were predicted to be targeted by serum miRNA more than other mRNAs. Moreover, serum miRNAs were predicted to target many more immune-related mRNA targets than non-serum miRNAs; however, these two biases in immune-related mRNAs and serum miRNAs appear to be completely independent. Conclusion Immune-related mRNAs have more miRNA binding sites in general, not just for serum miRNAs; likewise, serum miRNAs target many more mRNAs than non-serum miRNAs overall, regardless of whether they are immune related or not. Nevertheless, these two independent phenomena result in a significantly larger number of predicted serum miRNA–immune mRNA interactions than would be expected by chance. PMID:28203094

  7. Regulatory networks between neurotrophins and miRNAs in brain diseases and cancers.

    PubMed

    Shi, Jian

    2015-02-01

    Neurotrophins are involved in many physiological and pathological processes in the nervous system. They regulate and modify signal transduction, transcription and translation in neurons. It is recently demonstrated that the neurotrophin expression is regulated by microRNAs (miRNAs), changing our views on neurotrophins and miRNAs. Generally, miRNAs regulate neurotrophins and their receptors in at least two ways: (1) miRNAs bind directly to the 3' untranslated region (UTR) of isoform-specific mRNAs and post-transcriptionally regulate their expression; (2) miRNAs bind to the 3' UTR of the regulatory factors of neurotrophins and regulate their expression. On the other hand, neurotrophins can regulate miRNAs. The results of BNDF research show that neurotrophins regulate miRNAs in at least three ways: (1) ERK stimulation enhances the activation of TRBP (HIV-1 TAR RNA-binding protein) and Dicer, leading to the upregulation of miRNA biogenesis; (2) ERK-dependent upregulation of Lin28a (RNA-binding proteins) blocks select miRNA biogenesis; (3) transcriptional regulation of miRNA expression through activation of transcription factors, including CREB and NF-κB. These regulatory processes integrate positive and negative regulatory loops in neurotrophin and miRNA signaling pathways, and also expand the function of neurotrophins and miRNAs. In this review, we summarize the current knowledge of the regulatory networks between neurotrophins and miRNAs in brain diseases and cancers, for which novel cutting edge therapeutic, delivery and diagnostic approaches are emerging.

  8. Identification of miRNAs involved in pear fruit development and quality.

    PubMed

    Wu, Jun; Wang, Defu; Liu, Yufeng; Wang, Long; Qiao, Xin; Zhang, Shaoling

    2014-11-03

    MicroRNAs (miRNAs) are a class of small, endogenous RNAs that take part in regulating genes through mediating gene expressions at the post-transcriptional level in plants. Previous studies have reported miRNA identification in various plants ranging from model plants to perennial fruit trees. However, the role of miRNAs in pear (Pyrus bretschneideri) fruit development is not clear. Here, we investigated the miRNA profiles of pear fruits from different time stages during development with Illumina HiSeq 2000 platform and bioinformatics analysis. Quantitative real-time PCR was used to validate the expression levels of miRNAs. Both conserved and species-specific miRNAs in pear have been identified in this study. Total reads, ranging from 19,030,925 to 25,576,773, were obtained from six small RNA libraries constructed for different stages of fruit development after flowering. Comparative profiling showed that an average of 90 miRNAs was expressed with significant differences between various developmental stages. KEGG pathway analysis on 2,216 target genes of 188 known miRNAs and 1,127 target genes of 184 novel miRNAs showed that miRNAs are widely involved in the regulation of fruit development. Among these, a total of eleven miRNAs putatively participate in the pathway of lignin biosynthesis, nine miRNAs were identified to take part in sugar and acid metabolism, and MiR160 was identified to regulate auxin response factor. Comparative analysis of miRNAomes during pear fruit development is presented, and miRNAs were proved to be widely involved in the regulation of fruit development and formation of fruit quality, for example through lignin synthesis, sugar and acid metabolism, and hormone signaling. Combined with computational analysis and experimental confirmation, the research contributes valuable information for further functional research of microRNA in fruit development for pear and other species.

  9. URINE miRNAs: POTENTIAL BIOMARKERS FOR MONITORING PROGRESION OF EARLY STAGES OF DIABETIC NEPHROPATHY

    PubMed Central

    Yang, Yeyi; Xiao, Li; Li, Jun; Kanwar, Yashpal S.; Liu, Fuyou; Sun, Lin

    2013-01-01

    With a steep increase in the incidence of type 1 and 2 diabetes globally, diabetic nephropathy (DN) has now become the leading cause of renal failure in the world. There are no suitable biomarkers for the diagnosis of early stages of DN. In recent years, tremendous efforts are being made worldwide to delineate the role of micro RNAs in the pathogenesis of DN. Circulating miRNAs in serum, plasma, urine and other body fluids, which reflect a response to various pathophysiological stresses, are being investigated in the context of diabetic nephropathy. Delineation of the changes in miRNA levels in patients with DN may lead to a better understanding of the progression of the disease. We present here an exhaustive survey of the miRNA literature, highlighting various studies performed over the last decade. The aim is to assess if changes in various miRNAs could correlate with the progression of diabetic nephropathy. Based on the survey, we found that miRNA-377, miRNA-192, miRNA-216/217 and miRNA-144 are increased in body fluids of patients with DN, while miRNA-21 and miRNA-375 are decreased. Overall, there are a very few miRNAs that are kidney specific, and although significant differences were observed in the urinary excretion of certain miRNAs, they were not correlative to their levels in the blood or plasma. Thus, it is completely plausible that urine-specific miRNAs could serve as novel biomarkers for the diagnosis of early stages of diabetic nephropathy. PMID:23683774

  10. Combined miRNA profiling and proteomics demonstrates that different miRNAs target a common set of proteins to promote colorectal cancer metastasis.

    PubMed

    Torres, Sofía; Garcia-Palmero, Irene; Bartolomé, Rubén A; Fernandez-Aceñero, María Jesús; Molina, Elena; Calviño, Eva; Segura, Miguel F; Casal, J Ignacio

    2017-05-01

    The process of liver colonization in colorectal cancer remains poorly characterized. Here, we addressed the role of microRNA (miRNA) dysregulation in metastasis. We first compared miRNA expression profiles between colorectal cancer cell lines with different metastatic properties and then identified target proteins of the dysregulated miRNAs to establish their functions and prognostic value. We found that 38 miRNAs were differentially expressed between highly metastatic (KM12SM/SW620) and poorly metastatic (KM12C/SW480) cancer cell lines. After initial validation, we determined that three miRNAs (miR-424-3p, -503, and -1292) were overexpressed in metastatic colorectal cancer cell lines and human samples. Stable transduction of non-metastatic cells with each of the three miRNAs promoted metastatic properties in culture and increased liver colonization in vivo. Moreover, miR-424-3p and miR-1292 were associated with poor prognosis in human patients. A quantitative proteomic analysis of colorectal cancer cells transfected with miR-424-3p, miR-503, or miR-1292 identified alterations in 149, 129, or 121 proteins, respectively, with an extensive overlap of the target proteins of the three miRNAs. Importantly, down-regulation of two of these shared target proteins, CKB and UBA2, increased cell adhesion and proliferation in colorectal cancer cells. The capacity of distinct miRNAs to regulate the same mRNAs boosts the capacity of miRNAs to regulate cancer metastasis and underscores the necessity of targeting multiple miRNAs for effective cancer therapy. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

  11. Effects of form of nitrogen fertilization on the accumulation of Pb, As, Sc Ge and U in shoots of reed canary grass (Phalaris arundinacea L.)

    NASA Astrophysics Data System (ADS)

    Wiche, Oliver; Székely, Balázs; Moschner, Christin; Heilmeier, Hermann

    2015-04-01

    Nitrogen (N) fertilization is necessary for growth and development of plants but it may also causes an increased metal uptake by plants due to changes of physiochemical properties of the elements in soil. The research in phytoremediation and phytomining conducted so far has revealed that the effect of nitrogen fertilizers initially depends on the form of application, as N is the only element that can be readily utilized by plants in its cationic (ammonia) or anionic form (nitrate) causing several effects in soil-plant system. However, to our knowledge most of the recent studies only documented an improvement of yield parameters and the uptake of heavy metals by plants as a result of different forms of N-fertilization. Here we report the result of a field experiment were we tried to obtain more information about the effects of form of N-fertilization on uptake of As, Pb, Sc Ge and U in reed canary grass (Phalaris arundinacea L.). In this study, reed canary grass was grown on 15 plots (4 m² each) under field conditions on a semi-field lysimer at the off-site soil recycling and remediation center in Hirschfeld (Saxony, Germany). To test the effects of a fertilization with different N-forms on the accumulation, the plots plants received 5 g N / m² in three doses as NH4SO4, Mg(NO3)2 or NH4NO3. The geometrical arrangement of plots was randomized and every treatment was fivefold replicated. After a 50 day period of plant growth, the plants were harvested and concentrations of trace metals in the shoots were measured with ICP-MS. As a result of the different N-treatments we found that in plants treated with NH4SO4 concentrations of Pb and As as well as of Sc, Ge and U were significantly increased in plant tissues compared to plants treated with NH4NO3. Furthermore, no significant changes in mineral composition of plants between the Mg(NO3)2 and NH4NO3 treatments could be observed. Our interpretation of these results is that it might be an effect of the acidification of

  12. Neuropilin-1 is a receptor for extracellular miRNA and AGO2/miRNA complexes and mediates the internalization of miRNAs that modulate cell function.

    PubMed

    Prud'homme, Gerald J; Glinka, Yelena; Lichner, Zsuzsanna; Yousef, George M

    2016-10-18

    Extracellular miRNAs are increasingly studied as markers for specific diseases. They are released in biological fluids in a remarkably stable form, and may play a role in intercellular communication. They are thought to be protected against degradation by either encapsulation within microparticles, or by binding to proteins (mostly AGO2). The particulate forms may be internalized by endocytosis or membrane fusion, but the protein-bound forms require a receptor mechanism for their uptake. A major question is whether there are natural cell-membrane receptors that capture and internalize protein-bound functional miRNAs. We examined neuropilin-1 (NRP1), in view of its properties as a receptor for many ligands, including growth factors such as vascular endothelial growth factor (VEGF), and efficiency at mediating ligand internalization. It is expressed by endothelial cells, many other normal cell types, and cancer cells. Here, we report that NRP1 binds miRNAs with high affinity, and promotes their entry into the cell. Furthermore, the internalized miRNAs remain functional, as they specifically regulate proliferation and migration of cancer cells, as well as tube formation by human endothelial cells. Anti-NRP1 antibodies or NRP1 siRNA knockdown block miRNA effects, further confirming NRP1-mediated uptake. VEGF does not compete with miRNAs for binding to NRP1. In addition, NRP1 binds extracellular AGO2 (carrying miRNA or not), and internalizes AGO2/miRNA complexes. Because miRNA bound to AGO2 appears to the most abundant form in body fluids, this may have important physiological and pathological effects.

  13. Neuropilin-1 is a receptor for extracellular miRNA and AGO2/miRNA complexes and mediates the internalization of miRNAs that modulate cell function

    PubMed Central

    Prud'homme, Gerald J.; Glinka, Yelena; Lichner, Zsuzsanna; Yousef, George M.

    2016-01-01

    Extracellular miRNAs are increasingly studied as markers for specific diseases. They are released in biological fluids in a remarkably stable form, and may play a role in intercellular communication. They are thought to be protected against degradation by either encapsulation within microparticles, or by binding to proteins (mostly AGO2). The particulate forms may be internalized by endocytosis or membrane fusion, but the protein-bound forms require a receptor mechanism for their uptake. A major question is whether there are natural cell-membrane receptors that capture and internalize protein-bound functional miRNAs. We examined neuropilin-1 (NRP1), in view of its properties as a receptor for many ligands, including growth factors such as vascular endothelial growth factor (VEGF), and efficiency at mediating ligand internalization. It is expressed by endothelial cells, many other normal cell types, and cancer cells. Here, we report that NRP1 binds miRNAs with high affinity, and promotes their entry into the cell. Furthermore, the internalized miRNAs remain functional, as they specifically regulate proliferation and migration of cancer cells, as well as tube formation by human endothelial cells. Anti-NRP1 antibodies or NRP1 siRNA knockdown block miRNA effects, further confirming NRP1-mediated uptake. VEGF does not compete with miRNAs for binding to NRP1. In addition, NRP1 binds extracellular AGO2 (carrying miRNA or not), and internalizes AGO2/miRNA complexes. Because miRNA bound to AGO2 appears to the most abundant form in body fluids, this may have important physiological and pathological effects. PMID:27486976

  14. Identification and Expression Analyses of miRNAs from Two Contrasting Flower Color Cultivars of Canna by Deep Sequencing

    PubMed Central

    Yadav, Amrita; Mishra, Parneeta; Nautiyal, Chandra Shekhar

    2016-01-01

    miRNAs are endogenous small RNA (sRNA) that play critical roles in plant development processes. Canna is an ornamental plant belonging to family Cannaceae. Here, we report for the first time the identification and differential expression of miRNAs in two contrasting flower color cultivars of Canna, Tropical sunrise and Red president. A total of 313 known miRNAs belonging to 78 miRNA families were identified from both the cultivars. Thirty one miRNAs (17 miRNA families) were specific to Tropical sunrise and 43 miRNAs (10 miRNA families) were specific to Red president. Thirty two and 18 putative new miRNAs were identified from Tropical sunrise and Red president, respectively. One hundred and nine miRNAs were differentially expressed in the two cultivars targeting 1343 genes. Among these, 16 miRNAs families targeting60 genes were involved in flower development related traits and five miRNA families targeting five genes were involved in phenyl propanoid and pigment metabolic processes. We further validated the expression analysis of a few miRNA and their target genes by qRT-PCR. Transcription factors were the major miRNA targets identified. Target validation of a few randomly selected miRNAs by RLM-RACE was performed but was successful with only miR162. These findings will help in understanding flower development processes, particularly the color development in Canna. PMID:26799570

  15. Identification and Expression Analyses of miRNAs from Two Contrasting Flower Color Cultivars of Canna by Deep Sequencing.

    PubMed

    Roy, Sribash; Tripathi, Abhinandan Mani; Yadav, Amrita; Mishra, Parneeta; Nautiyal, Chandra Shekhar

    2016-01-01

    miRNAs are endogenous small RNA (sRNA) that play critical roles in plant development processes. Canna is an ornamental plant belonging to family Cannaceae. Here, we report for the first time the identification and differential expression of miRNAs in two contrasting flower color cultivars of Canna, Tropical sunrise and Red president. A total of 313 known miRNAs belonging to 78 miRNA families were identified from both the cultivars. Thirty one miRNAs (17 miRNA families) were specific to Tropical sunrise and 43 miRNAs (10 miRNA families) were specific to Red president. Thirty two and 18 putative new miRNAs were identified from Tropical sunrise and Red president, respectively. One hundred and nine miRNAs were differentially expressed in the two cultivars targeting 1343 genes. Among these, 16 miRNAs families targeting 60 genes were involved in flower development related traits and five miRNA families targeting five genes were involved in phenyl propanoid and pigment metabolic processes. We further validated the expression analysis of a few miRNA and their target genes by qRT-PCR. Transcription factors were the major miRNA targets identified. Target validation of a few randomly selected miRNAs by RLM-RACE was performed but was successful with only miR162. These findings will help in understanding flower development processes, particularly the color development in Canna.

  16. MatureBayes: A Probabilistic Algorithm for Identifying the Mature miRNA within Novel Precursors

    PubMed Central

    Gkirtzou, Katerina; Tsamardinos, Ioannis; Tsakalides, Panagiotis; Poirazi, Panayiota

    2010-01-01

    Background MicroRNAs (miRNAs) are small, single stranded RNAs with a key role in post-transcriptional regulation of thousands of genes across numerous species. While several computational methods are currently available for identifying miRNA genes, accurate prediction of the mature miRNA remains a challenge. Existing approaches fall short in predicting the location of mature miRNAs but also in finding the functional strand(s) of miRNA precursors. Methodology/Principal Findings Here, we present a computational tool that incorporates a Naive Bayes classifier to identify mature miRNA candidates based on sequence and secondary structure information of their miRNA precursors. We take into account both positive (true mature miRNAs) and negative (same-size non-mature miRNA sequences) examples to optimize sensitivity as well as specificity. Our method can accurately predict the start position of experimentally verified mature miRNAs for both human and mouse, achieving a significantly larger (often double) performance accuracy compared with two existing methods. Moreover, the method exhibits a very high generalization performance on miRNAs from two other organisms. More importantly, our method provides direct evidence about the features of miRNA precursors which may determine the location of the mature miRNA. We find that the triplet of positions 7, 8 and 9 from the mature miRNA end towards the closest hairpin have the largest discriminatory power, are relatively conserved in terms of sequence composition (mostly contain a Uracil) and are located within or in very close proximity to the hairpin loop, suggesting the existence of a possible recognition site for Dicer and associated proteins. Conclusions This work describes a novel algorithm for identifying the start position of mature miRNA(s) produced by miRNA precursors. Our tool has significantly better (often double) performance than two existing approaches and provides new insights about the potential use of specific

  17. miRNA Profiling of Naïve, Effector and Memory CD8 T Cells

    PubMed Central

    Wu, Haoquan; Neilson, Joel R.; Kumar, Priti; Manocha, Monika; Shankar, Premlata; Sharp, Phillip A.; Manjunath, N.

    2007-01-01

    microRNAs have recently emerged as master regulators of gene expression during development and cell differentiation. Although profound changes in gene expression also occur during antigen-induced T cell differentiation, the role of miRNAs in the process is not known. We compared the miRNA expression profiles between antigen-specific naïve, effector and memory CD8+ T cells using 3 different methods-small RNA cloning, miRNA microarray analysis and real-time PCR. Although many miRNAs were expressed in all the T cell subsets, the frequency of 7 miRNAs (miR-16, miR-21, miR-142-3p, miR-142-5p, miR-150, miR-15b and let-7f) alone accounted for ∼60% of all miRNAs, and their expression was several fold higher than the other expressed miRNAs. Global downregulation of miRNAs (including 6/7 dominantly expressed miRNAs) was observed in effector T cells compared to naïve cells and the miRNA expression levels tended to come back up in memory T cells. However, a few miRNAs, notably miR-21 were higher in effector and memory T cells compared to naïve T cells. These results suggest that concomitant with profound changes in gene expression, miRNA profile also changes dynamically during T cell differentiation. Sequence analysis of the cloned mature miRNAs revealed an extensive degree of end polymorphism. While 3′end polymorphisms dominated, heterogeneity at both ends, resembling drosha/dicer processing shift was also seen in miR-142, suggesting a possible novel mechanism to generate new miRNA and/or to diversify miRNA target selection. Overall, our results suggest that dynamic changes in the expression of miRNAs may be important for the regulation of gene expression during antigen-induced T cell differentiation. Our study also suggests possible novel mechanisms for miRNA biogenesis and function. PMID:17925868

  18. Intraindividual Temporal miRNA Variability in Serum, Plasma, and White Blood Cell Subpopulations.

    PubMed

    Ammerlaan, Wim; Betsou, Fay

    2016-10-01

    Blood microRNAs (miRNAs) are ideal biomarkers, and blood derivatives are often collected in the scope of miRNA research projects. However, knowledge of temporal variations of miRNAs in healthy individuals is lacking. In this study, miRNA variability was measured over a 1-year period in different blood derivatives, collected every 2-3 months from two healthy donors. There is a continuum of intraindividual temporal variability, with particularly stable (coefficient of variation [CV] <20%-30%) and particularly unstable (CV >100%-130%) miRNAs in serum, plasma, and specific white blood cell subpopulations. The temporal intraindividual variability of miRNAs should be taken into consideration in experimental design of biospecimen collections and validation of diagnostic biomarkers.

  19. Targeted delivery of miRNA therapeutics for cardiovascular diseases: opportunities and challenges.

    PubMed

    Kwekkeboom, Rick F J; Lei, Zhiyong; Doevendans, Pieter A; Musters, René J P; Sluijter, Joost P G

    2014-09-01

    Dysregulation of miRNA expression has been associated with many cardiovascular diseases in animal models, as well as in patients. In the present review, we summarize recent findings on the role of miRNAs in cardiovascular diseases and discuss the opportunities, possibilities and challenges of using miRNAs as future therapeutic targets. Furthermore, we focus on the different approaches that can be used to deliver these newly developed miRNA therapeutics to their sites of action. Since siRNAs are structurally homologous with the miRNA therapeutics, important lessons learned from siRNA delivery strategies are discussed that might be applicable to targeted delivery of miRNA therapeutics, thereby reducing costs and potential side effects, and improving efficacy.

  20. Exploring miRNA based approaches in cancer diagnostics and therapeutics.

    PubMed

    Mishra, Shivangi; Yadav, Tanuja; Rani, Vibha

    2016-02-01

    MicroRNAs (miRNAs), a highly conserved class of tissue specific, small non-protein coding RNAs maintain cell homeostasis by negative gene regulation. Proper controlling of miRNA expression is required for a balanced physiological environment, as these small molecules influence almost every genetic pathway from cell cycle checkpoint, cell proliferation to apoptosis, with a wide range of target genes. Deregulation in miRNAs expression correlates with various cancers by acting as tumor suppressors and oncogenes. Although promising therapies exist to control tumor development and progression, there is a lack of efficient diagnostic and therapeutic approaches for delineating various types of cancer. The molecularly different tumors can be differentiated by specific miRNA profiling as their phenotypic signatures, which can hence be exploited to surmount the diagnostic and therapeutic challenges. Present review discusses the involvement of miRNAs in oncogenesis with the analysis of patented research available on miRNAs.

  1. Formaldehyde exposure alters miRNA expression profiles in the olfactory bulb.

    PubMed

    Li, Guifa; Yang, Jing; Ling, Shucai

    2015-01-01

    It has been reported that inhaling formaldehyde (FA) causes damage to the central nervous system. However, it is unclear whether FA can disturb the function of the olfactory bulb. Using a microarray, we found that FA inhalation altered the miRNA expression profile. Functional enrichment analysis of the predicted targets of the changed miRNA showed that the enrichment canonical pathways and networks associated with cancer and transcriptional regulation. FA exposure disrupts miRNA expression profiles within the olfactory bulb.

  2. Dynamic regulation of novel and conserved miRNAs across various tissues of diverse Cucurbit spp.

    USDA-ARS?s Scientific Manuscript database

    MicroRNA genes (miRNAs) encoding small non-coding RNAs are abundant in plant genomes and play a key role in regulating several biological mechanisms. Five conserved miRNAs, miR156, miR168-1, miR168-2, miR164, and miR166 were selected for analysis from the 21 known plant miRNA families that were rec...

  3. Diverse miRNA spatial expression patterns suggest important roles in homeostasis and regeneration in planarians.

    PubMed

    González-Estévez, Cristina; Arseni, Varvara; Thambyrajah, Roshana S; Felix, Daniel A; Aboobaker, A Aziz

    2009-01-01

    miRNAs are an important class of non-protein coding small RNAs whose specific functions in animals are rapidly being elucidated. It is clear that miRNAs can play crucial roles in stem cell maintenance, cell fate determination and differentiation. We use planarians, which possess a large population of pluripotent somatic stem cells, as a powerful model system to study many aspects of stem cell biology and regeneration. In particular we wish to investigate the regulatory role miRNAs may have in planarian stem cell self renewal, proliferation and differentiation. Here, we characterized the differential spatial patterns of expression of miRNAs in whole and regenerating planarians by in situ hybridization to nascent miRNA transcripts. These miRNA expression patterns are the first which have been determined for a Lophotrocozoan animal. We have characterized the expression patterns of 42 miRNAs in adult planarians, constituting a complete range of tissue specific expression patterns. We also followed miRNA expression during planarian regeneration. The majority of planarian miRNAs were expressed either in areas where stem cells (neoblasts) are located and/or in the nervous system. Some miRNAs were definitively expressed in stem cells and dividing cells as confirmed by in situ hybridisation after irradiation. We also found miRNAs to be expressed in germ stem cells of the sexual strain. Together, these data suggest an important role for miRNAs in stem cell regulation and in neural cell differentiation in planarians.

  4. MicroRNA Key to Angiogenesis Regulation: miRNA Biology and Therapy.

    PubMed

    Tiwari, Ankit; Mukherjee, Bratati; Dixit, Manjusha

    2017-06-30

    Angiogenesis is involved in maintaining normal physiological processes like embryonic development, wound healing, inflammation and reproduction. Pathogenesis of various diseases like diabetic retinopathy, rheumatoid arthritis and cancer are associated with imbalanced angiogenesis. Angiogenic stimulators and inhibitors act together for keeping angiogenic switch in balance. Recently miRNAs have been found to regulate various stages of angiogenesis. miRNAs are 21-23 nucleotides long, single stranded, noncoding RNA molecules generated endogenously. miRNA's ability to target multiple genes within a signaling pathway makes them promising target for the development of second generation anti-angiogenesis drugs. This review was conceived with the notion of availability of specific and comprehensive knowledge about AngiomiRs at one place. This will facilitate the research in basic understanding and in the development of new drugs. In this review, we have summarized the biology and therapeutic potential of the miRNAs, which are involved in controlling angiogenesis process. In miRNA biology, we have provided the updated summary of miRNAs in the regulation of endothelial cells, showed role of miRNAs in the signaling pathways of angiogenesis and, discussed the gaps in complete knowledge of mechanism. We have also provided exclusive insights regarding therapeutic potential of these miRNAs, in angiogenesis related disorders. Additionally, we have discussed the challenges in miRNA based drug delivery and updated the current efforts in the development of miRNA delivery methods. Though much research is needed to discover the complete miRNA network regulating angiogenesis but once it is done, targeting miRNA may be considered as a potential candidate for therapeutic invention against angiogenesis related disorders. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  5. miRNA Transcriptome of Hypertrophic Skeletal Muscle with Overexpressed Myostatin Propeptide

    PubMed Central

    Jing, Lu; Li, Xinyun; Cao, Jianhua; Zhao, Shuhong

    2014-01-01

    MicroRNAs (miRNAs) play an imperative role in cell proliferation, differentiation, and cell metabolism through regulation of gene expression. Skeletal muscle hypertrophy that results from myostatin depression by its propeptide provides an interesting model to understand how miRNA transcriptome is involved in myostatin-based fiber hypertrophy. This study employed Solexa deep sequencing followed by Q-PCR methods to analyze miRNA transcriptome of skeletal muscle of myostatin propeptide transgenic mice in comparison with their littermate controls. A total of 461 mature known and 69 novel miRNAs were reported from this study. Fifty-seven miRNAs were expressed differentially between transgenic and littermate controls, of which most abundant miRNAs, miR-133a and 378a, were significantly differentially expressed. Expression profiling was validated on 8 known and 2 novel miRNAs. The miRNA targets prediction and pathway analysis showed that FST, SMAD3, TGFBR1, and AcvR1a genes play a vital role in skeletal muscle hypertrophy in the myostatin propeptide transgenic mice. It is predicted that miR-101 targeted to TGFBR1 and SMAD3, miR-425 to TGFBR2 and FST, and miR-199a to AcvR2a and TGF-β genes. In conclusion, the study offers initial miRNA profiling and methodology of miRNA targets prediction for myostatin-based hypertrophy. These differentially expressed miRNAs are proposed as candidate miRNAs for skeletal muscle hypertrophy. PMID:25147795

  6. Discovery of porcine miRNA-196a/b may influence porcine adipogenesis in longissimus dorsi muscle by miRNA sequencing.

    PubMed

    Liu, Linqing; Qian, Kun; Wang, Chonglong

    2017-04-01

    Intramuscular fat (IMF) is one of the fat traits that has economic importance in the pork industry. Longissimus dorsi muscle contains IMF and is suitable for studying adipogenesis. To discover further potential regulatory miRNAs that may influence adipogenesis, we analyzed miRNA in the longissimus dorsi muscle of Yorkshire (YY, lean-type) and Chinese Wannanhua (WH, fatty) pigs using miRNA sequencing (miRNA-seq). From this dataset, we identified 598 unique miRNAs comprising 325 pre-miRNAs and 273 novel pre-miRNAs through comparison with known miRNAs in miRBase version 21. We found 42 miRNAs including nine up- and 33 down-regulated between the YY and WH pigs. Moreover, we found two miRNAs, miR-196a/b (miR-196a, miR-196b-5p), that had the highest level of expression in WH pigs, and miR-196a/b may influence porcine adipogenesis in longissimus dorsi muscle through an adipocytokine signaling pathway.

  7. miRNA in multiple sclerosis: search for novel biomarkers.

    PubMed

    Gandhi, Roopali

    2015-08-01

    A major challenge in multiple sclerosis (MS) is to develop biomarkers that could help in understanding individual MS patients, i.e. whether they are a responder or non-responder to therapy, which medicine is more effective, and the degree to which they may be entering the progressive phase of disease. In the last few years, a lot of attention has been drawn toward identification of diagnostic, prognostic, process-specific, and treatment-related biomarkers for MS. In this review, we will focus on the micro RNAs (miRNAs) as potential candidates for MS biomarkers.

  8. Differential expression of miRNAs and their relation to active tuberculosis.

    PubMed

    Xu, Zhihong; Zhou, Aiping; Ni, Jinjing; Zhang, Qiufen; Wang, Ying; Lu, Jie; Wu, Wenjuan; Karakousis, Petros C; Lu, Shuihua; Yao, Yufeng

    2015-07-01

    The aim of this work was to screen miRNA signatures dysregulated in tuberculosis to improve our understanding of the biological role of miRNAs involved in the disease. Datasets deposited in publically available databases from microarray studies on infectious diseases and malignancies were retrieved, screened, and subjected to further analysis. Effect sizes were combined using the inverse-variance model and between-study heterogeneity was evaluated by the random effects model. 35 miRNAs were differentially expressed (12 up-regulated, 23 down-regulated; p < 0.05) by combining 15 datasets of tuberculosis and other infectious diseases. 15 miRNAs were found to be significantly differentially regulated (7 up-regulated, 8 down-regulated; p < 0.05) by combining 53 datasets of tuberculosis and malignancies. Most of the miRNA signatures identified in this study were found to be involved in immune responses and metabolism. Expression of these miRNA signatures in serum samples from TB subjects (n = 11) as well as healthy controls (n = 10) was examined by TaqMan miRNA array. Taken together, the results revealed differential expression of miRNAs in TB, but available datasets are limited and these miRNA signatures should be validated in future studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. MiRNAs: potential diagnostic and therapeutic targets for cerebral ischaemia.

    PubMed

    Zhu, Ruixia; Liu, Xu; Zhu, Ying; He, Zhiyi

    2016-01-01

    MiRNAs are short single-stranded non-coding RNAs that cause degradation or repression of target mRNAs by base pairing with their 3'-untranslated regions. Recent studies have shown that miRNAs play an important role in the occurrence and development of cerebral ischaemia, as well as exerting regulatory effects. Additionally, circulating miRNAs in peripheral blood, which are dysregulated following cerebral ischaemia, have recently been identified as useful biomarkers in diagnosis and prognosis of cerebral ischaemia. Single-nucleotide polymorphisms (SNPs) located in miRNA genes or target sites are likely to cause complex functional consequences by affecting miRNA biogenesis or target selection. Research on miRNA-SNPs is rapidly growing, and recent studies have identified a significant relationship between miRNAs and ischemic disease. We also address the latest advances in miRNA-based therapeutic approaches for ischemic disease. In conclusion, our review summarizes current research regarding miRNAs and cerebral ischaemia, focusing on the regulatory role of miRNAs in cerebral ischaemia, as well as the potential of miRNAs as biomarkers and therapeutic targets in cerebral ischaemia.

  10. Methods and matrices: approaches to identifying miRNAs for Nasopharyngeal carcinoma

    PubMed Central

    2014-01-01

    Background Nasopharyngeal carcinoma (NPC) is a solid tumor of the head and neck. Multimodal therapy is highly effective when NPC is detected early. However, due to the location of the tumor and the absence of clinical signs, early detection is difficult, making a biomarker for the early detection of NPC a priority. The dysregulation of small non-coding RNAs (miRNAs) during carcinogenesis is the focus of much current biomarker research. Herein, we examine several miRNA discovery methods using two sample matrices to identify circulating miRNAs (c-miRNAs) associated with NPC. Methods We tested two miRNA discovery workflows on two sample sources for miRNAs associated with NPC. In the first workflow, we assumed that NPC tumor tissue would be enriched for miRNAs, so we compared miRNA expression in FFPE from NPC cases and controls using microarray and RNA-Seq technologies. Candidate miRNAs from both technologies were verified by qPCR in FFPE and sera from an independent NPC sample set. In a second workflow, we directly interrogated NPC case and control sera by RNA-Seq for c-miRNAs associated with NPC, with candidate c-miRNAs verified by qPCR in the sera from the same independent NPC sample set. Results Both microarray and RNA-Seq narrowed the miRNA signature to 1-5% of the known mature human miRNAs. Moreover, these two methods produced similar results when applied to the same sample type (FFPE), with RNA-Seq additionally indicating “unknown” miRNAs associated with NPC. However, we found different miRNA profiles in NPC sera compared to FFPE using RNA-Seq, with the few overlapping miRNAs found to be significantly up-regulated in FFPE significantly down-regulated in sera (and vice versa). Despite the different miRNA profiles found in FFPE and sera, both profiles strongly associated with NPC, providing two potential sources for biomarker signatures for NPC. Conclusions We determined that the direct interrogation of sera by RNA-Seq was the most informative method for

  11. A compilation of Web-based research tools for miRNA analysis.

    PubMed

    Shukla, Vaibhav; Varghese, Vinay Koshy; Kabekkodu, Shama Prasada; Mallya, Sandeep; Satyamoorthy, Kapaettu

    2017-02-25

    Since the discovery of microRNAs (miRNAs), a class of noncoding RNAs that regulate the gene expression posttranscriptionally in sequence-specific manner, there has been a release of number of tools useful for both basic and advanced applications. This is because of the significance of miRNAs in many pathophysiological conditions including cancer. Numerous bioinformatics tools that have been developed for miRNA analysis have their utility for detection, expression, function, target prediction and many other related features. This review provides a comprehensive assessment of web-based tools for the miRNA analysis that does not require prior knowledge of any computing languages.

  12. Role of miRNAs in development and disease: Lessons learnt from small organisms.

    PubMed

    Chandra, Swati; Vimal, Divya; Sharma, Divya; Rai, Vipin; Gupta, Subash Chandra; Chowdhuri, D Kar

    2017-09-15

    MicroRNAs (miRNAs) constitute a class of small (18-22 nucleotides) non-coding RNAs that regulate gene expression at the post-transcriptional level. Caenorhabditis elegans, Drosophila melanogaster, and many other small organisms have been instrumental in deciphering the biological functions of miRNAs. While some miRNAs from small organisms are highly conserved across the taxa, others are organism specific. The miRNAs are known to play a crucial role during development and in various cellular functions such as cell survival, cell proliferation, and differentiation. The miRNAs associated with fragile X syndrome, Parkinson's disease, Alzheimer's disease, diabetes, cancer, malaria, infectious diseases and several other human diseases have been identified from small organisms. These organisms have been used as platforms in deciphering the functions of miRNAs in the pathogenesis of human diseases and to study miRNA biogenesis. Small organisms have also been used in the development of miRNA-based diagnostic, prognostic and therapeutic strategies. The molecular techniques such as genome sequencing, northern blot analysis, and quantitative RT-PCR, have been used in deciphering the functions of miRNAs in small organisms. How miRNAs from small organisms especially those from Drosophila and C. elegans regulate development and disease pathogenesis is the focus of this review. The outstanding questions raised by our current understanding are discussed. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. miRiadne: a web tool for consistent integration of miRNA nomenclature.

    PubMed

    Bonnal, Raoul J P; Rossi, Riccardo L; Carpi, Donatella; Ranzani, Valeria; Abrignani, Sergio; Pagani, Massimiliano

    2015-07-01

    The miRBase is the official miRNA repository which keeps the annotation updated on newly discovered miRNAs: it is also used as a reference for the design of miRNA profiling platforms. Nomenclature ambiguities generated by loosely updated platforms and design errors lead to incompatibilities among platforms, even from the same vendor. Published miRNA lists are thus generated with different profiling platforms that refer to diverse and not updated annotations. This greatly compromises searches, comparisons and analyses that rely on miRNA names only without taking into account the mature sequences, which is particularly critic when such analyses are carried over automatically. In this paper we introduce miRiadne, a web tool to harmonize miRNA nomenclature, which takes into account the original miRBase versions from 10 up to 21, and annotations of 40 common profiling platforms from nine brands that we manually curated. miRiadne uses the miRNA mature sequence to link miRBase versions and/or platforms to prevent nomenclature ambiguities. miRiadne was designed to simplify and support biologists and bioinformaticians in re-annotating their own miRNA lists and/or data sets. As Ariadne helped Theseus in escaping the mythological maze, miRiadne will help the miRNA researcher in escaping the nomenclature maze. miRiadne is freely accessible from the URL http://www.miriadne.org.

  14. Prognostic and Clinical Significance of miRNA-205 in Endometrioid Endometrial Cancer.

    PubMed

    Wilczynski, Milosz; Danielska, Justyna; Dzieniecka, Monika; Szymanska, Bozena; Wojciechowski, Michal; Malinowski, Andrzej

    2016-01-01

    Endometrial cancer is one of the most common malignancies of the reproductive female tract, with endometrioid endometrial cancer being the most frequent type. Despite the relatively favourable prognosis in cases of endometrial cancer, there is a necessity to evaluate clinical and prognostic utility of new molecular markers. MiRNAs are small, non-coding RNA molecules that take part in RNA silencing and post-transcriptional regulation of gene expression. Altered expression of miRNAs may be associated with cancer initiation, progression and metastatic capabilities. MiRNA-205 seems to be one of the key regulators of gene expression in endometrial cancer. In this study, we investigated clinical and prognostic role of miRNA-205 in endometrioid endometrial cancer. After total RNA extraction from 100 archival formalin-fixed paraffin-embedded tissues, real-time quantitative RT-PCR was used to define miRNA-205 expression levels. The aim of the study was to evaluate miRNA-205 expression levels in regard to patients' clinical and histopathological features, such as: survival rate, recurrence rate, staging, myometrial invasion, grading and lymph nodes involvement. Higher levels of miRNA-205 expression were observed in tumours with less than half of myometrial invasion and non-advanced cancers. Kaplan-Maier analysis revealed that higher levels of miRNA-205 were associated with better overall survival (p = 0,034). These results indicate potential clinical utility of miRNA-205 as a prognostic marker.

  15. Platelets confound the measurement of extracellular miRNA in archived plasma.

    PubMed

    Mitchell, Adam J; Gray, Warren D; Hayek, Salim S; Ko, Yi-An; Thomas, Sheena; Rooney, Kim; Awad, Mosaab; Roback, John D; Quyyumi, Arshed; Searles, Charles D

    2016-09-13

    Extracellular miRNAs are detectable in biofluids and represent a novel class of disease biomarker. Although many studies have utilized archived plasma for miRNA biomarker discovery, the effects of processing and storage have not been rigorously studied. Previous reports have suggested plasma samples are commonly contaminated by platelets, significantly confounding the measurement of extracellular miRNA, which was thought to be easily addressed by additional post-thaw plasma processing. In a case-control study of archived plasma, we noted a significant correlation between miRNA levels and platelet counts despite post-thaw processing. We thus examined the effects of a single freeze/thaw cycle on microparticles (MPs) and miRNA levels, and show that a single freeze/thaw cycle of plasma dramatically increases the number of platelet-derived MPs, contaminates the extracellular miRNA pool, and profoundly affects the levels of miRNAs detected. The measurement of extracellular miRNAs in archived samples is critically dependent on the removal of residual platelets prior to freezing plasma samples. Many previous clinical studies of extracellular miRNA in archived plasma should be interpreted with caution and future studies should avoid the effects of platelet contamination.

  16. Prognostic and Clinical Significance of miRNA-205 in Endometrioid Endometrial Cancer

    PubMed Central

    Wilczynski, Milosz; Wojciechowski, Michal; Malinowski, Andrzej

    2016-01-01

    Endometrial cancer is one of the most common malignancies of the reproductive female tract, with endometrioid endometrial cancer being the most frequent type. Despite the relatively favourable prognosis in cases of endometrial cancer, there is a necessity to evaluate clinical and prognostic utility of new molecular markers. MiRNAs are small, non-coding RNA molecules that take part in RNA silencing and post-transcriptional regulation of gene expression. Altered expression of miRNAs may be associated with cancer initiation, progression and metastatic capabilities. MiRNA-205 seems to be one of the key regulators of gene expression in endometrial cancer. In this study, we investigated clinical and prognostic role of miRNA-205 in endometrioid endometrial cancer. After total RNA extraction from 100 archival formalin-fixed paraffin-embedded tissues, real-time quantitative RT-PCR was used to define miRNA-205 expression levels. The aim of the study was to evaluate miRNA-205 expression levels in regard to patients’ clinical and histopathological features, such as: survival rate, recurrence rate, staging, myometrial invasion, grading and lymph nodes involvement. Higher levels of miRNA-205 expression were observed in tumours with less than half of myometrial invasion and non-advanced cancers. Kaplan-Maier analysis revealed that higher levels of miRNA-205 were associated with better overall survival (p = 0,034). These results indicate potential clinical utility of miRNA-205 as a prognostic marker. PMID:27737015

  17. Elsevier Trophoblast Research Award Lecture: origin, evolution and future of placenta miRNAs.

    PubMed

    Morales-Prieto, D M; Ospina-Prieto, S; Schmidt, A; Chaiwangyen, W; Markert, U R

    2014-02-01

    MicroRNAs (miRNAs) regulate the expression of a large number of genes in plants and animals. Placental miRNAs appeared late in evolution and can be found only in mammals. Nevertheless, these miRNAs are constantly under evolutionary pressure. As a consequence, miRNA sequences and their mRNA targets may differ between species, and some miRNAs can only be found in humans. Their expression can be tissue- or cell-specific and can vary time-dependently. Human placenta tissue exhibits a specific miRNA expression pattern that dynamically changes during pregnancy and is reflected in the maternal plasma. Some placental miRNAs are involved in or associated with major pregnancy disorders, such as preeclampsia, intrauterine growth restriction or preterm delivery and, therefore, have a strong potential for usage as sensitive and specific biomarkers. In this review we summarize current knowledge on the origin of placental miRNAs, their expression in humans with special regard to trophoblast cells, interspecies differences, and their future as biomarkers. It can be concluded that animal models for human reproduction have a different panel of miRNAs and targets, and can only partly reflect or predict the situation in humans. Copyright © 2013. Published by Elsevier Ltd.

  18. In-silico identification of miRNAs and their regulating target functions in Ocimum basilicum.

    PubMed

    Singh, Noopur; Sharma, Ashok

    2014-12-01

    microRNA is known to play an important role in growth and development of the plants and also in environmental stress. Ocimum basilicum (Basil) is a well known herb for its medicinal properties. In this study, we used in-silico approaches to identify miRNAs and their targets regulating different functions in O. basilicum using EST approach. Additionally, functional annotation, gene ontology and pathway analysis of identified target transcripts were also done. Seven miRNA families were identified. Meaningful regulations of target transcript by identified miRNAs were computationally evaluated. Four miRNA families have been reported by us for the first time from the Lamiaceae. Our results further confirmed that uracil was the predominant base in the first positions of identified mature miRNA sequence, while adenine and uracil were predominant in pre-miRNA sequences. Phylogenetic analysis was carried out to determine the relation between O. basilicum and other plant pre-miRNAs. Thirteen potential targets were evaluated for 4 miRNA families. Majority of the identified target transcripts regulated by miRNAs showed response to stress. miRNA 5021 was also indicated for playing an important role in the amino acid metabolism and co-factor metabolism in this plant. To the best of our knowledge this is the first in silico study describing miRNAs and their regulation in different metabolic pathways of O. basilicum.

  19. Uptake of dietary milk miRNAs by adult humans: a validation study

    PubMed Central

    Auerbach, Amanda; Vyas, Gopi; Li, Anne; Halushka, Marc; Witwer, Kenneth

    2016-01-01

    Breast milk is replete with nutritional content as well as nucleic acids including microRNAs (miRNAs). In a recent report, adult humans who drank bovine milk appeared to have increased circulating levels of miRNAs miR-29b-3p and miR-200c-3p. Since these miRNAs are homologous between human and cow, these results could be explained by xeno-miRNA influx, endogenous miRNA regulation, or both. More data were needed to validate the results and explore for additional milk-related alterations in circulating miRNAs. Samples from the published study were obtained, and 223 small RNA features were profiled with a custom OpenArray, followed by individual quantitative PCR assays for selected miRNAs. Additionally, small RNA sequencing (RNA-seq) data obtained from plasma samples of the same project were analyzed to find human and uniquely bovine miRNAs. OpenArray revealed no significantly altered miRNA signals after milk ingestion, and this was confirmed by qPCR. Plasma sequencing data contained no miR-29b or miR-200c reads and no intake-consistent mapping of uniquely bovine miRNAs. In conclusion, the results do not support transfer of dietary xenomiRs into the circulation of adult humans. PMID:27158459

  20. miRNome landscape analysis reveals a 30 miRNA core in retinoblastoma.

    PubMed

    Castro-Magdonel, Blanca Elena; Orjuela, Manuela; Camacho, Javier; García-Chéquer, Adda Jeanette; Cabrera-Muñoz, Lourdes; Sadowinski-Pine, Stanislaw; Durán-Figueroa, Noé; Orozco-Romero, María de Jesús; Velázquez-Wong, Ana Claudia; Hernández-Ángeles, Adriana; Hernández-Galván, Claudia; Lara-Molina, Citlali; Ponce-Castañeda, M Verónica

    2017-07-01

    miRNAs exert their effect through a negative regulatory mechanism silencing expression upon hybridizing to their target mRNA, and have a prominent position in the control of many cellular processes including carcinogenesis. Previous miRNA studies on retinoblastoma (Rb) have been limited to specific miRNAs reported in other tumors or to medium density arrays. Here we report expression analysis of the whole miRNome on 12 retinoblastoma tumor samples using a high throughput microarray platform including 2578 mature miRNAs. Twelve retinoblastoma tumor samples were analyzed using an Affymetrix platform including 2578 mature miRNAs. We applied RMA analysis to normalize raw data, obtained categorical data from detection call values, and also used signal intensity derived expression data. We used Diana-Tools-microT-CDS to find miRNA targets and ChromDraw to map miRNAs in chromosomes. We discovered a core-cluster of 30 miRNAs that were highly expressed in all the cases and a cluster of 993 miRNAs that were uniformly absent in all cases. Another 1022 miRNA were variably present in the samples reflecting heterogeneity between tumors. We explored mRNA targets, pathways and biological processes affected by some of these miRNAs. We propose that the core-cluster of 30 miRs represent miRNA machinery common to all Rb, and affecting most pathways considered hallmarks of cancer. In this core, we identified miR-3613 as a potential and critical down regulatory hub, because it is highly expressed in all the samples and its potential mRNA targets include at least 36 tumor suppressor genes, including RB1. In the variably expressed miRNA, 36 were differentially expressed between males and females. Some of the potential pathways targeted by these 36 miRNAs were associated with hormonal production. These findings indicate that Rb tumor samples share a common miRNA expression profile regardless of tumor heterogeneity, and shed light on potential novel therapeutic targets such as mir-3613 This

  1. Chronic ethanol feeding alters miRNA expression dynamics during liver regeneration

    PubMed Central

    Dippold, Rachael P.; Vadigepalli, Rajanikanth; Gonye, Gregory E.; Patra, Biswanath; Hoek, Jan B.

    2012-01-01

    Background Adaptation to chronic ethanol treatment of rats results in a changed functional state of the liver and greatly inhibits its regenerative ability, which may contribute to the progression of alcoholic liver disease. Methods In this study we investigated the effect of chronic ethanol intake on hepatic miRNA expression in male Sprague-Dawley rats during the initial 24 hrs of liver regeneration following 70% partial hepatectomy (PHx) using microRNA (miRNA) microarrays. miRNA expression during adaptation to ethanol was investigated using RT-qPCR. Nuclear Factor kappa B (NFκB) binding at target miRNA promoters was investigated with chromatin immunoprecipitation. Results Unsupervised clustering of miRNA expression profiles suggested that miRNA expression was more affected by chronic ethanol feeding than by the acute challenge of liver regeneration after PHx. Several miRNAs that were significantly altered by chronic ethanol feeding, including miRs-34a, -103, -107, and -122 have been reported to play a role in regulating hepatic metabolism and the onset of these miRNA changes occurred gradually during the time course of ethanol feeding. Chronic ethanol feeding also altered the dynamic miRNA profile during liver regeneration. Promoter analysis predicted a role for Nuclear Factor kappa B (NFκB) in the immediate early miRNA response to PHx. NFκB binding at target miRNA promoters in the chronic ethanol-fed group was significantly altered and these changes directly correlated with the observed expression dynamics of the target miRNA. Conclusions Chronic ethanol consumption alters the hepatic miRNA expression profile such that the response of the metabolism-associated miRNAs occurs during long-term adaptation to ethanol rather than as an acute transient response to ethanol metabolism. Additionally, the dynamic miRNA program during liver regeneration in response to PHx is altered in the chronically ethanol-fed liver and these differences reflect, in part, differences

  2. Mutant p53 inhibits miRNA biogenesis by interfering with the microprocessor complex.

    PubMed

    Garibaldi, F; Falcone, E; Trisciuoglio, D; Colombo, T; Lisek, K; Walerych, D; Del Sal, G; Paci, P; Bossi, G; Piaggio, G; Gurtner, A

    2016-07-21

    Downregulation of microRNAs (miRNAs) is commonly observed in cancers and promotes tumorigenesis suggesting that miRNAs may function as tumor suppressors. However, the mechanism through which miRNAs are regulated in cancer, and the connection between oncogenes and miRNA biogenesis remain poorly understood. The TP53 tumor-suppressor gene is mutated in half of human cancers resulting in an oncogene with gain-of-function activities. Here we demonstrate that mutant p53 (mutp53) oncoproteins modulate the biogenesis of a subset of miRNAs in cancer cells inhibiting their post-transcriptional maturation. Interestingly, among these miRNAs several are also downregulated in human tumors. By confocal, co-immunoprecipitation and RNA-chromatin immunoprecipitation experiments, we show that endogenous mutp53 binds and sequesters RNA helicases p72/82 from the microprocessor complex, interfering with Drosha-pri-miRNAs association. In agreement with this, the overexpression of p72 leads to an increase of mature miRNAs levels. Moreover, functional experiments demonstrate the oncosuppressive role of mutp53-dependent miRNAs (miR-517a, -519a, -218, -105). Our study highlights a previously undescribed mechanism by which mutp53 interferes with Drosha-p72/82 association leading, at least in part, to miRNA deregulation observed in cancer.

  3. Identification of associations between small molecule drugs and miRNAs based on functional similarity

    PubMed Central

    Dai, EnYu; Yang, Feng; Wang, Shuyuan; Chen, Xiaowen; Yang, Lei; Wang, Yuwen; Jiang, Wei

    2016-01-01

    MicroRNAs (miRNAs) are a class of small non-coding RNA molecules that regulate gene expression at post-transcriptional level. Increasing evidences show aberrant expression of miRNAs in varieties of diseases. Targeting the dysregulated miRNAs with small molecule drugs has become a novel therapy for many human diseases, especially cancer. Here, we proposed a novel computational approach to identify associations between small molecules and miRNAs based on functional similarity of differentially expressed genes. At the significance level of p < 0.01, we constructed the small molecule and miRNA functional similarity network involving 111 small molecules and 20 miRNAs. Moreover, we also predicted associations between drugs and diseases through integrating our identified small molecule-miRNA associations with experimentally validated disease related miRNAs. As a result, we identified 2265 associations between FDA approved drugs and diseases, in which ~35% associations have been validated by comprehensive literature reviews. For breast cancer, we identified 19 potential drugs, in which 12 drugs were supported by previous studies. In addition, we performed survival analysis for the patients from TCGA and GEO database, which indicated that the associated miRNAs of 4 drugs might be good prognosis markers in breast cancer. Collectively, this study proposed a novel approach to predict small molecule and miRNA associations based on functional similarity, which may pave a new way for miRNA-targeted therapy and drug repositioning. PMID:27232942

  4. Platelets confound the measurement of extracellular miRNA in archived plasma

    PubMed Central

    Mitchell, Adam J.; Gray, Warren D.; Hayek, Salim S.; Ko, Yi-An; Thomas, Sheena; Rooney, Kim; Awad, Mosaab; Roback, John D.; Quyyumi, Arshed; Searles, Charles D.

    2016-01-01

    Extracellular miRNAs are detectable in biofluids and represent a novel class of disease biomarker. Although many studies have utilized archived plasma for miRNA biomarker discovery, the effects of processing and storage have not been rigorously studied. Previous reports have suggested plasma samples are commonly contaminated by platelets, significantly confounding the measurement of extracellular miRNA, which was thought to be easily addressed by additional post-thaw plasma processing. In a case-control study of archived plasma, we noted a significant correlation between miRNA levels and platelet counts despite post-thaw processing. We thus examined the effects of a single freeze/thaw cycle on microparticles (MPs) and miRNA levels, and show that a single freeze/thaw cycle of plasma dramatically increases the number of platelet-derived MPs, contaminates the extracellular miRNA pool, and profoundly affects the levels of miRNAs detected. The measurement of extracellular miRNAs in archived samples is critically dependent on the removal of residual platelets prior to freezing plasma samples. Many previous clinical studies of extracellular miRNA in archived plasma should be interpreted with caution and future studies should avoid the effects of platelet contamination. PMID:27623086

  5. Methylation of miRNA genes in the response to temperature stress in Populus simonii

    PubMed Central

    Ci, Dong; Song, Yuepeng; Tian, Min; Zhang, Deqiang

    2015-01-01

    DNA methylation and miRNAs provide crucial regulation of the transcriptional and post-transcriptional responses to abiotic stress. In this study, we used methylation-sensitive amplification polymorphisms to identify 1066 sites that were differentially methylated in response to temperature stress in Populus simonii. Among these loci, BLAST searches of miRBase identified seven miRNA genes. Expression analysis by quantitative real-time PCR suggested that the methylation pattern of these miRNA genes probably influences their expression. Annotation of these miRNA genes in the sequenced genome of Populus trichocarpa found three target genes (Potri.007G090400, Potri.014G042200, and Potri.010G176000) for the miRNAs produced from five genes (Ptc-MIR396e and g, Ptc-MIR156i and j, and Ptc-MIR390c) respectively. The products of these target genes function in lipid metabolism to deplete lipid peroxide. We also constructed a network based on the interactions between DNA methylation and miRNAs, miRNAs and target genes, and the products of target genes and the metabolic factors that they affect, including H2O2, malondialdehyde, catalase (CAT), and superoxide dismutase. Our results suggested that DNA methylation probably regulates the expression of miRNA genes, thus affecting expression of their target genes, likely through the gene-silencing function of miRNAs, to maintain cell survival under abiotic stress conditions. PMID:26579167

  6. How HTLV-1 may subvert miRNAs for persistence and transformation

    PubMed Central

    Bouzar, Amel B; Willems, Luc

    2008-01-01

    Distinct mechanisms are used by viruses to interact with cellular miRNAs. The role of microRNAs in viral replication and persistence ranges from viral-encoded microRNAs to suppressors of RNA interference. Viruses can also exploit cellular miRNAs for influencing cellular metabolism to ensure efficient replication or latency. In particular, two recent studies provide examples of how HTLV-1 may co-opt or subvert cellular miRNAs for persistent replication and oncogenic purposes. The pathways modulated by these described miRNAs are critically involved in apoptosis, proliferation and innate immune response. PMID:19014483

  7. Computational identification of putative miRNAs and their target genes in pathogenic amoeba Naegleria fowleri.

    PubMed

    Padmashree, Dyavegowda; Swamy, Narayanaswamy Ramachandra

    2015-01-01

    Naegleria fowleri is a parasitic unicellular free living eukaryotic amoeba. The parasite spreads through contaminated water and causes primary amoebic meningoencephalitis (PAM). Therefore, it is of interest to understand its molecular pathogenesis. Hence, we analyzed the parasite genome for miRNAs (microRNAs) that are non-coding, single stranded RNA molecules. We identified 245 miRNAs using computational methods in N. fowleri, of which five miRNAs are conserved. The predicted miRNA targets were analyzed by using miRanda (software) and further studied the functions by subsequently annotating using AmiGo (a gene ontology web tool).

  8. miRNAs as biomarkers in colorectal cancer diagnosis and prognosis.

    PubMed

    Ju, Jingfang

    2010-05-01

    Since the discovery of noncoding small miRNAs and their function in controlling mRNA translational rate, the small non-coding miRNA world has become a research wonderland for cancer and other human diseases. Due to the critical regulatory function, miRNA can act as an oncogene or a tumor-suppressor gene. This review will cover some of the recent discoveries of the potential of miRNAs as cancer biomarkers in colorectal cancer, future challenges and solutions.

  9. Dissecting genetics of cutaneous miRNA in a mouse model of an autoimmune blistering disease.

    PubMed

    Gupta, Yask; Möller, Steffen; Witte, Mareike; Belheouane, Meriem; Sezin, Tanya; Hirose, Misa; Vorobyev, Artem; Niesar, Felix; Bischof, Julia; Ludwig, Ralf J; Zillikens, Detlef; Sadik, Christian D; Restle, Tobias; Häsler, Robert; Baines, John F; Ibrahim, Saleh M

    2016-02-16

    MicroRNAs (miRNAs) are small endogenous non-coding RNAs that control genes at post-transcriptional level. They are essential for development and tissue differentiation, and such altered miRNA expression patterns are linked to the pathogenesis of inflammation and cancer. There is evidence that miRNA expression is genetically controlled similar to the transcription of protein-coding genes and previous studies identified quantitative trait loci (QTL) for miRNA expression in the liver. So far, little attention has been paid to miRNA expression in the skin. Moreover, epistatic control of miRNA expression remains unknown. In this study, we characterize genetic regulation of cutaneous miRNA and their correlation with skin inflammation using a previously established murine autoimmune-prone advanced intercross line. We identified in silico 42 eQTL controlling the expression of 38 cutaneous miRNAs and furthermore found two chromosomal hot-spots on chromosomes 2 and 8 that control the expression of multiple miRNAs. Moreover, for 8 miRNAs an interacting effect from pairs of SNPs was observed. Combining the constraints on genes from the statistical interaction of their loci and further using curated protein interaction networks, the number of candidate genes for association of miRNAs was reduced to a set of several genes. A cluster analysis identified miR-379 and miR-223 to be associated with EBA severity/onset, where miR-379 was observed to be associated to loci on chromosome 6. The murine advanced intercross line allowed us to identify the genetic loci regulating multiple miRNA in skin. The recurrence of trans-eQTL and epistasis suggest that cutaneous miRNAs are regulated by yet an unexplored complex gene networks. Further, using co-expression analysis of miRNA expression levels we showed that multiple miRNA contribute to multiple pathways that might be involved in pathogenesis of autoimmune skin blistering disease. Specifically, we provide evidence that miRNA such as miR-223

  10. miRNA profiles in plasma from patients with sleep disorders reveal dysregulation of miRNAs in narcolepsy and other central hypersomnias.

    PubMed

    Holm, Anja; Bang-Berthelsen, Claus Heiner; Knudsen, Stine; Kornum, Birgitte R; Modvig, Signe; Jennum, Poul; Gammeltoft, Steen

    2014-09-01

    MicroRNAs (miRNAs) have been implicated in the pathogenesis of human diseases including neurological disorders. The aim is to address the involvement of miRNAs in the pathophysiology of central hypersomnias including autoimmune narcolepsy with cataplexy and hypocretin deficiency (type 1 narcolepsy), narcolepsy without cataplexy (type 2 narcolepsy), and idiopathic hypersomnia. We conducted high-throughput analysis of miRNA in plasma from three groups of patients-with type 1 narcolepsy, type 2 narcolepsy, and idiopathic hypersomnia, respectively-in comparison with healthy controls using quantitative real-time polymerase chain reaction (qPCR) panels. University hospital based sleep clinic and research laboratories. Twelve patients with type 1 narcolepsy, 12 patients with type 2 narcolepsy, 12 patients with idiopathic hypersomnia, and 12 healthy controls. By analyzing miRNA in plasma with qPCR we identified 50, 24, and 6 miRNAs that were different in patients with type 1 narcolepsy, type 2 narcolepsy, and idiopathic hypersomnia, respectively, compared with healthy controls. Twenty miRNA candidates who fulfilled the criteria of at least two-fold difference and p-value < 0.05 were selected to validate the miRNA changes in an independent cohort of patients. Four miRNAs differed significantly between type 1 narcolepsy patients and healthy controls. Levels of miR-30c, let-7f, and miR-26a were higher, whereas the level of miR-130a was lower in type 1 narcolepsy than healthy controls. The miRNA differences were not specific for type 1 narcolepsy, since the levels of the four miRNAs were also altered in patients with type 2 narcolepsy and idiopathic hypersomnia compared with healthy controls. The levels of four miRNAs differed in plasma from patients with type 1 narcolepsy, type 2 narcolepsy and idiopathic hypersomnia suggesting that alterations of miRNAs may be involved in the pathophysiology of central hypersomnias. © 2014 Associated Professional Sleep Societies, LLC.

  11. miRNA-197 and miRNA-223 Predict Cardiovascular Death in a Cohort of Patients with Symptomatic Coronary Artery Disease

    PubMed Central

    Appelbaum, Sebastian; Karakas, Mahir; Ojeda, Francisco; Lau, Denise M.; Hartmann, Tim; Lackner, Karl J.; Westermann, Dirk; Schnabel, Renate B.; Blankenberg, Stefan; Zeller, Tanja

    2015-01-01

    Background Circulating microRNAs (miRNAs) have been described as potential diagnostic biomarkers in cardiovascular disease and in particular, coronary artery disease (CAD). Few studies were undertaken to perform analyses with regard to risk stratification of future cardiovascular events. miR-126, miR-197 and miR-223 are involved in endovascular inflammation and platelet activation and have been described as biomarkers in the diagnosis of CAD. They were identified in a prospective study in relation to future myocardial infarction. Objectives The aim of our study was to further evaluate the prognostic value of these miRNAs in a large prospective cohort of patients with documented CAD. Methods Levels of miR-126, miR-197 and miR-223 were evaluated in serum samples of 873 CAD patients with respect to the endpoint cardiovascular death. miRNA quantification was performed using real time polymerase chain reaction (RT-qPCR). Results The median follow-up period was 4 years (IQR 2.78–5.04). The median age of all patients was 64 years (IQR 57–69) with 80.2% males. 38.9% of the patients presented with acute coronary syndrome (ACS), 61.1% were diagnosed with stable angina pectoris (SAP). Elevated levels of miRNA-197 and miRNA-223 reliably predicted future cardiovascular death in the overall group (miRNA-197: hazard ratio (HR) 1.77 per one standard deviation (SD) increase (95% confidence interval (CI) 1.20; 2.60), p = 0.004, C-index 0.78; miRNA-223: HR 2.23 per one SD increase (1.20; 4.14), p = 0.011, C-index 0.80). In ACS patients the prognostic power of both miRNAs was even higher (miRNA-197: HR 2.24 per one SD increase (1.25; 4.01), p = 0.006, C-index 0.89); miRA-223: HR 4.94 per one SD increase (1.42; 17.20), p = 0.012, C-index 0.89). Conclusion Serum-derived circulating miRNA-197 and miRNA-223 were identified as predictors for cardiovascular death in a large patient cohort with CAD. These results reinforce the assumption that circulating miRNAs are promising biomarkers

  12. Simultaneous inhibition of multiple oncogenic miRNAs by a multi-potent microRNA sponge.

    PubMed

    Jung, Jaeyun; Yeom, Chanjoo; Choi, Yeon-Sook; Kim, Sinae; Lee, EunJi; Park, Min Ji; Kang, Sang Wook; Kim, Sung Bae; Chang, Suhwan

    2015-08-21

    The roles of oncogenic miRNAs are widely recognized in many cancers. Inhibition of single miRNA using antagomiR can efficiently knock-down a specific miRNA. However, the effect is transient and often results in subtle phenotype, as there are other miRNAs contribute to tumorigenesis. Here we report a multi-potent miRNA sponge inhibiting multiple miRNAs simultaneously. As a model system, we targeted miR-21, miR-155 and miR-221/222, known as oncogenic miRNAs in multiple tumors including breast and pancreatic cancers. To achieve efficient knockdown, we generated perfect and bulged-matched miRNA binding sites (MBS) and introduced multiple copies of MBS, ranging from one to five, in the multi-potent miRNA sponge. Luciferase reporter assay showed the multi-potent miRNA sponge efficiently inhibited 4 miRNAs in breast and pancreatic cancer cells. Furthermore, a stable and inducible version of the multi-potent miRNA sponge cell line showed the miRNA sponge efficiently reduces the level of 4 target miRNAs and increase target protein level of these oncogenic miRNAs. Finally, we showed the miRNA sponge sensitize cells to cancer drug and attenuate cell migratory activity. Altogether, our study demonstrates the multi-potent miRNA sponge is a useful tool to examine the functional impact of simultaneous inhibition of multiple miRNAs and proposes a therapeutic potential.

  13. Use of radiometric indices to evaluate Zn and Pb stress in two grass species (Festuca rubra L. and Vulpia myuros L.).

    PubMed

    Gómez, J; Yunta, F; Esteban, E; Carpena, R O; Zornoza, P

    2016-11-01

    Vegetation indices obtained from radiometric measurements have been used to estimate the stress response of plants grown in contaminated sites. The phytotoxicity of Pb and Zn in Festuca rubra L. and Vulpia myuros L. plants grown under hydroponic conditions was evaluated using vegetation indices obtained from radiometric measurements. The plants were supplied with 3 mM Zn (+Zn), 500 μM Pb (+Pb) and 500 μM Pb with EDTA (+PbEDTA) for 3 months. Significantly higher Zn concentrations in F. rubra shoots compared with V. myuros shoots were detected for Zn and Pb treatments. EDTA increased Pb transport to the shoots for both grasses, while Pb-treated plants retained Pb primarily in the roots. All vegetation indices tested showed the highest differences in F. rubra under +PbEDTA treatment and minor effects under +Zn, whereas the major variations for V. myuros corresponded to +Zn treatment, followed by +PbEDTA. Red edge normalized difference vegetation index, yellowness index and anthocyanin concentration index were the most sensitive indices to report Zn and Pb phytotoxicity in these grasses. According to the results obtained, both metal concentrations and radiometric indices suggested that Pb is more phytotoxic to F. rubra, which tolerates high Zn levels, whereas V. myuros was strongly affected by high Zn levels and markedly tolerant to Pb, even when applied in a mobile form (PbEDTA). Both species could be used in the phytostabilization of Zn- and Pb-contaminated soils. The abilities of F. rubra to accumulate Zn and V. myuros to accumulate Pb in the roots would facilitate a more efficient phytoremediation strategy when used in combination.

  14. Search for signatures in miRNAs associated with cancer

    PubMed Central

    Kothandan, Ram; Biswas, Sumit

    2013-01-01

    Since the first discovery in the early 1990's, the predicted and validated population of microRNAs (miRNAs or miRs) has grown significantly. These small (~22 nucleotides long) regulators of gene expression have been implicated and associated with several genes in the cancer pathway as well. Globally, the identification and verification of microRNAs as biomarkers for cancer cell types has been the area of thrust for most miRNA biologists. However, there has been a noticeable vacuum when it comes to identifying a common signature or trademark that could be used to demarcate a miR to be associated with the development or suppression of cancer. To answer these queries, we report an in silico study involving the identification of global signatures in experimentally validated microRNAs which have been associated with cancer. This study has thrown light on the presence of significant common signatures, viz., - sequential and hybridization, which may distinguish a miR to be associated with cancer. Based on our analysis, we suggest the utility of such signatures in the design and development of algorithms for prediction of miRs involved in the cancer pathway. PMID:23861569

  15. Epigenetic regulation of normal human mammary cell type-specific miRNAs

    SciTech Connect

    Vrba, Lukas; Garbe, James C.; Stampfer, Martha R.; Futscher, Bernard W.

    2011-08-26

    Epigenetic mechanisms are important regulators of cell type–specific genes, including miRNAs. In order to identify cell type-specific miRNAs regulated by epigenetic mechanisms, we undertook a global analysis of miRNA expression and epigenetic states in three isogenic pairs of human mammary epithelial cells (HMEC) and human mammary fibroblasts (HMF), which represent two differentiated cell types typically present within a given organ, each with a distinct phenotype and a distinct epigenotype. While miRNA expression and epigenetic states showed strong interindividual concordance within a given cell type, almost 10% of the expressed miRNA showed a cell type–specific pattern of expression that was linked to the epigenetic state of their promoter. The tissue-specific miRNA genes were epigenetically repressed in nonexpressing cells by DNA methylation (38%) and H3K27me3 (58%), with only a small set of miRNAs (21%) showing a dual epigenetic repression where both DNA methylation and H3K27me3 were present at their promoters, such as MIR10A and MIR10B. Individual miRNA clusters of closely related miRNA gene families can each display cell type–specific repression by the same or complementary epigenetic mechanisms, such as the MIR200 family, and MIR205, where fibroblasts repress MIR200C/141 by DNA methylation, MIR200A/200B/429 by H3K27me3, and MIR205 by both DNA methylation and H3K27me3. Since deregulation of many of the epigenetically regulated miRNAs that we identified have been linked to disease processes such as cancer, it is predicted that compromise of the epigenetic control mechanisms is important for this process. Overall, these results highlight the importance of epigenetic regulation in the control of normal cell type–specific miRNA expression.

  16. Microevolution of nematode miRNAs reveals diverse modes of selection.

    PubMed

    Jovelin, Richard; Cutter, Asher D

    2014-10-28

    Micro-RNA (miRNA) genes encode abundant small regulatory RNAs that play key roles during development and in homeostasis by fine tuning and buffering gene expression. This layer of regulatory control over transcriptional networks is preserved by selection across deep evolutionary time, yet selection pressures on individual miRNA genes in contemporary populations remain poorly characterized in any organism. Here, we quantify nucleotide variability for 129 miRNAs in the genome of the nematode Caenorhabditis remanei to understand the microevolution of this important class of regulatory genes. Our analysis of three population samples and C. remanei's sister species revealed ongoing natural selection that constrains evolution of all sequence domains within miRNA hairpins. We also show that new miRNAs evolve faster than older miRNAs but that selection nevertheless favors their persistence. Despite the ongoing importance of purging of new mutations, we discover a trove of >400 natural miRNA sequence variants that include single nucleotide polymorphisms in seed motifs, indels that ablate miRNA functional domains, and origination of new miRNAs by duplication. Moreover, we demonstrate substantial nucleotide divergence of pre-miRNA hairpin alleles between populations and sister species. These findings from the first global survey of miRNA microevolution in Caenorhabditis support the idea that changes in gene expression, mediated through divergence in miRNA regulation, can contribute to phenotypic novelty and adaptation to specific environments in the present day as well as the distant past. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  17. Role of Alix in miRNA packaging during extracellular vesicle biogenesis

    PubMed Central

    IAVELLO, ALESSANDRA; FRECH, VALESKA S.L.; GAI, CHIARA; DEREGIBUS, MARIA CHIARA; QUESENBERRY, PETER J.; CAMUSSI, GIOVANNI

    2016-01-01

    Evidence indicates that Alix, an accessory protein of the endosomal sorting complex required for transport (ESCRT), is involved in the biogenesis of extracellular vesicles (EVs). EVs contain selected patterns of microRNAs (miRNAs or miRs); however, little is known about the mechanisms of miRNA enrichment in EVs. The aim of the present study was to evaluate whether Alix is involved in the packaging of miRNAs within EVs released by human liver stem-like cells (HLSCs). EVs released from HLSCs were enriched with miRNAs and expressed Alix and several RNA-binding proteins, including Argonaute 2 (Ago2), a member of the Argonaute family known to be involved in the transport and the processing of miRNAs. Co-immunoprecipitation experiments revealed an association between Alix and Ago2. The results from RT-qPCR indicated that in the Alix/Ago2 immunoprecipitates, miRNAs were detectable. EVs were instrumental in transferring selected miRNAs from HLSCs to human endothelial cells absent in the latter cells. Alix knockdown did not influence the number of EVs released by HLSCs, but it significantly decreased miRNA expression levels in the EVs and consequently their transfer to the endothelium. Our findings indicate that Alix binds to Ago2 and miRNAs, suggesting that it plays a key role in miRNA enrichment during EV biogenesis. These results may represent a novel function of Alix, demonstrating its involvement in the EV-mediated transfer of miRNAs. PMID:26935291

  18. Arabidopsis thaliana miRNAs promote embryo pattern formation beginning in the zygote.

    PubMed

    Armenta-Medina, Alma; Lepe-Soltero, Daniel; Xiang, Daoquan; Datla, Raju; Abreu-Goodger, Cei; Gillmor, C Stewart

    2017-09-12

    miRNAs are essential regulators of cell identity, yet their role in early embryo development in plants remains largely unexplored. To determine the earliest stage at which miRNAs act to promote pattern formation in embryogenesis, we examined a series of mutant alleles in the Arabidopsis thaliana miRNA biogenesis enzymes DICER-LIKE 1 (DCL1), SERRATE (SE), and HYPONASTIC LEAVES 1 (HYL1). Cellular and patterning defects were observed in dcl1, se and hyl1 embryos from the zygote through the globular stage of embryogenesis. To identify miRNAs that are expressed in early embryogenesis, we sequenced mRNAs from globular stage Columbia wild type (wt) and se-1 embryos, and identified transcripts potentially corresponding to 100 miRNA precursors. Considering genome location and transcript increase between wt and se-1, 39 of these MIRNAs are predicted to be bona fide early embryo miRNAs. Among these are conserved miRNAs such as miR156, miR159, miR160, miR161, miR164, miR165, miR166, miR167, miR168, miR171, miR319, miR390 and miR394, as well as miRNAs whose function has never been characterized. Our analysis demonstrates that miRNAs promote pattern formation beginning in the zygote, and provides a comprehensive dataset for functional studies of individual miRNAs in Arabidopsis embryogenesis. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Identification of novel and candidate miRNAs in rice by high throughput sequencing

    PubMed Central

    Sunkar, Ramanjulu; Zhou, Xuefeng; Zheng, Yun; Zhang, Weixiong; Zhu, Jian-Kang

    2008-01-01

    Background Small RNA-guided gene silencing at the transcriptional and post-transcriptional levels has emerged as an important mode of gene regulation in plants and animals. Thus far, conventional sequencing of small RNA libraries from rice led to the identification of most of the conserved miRNAs. Deep sequencing of small RNA libraries is an effective approach to uncover rare and lineage- and/or species-specific microRNAs (miRNAs) in any organism. Results In order to identify new miRNAs and possibly abiotic-stress regulated small RNAs in rice, three small RNA libraries were constructed from control rice seedlings and seedlings exposed to drought or salt stress, and then subjected to pyrosequencing. A total of 58,781, 43,003 and 80,990 unique genome-matching small RNAs were obtained from the control, drought and salt stress libraries, respectively. Sequence analysis confirmed the expression of most of the conserved miRNAs in rice. Importantly, 23 new miRNAs mostly each derived from a unique locus in rice genome were identified. Six of the new miRNAs are conserved in other monocots. Additionally, we identified 40 candidate miRNAs. Allowing not more than 3 mis-matches between a miRNA and its target mRNA, we predicted 20 targets for 9 of the new miRNAs. Conclusion Deep sequencing proved to be an effective strategy that allowed the discovery of 23 low-abundance new miRNAs and 40 candidate miRNAs in rice. PMID:18312648

  20. The roles of oncogenic miRNAs and their therapeutic importance in breast cancer.

    PubMed

    O'Bryan, Samia; Dong, Shengli; Mathis, J Michael; Alahari, Suresh K

    2017-02-01

    Since the discovery of tumour suppressive miRNA in 2002, the dysregulation of miRNAs was implicated in many cancers, exhibiting both tumour suppressive and oncogenic roles. Dysregulation of miRNAs was found to be involved in the initiation of oncogenesis, as well as the progression, invasion and metastasis of cancers. While normal miRNA inhibitory functions help regulate gene expression in the cell, oncogenic miRNA, when dysregulated can lead to suppression of critical pathways that control apoptosis, cell cycle progression, growth and proliferation. This suppression allows for the upregulation of pro-oncogenic factors that drive cell survival, growth and proliferation. Due to emerging discoveries, oncogenic miRNAs are proving to be a critical component in cancers, such as breast cancer, and may provide novel avenues for cancer treatment. In this article, we discuss the roles of the most studied oncogenic miRNAs in breast cancer including clusters and families involved as well as the less studied and recently discovered oncogenic miRNAs. These miRNAs provide valuable information into the complexity of regulatory elements affected by their overexpression and the overall impact in the progression of breast cancer. Also, identifying miRNAs causing or leading to resistance or sensitivity to current anti-cancer drugs prior to treatment may lead to an improvement in treatment selection and overall patient response. This review summarizes known and recently discovered miRNAs in literature found to have oncogenic roles in breast cancer initiation and the progression, invasion and metastasis of the disease.

  1. Repertoire and evolution of miRNA genes in four divergent nematode species.

    PubMed

    de Wit, Elzo; Linsen, Sam E V; Cuppen, Edwin; Berezikov, Eugene

    2009-11-01

    miRNAs are approximately 22-nt RNA molecules that play important roles in post-transcriptional regulation. We have performed small RNA sequencing in the nematodes Caenorhabditis elegans, C. briggsae, C. remanei, and Pristionchus pacificus, which have diverged up to 400 million years ago, to establish the repertoire and evolutionary dynamics of miRNAs in these species. In addition to previously known miRNA genes from C. elegans and C. briggsae we demonstrate expression of many of their homologs in C. remanei and P. pacificus, and identified in total more than 100 novel expressed miRNA genes, the majority of which belong to P. pacificus. Interestingly, more than half of all identified miRNA genes are conserved at the seed level in all four nematode species, whereas only a few miRNAs appear to be species specific. In our compendium of miRNAs we observed evidence for known mechanisms of miRNA evolution including antisense transcription and arm switching, as well as miRNA family expansion through gene duplication. In addition, we identified a novel mode of miRNA evolution, termed "hairpin shifting," in which an alternative hairpin is formed with up- or downstream sequences, leading to shifting of the hairpin and creation of novel miRNA* species. Finally, we identified 21U-RNAs in all four nematodes, including P. pacificus, where the upstream 21U-RNA motif is more diverged. The identification and systematic analysis of small RNA repertoire in four nematode species described here provides a valuable resource for understanding the evolutionary dynamics of miRNA-mediated gene regulation.

  2. Microarray analysis of colorectal cancer stromal tissue reveals upregulation of two oncogenic miRNA clusters.

    PubMed

    Nishida, Naohiro; Nagahara, Makoto; Sato, Tetsuya; Mimori, Koshi; Sudo, Tomoya; Tanaka, Fumiaki; Shibata, Kohei; Ishii, Hideshi; Sugihara, Kenichi; Doki, Yuichiro; Mori, Masaki

    2012-06-01

    Cancer stroma plays an important role in the progression of cancer. Although alterations in miRNA expression have been explored in various kinds of cancers, the expression of miRNAs in cancer stroma has not been explored in detail. Using a laser microdissection technique, we collected RNA samples specific for epithelium or stroma from 13 colorectal cancer tissues and four normal tissues, and miRNA microarray and gene expression microarray were carried out. The expression status of miRNAs was confirmed by reverse transcriptase PCR. Furthermore, we investigated whether miRNA expression status in stromal tissue could influence the clinicopathologic factors. Oncogenic miRNAs, including two miRNA clusters, miR-17-92a and miR-106b-25 cluster, were upregulated in cancer stromal tissues compared with normal stroma. Gene expression profiles from cDNA microarray analyses of the same stromal tissue samples revealed that putative targets of these miRNA clusters, predicted by Target Scan, such as TGFBR2, SMAD2, and BMP family genes, were significantly downregulated in cancer stromal tissue. Downregulated putative targets were also found to be involved in cytokine interaction and cellular adhesion. Importantly, expression of miR-25 and miR-92a in stromal tissues was associated with a variety of clinicopathologic factors. Oncogenic miRNAs were highly expressed in cancer stroma. Although further validation is required, the finding that stromal miRNA expression levels were associated with clinicopathologic factors suggests the possibility that miRNAs in cancer stroma are crucially involved in cancer progression.

  3. Comparative studies of two methods for miRNA isolation from milk whey.

    PubMed

    Jin, Xiao-lu; Wei, Zi-hai; Liu, Lan; Liu, Hong-yun; Liu, Jian-xin

    2015-06-01

    MicroRNAs (miRNAs) from milk whey have been considered for their potential as noninvasive biomarkers for milk quality control and disease diagnosis. However, standard protocols for miRNA isolation and quantification from milk whey are not well established. The objective of this study was to compare two methods for the isolation of miRNAs from milk whey. These two methods were modified phenol-based technique (Trizol LS(®) followed by phenol precipitation, the TP method) and combined phenol and column-based approach (Trizol LS(®) followed by cleanup using the miRNeasy kit, the TM method). Yield and quality of RNA were rigorously measured using a NanoDrop ND-1000 spectrophotometer and then the distribution of RNA was precisely detected in a Bioanalyzer 2100 instrument by microchip gel electrophoresis. Several endogenous miRNAs (bta-miR-141, bta-miR-146a, bta-miR-148a, bta-miR-200c, bta-miR-362, and bta-miR-375) and an exogenous spike-in synthetic control miRNA (cel-miR-39) were quantified by real-time polymerase chain reaction (PCR) to examine the apparent recovery efficiency of milk whey miRNAs. Both methods could successfully isolate sufficient small RNA (<200 nt) from milk whey, and their yields were quite similar. However, the quantification results show that the total miRNA recovery efficiency by the TM method is superior to that by the TP method. The TM method performed better than the TP for recovery of milk whey miRNA due to its consistency and good repeatability in endogenous and spike-in miRNA recovery. Additionally, quantitative recovery analysis of a spike-in miRNA may be more accurate to reflect the milk whey miRNA recovery efficiency than using traditional RNA quality analysis instruments (NanoDrop or Bioanalyzer 2100).

  4. Identification of miRNAs in Bovine Endometrium through RNAseq and Prediction of Regulated Pathways.

    PubMed

    Palma-Vera, S E; Sharbati, S; Einspanier, R

    2015-10-01

    Detection of miRNAs in reproductive tissues is a key step to understand their role in fertility. We hypothesize that miRNAs must be involved in pathways controlling endometrial physiology and defense against pathogens. In this study, we aimed to characterize miRNAs present in bovine endometrium and to predict regulated pathways. Cytobrush endometrial samples from four cows were collected at oestrous cycle days 1-5, 6-12, 13-18 and 19-21. RNA was extracted and sequenced using Ion Torrent (®) technology. After mapping of the reads to miRNA stem loops, rRNAs and tRNAs, data were normalized and analysed using DESeq2. Targets and pathways were predicted with miRmap and KEGG, respectively. Validation of miRNAs in tissue was done by RT-qPCR (miR-Q). A total of 221 identities were common among groups, accumulating more than 99% of miRNA expression. MiRNAs were predicted to regulate MAPK signalling pathway, lysosome and extracellular matrix (ECM)-receptor interaction. Eight miRNAs were validated by miR-Q, showing that let-7a-5p and let-7b were regulated across the oestrous cycle. This study demonstrated a high similarity in miRNA expression profile across the oestrous cycles in bovine endometrium. These miRNAs were predicted to regulate pathways involved in cell proliferation, differentiation, transport and catabolism. The number of pathways shared by different miRNAs indicates the broad range of regulation these molecules exhibit in the endometrium. © 2015 Blackwell Verlag GmbH.

  5. A common set of developmental miRNAs are upregulated in Nicotiana benthamiana by diverse begomoviruses

    PubMed Central

    2011-01-01

    Background Begomoviruses are single-stranded DNA viruses that cause economically important diseases of many crops throughout the world and induce symptoms in plants, including enations, leaf curling and stunting, that resemble developmental abnormalities. MicroRNAs (miRNAs) are small endogenous RNAs that are involved in a variety of activities, including plant development, signal transduction and protein degradation, as well as response to environmental stress, and pathogen invasion. Results The present study was aimed at understanding the deregulation of miRNAs upon begomovirus infection. Four distinct begomoviruses African cassava mosaic virus (ACMV), Cabbage leaf curl virus (CbLCuV), Tomato yellow leaf curl virus (TYLCV) and Cotton leaf curl Multan virus/Cotton leaf curl betasatellite (CLCuV/CLCuMB), were used in this study. Ten developmental miRNA were studied. N. benthamiana plants were inoculated with begomoviruses and their miRNA profiles were analysed by northern blotting using specific miRNA probes. The levels of most developmental miRNA were increased in N. benthamiana by TYLCV, CLCuMV/CLCuMB and CbLCuV infection with a common pattern despite their diverse genomic components. However, the increased levels of individual miRNAs differed for distinct begomoviruses, reflecting differences in severity of symptom phenotypes. Some of these miRNA were also common to ACMV infection. Conclusions Our results have shown a common pattern of miRNAs accumulation upon begomovirus infection. It was found that begomoviruses generally increase the accumulation of miRNA and thus result in the decreased translation of genes involved in the development of plants. Identification of common miRNAs that are deregulated upon begomovirus infection may provide novel targets for control strategies aimed at developing broad-spectrum resistance. PMID:21447165

  6. Distinct AGO1 and AGO2 associated miRNA profiles in human cells and blood plasma

    PubMed Central

    Turchinovich, Andrey; Burwinkel, Barbara

    2012-01-01

    Studies of miRNA association with Argonaute (AGO) proteins in mammalian cells have indicated lack of bias toward particular AGO. However, to our knowledge, the use of quantitative methods for studying miRNA association with different AGOs has not been reported so far. In this work we compared the total miRNA content in AGO1 and AGO2 immunoprecipitates obtained from MCF7 adenocarcinoma cells using TaqMan Low Density miRNA Arrays and successfully verified selected miRNAs with qPCR. For most of the miRNA species AGO1 and AGO2 profiles were well correlated, however, some miRNAs demonstrated consistent biases toward one of the Argonautes. Furthermore, miRNAs which were predominantly AGO2-associated derived mostly from sense strands of the corresponding pre-miRNAs while the majority of AGO1 biased miRNAs originated from antisense strands of the pre-miRNAs. Additionally, we show that circulating miRNA in human blood plasma can be immunoprecipitated with both AGO1 and AGO2 antibody. However, unlike in cell lysates, AGO1 and AGO2 associated miRNA profiles in plasma did not correlate, indicating that many cell types contribute to circulating miRNA (given that expression of AGO proteins is tissue specific). Furthermore, AGO-specific miRNA profiles in blood cells differed significantly from miRNAs profiles in plasma indicating that most circulating miRNAs are likely to derive from non-blood cells. Since circulating miRNAs hold great promise as biomarkers for numerous cancers and other diseases, we hypothesize that AGO-specific miRNA profiles might add an additional dimension to circulating miRNA-based diagnostics. PMID:22858679

  7. Identification of precursor transcripts for 6 novel miRNAs expands the diversity on the genomic organisation and expression of miRNA genes in rice

    PubMed Central

    Lacombe, Séverine; Nagasaki, Hiroshi; Santi, Carole; Duval, David; Piégu, Benoît; Bangratz, Martine; Breitler, Jean-Christophe; Guiderdoni, Emmanuel; Brugidou, Christophe; Hirsch, Judith; Cao, Xiaofeng; Brice, Claire; Panaud, Olivier; Karlowski, Wojciech M; Sato, Yutaka; Echeverria, Manuel

    2008-01-01

    Background The plant miRNAs represent an important class of endogenous small RNAs that guide cleavage of an mRNA target or repress its translation to control development and adaptation to stresses. MiRNAs are nuclear-encoded genes transcribed by RNA polymerase II, producing a primary precursor that is subsequently processed by DCL1 an RNase III Dicer-like protein. In rice hundreds of miRNAs have been described or predicted, but little is known on their genes and precursors which are important criteria to distinguish them from siRNAs. Here we develop a combination of experimental approaches to detect novel miRNAs in rice, identify their precursor transcripts and genes and predict or validate their mRNA targets. Results We produced four cDNA libraries from small RNA fractions extracted from distinct rice tissues. By in silico analysis we selected 6 potential novel miRNAs, and confirmed that their expression requires OsDCL1. We predicted their targets and used 5'RACE to validate cleavage for three of them, targeting a PPR, an SPX domain protein and a GT-like transcription factor respectively. In addition, we identified precursor transcripts for the 6 miRNAs expressed in rice, showing that these precursors can be efficiently processed using a transient expression assay in transfected Nicotiana benthamiana leaves. Most interestingly, we describe two precursors producing tandem miRNAs, but in distinct arrays. We focus on one of them encoding osa-miR159a.2, a novel miRNA produced from the same stem-loop structure encoding the conserved osa-miR159a.1. We show that this dual osa-miR159a.2-osa-miR159a.1 structure is conserved in distant rice species and maize. Finally we show that the predicted mRNA target of osa-miR159a.2 encoding a GT-like transcription factor is cleaved in vivo at the expected site. Conclusion The combination of approaches developed here identified six novel miRNAs expressed in rice which can be clearly distinguished from siRNAs. Importantly, we show that

  8. MiRNA need a TRIM regulation of miRNA activity by Trim-NHL proteins.

    PubMed

    Wulczyn, F Gregory; Cuevas, Elisa; Franzoni, Eleonora; Rybak, Agnieszka

    2010-01-01

    Trim-NHL proteins are defined by RING, B-Box and Coiled-coil protein motifs (referred to collectively as the Trim domain) coupled to an NHL domain. The C. elegans, D. melanogaster, mouse and human Trim-NHL proteins are potential and in several cases confirmed, E3 ubiquitin ligases. Current research is focused on identifying targets and pathways for Trim-NHL-mediated ubiquitination and in assessing the contribution of the NHL protein-protein interactiondomain for function and specificity. Several Trim-NHL proteins were discovered in screens for developmental genes in model organisms; mutations in one of the family members, Trim32, cause developmental disturbances in humans. In most instances, mutations that alter protein function map to the NHL domain. The NHL domain is a scaffold for the assembly of a translational repressor complex by the Brat proto-oncogene, a well-studied family member in Drosophila. The link to translational control is common to at least four Trim-NHLs that associate with miRNA pathway proteins. So far, two have been shown to repress (Mei-P26 and Lin41) and two to promote (NHL-2, Trim32) miRNA-mediated gene silencing. In this chapter we will describe structure-function relations for each of the proteins and then focus on the lessons being learned from these proteins about miRNA functions in development and in stem cell biology.

  9. miRNAs Need a Trim : Regulation of miRNA Activity by Trim-NHL Proteins.

    PubMed

    Wulczyn, F Gregory; Cuevas, Elisa; Franzoni, Eleonora; Rybak, Agnieszka

    2011-01-01

    Trim-NHL proteins are defined by RING, B-Box and Coiled-coil protein motifs (referred to collectively as the Trim domain) coupled to an NHL domain. The C. elegans, D. melanogaster, mouse and human Trim-NHL proteins are potential and in several cases confirmed, E3 ubiquitin ligases. Current research is focused on identifying targets and pathways for Trim-NHL-mediated ubiquitination and in assessing the contribution of the NHL protein-protein interaction domain for function and specificity. Several Trim-NHL proteins were discovered in screens for developmental genes in model organisms; mutations in one of the family members, Trim32, cause developmental disturbances in humans. In most instances, mutations that alter protein function map to the NHL domain. The NHL domain is a scaffold for the assembly of a translational repressor complex by the Brat proto-oncogene, a well-studied family member in Drosophila. The link to translational control is common to at least four Trim-NHLs that associate with miRNA pathway proteins. So far, two have been shown to repress (Mei-P26 and Lin41) and two to promote (NHL-2, Trim32) miRNA-mediated gene silencing. In this chapter we will describe structure-function relations for each of the proteins and then focus on the lessons being learned from these proteins about miRNA functions in development and in stem cell biology.

  10. Regulation of serum response factor by miRNA-200 and miRNA-9 modulates oligodendrocyte progenitor cell differentiation

    PubMed Central

    Buller, Benjamin; Chopp, Michael; Ueno, Yuji; Zhang, Li; Zhang, Rui Lan; Morris, Daniel; Zhang, Yi; Zhang, Zheng Gang

    2012-01-01

    Serum response factor (SRF) is a transcription factor that transactivates actin associated genes, and has been implicated in oligodendrocyte (OL) differentiation. To date, it has not been investigated in cerebral ischemia. We investigated the dynamics of SRF expression after stroke in vivo and the role of SRF in oligodendrocyte differentiation in vitro. Using immunohistochemistry, we found that SRF was upregulated in OLs and OL precursor cells (OPCs) after stroke. Moreover, upregulation of SRF was concurrent with downregulation of the microRNAs (miRNAs) miR-9 and the miR-200 family in the ischemic white matter region, the corpus callosum. Inhibition of SRF activation by CCG-1423, a specific inhibitor of SRF function, blocked OPCs from differentiating into OLs. Over-expression of miR-9 and miR-200 in cultured OPCs suppressed SRF expression and inhibited OPC differentiation. Moreover, co-expression of miR-9 and miR-200 attenuated activity of a luciferase reporter assay containing the Srf 3′ untranslated region (UTR). Collectively, this study is the first to show that stroke upregulates SRF expression in OPCs and OLs, and that SRF levels are mediated by miRNAs and regulate OPC differentiation. PMID:22907787

  11. Targeting of Runx2 by miRNA-135 and miRNA-203 Impairs Progression of Breast Cancer and Metastatic Bone Disease

    PubMed Central

    Taipaleenmäki, Hanna; Browne, Gillian; Akech, Jacqueline; Zustin, Jozef; van Wijnen, Andre J.; Stein, Janet L.; Hesse, Eric; Stein, Gary S.; Lian, Jane B.

    2015-01-01

    Progression of breast cancer to metastatic bone disease is linked to deregulated expression of the transcription factor Runx2. Therefore, our goal was to evaluate the potential for clinical use of Runx2-targeting microRNAs (miRNAs) to reduce tumor growth and bone metastatic burden. Expression analysis of a panel of miRNAs regulating Runx2 revealed a reciprocal relationship between the abundance of Runx2 protein and two miRNAs, miR-135 and miR-203. These miRNAs are highly expressed in normal breast epithelial cells where Runx2 is not detected, and absent in metastatic breast cancer cells and tissue biopsies that express Runx2. Reconstituting metastatic MDA-MB-231-Luc cells with miR-135 and miR-203 reduced the abundance of Runx2 and expression of the metastasis-promoting Runx2 target genes IL-11, MMP-13, and PTHrP. Additionally, tumor cell viability was decreased and migration suppressed in vitro. Orthotopic implantation of MDA-MB-231-luc cells delivered with miR-135 or miR-203, followed by an intratumoral administration of the synthetic miRNAs reduced the tumor growth and spontaneous metastasis to bone. Furthermore, intratibial injection of these miRNA-delivered cells impaired tumor growth in the bone environment and inhibited bone resorption. Importantly, reconstitution of Runx2 in MDA-MB-231-luc cells delivered with miR-135 and miR-203 reversed the inhibitory effect of the miRNAs on tumor growth and metastasis. Thus, we have identified that aberrant expression of Runx2 in aggressive tumor cells is related to the loss of specific Runx2-targeting miRNAs and that a clinically relevant replacement strategy by delivery of synthetic miRNAs is a candidate therapeutic approach to prevent metastatic bone disease by this route. PMID:25634212

  12. Identification of miRNA Signatures Associated with Epithelial Ovarian Cancer Chemoresistance with Further Biological and Functional Validation of Identified Key miRNAs

    DTIC Science & Technology

    2012-08-01

    physiological conditions, including pregnancy [2], diabetes [3], radiation sickness [4], and numerous forms of cancer [5]. In cancer , circulating miRNAs will...undetectable by RT-PCR (Ct > 40, data not shown). Figure 6. ARIA tests on ovarian cancer cell lines. (A) Relative fold change comparing...Epithelial Ovarian Cancer Chemoresistance with Further Biological and Functional Validation of Identified Key miRNAs PRINCIPAL INVESTIGATOR: Analisa

  13. Identification and Characterization of Salvia miltiorrhizain miRNAs in Response to Replanting Disease

    PubMed Central

    Zhu, Xiaole; Liu, Lin; He, Zhigui; Yang, Shushen; Liang, Zongsuo; Yan, Xijun; He, Yanfeng; Liu, Yan

    2016-01-01

    Replanting disease is a major factor limiting the artificial cultivation of the traditional Chinese medicinal herb Salvia miltiorrhiza. At present, little information is available regarding the role of miRNAs in response to replanting disease. In this study, two small RNA libraries obtained from first-year (FPR) and second-year plant (SPR) roots were subjected to a high-throughput sequencing method. Bioinformatics analysis revealed that 110 known and 7 novel miRNAs were annotated in the roots of S. miltiorrhiza. Moreover, 39 known and 2 novel miRNAs were identified and validated for differential expression in FPR compared with SPR. Thirty-one of these miRNAs were further analyzed by qRT-PCR, which revealed that 5 miRNAs negatively regulated the expression levels of 7 target genes involved in root development or stress responses. This study not only provides novel insights into the miRNA content of S. miltiorrhiza in response to replanting disease but also demonstrates that 5 miRNAs may be involved in these responses. Interactions among the differentially expressed miRNAs with their targets may form an important component of the molecular basis of replanting disease in S. miltiorrhiza. PMID:27483013

  14. Identification, evolution, and expression partitioning of miRNAs in allopolyploid Brassica napus

    PubMed Central

    Shen, Enhui; Zou, Jun; Hubertus Behrens, Falk; Chen, Li; Ye, Chuyu; Dai, Shutao; Li, Ruiyan; Ni, Meng; Jiang, Xiaoxue; Qiu, Jie; Liu, Yang; Wang, Weidi; Zhu, Qian-Hao; Chalhoub, Boulos; Bancroft, Ian; Meng, Jinling; Cai, Daguang; Fan, Longjiang

    2015-01-01

    The recently published genome of Brassica napus offers for the first time the opportunity to gain insights into the genomic organization and the evolution of miRNAs in oilseed rape. In this study, 12 small RNA libraries from two B. napus cultivars (Tapidor and Ningyou7) and their four double-haploid lines were sequenced, employing the newly sequenced B. napus genome, together with genomes of its progenitors Brassica rapa and Brassica oleracea. A total of 645 miRNAs including 280 conserved and 365 novel miRNAs were identified. Comparative analysis revealed a high level of genomic conservation of MIRNAs (75.9%) between the subgenomes of B. napus and its two progenitors’ genomes, and MIRNA lost/gain events (133) occurred in B. napus after its speciation. Furthermore, significant partitioning of miRNA expressions between the two subgenomes in B. napus was detected. The data of degradome sequencing, miRNA-mediated cleavage, and expression analyses support specific interactions between miRNAs and their targets in the modulation of diverse physiological processes in roots and leaves, as well as in biosynthesis of, for example, glucosinolates and lipids in oilseed rape. These data provide a first genome-wide view on the origin, evolution, and genomic organization of B. napus MIRNAs. PMID:26357884

  15. Identification, evolution, and expression partitioning of miRNAs in allopolyploid Brassica napus.

    PubMed

    Shen, Enhui; Zou, Jun; Hubertus Behrens, Falk; Chen, Li; Ye, Chuyu; Dai, Shutao; Li, Ruiyan; Ni, Meng; Jiang, Xiaoxue; Qiu, Jie; Liu, Yang; Wang, Weidi; Zhu, Qian-Hao; Chalhoub, Boulos; Bancroft, Ian; Meng, Jinling; Cai, Daguang; Fan, Longjiang

    2015-12-01

    The recently published genome of Brassica napus offers for the first time the opportunity to gain insights into the genomic organization and the evolution of miRNAs in oilseed rape. In this study, 12 small RNA libraries from two B. napus cultivars (Tapidor and Ningyou7) and their four double-haploid lines were sequenced, employing the newly sequenced B. napus genome, together with genomes of its progenitors Brassica rapa and Brassica oleracea. A total of 645 miRNAs including 280 conserved and 365 novel miRNAs were identified. Comparative analysis revealed a high level of genomic conservation of MIRNAs (75.9%) between the subgenomes of B. napus and its two progenitors' genomes, and MIRNA lost/gain events (133) occurred in B. napus after its speciation. Furthermore, significant partitioning of miRNA expressions between the two subgenomes in B. napus was detected. The data of degradome sequencing, miRNA-mediated cleavage, and expression analyses support specific interactions between miRNAs and their targets in the modulation of diverse physiological processes in roots and leaves, as well as in biosynthesis of, for example, glucosinolates and lipids in oilseed rape. These data provide a first genome-wide view on the origin, evolution, and genomic organization of B. napus MIRNAs. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  16. Identification of the Conserved and Novel miRNAs in Mulberry by High-Throughput Sequencing

    PubMed Central

    Jia, Ling; Zhang, Dayan; Qi, Xiwu; Ma, Bi; Xiang, Zhonghuia; He, Ningjia

    2014-01-01

    miRNAs are a class of non-coding endogenous small RNAs. They play vital roles in plant growth, development, and response to biotic and abiotic stress by negatively regulating genes. Mulberry trees are economically important species with multiple uses. However, to date, little is known about mulberry miRNAs and their target genes. In the present study, three small mulberry RNA libraries were constructed and sequenced using high-throughput sequencing technology. Results showed 85 conserved miRNAs belonging to 31 miRNA families and 262 novel miRNAs at 371 loci. Quantitative real-time PCR (qRT-PCR) analysis confirmed the expression pattern of 9 conserved and 5 novel miRNAs in leaves, bark, and male flowers. A total of 332 potential target genes were predicted to be associated with these 113 novel miRNAs. These results provide a basis for further understanding of mulberry miRNAs and the biological processes in which they are involved. PMID:25118991

  17. MiRNA expression signatures induced by Marek disease virus infection in chickens

    USDA-ARS?s Scientific Manuscript database

    MMicroRNAs (miRNAs) are small, non-coding RNAs that regulate gene expression at the post-transcriptional level. Emerging evidence suggests that differential miRNA expression is associated with viral infection and cancer. Marek's disease virus infection induces lymphoma in chickens. However, the host...

  18. Identification of Nutritional Stress-Responsive miRNAs in Phaseolus vulgaris

    USDA-ARS?s Scientific Manuscript database

    MicroRNAs (miRNAs) are key regulators for Arabidopsis development and stress responses. A hybridization approach using miRNAs-macroarrays was used to identify miRNAs that respond to nutritional stress in Phaseolus vulgaris. miRNAs-macroarrays were prepared by printing nylon filters with DNA syntheti...

  19. An integrated expression atlas of miRNAs and their promoters in human and mouse.

    PubMed

    de Rie, Derek; Abugessaisa, Imad; Alam, Tanvir; Arner, Erik; Arner, Peter; Ashoor, Haitham; Åström, Gaby; Babina, Magda; Bertin, Nicolas; Burroughs, A Maxwell; Carlisle, Ailsa J; Daub, Carsten O; Detmar, Michael; Deviatiiarov, Ruslan; Fort, Alexandre; Gebhard, Claudia; Goldowitz, Daniel; Guhl, Sven; Ha, Thomas J; Harshbarger, Jayson; Hasegawa, Akira; Hashimoto, Kosuke; Herlyn, Meenhard; Heutink, Peter; Hitchens, Kelly J; Hon, Chung Chau; Huang, Edward; Ishizu, Yuri; Kai, Chieko; Kasukawa, Takeya; Klinken, Peter; Lassmann, Timo; Lecellier, Charles-Henri; Lee, Weonju; Lizio, Marina; Makeev, Vsevolod; Mathelier, Anthony; Medvedeva, Yulia A; Mejhert, Niklas; Mungall, Christopher J; Noma, Shohei; Ohshima, Mitsuhiro; Okada-Hatakeyama, Mariko; Persson, Helena; Rizzu, Patrizia; Roudnicky, Filip; Sætrom, Pål; Sato, Hiroki; Severin, Jessica; Shin, Jay W; Swoboda, Rolf K; Tarui, Hiroshi; Toyoda, Hiroo; Vitting-Seerup, Kristoffer; Winteringham, Louise; Yamaguchi, Yoko; Yasuzawa, Kayoko; Yoneda, Misako; Yumoto, Noriko; Zabierowski, Susan; Zhang, Peter G; Wells, Christine A; Summers, Kim M; Kawaji, Hideya; Sandelin, Albin; Rehli, Michael; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R; de Hoon, Michiel J L

    2017-09-01

    MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libraries, with matching Cap Analysis Gene Expression (CAGE) data, from 396 human and 47 mouse RNA samples. Promoters were identified for 1,357 human and 804 mouse miRNAs and showed strong sequence conservation between species. We also found that primary and mature miRNA expression levels were correlated, allowing us to use the primary miRNA measurements as a proxy for mature miRNA levels in a total of 1,829 human and 1,029 mouse CAGE libraries. We thus provide a broad atlas of miRNA expression and promoters in primary mammalian cells, establishing a foundation for detailed analysis of miRNA expression patterns and transcriptional control regions.

  20. miRNAs regulated by estrogens, tamoxifen, and endocrine disruptors and their downstream gene targets

    PubMed Central

    Klinge, Carolyn M.

    2015-01-01

    MicroRNAs (miRNAs) are short (22 nucleotides), single-stranded, non-coding RNAs that form complimentary base-pairs with the 3’ untranslated region of target mRNAs within the RNA-induced silencing complex (RISC) and block translation and/or stimulate mRNA transcript degradation. The non-coding miRBase (release 21, June 2014) reports that human genome contains ~2,588 mature miRNAs which regulate ~ 60% of human protein-coding mRNAs. Dysregulation of miRNA expression has been implicated in estrogen-related diseases including breast and endometrial cancers. The mechanism for estrogen regulation of miRNA expression and the role of estrogen-regulated miRNAs in normal homeostasis, reproduction, lactation, and in cancer is an area of great research and clinical interest. Estrogens regulate miRNAs transcription through estrogen receptors α and β in a tissue-specific and cell-dependent manner. This review focuses primary on the regulation of miRNA expression by ligand-activated ERs and their bona fide gene targets and includes miRNAs regulation by tamoxifen and endocrine disrupting chemicals (EDCs) in breast cancer and cell lines. PMID:25659536

  1. Argonaute 2-dependent Regulation of Gene Expression by Single-stranded miRNA Mimics

    PubMed Central

    Matsui, Masayuki; Prakash, Thazha P; Corey, David R

    2016-01-01

    MicroRNAs (miRNAs) are small noncoding transcripts that regulate gene expression. Aberrant expression of miRNAs can affect development of cancer and other diseases. Synthetic miRNA mimics can modulate gene expression and offer an approach to therapy. Inside cells, mature miRNAs are produced as double-stranded RNAs and miRNA mimics typically retain both strands. This need for two strands has the potential to complicate drug development. Recently, synthetic chemically modified single-stranded silencing RNAs (ss-siRNA) have been shown to function through the RNAi pathway to induce gene silencing in cell culture and animals. Here, we test the hypothesis that single-stranded miRNA (ss-miRNA) can also mimic the function of miRNAs. We show that ss-miRNAs can act as miRNA mimics to silence the expression of target genes. Gene silencing requires expression of argonaute 2 (AGO2) protein and involves recruitment of AGO2 to the target transcripts. Chemically modified ss-miRNAs function effectively inside cells through endogenous RNAi pathways and broaden the options for miRNA-based oligonucleotide drug development. PMID:26903376

  2. Delivery and detection of dietary plant-based miRNAs in animal tissues

    USDA-ARS?s Scientific Manuscript database

    It has been proposed that genetic material, namely microRNAs (miRNAs), consumed in plant-based diets can affect animal gene expression. Though deep sequencing reveals the low-level presence of plant miRNAs in animal tissues, many groups have been thus far unable to replicate the finding that a rice ...

  3. miRNAs: Major modulators for crop growth and development under abiotic stresses.

    PubMed

    Noman, Ali; Fahad, Shah; Aqeel, Muhammad; Ali, Usman; Amanullah; Anwar, Sumera; Baloch, Shahbaz Khan; Zainab, Madiha

    2017-05-01

    Cumulatively, biotic and abiotic stresses of various magnitudes can decrease the production of crops by 70%. miRNAs have emerged as a genetic tool with enormous potential that can be exploited to understand stress tolerance at the molecular level and eventually regulate stress in crops. Plant miRNA targets frequently fit into diverse families of TFs that control the expression of genes related to a certain trait. As key machinery in gene regulatory networks, it is agreed that a broad understanding of miRNAs will greatly increase our understanding of plant responses to environmental stresses. miRNA-led stress regulatory networks are being considered as novel tools for the development of abiotic stress tolerance in crops. At this time, we need to expand our knowledge about the modulatory role of miRNAs during environmental fluctuations. It has become exceedingly clear that with increased understanding of the role of miRNAs during stress, the techniques for using miRNA-mediated gene regulation to enhance plant stress tolerance will become more effective and reliable. In this review we present: (1) miRNAs as a potential avenue for the modulation of abiotic stresses, and (2) summarize the research progress regarding plant responses to stress. Current progress is explained through discussion of the identification and validation of several miRNAs that enhance crop tolerance of salinity, drought, etc., while missing links on different aspects of miRNAs related to abiotic stress tolerance are noted.

  4. Preclinical Evaluation of An Anti-HCV miRNA Cluster for Treatment of HCV Infection

    PubMed Central

    Yang, Xiao; Marcucci, Katherine; Anguela, Xavier; Couto, Linda B.

    2013-01-01

    We developed a strategy to treat hepatitis C virus (HCV) infection by replacing five endogenous microRNA (miRNA) sequences of a natural miRNA cluster (miR-17–92) with sequences that are complementary to the HCV genome. This miRNA cluster (HCV-miR-Cluster 5) is delivered to cells using adeno-associated virus (AAV) vectors and the miRNAs are expressed in the liver, the site of HCV replication and assembly. AAV-HCV-miR-Cluster 5 inhibited bona fide HCV replication in vitro by up to 95% within 2 days, and the spread of HCV to uninfected cells was prevented by continuous expression of the anti-HCV miRNAs. Furthermore, the number of cells harboring HCV RNA replicons decreased dramatically by sustained expression of the anti-HCV miRNAs, suggesting that the vector is capable of curing cells of HCV. Delivery of AAV-HCV-miR-Cluster 5 to mice resulted in efficient transfer of the miRNA gene cluster and expression of all five miRNAs in liver tissue, at levels up to 1,300 copies/cell. These levels achieved up to 98% gene silencing of cognate HCV sequences, and no liver toxicity was observed, supporting the safety of this approach. Therefore, AAV-HCV-miR-Cluster 5 represents a different paradigm for the treatment of HCV infection. PMID:23295950

  5. Deep Sequencing Identification of Novel Glucocorticoid-Responsive miRNAs in Apoptotic Primary Lymphocytes

    PubMed Central

    Mav, Deepak; Scoltock, Alyson B.; Cidlowski, John A.

    2013-01-01

    Apoptosis of lymphocytes governs the response of the immune system to environmental stress and toxic insult. Signaling through the ubiquitously expressed glucocorticoid receptor, stress-induced glucocorticoid hormones induce apoptosis via mechanisms requiring altered gene expression. Several reports have detailed the changes in gene expression mediating glucocorticoid-induced apoptosis of lymphocytes. However, few studies have examined the role of non-coding miRNAs in this essential physiological process. Previously, using hybridization-based gene expression analysis and deep sequencing of small RNAs, we described the prevalent post-transcriptional repression of annotated miRNAs during glucocorticoid-induced apoptosis of lymphocytes. Here, we describe the development of a customized bioinformatics pipeline that facilitates the deep sequencing-mediated discovery of novel glucocorticoid-responsive miRNAs in apoptotic primary lymphocytes. This analysis identifies the potential presence of over 200 novel glucocorticoid-responsive miRNAs. We have validated the expression of two novel glucocorticoid-responsive miRNAs using small RNA-specific qPCR. Furthermore, through the use of Ingenuity Pathways Analysis (IPA) we determined that the putative targets of these novel validated miRNAs are predicted to regulate cell death processes. These findings identify two and predict the presence of additional novel glucocorticoid-responsive miRNAs in the rat transcriptome, suggesting a potential role for both annotated and novel miRNAs in glucocorticoid-induced apoptosis of lymphocytes. PMID:24250753

  6. Identification of putative miRNAs from the deep-branching unicellular flagellates.

    PubMed

    Huang, Po-Jung; Lin, Wei-Chen; Chen, Shih-Chieh; Lin, Yong-Han; Sun, Chin-Hung; Lyu, Ping-Chiang; Tang, Petrus

    2012-02-01

    MicroRNAs (miRNAs) are a class of extensively studied RNAi-associated small RNAs that play a critical role in eukaryotic gene regulation. However, knowledge on the miRNA and its regulation in unicellular eukaryotes is very limited. In order to obtain a better understanding on the origin of miRNA regulation system, we used deep-sequencing technology to investigate the miRNA expression pattern in four deep-branching unicellular flagellates: Giardia lamblia, Trichomonas vaginalis, Tritrichomonas foetus, and Pentatrichomonas hominis. In addition to the known miRNAs that have been described in G. lamblia and T. vaginalis, we identified 14 ancient animal miRNA families and 13 plant-specific families. Bioinformatics analysis also identified four novel miRNA candidates with reliable precursor structures derived from mature tRNAs. Our results indicated that miRNAs are likely to be a general feature for gene regulation throughout unicellular and multicellular eukaryotes and some of them may derive from unconventional ncRNAs such as snoRNA and tRNA.

  7. Future directions of extracellular vesicle-associated miRNAs in metastasis

    PubMed Central

    López, Jesús Adrián

    2017-01-01

    Numerous studies have demonstrated the dynamic cell-to-cell communication mediated by extracellular vesicles (EV) in cancer cell survival and metastasis development. EV content includes proteins, lipids, DNA, and RNA like microRNAs. Non-protein coding microRNAs play a very active role in almost all cellular processes targeting mRNAs for silencing. Different miRNA profiles have been found in different cancer types, and clarification of miRNAs packed in EV from different types of cancers will allow the understanding of metastasis and the application of miRNAs as biomolecules in diagnostic, prognostic and therapeutic approaches to fight cancer. The profound review of Dhondt et al., 2016, provides a wide view of EV miRNAs involved in various steps of the metastasis process to illustrate how the cancer cell interaction with the near and long distance microenvironment allows metastasis. These studies will surely conduce to additional patient studies to prove the relevance of EV miRNAs in metastasis in vivo. It remains to be elucidated how the tumoral cell sorts the miRNAs for secretion to send a message, and to well recognize the type of EV performing this message delivering. It will be very useful to identify whether miRNAs are delivered with post-transcriptional modifications since this is an important feature for miRNAs activity and stability. PMID:28361080

  8. New miRNAs network in human mesenchymal stem cells derived from skin and amniotic fluid.

    PubMed

    Lazzarini, R; Sorgentoni, G; Caffarini, M; Sayeed, M A; Olivieri, F; Di Primio, R; Orciani, M

    2016-09-01

    Mesenchymal stem cells (MSCs), isolated from different adult sources, have great appeal for therapeutic applications due to their simple isolation, extensive expansion potential, and high differentiative potential.In our previous studies we isolated MSCs form amniotic fluid (AF-MSCs) and skin (S-MSCs) and characterized them according to their phenotype, pluripotency, and mRNA/microRNAs (miRNAs) profiling using Card A from Life Technologies.Here, we enlarge the profiling of AF-MCSs and S-MSCs to the more recently discovered miRNAs (Card B by Life Technologies) to identify the miRNAs putative target genes and the relative signaling pathways. Card B, in fact, contains miRNAs whose role and target are not yet elucidated.The expression of the analyzed miRNAs is changing between S-MSCs and AF-MSCs, indicating that these two types of MSCs show differences potentially related to their source. Interestingly, the pathways targeted by the miRNAS deriving from Card B are the same found during the analysis of miRNAs from Card A.This result confirms the key role played by WNT and TGF-β pathways in stem cell fate, underlining as other miRNAs partially ignored up to now deserve to be reconsidered. In addition, this analysis allows including Adherens junction pathways among the mechanisms finely regulated in stem cell behavior. © The Author(s) 2015.

  9. Expressional analysis of immune-related miRNAs in breast milk.

    PubMed

    Na, R S; E, G X; Sun, W; Sun, X W; Qiu, X Y; Chen, L P; Huang, Y F

    2015-09-25

    Immune-related miRNAs in breast milk are extracellular miRNAs that are related to immune organ development and regulation of the immune function in infants and young animals. The goal of this study was to compare the expression levels of five immune-related miRNAs in breast milk in black goats, humans, and dairy cattle. The miRNAs from milk were extracted and the expression levels were assessed using quantitive RT-PCR methods. MiR-146, miR-155, miR-181a, miR-223, and miR-150 were all detected in Dazu black goat milk, and these miRNAs were significantly more highly expressed in colostrum than in mature milk of goats (P < 0.01), except for miR-150. Further, all five miRNAs were expressed in human colostrum, but patterns differed from those in goats: miR-146 and miR-155 were highly expressed (P < 0.01) in human colostrum, whereas miR-223 was abundant in goat colostrum (P < 0.01). In addition, five miRNAs were significantly higher in bovine mature milk than in goat milk (P < 0.01). Taken together, these results confirm that immune-related miRNAs are rich in breast milk with different expression levels depending on the lactation phase and species.

  10. MiRNA profiling of gastrointestinal stromal tumors by next-generation sequencing.

    PubMed

    Gyvyte, Ugne; Juzenas, Simonas; Salteniene, Violeta; Kupcinskas, Juozas; Poskiene, Lina; Kucinskas, Laimutis; Jarmalaite, Sonata; Stuopelyte, Kristina; Steponaitiene, Ruta; Hemmrich-Stanisak, Georg; Hübenthal, Matthias; Link, Alexander; Franke, Sabine; Franke, Andre; Pangonyte, Dalia; Lesauskaite, Vaiva; Kupcinskas, Limas; Skieceviciene, Jurgita

    2017-03-29

    Deregulation of miRNAs has been observed virtually in all major types of cancer, whereas the miRNA signature in GIST is not well characterized yet. In this study the first high-throughput miRNA profiling of 15 paired GIST and adjacent normal tissue samples was performed using small RNA-seq approach and differentially expressed miRNAs as well as isomiRNAs were defined. Highly significantly deregulated miRNAs were selected for validation by Taq-Man low-density array in replication group of 40 paired samples. Validated miRNAs were further subjected to enrichment analysis, which revealed significantly enriched KEGG pathways in the main GIST associated pathways. Further, we used an integrated analysis of miRNA-mRNA correlations for KIT and PDGFRA target genes and found a significant correlation between all of the enriched miRNAs and their target gene KIT. Results of the phenotype analysis showed miR-509-3p to be up-regulated in epithelioid and mixed cell types compared to spindle type, whereas miR-215-5p showed negative correlation with risk grade of GIST. These data reveal a detailed miRNA profile of GIST and highlight new candidates that may be important in the development of malignant disease.

  11. Application of miRNAs as Biomarkers of Exposure and Effects in Risk Evaluation

    EPA Science Inventory

    Of the known epigenetic mechanisms, non-coding RNA and more specifically, microRNA (miRNA), offer the most immediate promise for risk assessment applications because these molecules can serve as excellent biomarkers of toxicity. The advantages of miRNA versus more classical prot...

  12. Multiple miRNAs Jointly Regulate the Biosynthesis of Ecdysteroid in the Holometabolous Insects, Chilo suppressalis.

    PubMed

    He, Kang; Sun, Yang; Xiao, Huamei; Ge, Chang; Li, Fei; Han, Zhaojun

    2017-08-31

    The accurate rise and fall of active hormones is important for insect development. The ecdysteroids must be cleared in a timely manner. However, the mechanism of supressing the ecdysteroid biosynthesis at the right time remains unclear. Here, we sequenced a small RNA library of Chilo suppressalis and identified 300 miRNAs in this notorious rice insect pest. Microarray analysis yielded 54 differentially expressed miRNAs during metamorphosis development. Target prediction and in vitro dual luciferase assays confirmed that seven miRNAs (two conserved and five novel miRNAs) jointly targeted three Halloween genes in the ecdysteroid biosynthesis pathway. Overexpression of these seven miRNAs reduced the titre of 20-hydroxyecdysone (20E), induced mortality and retarded development, which could be rescued by treatment with 20E. Comparative analysis indicated that the miRNA regulation of metamorphosis development is a conserved process but that the miRNAs involved are highly divergent. In all, we present evidence that both conserved and lineage-specific miRNAs have crucial roles in regulating development in insects by controlling ecdysteroid biosynthesis, which is important for ensuring developmental convergence and evolutionary diversity. Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  13. Bicistronic gene transfer tools for delivery of miRNAs and protein coding sequences.

    PubMed

    Stoller, Michelle L; Chang, Henry C; Fekete, Donna M

    2013-09-05

    MicroRNAs (miRNAs) are a category of small RNAs that modulate levels of proteins via post-transcriptional inhibition. Currently, a standard strategy to overexpress miRNAs is as mature miRNA duplexes, although this method is cumbersome if multiple miRNAs need to be delivered. Many of these miRNAs are found within introns and processed through the RNA polymerase II pathway. We have designed a vector to exploit this naturally-occurring intronic pathway to deliver the three members of the sensory-specific miR-183 family from an artificial intron. In one version of the vector, the downstream exon encodes the reporter (GFP) while another version encodes a fusion protein created between the transcription factor Atoh1 and the hemaglutinin epitope, to distinguish it from endogenous Atoh1. In vitro analysis shows that the miRNAs contained within the artificial intron are processed and bind to their targets with specificity. The genes downstream are successfully translated into protein and identifiable through immunofluorescence. More importantly, Atoh1 is proven functional through in vitro assays. These results suggest that this cassette allows expression of miRNAs and proteins simultaneously, which provides the opportunity for joint delivery of specific translational repressors (miRNA) and possibly transcriptional activators (transcription factors). This ability is attractive for future gene therapy use.

  14. Two novel aspects of the kinetics of gene expression including miRNAs

    NASA Astrophysics Data System (ADS)

    Zhdanov, Vladimir

    2013-04-01

    In eukaryotic cells, many genes are transcribed into non-coding RNAs. Small RNAs or, more specifically, microRNAs (miRNAs) form an abundant sub-class of such RNAs. miRNAs are transcribed as long noncoding RNA and then generated via a processing pathway down to the 20-24-nucleotide length. The key ability of miRNAs is to associate with target mRNAs and to suppress their translation and/or facilitate degradation. Using the mean-field kinetic equations and Monte Carlo simulations, we analyze two aspects of this interplay. First, we describe the situation when the formation of mRNA or miRNA is periodically modulated by a transcription factor which itself is not perturbed by these species. Depending on the ratio between the mRNA and miRNA formation rates, the corresponding induced periodic kinetics are shown to be either nearly harmonic or shaped as anti-phase pulses. The second part of the work is related to recent experimental studies indicating that differentiation of stem cells often involves changes in gene transcription into miRNAs and/or the interference between miRNAs, mRNAs and proteins. In particular, the regulatory protein obtained via mRNA translation may suppress the miRNA formation, and the latter may suppress in turn the miRNA-mRNA association and degradation. The corresponding bistable kinetics are described in detail.

  15. Differential expression profiling of miRNAs between Marek’s disease resistant and susceptible chickens

    USDA-ARS?s Scientific Manuscript database

    Mounting evidence indicates microRNAs (miRNAs) play important roles in various biological processes including all aspects of cancer biology. The aim of this study was to profile and to assess the differences of miRNAs between the treatment groups of two lines of White Leghorns with or without viral ...

  16. Exosome-mediated delivery of functionally active miRNA-155 inhibitor to macrophages.

    PubMed

    Momen-Heravi, Fatemeh; Bala, Shashi; Bukong, Terence; Szabo, Gyongyi

    2014-10-01

    Exosomes, membranous nanovesicles, naturally carry bio-macromolecules and play pivotal roles in both physiological intercellular crosstalk and disease pathogenesis. Here, we showed that B cell-derived exosomes can function as vehicles to deliver exogenous miRNA-155 mimic or inhibitor into hepatocytes or macrophages, respectively. Stimulation of B cells significantly increased exosome production. Unlike in parental cells, baseline level of miRNA-155 was very low in exosomes derived from stimulated B cells. Exosomes loaded with a miRNA-155 mimic significantly increased miRNA-155 levels in primary mouse hepatocytes and the liver of miRNA-155 knockout mice. Treatment of RAW macrophages with miRNA-155 inhibitor loaded exosomes resulted in statistically significant reduction in LPS-induced TNFα production and partially prevented LPS-induced decrease in SOCS1 mRNA levels. Furthermore, exosome-mediated miRNA-155 inhibitor delivery resulted in functionally more efficient inhibition and less cellular toxicity compared to conventional transfection methods. Similar approaches could be useful in modification of target biomolecules in vitro and in vivo. From the clinical editor: In this study, exosome-based delivery of miRNA-155 mimicker or inhibitor was found to have significant biological response in hepatocytes and macrophages. Exosome-based approaches may be useful in the modification of other target biomolecules.

  17. Application of miRNAs as Biomarkers of Exposure and Effects in Risk Evaluation

    EPA Science Inventory

    Of the known epigenetic mechanisms, non-coding RNA and more specifically, microRNA (miRNA), offer the most immediate promise for risk assessment applications because these molecules can serve as excellent biomarkers of toxicity. The advantages of miRNA versus more classical prot...

  18. Mitochondrial miRNA (MitomiR): a new player in cardiovascular health.

    PubMed

    Srinivasan, Hemalatha; Das, Samarjit

    2015-10-01

    Cardiovascular disease is one of the major causes of human morbidity and mortality in the world. MicroRNAs (miRNAs) are small RNAs that regulate gene expression and are known to be involved in the pathogenesis of heart diseases, but the translocation phenomenon and the mode of action in mitochondria are largely unknown. Recent mitochondrial proteome analysis unveiled at least 2000 proteins, of which only 13 are made by the mitochondrial genome. There are numerous studies demonstrating the translocation of proteins into the mitochondria and also translocation of ribosomal RNA (viz., 5S rRNA) into mitochondria. Recent studies have suggested that miRNAs contain sequence elements that affect their subcellular localization, particularly nuclear localization. If there are sequence elements that direct miRNAs to the nucleus, it is also possible that similar sequence elements exist to direct miRNAs to the mitochondria. In this review we have summarized most of the miRNAs that have been shown to play an important role in mitochondrial function, either by regulating mitochondrial genes or by regulating nuclear genes that are known to influence mitochondrial function. While the focus of this review is cardiovascular diseases, we also illustrate the role of mitochondrial miRNA (MitomiR) in the initiation and progression of various diseases, including cardiovascular diseases, metabolic diseases, and cancer. Our goal here is to summarize the miRNAs that are localized to the mitochondrial fraction of cells, and how these miRNAs modulate cardiovascular health.

  19. Apple miRNAs and tasiRNAs with novel regulatory networks

    USDA-ARS?s Scientific Manuscript database

    MiRNAs, negatively affecting gene expression at the post-transcriptional levels, have been shown to control numerous genes involved in various biological and metabolic processes. To date, the identification of miRNAs in plants focused on certain model plants, such as Arabidopsis and rice. Investig...

  20. Micromanaging metabolism-a role for miRNAs in teleost energy metabolism.

    PubMed

    Mennigen, Jan A

    2016-09-01

    MicroRNAs (miRNAs) are small, non-protein coding RNA sequences, which are found in most eukaryotes. Since their initial discovery, miRNAs have emerged as important regulators of many biological processes. One of the most important processes profoundly regulated by miRNAs is energy metabolism. Traditionally, metabolic functions of miRNAs have been studied in genome-sequenced mammalian organisms, especially the mouse model. However, partially driven by commercial interest in aquaculture, increasingly feasible large-scale molecular techniques have resulted in the characterization of miRNA repertoires, and importantly, several genome sequences of several (commercially important) teleost species, which also hold important roles as research models in the comparative physiology of energy metabolism. This review aims to introduce the recent advances in miRNA research in teleost fish and to describe the current knowledge of miRNA function in teleost energy metabolism. The most pressing research needs and questions to determine metabolic roles of miRNAs in teleost models are presented, as well as applicable technical approaches and current bottlenecks. Rainbow trout, which possess the advantages of newly available molecular tools and a long history as comparative research model in teleost energy metabolism, are discussed as a promising research model to address these questions. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. Dissecting the regulation rules of cancer-related miRNAs based on network analysis

    PubMed Central

    Liu, Zhongyu; Guo, Yanzhi; Pu, Xuemei; Li, Menglong

    2016-01-01

    miRNAs (microRNAs) are a set of endogenous and small non-coding RNAs which specifically induce degradation of target mRNAs or inhibit protein translation to control gene expression. Obviously, aberrant miRNA expression in human cells will lead to a serious of changes in protein-protein interaction network (PPIN), thus to activate or inactivate some pathways related to various diseases, especially carcinogenesis. In this study, we systematically constructed the miRNA-regulated co-expressed protein-protein interaction network (CePPIN) for 17 cancers firstly. We investigated the topological parameters and functional annotation for the proteins in CePPIN, especially for those miRNA targets. We found that targets regulated by more miRNAs tend to play a more important role in the forming process of cancers. We further elucidated the miRNA regulation rules in PPIN from a more systematical perspective. By GO and KEGG pathway analysis, miRNA targets are involved in various cellular processes mostly related to cell cycle, such as cell proliferation, growth, differentiation, etc. Through the Pfam classification, we found that miRNAs belonging to the same family tend to have targets from the same family which displays the synergistic function of these miRNAs. Finally, the case study on miR-519d and miR-21-regulated sub-network was performed to support our findings. PMID:27694936

  2. miRNA-21 and miRNA-34a Are Potential Minimally Invasive Biomarkers for the Diagnosis of Pancreatic Ductal Adenocarcinoma.

    PubMed

    Alemar, Bárbara; Izetti, Patrícia; Gregório, Cleandra; Macedo, Gabriel S; Castro, Mauro Antonio Alves; Osvaldt, Alessandro Bersch; Matte, Ursula; Ashton-Prolla, Patricia

    2016-01-01

    Pancreatic ductal adenocarcinoma (PDAC) is one of the most deadly cancers, and its diagnosis often requires invasive procedures. Deregulated miRNA expression has been described in patients with PDAC. In this study, we analyzed the expression levels of 6 miRNAs (miR-21, -34a, -155, -196a, -200b, and -376a involved in PDAC tumorigenesis) in serum and salivary samples to assess their potential role as circulating diagnostics biomarkers. Serum and salivary samples were collected from patients with PDAC and healthy controls, and miRNA levels were quantified using qRT-PCR. Twenty-four patients with PDAC and 10 healthy controls were recruited. A significant difference between PDAC and healthy groups was observed for the expression of miR-21 and miR-34a (P < 0.001 and P = 0.001) in serum samples. Both miRNAs accurately discriminated between the 2 groups, with an area under the curve for miR-21 and miR-34a of 0.889 (P = 0.001) and 0.865 (P = 0.002), respectively. In general, the expression of miRNAs between salivary samples did not differ. Serum miR-21 and miR-34a are potentially useful diagnostic biomarkers of PDAC. In addition, our results suggest that these miRNAs are not differentially expressed in saliva, making them unsuitable for use as noninvasive biomarkers for diagnostic purposes.

  3. Inference of miRNA targets using evolutionary conservation and pathway analysis

    PubMed Central

    Gaidatzis, Dimos; van Nimwegen, Erik; Hausser, Jean; Zavolan, Mihaela

    2007-01-01

    Background MicroRNAs have emerged as important regulatory genes in a variety of cellular processes and, in recent years, hundreds of such genes have been discovered in animals. In contrast, functional annotations are available only for a very small fraction of these miRNAs, and even in these cases only partially. Results We developed a general Bayesian method for the inference of miRNA target sites, in which, for each miRNA, we explicitly model the evolution of orthologous target sites in a set of related species. Using this method we predict target sites for all known miRNAs in flies, worms, fish, and mammals. By comparing our predictions in fly with a reference set of experimentally tested miRNA-mRNA interactions we show that our general method performs at least as well as the most accurate methods available to date, including ones specifically tailored for target prediction in fly. An important novel feature of our model is that it explicitly infers the phylogenetic distribution of functional target sites, independently for each miRNA. This allows us to infer species-specific and clade-specific miRNA targeting. We also show that, in long human 3' UTRs, miRNA target sites occur preferentially near the start and near the end of the 3' UTR. To characterize miRNA function beyond the predicted lists of targets we further present a method to infer significant associations between the sets of targets predicted for individual miRNAs and specific biochemical pathways, in particular those of the KEGG pathway database. We show that this approach retrieves several known functional miRNA-mRNA associations, and predicts novel functions for known miRNAs in cell growth and in development. Conclusion We have presented a Bayesian target prediction algorithm without any tunable parameters, that can be applied to sequences from any clade of species. The algorithm automatically infers the phylogenetic distribution of functional sites for each miRNA, and assigns a posterior

  4. miRNAs target databases: developmental methods and target identification techniques with functional annotations.

    PubMed

    Singh, Nagendra Kumar

    2017-06-01

    microRNA (miRNA) regulates diverse biological mechanisms and metabolisms in plants and animals. Thus, the discoveries of miRNA has revolutionized the life sciences and medical research.The miRNA represses and cleaves the targeted mRNA by binding perfect or near perfect or imperfect complementary base pairs by RNA-induced silencing complex (RISC) formation during biogenesis process. One miRNA interacts with one or more mRNA genes and vice versa, hence takes part in causing various diseases. In this paper, the different microRNA target databases and their functional annotations developed by various researchers have been reviewed. The concurrent research review aims at comprehending the significance of miRNA and presenting the existing status of annotated miRNA target resources built by researchers henceforth discovering the knowledge for diagnosis and prognosis. This review discusses the applications and developmental methodologies for constructing target database as well as the utility of user interface design. An integrated architecture is drawn and a graphically comparative study of present status of miRNA targets in diverse diseases and various biological processes is performed. These databases comprise of information such as miRNA target-associated disease, transcription factor binding sites (TFBSs) in miRNA genomic locations, polymorphism in miRNA target, A-to-I edited target, Gene Ontology (GO), genome annotations, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, target expression analysis, TF-miRNA and miRNA-mRNA interaction networks, drugs-targets interactions, etc. miRNA target databases contain diverse experimentally and computationally predicted target through various algorithms. The comparison of various miRNA target database has been performed on various parameters. The computationally predicted target databases suffer from false positive information as there is no common theory for prediction of miRNA targets. The review conclusion emphasizes

  5. The Sequence and Structure Determine the Function of Mature Human miRNAs

    PubMed Central

    Wawrzyniak, Dariusz; Jeleniewicz, Jaroslaw; Barciszewska, Miroslawa Z.; Barciszewski, Jan

    2016-01-01

    Micro RNAs (miRNAs) (19–25 nucleotides in length) belong to the group of non-coding RNAs are the most abundant group of posttranscriptional regulators in multicellular organisms. They affect a gene expression by binding of fully or partially complementary sequences to the 3’-UTR of target mRNA. Furthermore, miRNAs present a mechanism by which genes with diverse functions on multiple pathways can be simultaneously regulated at the post-transcriptional level. However, little is known about the specific pathways through which miRNAs with specific sequence or structural motifs regulate the cellular processes. In this paper we showed the broad and deep characteristics of mature miRNAs according to their sequence and structural motifs. We investigated a distinct group of miRNAs characterized by the presence of specific sequence motifs, such as UGUGU, GU-repeats and purine/pyrimidine contents. Using computational function and pathway analysis of their targeted genes, we were able to observe the relevance of sequence and the type of targeted mRNAs. As the consequence of the sequence analysis we finally provide the comprehensive description of pathways, biological processes and proteins associated with the distinct group of characterized miRNAs. Here, we found that the specific group of miRNAs with UGUGU can activate the targets associated to the interferon induction pathway or pathways prominently observed during carcinogenesis. GU-rich miRNAs are prone to regulate mostly processes in neurogenesis, whereas purine/pyrimidine rich miRNAs could be involved rather in transport and/or degradation of RNAs. Additionally, we have also analyzed the simple sequence repeats (SSRs). Their variation within mature miRNAs might be critical for normal miRNA regular activity. Expansion or contraction of SSRs in mature miRNA might directly affect its mRNA interaction or even change the function of that distinct miRNA. Our results prove that due to the specific sequence features, these

  6. Involvement of miRNAs in equine follicle development.

    PubMed

    Schauer, S N; Sontakke, S D; Watson, E D; Esteves, C L; Donadeu, F X

    2013-09-01

    Previous evidence from in vitro studies suggests specific roles for a subset of miRNAs, including miR-21, miR-23a, miR-145, miR-503, miR-224, miR-383, miR-378, miR-132, and miR-212, in regulating ovarian follicle development. The objective of this study was to determine changes in the levels of these miRNAs in relation to follicle selection, maturation, and ovulation in the monovular equine ovary. In Experiment 1, follicular fluid was aspirated during ovulatory cycles from the dominant (DO) and largest subordinate (S) follicles of an ovulatory wave and the dominant (DA) follicle of a mid-cycle anovulatory wave (n=6 mares). Follicular fluid levels of progesterone and estradiol were lower (P<0.01) in S follicles than in DO follicles, whereas mean levels of IGF1 were lower (P<0.01) in S and DA follicles than in DO follicles. Relative to DO and DA follicles, S follicles had higher (P≤0.01) follicular fluid levels of miR-145 and miR-378. In Experiment 2, follicular fluid and granulosa cells were aspirated from dominant follicles before (DO) and 24 h after (L) administration of an ovulatory dose of hCG (n=5 mares/group). Relative to DO follicles, L follicles had higher follicular fluid levels of progesterone (P=0.05) and lower granulosa cell levels of CYP19A1 and LHCGR (P<0.005). Levels of miR-21, miR-132, miR-212, and miR-224 were increased (P<0.05) in L follicles; this was associated with reduced expression of the putative miRNA targets, PTEN, RASA1, and SMAD4. These novel results may indicate a physiological involvement of miR-21, miR-145, miR-224, miR-378, miR-132, and miR-212 in the regulation of cell survival, steroidogenesis, and differentiation during follicle selection and ovulation in the monovular ovary.

  7. Shen 4-marker miRNA panel for lung cancer — EDRN Public Portal

    Cancer.gov

    We initially validated expressions of a set of miRNAs in paired lung tumor tissues and plasma specimens from 28 stage I NSCLC patients by real-time quantitative reverse transcription PCR, and then evaluated diagnostic value of the plasma miRNAs in a cohort of 58 NSCLC patients and 29 healthy individuals. The altered miRNA expressions were reproducibly confirmed in the tumor tissues. The miRNAs were stably present and reliably measurable in plasma. A logistic regression model with the best prediction was defined on the basis of the four genes (miRNA-21, -126, -210, and 486-5p), yielding 86.22% sensitivity and 96.55% specificity in distinguishing NSCLC patients from the healthy controls. (Lab Invest. 2011 Apr;91(4):579-87, PMID: 21116241)

  8. Age-Associated Changes in miRNA Expression Profiles in Thymopoiesis

    PubMed Central

    Virts, Elizabeth L.; Thoman, Marilyn L.

    2010-01-01

    During adult life, the thymus involutes and thymic output of mature T cells drastically declines. The molecular events underlying this process are not well understood. Here, we present evidence of the importance of miRNAs in regulating T cell differentiation in the aged. miRNAs are a wide-ranging regulatory element influencing gene expression throughout the lifetime of the organism. To establish whether they play a role in the age-specific thymic decline, the miRNA expression pattern was examined in TN subsets of young and aged mice. Fifty-two percent of the miRNAs exhibited elevated expression levels in the aged TN1 cells. This expression profile leads us to hypothesize that the large number of highly expressed miRNAs, indicative of rigidly controlled protein expression, limits the developmental potential of this population and results in the age-induced decline in thymopoiesis. PMID:20934450

  9. MiRNA-21 has effects to protect kidney injury induced by sepsis.

    PubMed

    Fu, Dian; Dong, Jie; Li, Ping; Tang, Chaopeng; Cheng, Wen; Xu, Zhenyu; Zhou, Wenquan; Ge, Jingping; Xia, Chen; Zhang, Zhengyu

    2017-10-01

    To investigate the miRNA-21 over-expression in the acute kidney injury induced by sepsis, we developed a sepsis induced in vitro model by lip polysaccharide (LPS) and in vovo model by cecal ligation and puncture (CLP) surgery. LPS or CLP surgery induced kidney cell apoptosis increasing. However, the kidney injury indexes of miRNA groups which were transfected with miRNA-21 were significantly suppressed. In further study, the relative proteins expressions were evaluated to explain the miRNA-21 mechanism to improve sepsis induced kidney cell apoptosis. The results were shown that miRNA-21 over-expression had effects to protect kidney cell apoptosis induced by sepsis via PTEN/PI3K/AKT signaling pathway. Copyright © 2017. Published by Elsevier Masson SAS.

  10. Altered miRNA expression in the cervix during pregnancy associated with lead and mercury exposure

    PubMed Central

    Sanders, Alison P; Burris, Heather H; Just, Allan C; Motta, Valeria; Amarasiriwardena, Chitra; Svensson, Katherine; Oken, Emily; Solano-Gonzalez, Maritsa; Mercado-Garcia, Adriana; Pantic, Ivan; Schwartz, Joel; Tellez-Rojo, Martha M; Baccarelli, Andrea A; Wright, Robert O

    2015-01-01

    Aim: Toxic metals including lead and mercury are associated with adverse pregnancy outcomes. This study aimed to assess the association between miRNA expression in the cervix during pregnancy with lead and mercury levels. Materials & methods: We obtained cervical swabs from pregnant women (n = 60) and quantified cervical miRNA expression. Women's blood lead, bone lead and toenail mercury levels were analyzed. We performed linear regression to examine the association between metal levels and expression of 74 miRNAs adjusting for covariates. Results: Seventeen miRNAs were negatively associated with toenail mercury levels, and tibial bone lead levels were associated with decreased expression of miR-575 and miR-4286. Conclusion: The findings highlight miRNAs in the human cervix as novel responders to maternal chemical exposure during pregnancy. PMID:26418635

  11. Profiling Circulating miRNAs from the Plasma of Individuals with Metabolic Syndrome.

    PubMed

    O'Neill, Sadhbh; O'Driscoll, Lorraine

    2017-01-01

    The technique of RT-qPCR (real time-quantitative polymerase chain reaction) is invaluable in miRNA research both at the profiling and individual RT-qPCR stages. At the profiling stage, numerous miRNAs are looked at in the plasma of numerous individuals from two or more cohorts (i.e., control vs. case). The miRNAs of interest would be either upregulated or downregulated by more than twofold in the case cohort compared to the control cohort. Profiling human specimens for miRNA biomarkers has exploded over the last decade, with researchers profiling plasma, serum, urine, and also the miRNA content of extracellular vesicles, which are also isolated from human specimens. RT-qPCR is a relatively easy technique; however, sample preparation from plasma to RNA to RNA input in RT reaction requires accuracy and precision.

  12. MotomiRs: miRNAs in Motor Neuron Function and Disease

    PubMed Central

    Hawley, Zachary C. E.; Campos-Melo, Danae; Droppelmann, Cristian A.; Strong, Michael J.

    2017-01-01

    MiRNAs are key regulators of the mammalian transcriptome that have been increasingly linked to degenerative diseases of the motor neurons. Although many of the miRNAs currently incriminated as participants in the pathogenesis of these diseases are also important to the normal development and function of motor neurons, at present there is no knowledge of the complete miRNA profile of motor neurons. In this review, we examine the current understanding with respect to miRNAs that are specifically required for motor neuron development, function and viability, and provide evidence that these should be considered as a functional network of miRNAs which we have collectively termed MotomiRs. We will also summarize those MotomiRs currently known to be associated with both amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA), and discuss their potential use as biomarkers. PMID:28522960

  13. MotomiRs: miRNAs in Motor Neuron Function and Disease.

    PubMed

    Hawley, Zachary C E; Campos-Melo, Danae; Droppelmann, Cristian A; Strong, Michael J

    2017-01-01

    MiRNAs are key regulators of the mammalian transcriptome that have been increasingly linked to degenerative diseases of the motor neurons. Although many of the miRNAs currently incriminated as participants in the pathogenesis of these diseases are also important to the normal development and function of motor neurons, at present there is no knowledge of the complete miRNA profile of motor neurons. In this review, we examine the current understanding with respect to miRNAs that are specifically required for motor neuron development, function and viability, and provide evidence that these should be considered as a functional network of miRNAs which we have collectively termed MotomiRs. We will also summarize those MotomiRs currently known to be associated with both amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA), and discuss their potential use as biomarkers.

  14. Identification of potential miRNAs and their targets in Vriesea carinata (Poales, Bromeliaceae).

    PubMed

    Guzman, Frank; Almerão, Mauricio Pereira; Korbes, Ana Paula; Christoff, Ana Paula; Zanella, Camila Martini; Bered, Fernanda; Margis, Rogério

    2013-09-01

    The miRNAs play important roles in regulation of gene expression at the post-transcriptional level. A small RNA and RNA-seq of libraries were constructed to identify miRNAs in Vriesea carinata, a native bromeliad species from Brazilian Atlantic Rainforest. Illumina technology was used to perform high throughput sequencing and data was analyzed using bioinformatics tools. We obtained 2,191,509 mature miRNAs sequences representing 54 conserved families in plant species. Further analysis allowed the prediction of secondary structures for 19 conserved and 16 novel miRNAs. Potential targets were predicted from pre-miRNAs by sequence homology and validated using RTqPCR approach. This study provides the first identification of miRNAs and their potential targets of a bromeliad species.

  15. Capture and Identification of miRNA Targets by Biotin Pulldown and RNA-seq.

    PubMed

    Tan, Shen Mynn; Lieberman, Judy

    2016-01-01

    MicroRNAs (miRNAs) are small noncoding RNAs that regulate the stability and expression of target RNAs in a sequence-dependent manner. Identifying miRNA-regulated genes is key to understanding miRNA function. Here, we describe an unbiased biochemical pulldown method to identify with high-specificity miRNA targets. Regulated transcripts are enriched in streptavidin-captured mRNAs that bind to a transfected biotinylated miRNA mimic. The method is relatively simple, does not involve cross-linking and can be performed with only a million cells. Addition of an on-bead RNase digestion step also identifies miRNA recognition elements (MRE).

  16. Regulation of cancer metastasis by cell-free miRNAs

    PubMed Central

    Alečković, Maša; Kang, Yibin

    2014-01-01

    MicroRNAs (miRNAs) are integral molecules in the regulation of numerous physiological cellular processes that have emerged as critical players in cancer initiation and metastatic progression, both by promoting and suppressing metastasis. Recently, cell-free miRNAs shed from cancer cells into circulation have been reported in cancer patients, raising hope for development of novel biomarkers that can be routinely measured in easily accessible samples. In fact, establishing miRNA expression in the circulation likely has advantages over determination in primary tumor tissue, further augmenting the potential applications of miRNA detection in oncological practice. In addition, secretion of miRNAs impacting distant cell signaling or promoting the formation of a niche that sustains a distant tumor microenvironment allows for new treatment approaches to thwart cancer progression. PMID:25450578

  17. siRNA and miRNA processing: new functions for Cajal bodies.

    PubMed

    Pontes, Olga; Pikaard, Craig S

    2008-04-01

    In diverse eukaryotes, micro-RNAs (miRNAs) and small interfering RNAs (siRNAs) regulate important processes that include mRNA inactivation, viral defense, chromatin modification, and transposon silencing. Recently, nucleolus-associated Cajal bodies in plants have been implicated as sites of siRNA and miRNA biogenesis, whereas in animals siRNA and miRNA dicing occurs in the cytoplasm. The plant nucleolus also contains proteins of the nonsense-mediated mRNA decay pathway that in animals are found associated with cytoplasmic processing bodies (P-bodies). P-bodies also function in the degradation of mRNAs subjected to miRNA and siRNA targeting. Collectively, these observations suggest interesting variations in the way siRNAs and miRNAs can accomplish their similar functions in plants and animals.

  18. Assessing sample and miRNA profile quality in serum and plasma or other biofluids.

    PubMed

    Blondal, Thorarinn; Jensby Nielsen, Søren; Baker, Adam; Andreasen, Ditte; Mouritzen, Peter; Wrang Teilum, Maria; Dahlsveen, Ina K

    2013-01-01

    MicroRNAs (miRNAs) constitute a class of small cellular RNAs (typically 21-23nt) that function as post-transcriptional regulators of gene expression. Current estimates indicate that more than one third of the cellular transcriptome is regulated by miRNAs, although they are relatively few in number (less than 2000 human miRNAs). The high relative stability of miRNA in common clinical tissues and biofluids (e.g. plasma, serum, urine, saliva, etc.) and the ability of miRNA expression profiles to accurately classify discrete tissue types and disease states have positioned miRNA quantification as a promising new tool for a wide range of diagnostic applications. Furthermore miRNAs have been shown to be rapidly released from tissues into the circulation with the development of pathology. To facilitate discovery and clinical development of miRNA-based biomarkers, we developed a genome-wide Locked Nucleic Acid (LNA™)-based miRNA qPCR platform with unparalleled sensitivity and robustness. The platform allows high-throughput profiling of miRNAs from important clinical sources without the need for pre-amplification. Using this system, we have profiled thousands of biofluid samples including blood derived plasma and serum. An extensive quality control (QC) system has been implemented in order to secure technical excellence and reveal any unwanted bias coming from pre-analytical or analytical variables. We present our approaches to sample and RNA QC as well as data QC and normalization. Specifically we have developed normal reference ranges for circulating miRNAs in serum and plasma as well as a hemolysis indicator based on microRNA expression.

  19. miRNA Expression in Control and FSHD Fetal Human Muscle Biopsies

    PubMed Central

    Portilho, Débora Morueco; Alves, Marcelo Ribeiro; Kratassiouk, Gueorgui; Roche, Stéphane; Magdinier, Frédérique; de Santana, Eliane Corrêa; Polesskaya, Anna; Harel-Bellan, Annick; Mouly, Vincent; Savino, Wilson; Butler-Browne, Gillian; Dumonceaux, Julie

    2015-01-01

    Background Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal-dominant disorder and is one of the most common forms of muscular dystrophy. We have recently shown that some hallmarks of FSHD are already expressed in fetal FSHD biopsies, thus opening a new field of investigation for mechanisms leading to FSHD. As microRNAs (miRNAs) play an important role in myogenesis and muscle disorders, in this study we compared miRNAs expression levels during normal and FSHD muscle development. Methods Muscle biopsies were obtained from quadriceps of both healthy control and FSHD1 fetuses with ages ranging from 14 to 33 weeks of development. miRNA expression profiles were analyzed using TaqMan Human MicroRNA Arrays. Results During human skeletal muscle development, in control muscle biopsies we observed changes for 4 miRNAs potentially involved in secondary muscle fiber formation and 5 miRNAs potentially involved in fiber maturation. When we compared the miRNA profiles obtained from control and FSHD biopsies, we did not observe any differences in the muscle specific miRNAs. However, we identified 8 miRNAs exclusively expressed in FSHD1 samples (miR-330, miR-331-5p, miR-34a, miR-380-3p, miR-516b, miR-582-5p, miR-517* and miR-625) which could represent new biomarkers for this disease. Their putative targets are mainly involved in muscle development and morphogenesis. Interestingly, these FSHD1 specific miRNAs do not target the genes previously described to be involved in FSHD. Conclusions This work provides new candidate mechanisms potentially involved in the onset of FSHD pathology. Whether these FSHD specific miRNAs