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Sample records for festuca arundinacea mirnas

  1. Tall fescue (Festuca arundinacea Schreb.).

    PubMed

    Ge, Yaxin; Wang, Zeng-Yu

    2015-01-01

    Tall fescue (Festuca arundinacea Schreb.) is the predominant cool-season perennial grass in the United States. It is widely used for both forage and turf purposes. This chapter describes a protocol that allows for the generation of a large number of transgenic tall fescue plants by Agrobacterium tumefaciens-mediated transformation. Embryogenic calli induced from caryopsis are used as explants for inoculation with A. tumefaciens. The Agrobacterium strain used is EHA105. Hygromycin phosphotransferase gene (hph) is used as the selectable marker, and hygromycin is used as the selection agent. Calli resistant to hygromycin are obtained after 4-6 weeks of selection. Soil-grown tall fescue plants can be regenerated 4-5 months after Agrobacterium tumefaciens-mediated transformation. PMID:25416272

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  3. Utilizing genetically diverse Festuca arundinaceae recoveries from a Lolium multiflorum x Festuca arundinaceae population to evaluate endophyte interaction and performance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Development of cool-season perennial grass forages exhibiting adaptation and persistence to the environmental extremes of the southern plains region of the USA would provide an important contribution toward sustaining the regions grazing livestock industry. Festuca arundinaceae, a sustainable cool-...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  5. Mg and K Effects on Cation Uptake and Dry Matter Accumulation in Tall Fescue (Festuca Arundinacea)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    HiMag tall fescue (Lolium arundinaceum (Schreb.) S.J. Darbyshire = Festuca arundinacea Schreb) was selected for high Mg concentration to reduce grass tetany risk to ruminants; however, the mechanism of increased Mg uptake into shoots is unknown. The objective was to determine cation concentrations ...

  6. Utilization of flow cytometry for festulolium breeding (Lolium multiflorum (2x) × Festuca arundinacea (6x))

    PubMed Central

    Akiyama, Yukio; Ueyama, Yasufumi; Hamada, Seiya; Kubota, Akito; Kato, Daisuke; Yamada-Akiyama, Hitomi; Takahara, Yoshinori; Fujimori, Masahiro

    2016-01-01

    Festulolium is a hybrid between Festuca and Lolium species that has valuable agronomic traits from both grass species. The purpose of our breeding program is to produce hexaploid festulolium that introduces tolerance to summer depression into Italian ryegrass (Lolium multiflorum) by crossing it with tall fescue (Festuca arundinacea). However, we found the DNA ploidy of hexaploids was not stable and was reduced in successive generations. We aimed to find out how to obtain stable high-ploidy festulolium. F1 hybrids of L. multiflorum and F. arundinacea were produced. The F3 generation was produced from putative hexaploid F2 individuals by open pollination. The F4 to F6 generations were obtained by polycrossing. The DNA ploidy levels of F2 to F6 individuals were estimated by flow cytometry. Cytological characteristics of the F5 and F6 individuals were investigated by FISH and GISH. The DNA ploidy level of hexaploid festulolium was reduced and stabilized at almost the same level as a tetraploid. Seed fertility was inversely correlated with an increase in ploidy level. GISH revealed no preferential Lolium transmission. FISH with a telomere probe revealed that counting the exact number of chromosomes in festulolium was difficult. DNA ploidy level was strongly correlated with the number of chromosomes. PMID:27162495

  7. Utilization of flow cytometry for festulolium breeding (Lolium multiflorum (2x) × Festuca arundinacea (6x)).

    PubMed

    Akiyama, Yukio; Ueyama, Yasufumi; Hamada, Seiya; Kubota, Akito; Kato, Daisuke; Yamada-Akiyama, Hitomi; Takahara, Yoshinori; Fujimori, Masahiro

    2016-03-01

    Festulolium is a hybrid between Festuca and Lolium species that has valuable agronomic traits from both grass species. The purpose of our breeding program is to produce hexaploid festulolium that introduces tolerance to summer depression into Italian ryegrass (Lolium multiflorum) by crossing it with tall fescue (Festuca arundinacea). However, we found the DNA ploidy of hexaploids was not stable and was reduced in successive generations. We aimed to find out how to obtain stable high-ploidy festulolium. F1 hybrids of L. multiflorum and F. arundinacea were produced. The F3 generation was produced from putative hexaploid F2 individuals by open pollination. The F4 to F6 generations were obtained by polycrossing. The DNA ploidy levels of F2 to F6 individuals were estimated by flow cytometry. Cytological characteristics of the F5 and F6 individuals were investigated by FISH and GISH. The DNA ploidy level of hexaploid festulolium was reduced and stabilized at almost the same level as a tetraploid. Seed fertility was inversely correlated with an increase in ploidy level. GISH revealed no preferential Lolium transmission. FISH with a telomere probe revealed that counting the exact number of chromosomes in festulolium was difficult. DNA ploidy level was strongly correlated with the number of chromosomes. PMID:27162495

  8. Effect of Light Crude Oil-Contaminated Soil on Growth and Germination of Festuca arundinacea

    NASA Astrophysics Data System (ADS)

    Minai-Tehrani, Dariush; Shahriari, Malek-Hossein; Savaghebi-Firoozabadi, Gholamreza

    In this study the effect of different concentrations of light crude oil (up to 10%) on the growth and germination of Festuca arundinacea (Tall fescue) was studied. Present results showed that the germination number and dry biomass of the plant decreased by increasing light crude oil concentration in the soil. The biomass was higher in 1% crude oil sample while it was lower in 10% crude oil sample. The length of leaves reduced in higher crude oil concentration in comparison with the control. Total and oil-degrading colony count of soil showed that the microbial population in 7 and 10% samples was higher than the control and low concentrations of crude oil (1 and 3% samples). The crude oil reduction in the vegetated and the non-vegetated samples was higher in 1% sample. All vegetated samples had higher crude oil reduction than non-vegetated samples. The higher reduction was occurred at 1% sample, while the lower reduction was seen at 10% sample.

  9. Ozone and sulfur dioxide effects on tall fescue. II. Alteration of quality constituents. [Festuca arundinacea

    SciTech Connect

    Flagler, R.B.; Youngner, V.B.

    1985-01-01

    A greenhouse study was conducted to determine whether ozone (O/sub 3/) and sulfur dioxide (SO/sub 2/) might alter forage quality parameters of tall fescue (Festuca arundinacea Schreb. Alta). Plants were exposed weekly to four O/sub 3/ treatments, 0, 0.10, 0.20, and 0.30 ..mu..L L/sup -1/; with or without 0.10 ..mu..L L/sup -1/ SO/sub 2/, 6 h d/sup -1/ for 12 weeks. Ozone had a much greater impact on forage quality than did SO/sub 2/. Ozone increased protein content on a g kg/sup -1/ basis and decreased protein on a weight per plant basis. Ozone reduced crude fat, crude fiber, and total nonstructural carbohydrate contents of the forage. Crude ash content increased due to O/sub 3/ exposure. On a weight per plant basis, O/sub 3/ decreased the forage concentration of Ca, Mg, and P. Ozone increased Ca concentration of herbage. Sulfur dioxide increased ash content of the forage. Phosphorus concentration and weight per plant of Mg and P were all reduced by SO/sub 2/ Significant pollutant interactions occurred for crude fiber, crude ash, total Mg, and total P contents of forage. While treatments resulted in some apparent increases in forage quality, these were at the expense of yield. The most adverse effects on forage quality were an increase in ash content which resulted from an interaction of SO/sub 2/ with O/sub 3/, and a reduction in soluble carbohydrate content of shoots due to O/sub 3/.

  10. Identification and characterization of a salt stress-inducible zinc finger protein from Festuca arundinacea

    PubMed Central

    2012-01-01

    Background Increased biotic and abiotic plant stresses due to climate change together with an expected global human population of over 9 billion by 2050 intensifies the demand for agricultural production on marginal lands. Soil salinity is one of the major abiotic stresses responsible for reduced crop productivity worldwide and the salinization of arable land has dramatically increased over the last few decades. Consequently, as land becomes less amenable for conventional agriculture, plants grown on marginal soils will be exposed to higher levels of soil salinity. Forage grasses are a critical component of feed used in livestock production worldwide, with many of these same species of grasses being utilized for lawns, erosion prevention, and recreation. Consequently, it is important to develop a better understanding of salt tolerance in forage and related grass species. Findings A gene encoding a ZnF protein was identified during the analysis of a salt-stress suppression subtractive hybridization (SSH) expression library from the forage grass species Festuca arundinacea. The expression pattern of FaZnF was compared to that of the well characterized gene for delta 1-pyrroline-5-carboxylate synthetase (P5CS), a key enzyme in proline biosynthesis, which was also identified in the salt-stress SSH library. The FaZnF and P5CS genes were both up-regulated in response to salt and drought stresses suggesting a role in dehydration stress. FaZnF was also up-regulated in response to heat and wounding, suggesting that it might have a more general function in multiple abiotic stress responses. Additionally, potential downstream targets of FaZnF (a MAPK [Mitogen-Activated Protein Kinase], GST [Glutathione-S-Transferase] and lipoxygenase L2) were found to be up-regulated in calli overexpressing FaZnF when compared to control cell lines. Conclusions This work provides evidence that FaZnF is an AN1/A20 zinc finger protein that is involved in the regulation of at least two pathways

  11. 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

  12. Variation and genetic structure of Tunisian Festuca arundinacea populations based on inter-simple sequence repeat pattern.

    PubMed

    Chtourou-Ghorbel, N; Elazreg, H; Ghariani, S; Ben Mheni, N; Sekmani, M; Chakroun, M; Trifi-Farah, N

    2015-01-01

    Tunisian tall fescue (Festuca arundinacea Schreb.) is an important grass for forages or soil conservation, particularly in marginal sites. Inter-simple sequence repeats were used to estimate genetic diversity within and among 8 natural populations and 1 cultivar from Northern Tunisia. A total of 181 polymorphic inter-simple sequence repeat markers were generated using 7 primers. Shannon's index and analysis of molecular variance evidenced a high molecular polymorphism at intra-specific levels for wild and cultivated accessions, showing that Tunisian tall fescue germplasm constitutes an important pool of diversity. Within-population variation accounted for 39.42% of the total variation, but no regional differentiation was discernible to designate close relationships between regions. Most of the variation (GST = 67%) occurred between populations, rather than within populations. The ɸST (0.60) revealed high population structuring. Additionally, the population structure was independent of the geographic origin and was not affected by environmental factors. The unweighted pair group method with arithmetic mean tree based on genetic similarity and principal coordinate analysis based on coefficient similarity illustrated that continental populations from the proximate localities of Beja and Jendouba were genetically closely related, while the wild Skalba population from the littoral Tunisian locality was the most diverse from the others. Moreover, great molecular similarity of the spontaneous population Sedjnane originated from the mountain areas was revealed with the local cultivar Mornag. The observed genetic diversity can be used to implement conservation strategies and breeding programs for improving forage crops in Tunisia. PMID:25966071

  13. 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.

  14. 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

  15. Responses of tall fescue (Festuca arundinacea) to growth in naphthalene-contaminated sand: xenobiotic stress versus water stress.

    PubMed

    Balasubramaniyam, Anuluxshy; Chapman, Mark M; Harvey, Patricia J

    2015-05-01

    The adaptations of tall fescue (Festuca arundinacea) arising from growth in naphthalene-contaminated sand (0.8 g kg(-1) sand dry weight (dw)) were investigated in the contexts of xenobiotic stress and water stress. The transfer of polycyclic aromatic hydrocarbons (PAHs) across the root endodermis was investigated using the hydrophobic Nile red stain as a PAH homologue. Nile red was applied to the epidermis of a living root to visualise uptake into the root through the transpiration stream, and the distance travelled by the stain into the root tissues was investigated using epi-fluorescence microscopy (Nikon Eclipse 90i). The results showed that the Nile red applied to the roots grown in naphthalene-contaminated sand was unable to penetrate the roots beyond the endodermis, whereas those grown in 'clean' sand showed evidence of uptake into the xylem vessels beyond the endodermis. Furthermore, partial collapse was observed in the cortex of naphthalene-treated roots, suggesting drought stress. Interestingly, the treated plants showed visual resilience to drought stress whilst the leaves of the control plants showed signs of wilting. PMID:25874421

  16. 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. PMID:25774160

  17. 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

  18. 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.

  19. Changes in the abundance of sugars and sugar-like compounds in tall fescue (Festuca arundinacea) due to growth in naphthalene-treated sand.

    PubMed

    Balasubramaniyam, Anuluxshy; Harvey, Patricia J

    2015-04-01

    The hydrophilic metabolome of tall fescue (Festuca arundinacea) adapted to grow in naphthalene-treated sand (0.8 g kg(-1) sand dw) was analysed using gas chromatography-mass spectrometry, and peaks corresponding to the more abundant compounds were tentatively identified from analysis of their mass spectral features and reference to the NIST Mass Spectral Database. Particular attention was paid to sugars as they are known to play important roles as stress regulators in plants. The results showed that the abundance of sugars was greater in the roots but lesser in the shoots of treated plants when compared to their control counterparts. The results for indole acetic acid (IAA) were notable: IAA was prominently less in the treated roots compared to shoots, and in treated shoots, IAA was particularly subdued compared to untreated shoots consistent with IAA degradation in treated plant tissues. The differences in the molecular phenotype between control and treated plants were expressed in root structural differences. The treated roots were modified to have greater suberisation, enhanced thickening in the endodermis and distortions in the cortical zone as demonstrated through scanning electron and epi-fluorescence microscopy. PMID:25391233

  20. Characterization of Proanthocyanidins from Seeds of Perennial Ryegrass (Lolium perenne L.) and Tall Fescue (Festuca arundinacea) by Liquid Chromatography-Mass Spectrometry.

    PubMed

    Fraser, Karl; Collette, Vern; Hancock, Kerry R

    2016-09-01

    Perennial ryegrass (Lolium perenne) and tall fescue (Festuca arundinacea) are forage species of the grass family (Poaceae) that are key components of temperate pasture-based agricultural systems. Proanthocyanidins (PAs) are oligomeric flavonoids that, when provided as part of a farm animal's diet, have been reported to improve animal production and health. Up to now, forage grasses have been deemed not to produce PAs. This paper reports for the first time the detection of polymerized PAs in aqueous methanolic extracts of seed tissue of both perennial ryegrass and tall fescue, using LC-MS/MS. We have determined the structure of the PAs to be trans-flavan-3-ol-based, consisting predominately of afzelechin and catechin and linked primarily by B-type bonds. Investigations into the leaf tissue of both species failed to detect any PAs. This discovery opens the possibility of using genetic engineering tools to achieve tannin accumulation in leaf tissue of perennial ryegrass and tall fescue. PMID:27532250

  1. 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

  2. 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. PMID:27504113

  3. Ascorbic acid mitigation of water stress-inhibition of root growth in association with oxidative defense in tall fescue (Festuca arundinacea Schreb.)

    PubMed Central

    Xu, Yi; Xu, Qian; Huang, Bingru

    2015-01-01

    Root growth inhibition by water stress may be related to oxidative damages. The objectives of this study were to determine whether exogenous application of ascorbic acid (ASA) could mitigate root growth decline due to water stress and whether ASA effects on root growth could be regulated through activating non-enzymatic or enzymatic antioxidant systems in perennial grass species. Tall fescue (Festuca arundinacea Schreb. cv. “K-31”) plants were grown in nutrient solution, and polyethylene glycol (PEG)-8000 was added into the solution to induce water stress. For exogenous ASA treatment, ASA (5 mM) was added into the solution with or without PEG-8000. Plants treated with ASA under water stress showed significantly increased root growth rate, and those roots had significantly lower content of reactive oxygen species (ROS) (H2O2 and O2− content) than those without ASA treatment. Malondialdehyde content in root tips treated with ASA under water stress was also significantly reduced compared with those under water stress alone. In addition, free ascorbate and total ascorbate content were significantly higher in roots treated with ASA under water stress than those without ASA treatment. The enzymatic activities for ROS scavenging-related genes were not significantly altered by ASA treatment under water stress, while transcript abundances of genes encoding superoxide dismutase, catalase, ascorbate peroxidase, glutathione reductase, dehydroascorbate reductase, and monohydroascorbate reductase showed significant decreases in the root elongation zone and significant increases in the root maturation zone treated with ASA under water stress. Transcripts of genes for expansins and xyloglucan endotransglycosylases showed increased abundances in ASA-treated root maturation zone under water stress, indicating that ASA could accelerated cell wall loosening and cell expansion. The results suggested that exogenous treatment of roots with ASA enhanced root elongation under water

  4. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  6. MOLECULAR DETECTION, CLASSIFICATION, AND PHYLOGENETIC ANALYSIS OF SUBGROUP 16SRI-C PHYTOPLASMAS DETECTED IN DISEASED POA AND FESTUCA IN LITHUANIA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phytoplasma strains were detected in two grass species, Poa pratensis L. (common meadow grass) and Festuca arundinacea Schreb. (tall fescue), exhibiting yellows disease symptoms in Lithuania. Analysis of amplified 16S rDNAs revealed that the phytoplasmas associated with these diseases, designated as...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  8. Transcriptomes of Lolium/Schedonorus/Festuca species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  9. Transcriptomes of Lolium/Schedonorus/Festuca Species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  10. Transcriptomes of Lolium/Schedonorus/Festuca species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  11. 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

  12. 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

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

    PubMed

    Lou, Yanhong; Hu, Longxing; 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

  14. 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

  15. 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

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

    PubMed

    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

  17. 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

  18. Viral miRNAs.

    PubMed

    Plaisance-Bonstaff, Karlie; Renne, Rolf

    2011-01-01

    Since 2004, more than 200 microRNAs (miRNAs) have been discovered in double-stranded DNA viruses, mainly herpesviruses and polyomaviruses (Nucleic Acids Res 32:D109-D111, 2004). miRNAs are short 22  ±  3 nt RNA molecules that posttranscriptionally regulate gene expression by binding to 3'-untranslated regions (3'UTR) of target mRNAs, thereby inducing translational silencing and/or transcript degradation (Nature 431:350-355, 2004; Cell 116:281-297, 2004). Since miRNAs require only limited complementarity for binding, miRNA targets are difficult to determine (Mol Cell 27:91-105, 2007). To date, targets have only been experimentally verified for relatively few viral miRNAs, which either target viral or host cellular gene expression: For example, SV40 and related polyomaviruses encode miRNAs which target viral large T antigen expression (Nature 435:682-686, 2005; J Virol 79:13094-13104, 2005; Virology 383:183-187, 2009; J Virol 82:9823-9828, 2008) and miRNAs of α-, β-, and γ-herpesviruses have been implicated in regulating the transition from latent to lytic gene expression, a key step in the herpesvirus life cycle. Viral miRNAs have also been shown to target various host cellular genes. Although this field is just beginning to unravel the multiple roles of viral miRNA in biology and pathogenesis, the current data strongly suggest that virally encoded miRNAs are able to regulate fundamental biological processes such as immune recognition, promotion of cell survival, angiogenesis, proliferation, and cell differentiation. This chapter aims to summarize our current knowledge of viral miRNAs, their targets and function, and the challenges lying ahead to decipher their role in viral biology, pathogenesis, and for γ-herepsvirus-encoded miRNAs, potentially tumorigenesis. PMID:21431678

  19. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  1. DNA Markers and Sequences Reveal Geographic Races of Reed Canarygrass (Phalaris arundinacea)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Reed canarygrass (Phalaris arundinacea L.) is a cool-season perennial with a circumglobal distribution in the northern hemisphere, native to Europe, Asia, and North America. Repeated introductions of European germplasm into North America have created confusion over the origins of reed canarygrass g...

  2. 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

  3. 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

  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

    2016-01-01

    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. PMID:27005474

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

    PubMed

    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

  6. 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

  7. 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

    2015-01-01

    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

  8. 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

  9. 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. PMID:24696578

  10. 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

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

    PubMed

    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

  12. 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

  13. miRNAs Related to Skeletal Diseases.

    PubMed

    Seeliger, Claudine; Balmayor, Elizabeth R; van Griensven, Martijn

    2016-09-01

    miRNAs as non-coding, short, double-stranded RNA segments are important for cellular biological functions, such as proliferation, differentiation, and apoptosis. miRNAs mainly contribute to the inhibition of important protein translations through their cleavage or direct repression of target messenger RNAs expressions. In the last decade, miRNAs got in the focus of interest with new publications on miRNAs in the context of different diseases. For many types of cancer or myocardial damage, typical signatures of local or systemically circulating miRNAs have already been described. However, little is known about miRNA expressions and their molecular effect in skeletal diseases. An overview of published studies reporting miRNAs detection linked with skeletal diseases was conducted. All regulated miRNAs were summarized and their molecular interactions were illustrated. This review summarizes the involvement and interaction of miRNAs in different skeletal diseases. Thereby, 59 miRNAs were described to be deregulated in tissue, cells, or in the circulation of osteoarthritis (OA), 23 miRNAs deregulated in osteoporosis, and 107 miRNAs deregulated in osteosarcoma (OS). The molecular influences of miRNAs regarding OA, osteoporosis, and OS were illustrated. Specific miRNA signatures for skeletal diseases are described in the literature. Some overlapped, but also unique ones for each disease exist. These miRNAs may present useful targets for the development of new therapeutic approaches and are candidates for diagnostic evaluations. PMID:27418331

  14. 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. PMID:25659333

  15. Epichloae infection in a native South African grass, Festuca costata Nees.

    PubMed

    McGranahan, D A; Burgdorf, R; Kirkman, K P

    2015-07-01

    Fungal endophytes have been documented in almost all terrestrial plant groups. Although the endophyte infection syndrome in agronomic cultivars is well studied, relatively little work addresses questions of spatial ecology and fire effects on epichloae endophyte infection in native grasses, and none, to our knowledge, in sub-Saharan Africa. We sampled seven populations of the native Festuca costata Nees along the spline of the Drakensberg range in South Africa at several spatial scales, including both recently burned and unburned stands. We tested epichloae presence and prevalence with immunoblot assays, PCR and genetic sequencing. We found epichloae endophytes were present and prevalent (38-98% infection rates depending on location). Variation in infection rates occurred primarily among locations, but also among bunches. There was little evidence that endophyte infection rates varied with fire. Novel evidence of epichloae infection of a native Festuca in South Africa opens the door to several new research questions, from the phylogenetic relationship between epichloae of sub-Saharan Africa and other continents to the ecological advantages or disadvantages that endophytes confer upon their hosts, especially in a fire-prone ecosystem vulnerable to global environmental change. PMID:25619128

  16. Genetic Differentiation and Hybridization Among Festuca Idahoensis, F. Roemeri, and F. Ovina Detected From AFLP, ITS, and Chloroplast DNA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    North American forms of the F. ovina complex, Festuca idahoensis and F. roemert are distributed broadly east and narrowly west of the Cascade Mountains, respectively. The psbA-trnH and rps16-trnK chloroplast DNA intergenic sequences, 18S-5.8S-26S nuclear ribosomal DNA internal transcribed spacer (I...

  17. 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. PMID:22038480

  18. Diversity of AMF associated with Ammophila arenaria ssp. arundinacea in Portuguese sand dunes.

    PubMed

    Rodríguez-Echeverría, Susana; Freitas, Helena

    2006-11-01

    Dune vegetation is essential for the formation and preservation of sand dunes and the protection of the coast line. Coastal sand dunes are harsh environments where arbuscular mycorrhizal fungi (AMF) play an important role in promoting plant establishment and growth. We present a study of the diversity of AMF associated with A. arenaria ssp. arundinacea in two locations of the Portuguese coast under a Mediterranean climate. These two locations were selected to compare a well-preserved dune system from a protected area with a degraded dune system from a public beach. AMF diversity was assessed mainly by cloning and sequencing of a fragment of the ribosomal SSU using the primer NS31 and AM1. Most of the 89 AMF clones obtained from the rhizosphere and roots of A. arenaria belonged to the genus Glomus, the largest clade within the Glomeromycota. Higher AMF diversity was found in the least disturbed site, in which spores of Scutellospora persica, Glomus constrictum and Glomus globiferum were found in the rhizosphere of A. arenaria. PMID:17043895

  19. Characterization of two Agrostis-Festuca alpine pastures and their influence on cheese composition.

    PubMed

    Povolo, Milena; Pelizzola, Valeria; Passolungo, Luigi; Biazzi, Elisa; Tava, Aldo; Contarini, Giovanna

    2013-01-16

    Recently, there has been a renewed interest in mountain farming, and several studies have been carried out on milk and cheese obtained in the unique environmental conditions of the Alps, a 1300 km mountain chain, located in the north of Italy. In this paper, the influence, on some cheese constituents, of two very similar mountain grasslands, both dominated by Festuca - Agrostis , was investigated. The two pastures were located in the same area in the southeastern Italian alpine region and differed in sunshine orientation and exposure. Milk obtained from cows grazing on these pastures was used to produce a semi-hard traditional cheese. The differences observed between the cheeses of the two areas for both some hydrocarbons (1-phytene and 2-phytene) and trans-fatty acids can be explained by a different rumen environment created by the botanical composition of the two pastures. The multidisciplinary approach can be considered a successful strategy, suitable for studying markers of authenticity. PMID:23259614

  20. Volatile constituents of Festuca nigrescens, Phleum alpinum and Poa alpina from N. W. Italian Alpine pastures.

    PubMed

    Tava, Aldo; Cecotti, Roberto; Grecchi, Maris; Falchero, Luca; Coppa, Mauro; Lombardi, Giampiero

    2011-01-01

    The composition of the volatile fractions of three important grasses from sub-alpine N.W. Italian pastures, namely Festuca nigrescens Lam. non Gaudin (chewing fescue), Phleum alpinum L. (alpine timothy) and Poa alpina L. (alpine bluegrass) was investigated. The fresh aerial parts were collected at the flowering stage during the summer season. The volatile oils obtained from green tissues by steam distillation in a Clevenger-type apparatus, were analyzed by GC/FID and GC/MS. The oil yield was 0.04 +/- 0.01% weight/fresh weight bases for each of the investigated species. Several classes of compounds were found in the volatile fractions, including aldehydes, alcohols, acids, hydrocarbons, esters, ketones, terpenes, and phenolics. Qualitative and quantitative differences were observed. PMID:21366056

  1. 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.

  2. Estrogenic activity of a hydro-alcoholic extract of Bambusa arundinaceae leaves on female wistar rats

    PubMed Central

    Jawaid, Talha; Awasthi, Akanksha; Kamal, Mehnaz

    2015-01-01

    To study the estrogenic activity of the hydro-alcoholic extract of Bambusa arundinaceae leaves (HEBA) in female Wistar rats. The dried powdered leaves were extracted with hydroalcoholic mixture (60%), and the resultant extract was subjected for phytochemical analyses to identify different phytoconstituents. HEBA were administered to ovariectomized rats for 7 days at three different doses (viz., 200, 300, 400 mg/kg body weight, p.o.) and their estrogenic activity were compared with each of daily treatment with 0.2 mg/kg body weight, i.p. conjugated equine estrogen as a positive control or olive oil as a negative control. Estrogenic activity was evaluated by doing uterotropic assay, vaginal cytology and measurement of vaginal opening in female Wistar rats. Oral administration of HEBA in ovariectomized immature and mature female Wistar rats in a dose of 400 mg/kg b.w. resulted in significant increase in the uterine wet weight (in mg) (224.82 ± 7.01) and (912.25 ± 27.22) when compared with ovariectomized control rats (111.52 ± 3.17) and (506.67 ± 21.39). HEBA (400 mg/kg b.w., p.o.) treated rats, showing only cornified epithelial cells which was an indication of the presence of the estrogen and also showed 100% vaginal opening. It was observed that HEBA possess significant estrogenic activity at 400 mg/kg b.w., p.o. which was evident by uterotropic assay, measurement of vaginal opening, and histopathological changes. PMID:25709965

  3. 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. PMID:22048544

  4. 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

  5. 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

  6. 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

  7. miRNA and Vascular Cell Movement

    PubMed Central

    Yue, Junming

    2011-01-01

    miRNAs are a new class of endogenous small RNAs that negatively regulate gene expression at the posttranscriptional level. Accumulating experimental evidence shows that miRNAs regulate cellular apoptosis, proliferation, differentiation, and migration. Dysregulation of miRNA expression leads to various human diseases including cancer and cardiovascular disease. miRNA maturation is regulated at multiple steps by different mechanisms, including miRNA editing, hairpin loop binding, self-regulation, and cross-talk with other signaling pathways. Vascular cell movement plays a pivotal role in the development of various cancers and cardiovascular diseases. miRNAs have been found to regulate vascular cell movement. Presently the chemically synthesized antagomir, miRNA mimics have been widely used in investigating the biological functions of miRNA genes. The viral vectors, including adenoviral, lentiviral, and adeno-associated viral vectors, have been used to efficiently overexpress or knockdown miRNAs in vitro and in vivo. Therefore, targeting vascular cell movement using miRNA-based drug or gene therapy would provide a novel therapeutic approach in the treatment of cancers and vascular diseases. PMID:21241758

  8. 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

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

    PubMed

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

    2016-01-01

    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. PMID:26732371

  10. 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

  11. Relative effects of irrigation and intense shade on productivity of alley-cropped tall fescue herbage

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The comparative effects of reduced irradiance and soil water on alley cropped herbage are poorly understood. Our objective was to determine effects of irrigation on herbage productivity when tall fescue [Lolium arundinaceum (Schreb.) Darbysh. = Festuca arundinacea Schreb. var. arundinacea Schreb.] ...

  12. Prediction of miRNA targets.

    PubMed

    Oulas, Anastasis; Karathanasis, Nestoras; Louloupi, Annita; Pavlopoulos, Georgios A; Poirazi, Panayiota; Kalantidis, Kriton; Iliopoulos, Ioannis

    2015-01-01

    Computational methods for miRNA target prediction are currently undergoing extensive review and evaluation. There is still a great need for improvement of these tools and bioinformatics approaches are looking towards high-throughput experiments in order to validate predictions. The combination of large-scale techniques with computational tools will not only provide greater credence to computational predictions but also lead to the better understanding of specific biological questions. Current miRNA target prediction tools utilize probabilistic learning algorithms, machine learning methods and even empirical biologically defined rules in order to build models based on experimentally verified miRNA targets. Large-scale protein downregulation assays and next-generation sequencing (NGS) are now being used to validate methodologies and compare the performance of existing tools. Tools that exhibit greater correlation between computational predictions and protein downregulation or RNA downregulation are considered the state of the art. Moreover, efficiency in prediction of miRNA targets that are concurrently verified experimentally provides additional validity to computational predictions and further highlights the competitive advantage of specific tools and their efficacy in extracting biologically significant results. In this review paper, we discuss the computational methods for miRNA target prediction and provide a detailed comparison of methodologies and features utilized by each specific tool. Moreover, we provide an overview of current state-of-the-art high-throughput methods used in miRNA target prediction. PMID:25577381

  13. Telomere Length, TERT, and miRNA Expression.

    PubMed

    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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  15. Deletion of the Fungal Gene soft Disrupts Mutualistic Symbiosis between the Grass Endophyte Epichloë festucae and the Host Plant

    PubMed Central

    Charlton, Nikki D.; Shoji, Jun-Ya; Ghimire, Sita R.; Nakashima, Jin

    2012-01-01

    Hyphal anastomosis, or vegetative hyphal fusion, establishes the interconnection of individual hyphal strands into an integrated network of a fungal mycelium. In contrast to recent advances in the understanding of the molecular basis for hyphal anastomosis, knowledge of the physiological role of hyphal anastomosis in the natural habitats of filamentous fungi is still very limited. To investigate the role of hyphal anastomosis in fungal endophyte-plant interactions, we generated mutant strains lacking the Epichloë festucae soft (so) gene, an ortholog of the hyphal anastomosis gene so in the endophytic fungus E. festucae. The E. festucae Δso mutant strains grew similarly to the wild-type strain in culture but with reduced aerial hyphae and completely lacked hyphal anastomosis. The most striking phenotype of the E. festucae Δso mutant strain was that it failed to establish a mutualistic symbiosis with the tall fescue plant host (Lolium arundinaceum); instead, it killed the host plant within 2 months after the initial infection. Microscopic examination revealed that the death of the tall fescue plant host was associated with the distortion and disorganization of plant cells. This study suggests that hyphal anastomosis may have an important role in the establishment/maintenance of fungal endophyte-host plant mutualistic symbiosis. PMID:23042130

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A bunt fungus infecting commercial perennial ryegrass (Lolium perenne) from Australia and chewings fescue (Festuca rubra) from the U.S.A. exhibits a spore germination pattern that is unique from other reticulately-spored species of Tilletia infecting hosts in the grass subfamily Pooideae. Teliospor...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  18. miRNAs in Bone Development

    PubMed Central

    Papaioannou, Garyfallia

    2015-01-01

    Skeletal development is a multistage process during which mesenchymal progenitor cells undergo proliferation and differentiation and subsequently give rise to bone and cartilage forming cells. Each step is regulated by various transcription factors and signaling molecules. microRNAs are small non-coding RNAs that post-transcriptionally regulate gene expression. Several in vivo and in vitro studies have shown that miRNAs play significant roles in skeletal development. Identifying their functions may give insights into the treatment of developmental disorders of the skeleton. This review summarizes miRNAs that have been shown to participate in various stages of skeletal development by targeting crucial factors. PMID:27019617

  19. Risk miRNA screening of ovarian cancer based on miRNA functional synergistic network

    PubMed Central

    2014-01-01

    Background miRNAs are proved to have causal roles in tumorgenesis involving various types of human cancers, but the mechanism is not clear. We aimed to explore the effect of miRNAs on the development of ovarian cancer and the underlying mechanism. Methods The miRNA expression profile GSE31801 was downloaded from GEO (Gene Expression Omnibus) database. Firstly, the differentially expressed miRNAs were screened. Target genes of the miRNAs were collected from TargetScan, PicTar, miRanda, and DIANA-microT database, then the miRNA-miRNA co-regulating network was constructed using miRNA pairs with common regulated target genes. Next, the functional modules in the network were studied, the miRNA pairs regulated at least one modules were enriched to form the miRNA functional synergistic network (MFSN). Results Risk miRNA were selected in MFSN according to the topological structure. Transcript factors (TFs) in MFSN were identified, followed by the miRNA-transcript factor networks construction. Totally, 42 up- and 61 down-regulated differentially expressed miRNAs were identified, of which 68 formed 2292 miRNA pairs in the miRNA-miRNA co-regulating network. GO: 0007268 (synaptic transmission) and GO: 0019226 (transmission of nerve impulse) were the two common functions of miRNAs in MFSN, and hsa-miR-579 (36), hsa-miR-942 (31), hsa-miR-105 (31), hsa-miR-150 (34), and hsa-miR-27a* (32) were selected as the hub nodes in MFSN. Conclusions In all, 17 TFs, including CREM, ERG, and CREB1 were screened as the cancer related TFs in MFSN. Other TFs, such as BIN1, FOXN3, FOXK1, FOXP2, and ESRRG with high degrees may be inhibited in ovarian cancer. MFSN gave us a new shed light on the mechanism studies in ovarian cancer. PMID:24444095

  20. RNA Binding Proteins in the miRNA Pathway

    PubMed Central

    Connerty, Patrick; Ahadi, Alireza; Hutvagner, Gyorgy

    2015-01-01

    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. PMID:26712751

  1. Combination of miRNA499 and miRNA133 Exerts a Synergic Effect on Cardiac Differentiation

    PubMed Central

    Pisano, Federica; Altomare, Claudia; Cervio, Elisabetta; Barile, Lucio; Rocchetti, Marcella; Ciuffreda, Maria Chiara; Malpasso, Giuseppe; Copes, Francesco; Mura, Manuela; Danieli, Patrizia; Viarengo, Gianluca; Zaza, Antonio; Gnecchi, Massimiliano

    2015-01-01

    Several studies have demonstrated that miRNA are involved in cardiac development, stem cell maintenance, and differentiation. In particular, it has been shown that miRNA133, miRNA1, and miRNA499 are involved in progenitor cell differentiation into cardiomyocytes. However, it is unknown whether different miRNA may act synergistically to improve cardiac differentiation. We used mouse P19 cells as a cardiogenic differentiation model. miRNA499, miRNA1, or miRNA133 were transiently over-expressed in P19 cells individually or in different combinations. The over-expression of miRNA499 alone increased the number of beating cells and the association of miRNA499 with miRNA133 exerted a synergistic effect, further increasing the number of beating cells. Real-time polymerase chain reaction showed that the combination of miRNA499 + 133 enhanced the expression of cardiac genes compared with controls. Western blot and immunocytochemistry for connexin43 and cardiac troponin T confirmed these findings. Importantly, caffeine responsiveness, a clear functional parameter of cardiac differentiation, was increased by miRNA499 in association with miRNA133 and was directly correlated with the activation of the cardiac troponin I isoform promoter. Cyclic contractions were reversibly abolished by extracellular calcium depletion, nifedipine, ryanodine, and IP3R blockade. Finally, we demonstrated that the use of miRNA499 + 133 induced cardiac differentiation even in the absence of dimethyl sulfoxide. Our results show that the areas spontaneously contracting possess electrophysiological and pharmacological characteristics compatible with true cardiac excitation-contraction coupling. The translational relevance of our findings was reinforced by the demonstration that the over-expression of miRNA499 and miRNA133 was also able to induce the differentiation of human mesenchymal stromal cells toward the cardiac lineage. Stem Cells 2015;33:1187–1199 PMID:25534971

  2. Combination of miRNA499 and miRNA133 exerts a synergic effect on cardiac differentiation.

    PubMed

    Pisano, Federica; Altomare, Claudia; Cervio, Elisabetta; Barile, Lucio; Rocchetti, Marcella; Ciuffreda, Maria Chiara; Malpasso, Giuseppe; Copes, Francesco; Mura, Manuela; Danieli, Patrizia; Viarengo, Gianluca; Zaza, Antonio; Gnecchi, Massimiliano

    2015-04-01

    Several studies have demonstrated that miRNA are involved in cardiac development, stem cell maintenance, and differentiation. In particular, it has been shown that miRNA133, miRNA1, and miRNA499 are involved in progenitor cell differentiation into cardiomyocytes. However, it is unknown whether different miRNA may act synergistically to improve cardiac differentiation. We used mouse P19 cells as a cardiogenic differentiation model. miRNA499, miRNA1, or miRNA133 were transiently over-expressed in P19 cells individually or in different combinations. The over-expression of miRNA499 alone increased the number of beating cells and the association of miRNA499 with miRNA133 exerted a synergistic effect, further increasing the number of beating cells. Real-time polymerase chain reaction showed that the combination of miRNA499 + 133 enhanced the expression of cardiac genes compared with controls. Western blot and immunocytochemistry for connexin43 and cardiac troponin T confirmed these findings. Importantly, caffeine responsiveness, a clear functional parameter of cardiac differentiation, was increased by miRNA499 in association with miRNA133 and was directly correlated with the activation of the cardiac troponin I isoform promoter. Cyclic contractions were reversibly abolished by extracellular calcium depletion, nifedipine, ryanodine, and IP3R blockade. Finally, we demonstrated that the use of miRNA499 + 133 induced cardiac differentiation even in the absence of dimethyl sulfoxide. Our results show that the areas spontaneously contracting possess electrophysiological and pharmacological characteristics compatible with true cardiac excitation-contraction coupling. The translational relevance of our findings was reinforced by the demonstration that the over-expression of miRNA499 and miRNA133 was also able to induce the differentiation of human mesenchymal stromal cells toward the cardiac lineage. PMID:25534971

  3. 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

  4. PGC-Enriched miRNAs Control Germ Cell Development

    PubMed Central

    Bhin, Jinhyuk; Jeong, Hoe-Su; Kim, Jong Soo; Shin, Jeong Oh; Hong, Ki Sung; Jung, Han-Sung; Kim, Changhoon; Hwang, Daehee; Kim, Kye-Seong

    2015-01-01

    Non-coding microRNAs (miRNAs) regulate the translation of target messenger RNAs (mRNAs) involved in the growth and development of a variety of cells, including primordial germ cells (PGCs) which play an essential role in germ cell development. However, the target mRNAs and the regulatory networks influenced by miRNAs in PGCs remain unclear. Here, we demonstrate a novel miRNAs control PGC development through targeting mRNAs involved in various cellular pathways. We reveal the PGC-enriched expression patterns of nine miRNAs, including miR-10b, -18a, -93, -106b, -126-3p, -127, -181a, -181b, and -301, using miRNA expression analysis along with mRNA microarray analysis in PGCs, embryonic gonads, and postnatal testes. These miRNAs are highly expressed in PGCs, as demonstrated by Northern blotting, miRNA in situ hybridization assay, and miRNA qPCR analysis. This integrative study utilizing mRNA microarray analysis and miRNA target prediction demonstrates the regulatory networks through which these miRNAs regulate their potential target genes during PGC development. The elucidated networks of miRNAs disclose a coordinated molecular mechanism by which these miRNAs regulate distinct cellular pathways in PGCs that determine germ cell development. PMID:26442865

  5. How nitrogen and sulphur addition, and a single drought event affect root phosphatase activity in Phalaris arundinacea.

    PubMed

    Robroek, Bjorn J M; Adema, Erwin B; Venterink, Harry Olde; Leonardson, Lars; Wassen, Martin J

    2009-03-15

    Conservation and restoration of fens and fen meadows often aim to reduce soil nutrients, mainly nitrogen (N) and phosphorus (P). The biogeochemistry of P has received much attention as P-enrichment is expected to negatively impact on species diversity in wetlands. It is known that N, sulphur (S) and hydrological conditions affect the biogeochemistry of P, yet their interactive effects on P-dynamics are largely unknown. Additionally, in Europe, climate change has been predicted to lead to increases in summer drought. We performed a greenhouse experiment to elucidate the interactive effects of N, S and a single drought event on the P-availability for Phalaris arundinacea. Additionally, the response of plant phosphatase activity to these factors was measured over the two year experimental period. In contrast to results from earlier experiments, our treatments hardly affected soil P-availability. This may be explained by the higher pH in our soils, hampering the formation of Fe-P or Fe-Al complexes. Addition of S, however, decreased the plants N:P ratio, indicating an effect of S on the N:P stoichiometry and an effect on the plant's P-demand. Phosphatase activity increased significantly after addition of S, but was not affected by the addition of N or a single drought event. Root phosphatase activity was also positively related to plant tissue N and P concentrations, plant N and P uptake, and plant aboveground biomass, suggesting that the phosphatase enzyme influences P-biogeochemistry. Our results demonstrated that it is difficult to predict the effects of wetland restoration, since the involved mechanisms are not fully understood. Short-term and long-term effects on root phosphatase activity may differ considerably. Additionally, the addition of S can lead to unexpected effects on the biogeochemistry of P. Our results showed that natural resource managers should be careful when restoring degraded fens or preventing desiccation of fen ecosystems. PMID:19101022

  6. 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

  7. Identification of Aberrantly Expressed miRNAs in Gastric Cancer

    PubMed Central

    Liu, Dan; Hu, Xiaowei; Zhou, Hongfeng; Shi, Guangyue; Wu, Jin

    2014-01-01

    The noncoding components of the genome, including miRNA, can contribute to pathogenesis of gastric cancer. Their expression has been profiled in many human cancers, but there are a few published studies in gastric cancer. It is necessary to identify novel aberrantly expressed miRNAs in gastric cancer. In this study, the expression profile of 1891 miRNAs was analyzed using a miRCURY array LNA miRNA chip from three gastric cancer tissues and three normal tissues. The expression levels of 4 miRNAs were compared by real-time PCR between cancerous and normal tissues. We found that 31 miRNAs are upregulated in gastric cancer (P < 0.05) and 10 miRNAs have never been reported by other studies; 30 miRNA are downregulated (P < 0.05) in gastric cancer tissues. Gene ontology analysis revealed that those dysregulated miRNAs mainly take part in regulating cell proliferation. The levels of has-miR-105, -213∗, -514b, and -548n were tested by real-time PCR and have high levels in cancerous tissues. Here, we report a miRNA profile of gastric cancer and provide new perspective to understand this malignant disease. This novel information suggests the potential roles of these miRNAs in the diagnosis, prognosis biomarkers, or therapy targets of gastric cancer. PMID:24982669

  8. Widespread evidence of viral miRNAs targeting host pathways

    PubMed Central

    2013-01-01

    Background MicroRNAs (miRNA) are regulatory genes that target and repress other RNA molecules via sequence-specific binding. Several biological processes are regulated across many organisms by evolutionarily conserved miRNAs. Plants and invertebrates employ their miRNA in defense against viruses by targeting and degrading viral products. Viruses also encode miRNAs and there is evidence to suggest that virus-encoded miRNAs target specific host genes and pathways that may be beneficial for their infectivity and/or proliferation. However, it is not clear whether there are general patterns underlying cellular targets of viral miRNAs. Results Here we show that for several of the 135 known viral miRNAs in human viruses, the human genes targeted by the viral miRNA are enriched for specific host pathways whose targeting is likely beneficial to the virus. Given that viral miRNAs continue to be discovered as technologies evolve, we extended the investigation to 6809 putative miRNAs encoded by 23 human viruses. Our analysis further suggests that human viruses have evolved their miRNA repertoire to target specific human pathways, such as cell growth, axon guidance, and cell differentiation. Interestingly, many of the same pathways are also targeted in mice by miRNAs encoded by murine viruses. Furthermore, Human Cytomegalovirus (CMV) miRNAs that target specific human pathways exhibit increased conservation across CMV strains. Conclusions Overall, our results suggest that viruses may have evolved their miRNA repertoire to target specific host pathways as a means for their survival. PMID:23369080

  9. ProA, a transcriptional regulator of fungal fruiting body development, regulates leaf hyphal network development in the Epichloë festucae-Lolium perenne symbiosis.

    PubMed

    Tanaka, Aiko; Cartwright, Gemma M; Saikia, Sanjay; Kayano, Yuka; Takemoto, Daigo; Kato, Masashi; Tsuge, Takashi; Scott, Barry

    2013-11-01

    Transcription factors containing a Zn(II)2 Cys6 binuclear cluster DNA-binding domain are unique to fungi and are key regulators of fungal growth and development. The C6-Zn transcription factor, Pro1, in Sordaria macrospora is crucial for maturation of sexual fruiting bodies. In a forward genetic screen to identify Epichloë festucae symbiosis genes we identified a mutant with an insertion in proA. Plants infected with the proA mutant underwent premature senescence. Hyphae of ΔproA had a proliferative pattern of growth within the leaves of Lolium perenne. Targeted deletion of proA recapitulated this phenotype and introduction of a wild-type gene complemented the mutation. ΔproA was defective in hyphal fusion. qPCR analysis of E. festucae homologues of S. macrospora genes differentially expressed in Δpro1 identified esdC, encoding a glycogen-binding protein, as a target of ProA. Electrophoretic mobility shift assay analysis identified two binding sites for ProA in the intergenic region of esdC and a divergently transcribed gene, EF320. Both esdC and EF320 are highly expressed in a wild-type E. festucae-grass association but downregulated in a proA-mutant association. These results show that ProA is a key regulator of in planta specific growth of E. festucae, and therefore crucial for maintaining a mutualistic symbiotic interaction. PMID:23998652

  10. 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. PMID:26678076

  11. 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. PMID:22433074

  12. Circulating miRNAs as Potential Marker for Pulmonary Hypertension

    PubMed Central

    Wei, Chuanyu; Henderson, Heather; Spradley, Christopher; Li, Li; Kim, Il-Kwon; Kumar, Sandeep; Hong, Nayeon; Arroliga, Alejandro C.; Gupta, Sudhiranjan

    2013-01-01

    MircoRNAs (miRNAs) are small non-coding RNAs that govern the gene expression and, play significant role in the pathogenesis of heart failure. The detection of miRNAs in circulation of pulmonary hypertensive (PH) human subjects remains elusive. In the current study, we determined the pattern of miRNAs of mild-to-severe human PH subjects and, compared them with the control subjects by miRNA array. Blood was obtained using fluoroscopic and waveform guided catheterization from the distal (pulmonary artery) port of the catheter. A total 40 human subjects were included in the study and, the degree of PH was determined by mean pulmonary arterial pressure. Among several miRNAs in the array, we validated 14 miRNAs and, the data were consistent with the array profile. We identified several novel downregulated miRNAs (miR-451, miR-1246) and upregulated miRNAs (miR-23b, miR-130a and miR-191) in the circulation of PH subjects. Our study showed novel set of miRNAs which are dysregulated in PH and, are directly proportional to the degree of PH. These miRNAs may be considered as potential biomarker for early detection of PH. PMID:23717609

  13. 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. PMID:24234763

  14. PlantMirnaT: miRNA and mRNA integrated analysis fully utilizing characteristics of plant sequencing data.

    PubMed

    Rhee, S; Chae, H; Kim, S

    2015-07-15

    miRNA is known to regulate up to several hundreds coding genes, thus the integrated analysis of miRNA and mRNA expression data is an important problem. Unfortunately, the integrated analysis is challenging since it needs to consider expression data of two different types, miRNA and mRNA, and target relationship between miRNA and mRNA is not clear, especially when microarray data is used. Fortunately, due to the low sequencing cost, small RNA and RNA sequencing are routinely processed and we may be able to infer regulation relationships between miRNAs and mRNAs more accurately by using sequencing data. However, no method is developed specifically for sequencing data. Thus we developed PlantMirnaT, a new miRNA-mRNA integrated analysis system. To fully leverage the power of sequencing data, three major features are developed and implemented in PlantMirnaT. First, we implemented a plant-specific short read mapping tool based on recent discoveries on miRNA target relationship in plant. Second, we designed and implemented an algorithm considering miRNA targets in the full intragenic region, not just 3' UTR. Lastly but most importantly, our algorithm is designed to consider quantity of miRNA expression and its distribution on target mRNAs. The new algorithm was used to characterize rice under drought condition using our proprietary data. Our algorithm successfully discovered that two miRNAs, miRNA1425-5p, miRNA 398b, that are involved in suppression of glucose pathway in a naturally drought resistant rice, Vandana. The system can be downloaded at https://sites.google.com/site/biohealthinformaticslab/resources. PMID:25863133

  15. 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

  16. 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

  17. 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

  18. 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

    2016-05-01

    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

  19. 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.

  20. 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. PMID:25366556

  1. Exploration of miRNA families for hypotheses generation.

    PubMed

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

    2013-01-01

    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. PMID:24126940

  2. 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. PMID:21171923

  3. miRNAs: roles and clinical applications in vascular disease

    PubMed Central

    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. PMID:21171923

  4. MiRNA in atopic dermatitis

    PubMed Central

    Rudnicka, Lidia; Samochocki, Zbigniew

    2016-01-01

    MicroRNAs are relatively new molecules that have been widely studied in recent years as to determine their exact function in the human body. It is suggested that microRNAs control approx. 30% of all genes, making them one of the largest groups that control the expression of proteins. Various functions of miRNAs have already been described. In skin diseases, there are more and more studies describing an altered expression of microRNAs in the skin or serum. Relatively little is known about the function of these molecules in atopic dermatitis, which prompted us to gather current reports on this subject. PMID:27512348

  5. 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. PMID:25557441

  6. Patterns of MiRNA Expression in Arctic Charr Development

    PubMed Central

    Kapralova, Kalina H.; Franzdóttir, Sigrídur Rut; Jónsson, Hákon; Snorrason, Sigurður S.; Jónsson, Zophonías O.

    2014-01-01

    Micro-RNAs (miRNAs) are now recognized as a major class of developmental regulators. Sequences of many miRNAs are highly conserved, yet they often exhibit temporal and spatial heterogeneity in expression among species and have been proposed as an important reservoir for adaptive evolution and divergence. With this in mind we studied miRNA expression during embryonic development of offspring from two contrasting morphs of the highly polymorphic salmonid Arctic charr (Salvelinus alpinus), a small benthic morph from Lake Thingvallavatn (SB) and an aquaculture stock (AC). These morphs differ extensively in morphology and adult body size. We established offspring groups of the two morphs and sampled at several time points during development. Four time points (3 embryonic and one just before first feeding) were selected for high-throughput small-RNA sequencing. We identified a total of 326 conserved and 427 novel miRNA candidates in Arctic charr, of which 51 conserved and 6 novel miRNA candidates were differentially expressed among developmental stages. Furthermore, 53 known and 19 novel miRNAs showed significantly different levels of expression in the two contrasting morphs. Hierarchical clustering of the 53 conserved miRNAs revealed that the expression differences are confined to the embryonic stages, where miRNAs such as sal-miR-130, 30, 451, 133, 26 and 199a were highly expressed in AC, whereas sal-miR-146, 183, 206 and 196a were highly expressed in SB embryos. The majority of these miRNAs have previously been found to be involved in key developmental processes in other species such as development of brain and sensory epithelia, skeletogenesis and myogenesis. Four of the novel miRNA candidates were only detected in either AC or SB. miRNA candidates identified in this study will be combined with available mRNA expression data to identify potential targets and involvement in developmental regulation. PMID:25170615

  7. Structure and activity of putative intronic miRNA promoters.

    PubMed

    Monteys, Alex Mas; Spengler, Ryan M; Wan, Ji; Tecedor, Luis; Lennox, Kimberly A; Xing, Yi; Davidson, Beverly L

    2010-03-01

    MicroRNAs (miRNAs) are RNA sequences of approximately 22 nucleotides that mediate post-transcriptional regulation of specific mRNAs. miRNA sequences are dispersed throughout the genome and are classified as intergenic (between genes) or intronic (embedded into a gene). Intergenic miRNAs are expressed by their own promoter, and until recently, it was supposed that intronic miRNAs are transcribed from their host gene. Here, we performed a genomic analysis of currently known intronic miRNA regions and observed that approximately 35% of intronic miRNAs have upstream regulatory elements consistent with promoter function. Among all intronic miRNAs, 30% have associated Pol II regulatory elements, including transcription start sites, CpG islands, expression sequence tags, and conserved transcription factor binding sites, while 5% contain RNA Pol III regulatory elements (A/B box sequences). We cloned intronic regions encompassing miRNAs and their upstream Pol II (miR-107, miR-126, miR-208b, miR-548f-2, miR-569, and miR-590) or Pol III (miR-566 and miR-128-2) sequences into a promoterless plasmid, and confirmed that miRNA expression occurs independent of host gene transcription. For miR-128-2, a miRNA overexpressed in acute lymphoblastic leukemia, ChIP analysis suggests dual regulation by both intronic (Pol III) and host gene (Pol II) promoters. These data support complex regulation of intronic miRNA expression, and have relevance to disregulation in disease settings. PMID:20075166

  8. miRNAs and Melanoma: How Are They Connected?

    PubMed Central

    da Cruz, Adriana Taveira; Jasiulionis, Miriam Galvonas

    2012-01-01

    miRNAs are non-coding RNAs that bind to mRNA targets and disturb their stability and/or translation, thus acting in gene posttranscriptional regulation. It is predicted that over 30% of mRNAs are regulated by miRNAs. Therefore these molecules are considered essential in the processing of many biological responses, such as cell proliferation, apoptosis, and stress responsiveness. As miRNAs participate of virtually all cellular pathways, their deregulation is critical to cancer development. Consequently, loss or gain of miRNAs function may contribute to tumor progression. Little is known about the regulation of miRNAs and understanding the events that lead to changes in their expression may provide new perspectives for cancer treatment. Among distinct types of cancer, melanoma has special implications. It is characterized as a complex disease, originated from a malignant transformation of melanocytes. Despite being rare, its metastatic form is usually incurable, which makes melanoma the major death cause of all skin cancers. Some molecular pathways are frequently disrupted in melanoma, and miRNAs probably have a decisive role on these alterations. Therefore, this review aims to discuss new findings about miRNAs in melanoma fields, underlying epigenetic processes, and also to argue possibilities of using miRNAs in melanoma diagnosis and therapy. PMID:21860617

  9. Genome-wide characterization of maize miRNA genes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  10. Oscillating primary transcripts harbor miRNAs with circadian functions

    PubMed Central

    Wang, Haifang; Fan, Zenghua; Zhao, Meng; Li, Juan; Lu, Minghua; Liu, Wei; Ying, Hao; Liu, Mofang; Yan, Jun

    2016-01-01

    The roles of miRNAs as important post-transcriptional regulators in the circadian clock have been suggested in several studies. But the search for circadian miRNAs has led to disparate results. Here we demonstrated that at least 57 miRNA primary transcripts are rhythmically transcribed in mouse liver. Most of these transcripts are under the regulation of circadian transcription factors such as BMAL1/CLOCK and REV-ERBα/β. However, the mature miRNAs derived from these transcripts are either not oscillating or oscillating at low amplitudes, which could explain the inconsistency of different circadian miRNA studies. In order to show that these circadian primary transcripts can give rise to miRNAs with circadian functions, we over-expressed one of them, miR-378, in mouse by adenovirus injection. We found a significant over-representation of circadian oscillating genes under-expressed by miR-378 over-expression in liver. In particular, we observed that miR-378 modulates the oscillation amplitudes of Cdkn1a in the control of cell cycle and Por in the regulation of oxidation reduction by forming partnership with different circadian transcription factors. Our study suggests that circadian transcription of miRNA at primary transcript level can be a good indicator for circadian miRNA functions. PMID:26898952

  11. 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. PMID:26529380

  12. Identification of extracellular siderophores and a related peptide from the endophytic fungus Epichloë festucae in culture and endophyte-infected Lolium perenne

    PubMed Central

    Koulman, Albert; Lee, T. Verne; Fraser, Karl; Johnson, Linda; Arcus, Vickery; Lott, J. Shaun; Rasmussen, Susanne; Lane, Geoffrey

    2012-01-01

    A number of genes encoding non-ribosomal peptide synthetases (NRPSs) have been identified in fungi of Epichloë/Neotyphodium species, endophytes of Pooid grasses, including sidN, putatively encoding a ferrichrome siderophore-synthesizing NRPS. Targeted gene replacement and complementation of sidN in Epichloë festucae has established that extracellular siderophore epichloënin A is the major product of the SidN enzyme complex (Johnson et al., 2007a). We report here high resolution mass spectrometric fragmentation experiments and NMR analysis of an isolated fraction establishing that epichloënin A is a siderophore of the ferrichrome family, comprising a cyclic sequence of four glycines, a glutamine and three Nδ-trans-anhydromevalonyl–Nδ-hydroxyornithine (AMHO) moieties. Epichloënin A is unusual among ferrichrome siderophores in comprising an octapeptide rather than hexapeptide sequence, and in incorporating a glutamine residue. During this investigation we have established that desferrichrome siderophores with pendant trans-AMHO groups can be distinguished from those with pendant cis-AMHO groups by the characteristic neutral loss of an hydroxyornithine moiety in the MS/MS spectrum. A minor component, epichloënin B, has been characterized as the triglycine variant by mass spectrometry. A peptide characterized by mass spectrometry as the putative deoxygenation product, epichloëamide has been detected together with ferriepichloënin A in guttation fluid from ryegrass (Lolium perenne) plants infected with wild-type E. festucae, but not in plants infected with the ΔsidN mutant strain, and also detected at trace levels in wild-type E. festucae fungal culture. PMID:22196939

  13. Host settling behavior, reproductive performance, and effects on plant growth of an exotic cereal aphid, Metopolophium festucae subsp. cerealium (Hemiptera: Aphididae).

    PubMed

    Davis, T S; Wu, Y; Eigenbrode, S D

    2014-06-01

    The cereal aphid Metopolophium festucae subsp. cerealium (Stroyan) is a recent addition to North America, but little is known about this species in its exotic habitat. We surveyed aphid populations for 3 years (2011-2013) to investigate changes in aphid density in the Pacific Northwest United States. We tested aphid host settling preference and fecundity on eight grass species, four native grasses (bluebunch wheatgrass, blue wild rye, Idaho fescue, and rough fescue) and four cereal crops (corn, wheat, barley, and oat), and evaluated the effects of aphid feeding on plant biomass. Four important findings emerged: 1) aphid prevalence in sweep net samples increased from 2011 to 2012, but remained stable from 2012 to 2013; 2) aphids preferentially settled on wheat and avoided corn, but aphids did not discriminate between barley, oat, and native grasses; 3) aphid fecundity was high on wheat and barley, intermediate on oat and blue wild rye, low on Idaho fescue, rough fescue, and bluebunch wheatgrass, and aphids did not reproduce at all on corn; and 4) barley, corn, oats, Idaho fescue, and blue wild rye were not susceptible to aphid feeding damage, but wheat, rough fescue, and bluebunch wheatgrass were susceptible to aphid feeding damage. Our results suggest that wheat and barley are preferred by M. festucae cerealium, and that aphids reproduce most rapidly on these hosts and cause significant reductions in wheat but not barley growth. Also, M. festucae cerealium appears capable of surviving on native grasses, although only bluebunch wheatgrass and rough fescue were susceptible to aphid feeding damage. PMID:24874155

  14. 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

  15. Modulation of Host miRNAs by Intracellular Bacterial Pathogens.

    PubMed

    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

  16. PEI-complexed LNA antiseeds as miRNA inhibitors

    PubMed Central

    Thomas, Maren; Lange-Grünweller, Kerstin; Dayyoub, Eyas; Bakowsky, Udo; Weirauch, Ulrike; Aigner, Achim; Hartmann, Roland K.; Grünweller, Arnold

    2012-01-01

    Antisense inhibition of oncogenic or other disease-related miRNAs and miRNA families in vivo may provide novel therapeutic strategies. However, this approach relies on the development of potent miRNA inhibitors and their efficient delivery into cells. Here, we introduce short seed-directed LNA oligonucleotides (12- or 14-mer antiseeds) with a phosphodiester backbone (PO) for efficient miRNA inhibition. We have analyzed such LNA (PO) antiseeds using a let-7a-controlled luciferase reporter assay and identified them as active miRNA inhibitors in vitro. Moreover, LNA (PO) 14-mer antiseeds against ongogenic miR-17–5p and miR-20a derepress endogenous p21 expression more persistently than corresponding miRNA hairpin inhibitors, which are often used to inhibit miRNA function. Further analysis of the antiseed-mediated derepression of p21 in luciferase reporter constructs - containing the 3′-UTR of p21 and harboring two binding sites for miRNAs of the miR-106b family - provided evidence that the LNA antiseeds inhibit miRNA families while hairpin inhibitors act in a miRNA-specific manner. The derepression caused by LNA antiseeds is specific, as demonstrated via seed mutagenesis of the miR-106b target sites. Importantly, we show functional delivery of LNA (PO) 14-mer antiseeds into cells upon complexation with polyethylenimine (PEI F25-LMW), which leads to the formation of polymeric nanoparticles. In contrast, attempts to deliver a functional seed-directed tiny LNA 8-mer with a phosphorothioate backbone (PS) by formulation with PEI F25-LMW remained unsuccessful. In conclusion, LNA (PO) 14-mer antiseeds are attractive miRNA inhibitors, and their PEI-based delivery may represent a promising new strategy for therapeutic applications. PMID:22894918

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  18. 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

    2016-02-01

    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. PMID:26907327

  19. Serum miRNA-499 and miRNA-210: A potential role in early diagnosis of acute coronary syndrome.

    PubMed

    Shalaby, Sally M; El-Shal, Amal S; Shoukry, Amira; Khedr, Mohamad H; Abdelraheim, Nader

    2016-08-01

    In clinical practice, there is still a need for novel biomarkers, which can reliably rule in or rule out acute coronary syndrome (ACS) immediately on admission. This is of particular interest in patients with unstable angina (UA) and non-ST-segment elevation myocardial infarction (NSTEMI) in whom diagnostic uncertainty is high. The aim of the present study is to evaluate the potential role of miRNA-499 and miRNA-210 as novel molecular biomarkers for early diagnosis of UA and NSTEMI suspected patients presented at the emergency unit. A total of 110 patients presenting to the intensive care unit (ICU) within 24 h of onset of chest pain suggestive of ACS were enrolled in the study. They included 37 UA, 48 NSTEMI and 25 noncardiac chest pain (NCCP) patients. Immediately at enrollment, blood samples were taken for estimation of serum miRNA-499 and miRNA-210 expression levels by real time PCR. miRNA-499 and miRNA-210 expression levels were significantly increased in UA and NSTEMI patients compared with NCCP patients (P < 0.001). Receiver operating characteristic (ROC) curve analysis revealed that the area under curve (AUC) of miR-499 for the diagnosis of UA and NSTEMI was 0.98 and 0.97, respectively; while the AUC of miRNA-210 was 0.84 and 0.90, respectively. The important finding of our study was that the AUC of miRNA-499 for the diagnosis of ACS patients with symptoms onset <3 h was 0.89, while the AUC of miRNA-210 was 0.86. Interestingly, combining miRNA-499 and miRNA-210 significantly improved the diagnostic value by increasing the AUC to 0.96, P < 0.001. In conclusion, serum miRNA-499 and miRNA-210 are associated with UA and NSTEMI and with those presenting within 3 h of symptom onset. Both miRNAs might be potentially novel biomarkers for accelerating the diagnosis of ACS patients in emergency unit. © 2016 IUBMB Life, 68(8):673-682, 2016. PMID:27346801

  20. miRNA 206 and miRNA 574-5p are highly expression in coronary artery disease

    PubMed Central

    Zhou, Jianqing; Shao, Guofeng; Chen, Xiaoliang; Yang, Xi; Huang, Xiaoyan; Peng, Ping; Ba, Yanna; Zhang, Lin; Jehangir, Tashina; Bu, Shizhong; Liu, Ningsheng; Lian, Jiangfang

    2015-01-01

    Coronary artery disease (CAD) is the leading cause of human morbidity and mortality worldwide. Innovative diagnostic biomarkers are a pressing need for this disease. miRNAs profiling is an innovative method of identifying biomarkers for many diseases and could be proven as a powerful tool in the diagnosis and treatment of CAD. We performed miRNA microarray analysis from the plasma of three CAD patients and three healthy controls. Subsequently, we performed quantitative real-time PCR (qRT-PCR) analysis of miRNA expression in plasma of another 67 CAD patients and 67 healthy controls. We identified two miRNAs (miR-206 and miR-574-5p) that were significantly up-regulated in CAD patients as compared with healthy controls (P<0.05). The receiver operating characteristic (ROC) curves indicated these two miRNAs had great potential to provide sensitive and specific diagnostic value for CAD. PMID:26685009

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

    PubMed

    Tilghman, Syreeta L; Rhodes, Lyndsay V; Bratton, Melyssa R; Carriere, Patrick; Preyan, Lynez C; Boue, Stephen M; Vasaitis, Tadas Sean; McLachlan, John A; Burow, Matthew E

    2013-02-01

    There is growing interest in the diverse signaling pathways that regulate and affect breast tumorigenesis, including the role of phytochemicals and the emerging role of microRNAs (miRNAs). Recent studies demonstrate that miRNAs regulate fundamental cellular and developmental processes at the transcriptional and translational level under normal and disease conditions. While there is growing evidence to support the role of phytoalexin-mediated miRNA regulation of cancer, few reports address this role in breast cancer. Recent reports by our group and others demonstrate that natural products, including stilbenes, curcumin, and glyceollins, could alter the expression of specific miRNAs, which may lead to increased sensitivity of cancer cells to conventional anti-cancer agents and, therefore, hormone-dependent and hormone-independent tumor growth inhibition. This review will discuss how dietary intake of natural products, by regulating specific miRNAs, contribute to the prevention and treatment of breast cancer. PMID:23395943

  2. Phytoalexins, miRNAs and Breast Cancer: A Review of Phytochemical-mediated miRNA Regulation in Breast Cancer

    PubMed Central

    Rhodes, Lyndsay V.; Bratton, Melyssa R.; Carriere, Patrick; Preyan, Lynez C.; Boue, Stephen M.; Vasaitis, Tadas Sean; McLachlan, John A.; Burow, Matthew E.

    2013-01-01

    There is growing interest in the diverse signaling pathways that regulate and affect breast tumorigenesis, including the role of phytochemicals and the emerging role of microRNAs (miRNAs). Recent studies demonstrate that miRNAs regulate fundamental cellular and developmental processes at the transcriptional and translational level under normal and disease conditions. While there is growing evidence to support the role of phytoalexin-mediated miRNA regulation of cancer, few reports address this role in breast cancer. Recent reports by our group and others demonstrate that natural products, including stilbenes, curcumin, and glyceollins, could alter the expression of specific miRNAs, which may lead to increased sensitivity of cancer cells to conventional anti-cancer agents and, therefore, hormone-dependent and hormone-independent tumor growth inhibition. This review will discuss how dietary intake of natural products, by regulating specific miRNAs, contribute to the prevention and treatment of breast cancer. PMID:23395943

  3. [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. PMID:26817318

  4. Milk miRNAs: simple nutrients or systemic functional regulators?

    PubMed

    Melnik, Bodo C; Kakulas, Foteini; Geddes, Donna T; Hartmann, Peter E; John, Swen Malte; Carrera-Bastos, Pedro; Cordain, Loren; Schmitz, Gerd

    2016-01-01

    Milk is rich in miRNAs that appear to play important roles in the postnatal development of all mammals. Currently, two competing hypotheses exist: the functional hypothesis, which proposes that milk miRNAs are transferred to the offspring and exert physiological regulatory functions, and the nutritional hypothesis, which suggests that these molecules do not reach the systemic circulation of the milk recipient, but merely provide nutrition without conferring active regulatory signals to the offspring. The functional hypothesis is based on indirect evidence and requires further investigation. The nutritional hypothesis is primarily based on three mouse models, which are inherently problematic: 1) miRNA-375 KO mice, 2) miRNA-200c/141 KO mice, and 3) transgenic mice presenting high levels of miRNA-30b in milk. This article presents circumstantial evidence that these mouse models may all be inappropriate to study the physiological traffic of milk miRNAs to the newborn mammal, and calls for new studies using more relevant mouse models or human milk to address the fate and role of milk miRNAs in the offspring and the adult consumer of cow's milk. PMID:27330539

  5. Finding cancer-associated miRNAs: methods and tools.

    PubMed

    Oulas, Anastasis; Karathanasis, Nestoras; Louloupi, Annita; Poirazi, Panayiota

    2011-09-01

    Changes in the structure and/or the expression of protein coding genes were thought to be the major cause of cancer for many decades. The recent discovery of non-coding RNA (ncRNA) transcripts (i.e., microRNAs) suggests that the molecular biology of cancer is far more complex. MicroRNAs (miRNAs) have been under investigation due to their involvement in carcinogenesis, often taking up roles of tumor suppressors or oncogenes. Due to the slow nature of experimental identification of miRNA genes, computational procedures have been applied as a valuable complement to cloning. Numerous computational tools, implemented to recognize the features of miRNA biogenesis, have resulted in the prediction of novel miRNA genes. Computational approaches provide clues as to which are the dominant features that characterize these regulatory units and furthermore act by narrowing down the search space making experimental verification faster and cheaper. In combination with large scale, high throughput methods, such as deep sequencing, computational methods have aided in the discovery of putative molecular signatures of miRNA deregulation in human tumors. This review focuses on existing computational methods for identifying miRNA genes, provides an overview of the methodology undertaken by these tools, and underlies their contribution towards unraveling the role of miRNAs in cancer. PMID:21607762

  6. miRNA and methylation: a multifaceted liaison.

    PubMed

    Chhabra, Ravindresh

    2015-01-19

    miRNAs and DNA methylation are both critical regulators of gene expression. Aberration in miRNA expression or DNA methylation is a causal factor for numerous pathological conditions. DNA methylation can inhibit the transcription of miRNAs, just like coding genes, by methylating the CpG islands in the promoter regions of miRNAs. Conversely, certain miRNAs can directly target DNA methyltransferases and bring about their inhibition, thereby affecting the whole genome methylation pattern. Recently, methylation patterns have also been revealed in mRNA. Surprisingly, the two most commonly studied methylation states in mRNA (m6A and m5C) are found to be enriched in 3'-UTRs (untranslated regions), the target site for the majority of miRNAs. Whereas m5C is reported to stabilise mRNA, m6A has a destabilising effect on mRNA. However, the effect of mRNA methylation on its interaction with miRNAs is largely unexplored. The review highlights the complex interplay between microRNA and methylation at DNA and mRNA level. PMID:25469751

  7. Exosomal miRNAs as cancer biomarkers and therapeutic targets

    PubMed Central

    Thind, Arron; Wilson, Clive

    2016-01-01

    Intercommunication between cancer cells and with their surrounding and distant environments is key to the survival, progression and metastasis of the tumour. Exosomes play a role in this communication process. MicroRNA (miRNA) expression is frequently dysregulated in tumour cells and can be reflected by distinct exosomal miRNA (ex-miRNA) profiles isolated from the bodily fluids of cancer patients. Here, the potential of ex-miRNA as a cancer biomarker and therapeutic target is critically analysed. Exosomes are a stable source of miRNA in bodily fluids but, despite a number of methods for exosome extraction and miRNA quantification, their suitability for diagnostics in a clinical setting is questionable. Furthermore, exosomally transferred miRNAs can alter the behaviour of recipient tumour and stromal cells to promote oncogenesis, highlighting a role in cell communication in cancer. However, our incomplete understanding of exosome biogenesis and miRNA loading mechanisms means that strategies to target exosomes or their transferred miRNAs are limited and not specific to tumour cells. Therefore, if ex-miRNA is to be employed in novel non-invasive diagnostic approaches and as a therapeutic target in cancer, two further advances are necessary: in methods to isolate and detect ex-miRNA, and a better understanding of their biogenesis and functions in tumour-cell communication. PMID:27440105

  8. Exosomal miRNAs as cancer biomarkers and therapeutic targets.

    PubMed

    Thind, Arron; Wilson, Clive

    2016-01-01

    Intercommunication between cancer cells and with their surrounding and distant environments is key to the survival, progression and metastasis of the tumour. Exosomes play a role in this communication process. MicroRNA (miRNA) expression is frequently dysregulated in tumour cells and can be reflected by distinct exosomal miRNA (ex-miRNA) profiles isolated from the bodily fluids of cancer patients. Here, the potential of ex-miRNA as a cancer biomarker and therapeutic target is critically analysed. Exosomes are a stable source of miRNA in bodily fluids but, despite a number of methods for exosome extraction and miRNA quantification, their suitability for diagnostics in a clinical setting is questionable. Furthermore, exosomally transferred miRNAs can alter the behaviour of recipient tumour and stromal cells to promote oncogenesis, highlighting a role in cell communication in cancer. However, our incomplete understanding of exosome biogenesis and miRNA loading mechanisms means that strategies to target exosomes or their transferred miRNAs are limited and not specific to tumour cells. Therefore, if ex-miRNA is to be employed in novel non-invasive diagnostic approaches and as a therapeutic target in cancer, two further advances are necessary: in methods to isolate and detect ex-miRNA, and a better understanding of their biogenesis and functions in tumour-cell communication. PMID:27440105

  9. miRNAs: Key Players in Neurodegenerative Disorders and Epilepsy.

    PubMed

    Karnati, Hanuma Kumar; Panigrahi, Manas Kumar; Gutti, Ravi Kumar; Greig, Nigel H; Tamargo, Ian A

    2015-01-01

    MicroRNAs (miRNAs) are endogenous, ∼22 nucleotide, non-coding RNA molecules that function as post-transcriptional regulators of gene expression. miRNA dysregulation has been observed in cancer and in neurodegenerative disorders such as Alzheimer's, Parkinson's, and Huntington's diseases, amyotrophic lateral sclerosis, and the neurological disorder, epilepsy. Neuronal degradation and death are important hallmarks of neurodegenerative disorders. Additionally, abnormalities in metabolism, synapsis and axonal transport have been associated with Alzheimer's disease, Parkinson's disease, and frontotemporal dementia. A number of recently published studies have demonstrated the importance of miRNAs in the nervous system and have contributed to the growing body of evidence on miRNA dysregulation in neurological disorders. Knowledge of the expressions and activities of such miRNAs may aid in the development of novel therapeutics. In this review, we discuss the significance of miRNA dysregulation in the development of neurodegenerative disorders and the use of miRNAs as targets for therapeutic intervention. PMID:26402105

  10. Mechanisms of regulation of mature miRNAs.

    PubMed

    Towler, Benjamin P; Jones, Christopher I; Newbury, Sarah F

    2015-12-01

    miRNAs are short RNA molecules of ∼22-nt in length that play important roles in post-transcriptional control of gene expression. miRNAs normally function as negative regulators of mRNA expression by binding complementary sequences in the 3'-UTR of target mRNAs and causing translational repression and/or target degradation. Much research has been undertaken to enhance understanding of the biogenesis, function and targeting of miRNAs. However, until recently, the mechanisms underlying the regulation of the levels of mature miRNAs themselves have been largely overlooked. Although it has generally been assumed that miRNAs are stable molecules, recent evidence indicates that the stability of specific mature miRNAs can be regulated during key cellular and developmental processes in certain cell types. Here we discuss the current knowledge of the mechanisms by which mature miRNAs are regulated in the cell and the factors that contribute to the control of their stability. PMID:26614662

  11. 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. PMID:26874020

  12. 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

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

    PubMed Central

    2013-01-01

    Background 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). Results 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. Conclusions 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. PMID:23937676

  14. Infiltration related miRNAs in bladder urothelial carcinoma.

    PubMed

    Xie, Peng; Xu, Feng; Cheng, Wen; Gao, Jianping; Zhang, Zhengyu; Ge, Jingping; Wei, Zhifeng; Xu, Xiaofeng; Liu, Youhuang

    2012-08-01

    This study aimed to investigate infiltration related microRNAs (miRNAs) in bladder urothelial carcinoma (BUC). Twenty patients with BUC were enrolled and divided into 2 groups according to infiltration or not: infiltrating BUC group (n=12) and non-infiltrating BUC group (n=8). Gene chip was used to detect infiltration related miRNAs in the BUC samples. In other recruited 17 patients with BUC who were divided into infiltrating BUC samples (n=14) and non-infiltrating BUC samples (n=3), and in 4 BUC cell lines (EJ, 5637, T24 and BIU-87), the expression of miRNAs was assayed by using reverse transcription-polymerase chain reaction (RT-PCR). In infiltrating BUC group, as compared with non-infiltrating BUC group, there were 7 differentially expressed miRNAs: hsa-miR-29c, hsa-miR-200a, hsa-miR-378, hsa-miR-429, hsa-miR-200c and hsa-miR-141 were up-regulated, while hsa-miR-451 was down-regulated. In the BUC samples, the results of RT-PCR were consistent with those by the miRNA array. In the cancer cell lines, RT-PCR in T24 only revealed the similar expression pattern of miRNAs to that by the miRNA array. It is suggested that infiltration of BUC is related with different expression of miRNAs, which may provide a novel platform for further study on function and action mechanism of miRNAs. PMID:22886973

  15. tRFs: miRNAs in disguise.

    PubMed

    Venkatesh, Thejaswini; Suresh, Padmanaban S; Tsutsumi, Rie

    2016-04-01

    tRFs and tiRNAs are two new classes of regulatory non-coding small RNAs that are derived from the cleavage of pre-existing tRNAs. tRFs are 18-22 nt long and are classified into the tRF-5, tRF-3, and tRF-1 series. Here, we discuss in detail the regulatory roles of tRFs in translation, viral infections, and carcinogenesis. Moreover, we have reviewed the association of tRFs with Argonaute proteins, including their potential to function as miRNAs. Interestingly, few miRNAs are generated from pre-existing tRNAs. Hence, tRNAs generate similar-sized tRFs and miRNAs, leading to misannotations due to cross mapping of tRFs and tRNA-derived miRNAs during deep sequencing data analysis. Therefore, it is important to catalogue the overlapping sequences between tRNA-derived miRNAs and tRFs. We have catalogued the miRNAs that overlap with tRFs sequences in humans using miRBase. We identified 20 tRNA-derived miRNAs that share sequences with tRFs. Of the 20 miRNAs, 5 miRNAs (miR-3182, miR-4521, miR-1260a, miR-1260b, and miR-7977) showed significant prediction scores. Furthermore, we have identified a lysine degradation pathway as a common regulatory pathway for miR-1260a, miR-1260b, and miR-3182 by using DIANA-mirPath. PMID:26743126

  16. Functions of miRNAs during Mammalian Heart Development

    PubMed Central

    Yan, Shun; Jiao, Kai

    2016-01-01

    MicroRNAs (miRNAs) play essential roles during mammalian heart development and have emerged as attractive therapeutic targets for cardiovascular diseases. The mammalian embryonic heart is mainly derived from four major cell types during development. These include cardiomyocytes, endocardial cells, epicardial cells, and neural crest cells. Recent data have identified various miRNAs as critical regulators of the proper differentiation, proliferation, and survival of these cell types. In this review, we briefly introduce the contemporary understanding of mammalian cardiac development. We also focus on recent developments in the field of cardiac miRNAs and their functions during the development of different cell types. PMID:27213371

  17. 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

  18. N6-adenosine methylation in MiRNAs.

    PubMed

    Berulava, Tea; Rahmann, Sven; Rademacher, Katrin; Klein-Hitpass, Ludgar; Horsthemke, Bernhard

    2015-01-01

    Methylation of N6-adenosine (m6A) has been observed in many different classes of RNA, but its prevalence in microRNAs (miRNAs) has not yet been studied. Here we show that a knockdown of the m6A demethylase FTO affects the steady-state levels of several miRNAs. Moreover, RNA immunoprecipitation with an anti-m6A-antibody followed by RNA-seq revealed that a significant fraction of miRNAs contains m6A. By motif searches we have discovered consensus sequences discriminating between methylated and unmethylated miRNAs. The epigenetic modification of an epigenetic modifier as described here adds a new layer to the complexity of the posttranscriptional regulation of gene expression. PMID:25723394

  19. N6-Adenosine Methylation in MiRNAs

    PubMed Central

    Berulava, Tea; Rahmann, Sven; Rademacher, Katrin; Klein-Hitpass, Ludgar; Horsthemke, Bernhard

    2015-01-01

    Methylation of N6-adenosine (m6A) has been observed in many different classes of RNA, but its prevalence in microRNAs (miRNAs) has not yet been studied. Here we show that a knockdown of the m6A demethylase FTO affects the steady-state levels of several miRNAs. Moreover, RNA immunoprecipitation with an anti-m6A-antibody followed by RNA-seq revealed that a significant fraction of miRNAs contains m6A. By motif searches we have discovered consensus sequences discriminating between methylated and unmethylated miRNAs. The epigenetic modification of an epigenetic modifier as described here adds a new layer to the complexity of the posttranscriptional regulation of gene expression. PMID:25723394

  20. Impact of miRNAs on cardiovascular aging.

    PubMed

    Lee, Seahyoung; Choi, Eunhyun; Cha, Min-Ji; Park, Ae-Jun; Yoon, Cheesoon; Hwang, Ki-Chul

    2015-09-01

    Aging is a multidimensional process that leads to an increased risk of developing severe diseases, such as cancer and cardiovascular, neurodegenerative, and immunological diseases. Recently, small non-coding RNAs known as microRNAs (miRNAs) have been shown to regulate gene expression, which contributes to many physiological and pathophysiological processes in humans. Increasing evidence suggests that changes in miRNA expression profiles contribute to cellular senescence, aging and aging-related diseases. However, only a few miRNAs whose functions have been elucidated have been associated with aging and/or aging-related diseases. This article reviews the currently available findings regarding the roles of aging-related miRNAs, with a focus on cardiac and cardiovascular aging. PMID:26512249

  1. 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. PMID:26015318

  2. A systematic analysis of the skeletal muscle miRNA transcriptome of chicken varieties with divergent skeletal muscle growth identifies novel miRNAs and differentially expressed miRNAs

    PubMed Central

    2011-01-01

    Background Functional studies have demonstrated that microRNAs (miRNAs or miRs) play critical roles in a wide spectrum of biological processes including development and disease pathogenesis. To investigate the functional roles that miRNAs play during chicken skeletal muscle development, the miRNA transcriptomes of skeletal muscles from broiler and layer chickens were profiled using Solexa deep sequencing. Results Some miRNAs have multiple isoforms and several miRNAs* are present at higher levels than their corresponding miRNAs. Thirty three novel and 189 known chicken miRNAs were identified using computational approaches. Subsequent miRNA transcriptome comparisons and real-time PCR validation experiments revealed 17 miRNAs that were differentially expressed between broilers and layers, and a number of targets of these miRNAs have been implicated in myogenesis regulation. Using integrative miRNA target-prediction and network-analysis approaches an interaction network of differentially expressed and muscle-related miRNAs and their putative targets was constructed, and miRNAs that could contribute to the divergent muscle growth of broiler and layer chickens by targeting the ACVR2B gene were identified, which can causes dramatic increases in muscle mass. Conclusions The present study provides the first transcriptome profiling-based evaluation of miRNA function during skeletal muscle development in chicken. Systematic predictions aided the identification of potential miRNAs and their targets, which could contribute to divergent muscle growth in broiler and layer chickens. Furthermore, these predictions generated information that can be utilized in further research investigating the involvement of interaction networks, containing miRNAs and their targets, in the regulation of muscle development. PMID:21486491

  3. 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

  4. Exploring the miRNA Regulatory Network Using Evolutionary Correlations

    PubMed Central

    Obermayer, Benedikt; Levine, Erel

    2014-01-01

    Post-transcriptional regulation by miRNAs is a widespread and highly conserved phenomenon in metazoans, with several hundreds to thousands of conserved binding sites for each miRNA, and up to two thirds of all genes under miRNA regulation. At the same time, the effect of miRNA regulation on mRNA and protein levels is usually quite modest and associated phenotypes are often weak or subtle. This has given rise to the notion that the highly interconnected miRNA regulatory network exerts its function less through any individual link and more via collective effects that lead to a functional interdependence of network links. We present a Bayesian framework to quantify conservation of miRNA target sites using vertebrate whole-genome alignments. The increased statistical power of our phylogenetic model allows detection of evolutionary correlation in the conservation patterns of site pairs. Such correlations could result from collective functions in the regulatory network. For instance, co-conservation of target site pairs supports a selective benefit of combinatorial regulation by multiple miRNAs. We find that some miRNA families are under pronounced co-targeting constraints, indicating a high connectivity in the regulatory network, while others appear to function in a more isolated way. By analyzing coordinated targeting of different curated gene sets, we observe distinct evolutionary signatures for protein complexes and signaling pathways that could reflect differences in control strategies. Our method is easily scalable to analyze upcoming larger data sets, and readily adaptable to detect high-level selective constraints between other genomic loci. We thus provide a proof-of-principle method to understand regulatory networks from an evolutionary perspective. PMID:25299225

  5. The Role of miRNA in Haematological Malignancy

    PubMed Central

    Gounaris-Shannon, Stephanie

    2013-01-01

    Currently, there are over 1,800 annotated human miRNAs, many of which have tissue-specific expression. Numerous studies have highlighted their role in haematopoietic differentiation and proliferation, acting as master regulators of haematopoietic stem cell function. Aberrant expression of miRNAs has been observed in haematological cancers, exhibiting unique expression signatures in comparison to normal counterparts. Functional and target analyses as well as animal models have attempted to annotate how different miRNA may contribute to the pathophysiology of these malignancies from modulating cancer associated genes, functioning directly as oncogenes or tumour suppressor genes or acting as bystanders or regulators of the epigenetic mechanisms in cancer. miRNAs have also been shown to play a role in modulating drug resistance and determining prognosis between the various subtypes of blood cancers. This review discusses the important role that miRNAs play in haematological malignancies by exploring associations that exist between the two and trying to examine evidence of causality to support the tantalising possibility that miRNAs might serve as therapeutic targets in blood cancers. PMID:24416592

  6. 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

  7. miRNAs in the Pathogenesis of Systemic Lupus Erythematosus

    PubMed Central

    Qu, Bo; Shen, Nan

    2015-01-01

    MicroRNAs (miRNAs) were first discovered as regulatory RNAs that controlled the timing of the larval development of Caenorhabditis elegans. Since then, nearly 30,000 mature miRNA products have been found in many species, including plants, warms, flies and mammals. Currently, miRNAs are well established as endogenous small (~22 nt) noncoding RNAs, which have functions in regulating mRNA stability and translation. Owing to intensive investigations during the last decade, miRNAs were found to play essential roles in regulating many physiological and pathological processes. Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by elevated autoantibodies against nuclear antigens and excessive inflammatory responses affecting multiple organs. Although efforts were taken and theories were produced to elucidate the pathogenesis of SLE, we still lack sufficient knowledge about the disease for developing effective therapies for lupus patients. Recent advances indicate that miRNAs are involved in the development of SLE, which gives us new insights into the pathogenesis of SLE and might lead to the finding of new therapeutic targets. Here, we will review recent discoveries about how miRNAs are involved in the pathogenesis of SLE and how it can promote the development of new therapy. PMID:25927578

  8. New insights about miRNAs in cystic fibrosis.

    PubMed

    Sonneville, Florence; Ruffin, Manon; Guillot, Loïc; Rousselet, Nathalie; Le Rouzic, Philippe; Corvol, Harriet; Tabary, Olivier

    2015-04-01

    The molecular basis of cystic fibrosis (CF) is a mutation-related defect in the epithelial-cell chloride channel called CF transmembrane conductance regulator (CFTR). This defect alters chloride ion transport and impairs water transport across the cell membrane. Marked clinical heterogeneity occurs even among patients carrying the same mutation in the CFTR gene. Recent studies suggest that such heterogeneity could be related to epigenetic factors and/or miRNAs, which are small noncoding RNAs that modulate the expression of various proteins via post-transcriptional inhibition of gene expression. In the respiratory system, it has been shown that the dysregulation of miRNAs could participate in and lead to pathogenicity in several diseases. In CF airways, recent studies have proposed that miRNAs may modulate disease progression by affecting the production of either CFTR or various proteins that are dysregulated in the CF lung. Herein, we provide an overview of studies showing how miRNAs may modulate CF pathology and the efforts to develop miRNA-based treatments and/or to consider miRNAs as biomarkers. The identification of miRNAs involved in CF disease progression opens up new avenues toward treatments targeting selected clinical components of CF, independently from the CFTR mutation. PMID:25687559

  9. Polysome arrest restricts miRNA turnover by preventing exosomal export of miRNA in growth-retarded mammalian cells

    PubMed Central

    Ghosh, Souvik; Bose, Mainak; Ray, Anirban; Bhattacharyya, Suvendra N.

    2015-01-01

    MicroRNAs (miRNAs) are tiny posttranscriptional regulators of gene expression in metazoan cells, where activity and abundance of miRNAs are tightly controlled. Regulated turnover of these regulatory RNAs is important to optimize cellular response to external stimuli. We report that the stability of mature miRNAs increases inversely with cell proliferation, and the increased number of microribonucleoproteins (miRNPs) in growth-restricted mammalian cells are in turn associated with polysomes. This heightened association of miRNA with polysomes also elicits reduced degradation of target mRNAs and impaired extracellular export of miRNA via exosomes. Overall polysome sequestration contributes to an increase of cellular miRNA levels but without an increase in miRNA activity. Therefore miRNA activity and turnover can be controlled by subcellular distribution of miRNPs that may get differentially regulated as a function of cell growth in mammalian cells. PMID:25609084

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

    PubMed

    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

  11. 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

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

    PubMed

    Gambari, Roberto; Brognara, Eleonora; Spandidos, Demetrios A; Fabbri, Enrica

    2016-07-01

    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

  13. Content of Heavy Metals in the Reed Canarygrass (Phalaris Arundinacea L.) in the First Year of Harvest

    NASA Astrophysics Data System (ADS)

    Poisa, Liena; Adamovics, Aleksandrs; Platace, Rasma

    2010-01-01

    One of the major factors in achieving more biofuel is the amount of crop yield, but that is not synonymous with the yield quality. Plants are contaminated by heavy metals not only through the soil, but also from atmospheric pollution. The aim of this research was to establish the amount of heavy metals in the dry matter of reed canarygrass (Phalaris arundinacea L.). The Marathon variety of reed canarygrass was studied with two sowing periods and four N-fertilizer rate applications. The concentration level of arsenic (As), cadmium (Cd), lead (Pb) and titanium (Ti) in the samples of reed canarygrass were analysed with the coupled plasma optical emission spectrometer Perkin Elmer 2100 DV. The samples of reed canarygrass taken in April had a greater concentration of As, Cd, Pb, which means that the plants absorb the heavy metals also from the snow covering. The first year yield of reed canarygrass established a fundamental negative correlation between the amount of As, Cd, Pb and the ash content. The samples taken in April have a greater heavy metal contamination, than the samples taken in October. The sowing period fundamentally affected the concentration of lead in reed canarygrass samples, but the level of N-fertilizer rate application affected the amount of cadmium and arsenic.

  14. 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.

  15. Detecting miRNA Mentions and Relations in Biomedical Literature

    PubMed Central

    Bagewadi, Shweta; Bobić, Tamara; Hofmann-Apitius, Martin; Fluck, Juliane; Klinger, Roman

    2015-01-01

    Introduction: MicroRNAs (miRNAs) have demonstrated their potential as post-transcriptional gene expression regulators, participating in a wide spectrum of regulatory events such as apoptosis, differentiation, and stress response. Apart from the role of miRNAs in normal physiology, their dysregulation is implicated in a vast array of diseases. Dissection of miRNA-related associations are valuable for contemplating their mechanism in diseases, leading to the discovery of novel miRNAs for disease prognosis, diagnosis, and therapy. Motivation: Apart from databases and prediction tools, miRNA-related information is largely available as unstructured text. Manual retrieval of these associations can be labor-intensive due to steadily growing number of publications. Additionally, most of the published miRNA entity recognition methods are keyword based, further subjected to manual inspection for retrieval of relations. Despite the fact that several databases host miRNA-associations derived from text, lower sensitivity and lack of published details for miRNA entity recognition and associated relations identification has motivated the need for developing comprehensive methods that are freely available for the scientific community. Additionally, the lack of a standard corpus for miRNA-relations has caused difficulty in evaluating the available systems. We propose methods to automatically extract mentions of miRNAs, species, genes/proteins, disease, and relations from scientific literature. Our generated corpora, along with dictionaries, and miRNA regular expression are freely available for academic purposes. To our knowledge, these resources are the most comprehensive developed so far. Results: The identification of specific miRNA mentions reaches a recall of 0.94 and precision of 0.93.  Extraction of miRNA-disease and miRNA-gene relations lead to an F 1 score of up to 0.76. A comparison of the information extracted by our approach to the databases miR2Disease and miRSel for

  16. Modulation of miRNAs in Pulmonary Hypertension

    PubMed Central

    Gupta, Sudhiranjan; Li, Li

    2015-01-01

    MicroRNAs (miRNAs) have emerged as a new class of posttranscriptional regulators of many cardiac and vascular diseases. They are a class of small, noncoding RNAs that contributes crucial roles typically through binding of the 3′-untranslated region of mRNA. A single miRNA may influence several signaling pathways associated with cardiac remodeling by targeting multiple genes. Pulmonary hypertension (PH) is a rare disorder characterized by progressive obliteration of pulmonary (micro) vasculature that results in elevated vascular resistance, leading to right ventricular hypertrophy (RVH) and RV failure. The pathology of PH involves vascular cell remodeling including pulmonary arterial endothelial cell (PAEC) dysfunction and pulmonary arterial smooth muscle cell (PASMC) proliferation. There is no cure for this disease. Thus, novel intervention pathways that govern PH induced RVH may result in new treatment modalities. Current therapies are limited to reverse the vascular remodeling. Recent studies have demonstrated the roles of various miRNAs in the pathogenesis of PH and pulmonary disorders. This review provides an overview of recent discoveries on the role of miRNAs in the pathogenesis of PH and discusses the potential for miRNAs as therapeutic targets and biomarkers of PH at clinical setting. PMID:25861465

  17. The miRNA biogenesis in marine bivalves.

    PubMed

    Rosani, Umberto; Pallavicini, Alberto; Venier, Paola

    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

  18. 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

  19. The Role of miRNAs in Cartilage Homeostasis

    PubMed Central

    Li, Yong Ping; Wei, Xiao Chun; Li1, Peng Cu; Chen, Chun Wei; Wang, Xiao Hu; Jiao, Qiang; Wang, Dong Ming; Wei, Fang Yuan; Zhang, Jian Zhong; Wei, Lei

    2015-01-01

    Osteoarthritis (OA) is an age-related disease with poorly understood pathogenesis. Recent studies have demonstrated that miRNA might play a key role in OA initiation and development. We reviewed recent publications and elucidated the connection between miRNA and OA cartilage anabolic and catabolic signals, including four signaling pathways: TGF-β/Smads and BMPs signaling, associated with cartilage anabolism; and MAPK and NF-KB signaling, associated with cartilage catabolism. We also explored the relationships with MMP, ADAMTS and NOS (NitricOxide Synthases) families, as well as with the catabolic cytokines IL-1 and TNF-α. The potential role of miRNAs in biological processes such as cartilage degeneration, chondrocyte proliferation, and differentiation is discussed. Collective evidence indicates that miRNAs play a critical role in cartilage degeneration. These findings will aid in understanding the molecular network that governs articular cartilage homeostasis and in to elucidate the role of miRNA in the pathogenesis of OA. PMID:27019614

  20. miRNA therapeutics in cardiovascular diseases: promises and problems

    PubMed Central

    Nouraee, Nazila; Mowla, Seyed J.

    2015-01-01

    microRNAs (miRNAs) are a novel class of non-coding RNAs which found their way into the clinic due to their fundamental roles in cellular processes such as differentiation, proliferation, and apoptosis. Recently, miRNAs have been known as micromodulators in cellular communications being involved in cell signaling and microenvironment remodeling. In this review, we will focus on the role of miRNAs in cardiovascular diseases (CVDs) and their reliability as diagnostic and therapeutic biomarkers in these conditions. CVDs comprise a variety of blood vessels and heart disorders with a high rate of morbidity and mortality worldwide. This necessitates introduction of novel molecular biomarkers for early detection, prevention, or treatment of these diseases. miRNAs, due to their stability, tissue-specific expression pattern and secretion to the corresponding body fluids, are attractive targets for cardiovascular-associated therapeutics. Explaining the challenges ahead of miRNA-based therapies, we will discuss the exosomes as delivery packages for miRNA drugs and promising novel strategies for the future of miRNA-based therapeutics. These approaches provide insights to the future of personalized medicine for the treatment of CVDs. PMID:26175755

  1. 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

  2. miRNAs in atherosclerotic plaque initiation, progression, and rupture.

    PubMed

    Andreou, Ioannis; Sun, Xinghui; Stone, Peter H; Edelman, Elazer R; Feinberg, Mark W

    2015-05-01

    Atherosclerosis is a chronic immune-inflammatory disorder that integrates multiple cell types and a diverse set of inflammatory mediators. miRNAs are emerging as important post-transcriptional regulators of gene expression in most, if not all, vertebrate cells, and constitute central players in many physiological and pathological processes. Rapidly accumulating experimental studies reveal their key role in cellular and molecular processes related to the development of atherosclerosis. We review current evidence for the involvement of miRNAs in early atherosclerotic lesion formation and in plaque rupture and erosion. We conclude with a perspective on the clinical relevance, therapeutic opportunities, and future challenges of miRNA biology in understanding the pathogenesis of this complex disease. PMID:25771097

  3. Control of mitochondrial activity by miRNAs

    PubMed Central

    Li, Peifeng; Jiao, Jianqing; Gao, Guifeng; Prabhakar, Bellur S.

    2012-01-01

    Mitochondria supply energy for physiological function and they participate in the regulation of other cellular events including apoptosis, calcium homeostasis and production of reactive oxygen species. Thus, mitochondria play a critical role in the cells. However, dysfunction of mitochondria is related to a variety of pathological processes and diseases. MicroRNAs (miRNAs) are a class of small noncoding RNAs about 22 nucleotides long, and they can bind to the 3′ un-translated region (3′UTR) of mRNAs, thereby inhibiting mRNA translation or promoting mRNA degradation. We summarize the molecular regulation of mitochondrial metabolism, structure and function by miRNAs. Modulation of miRNAs levels may provide a new therapeutic approach for the treatment of mitochondria-related diseases. PMID:22135235

  4. miRNAs in atherosclerotic plaque initiation, progression, and rupture

    PubMed Central

    Andreou, Ioannis; Sun, Xinghui; Stone, Peter H.; Edelman, Elazer R.; Feinberg, Mark W.

    2015-01-01

    Atherosclerosis is a chronic immune-inflammatory disorder that integrates multiple cell types and a diverse set of inflammatory mediators. miRNAs are emerging as important post-transcriptional regulators of gene expression in most, if not all, vertebrate cells and constitute central players in many physiological and pathological processes. Rapidly accumulating experimental studies reveal their key role in cellular and molecular processes related to the development of atherosclerosis. Here, we review the current evidence for the involvement of miRNAs in early atherosclerotic lesion formation to plaque rupture and erosion. We conclude with a perspective on the clinical relevance, therapeutic opportunities, and future challenges of miRNA biology in the pathogenesis of this complex disease. PMID:25771097

  5. Key principles of miRNA involvement in human diseases

    PubMed Central

    Giza, Dana Elena; Vasilescu, Catalin; Calin, George A.

    2015-01-01

    Although rapid progress in our understanding of the functions of miRNA has been made by experimentation and computational approach, a considerable effort still has to be done in determining the general principles that govern the miRNA’s mode of action in human diseases. We will further discuss how these principles are being progressively approached by molecular studies, as well as the importance of miRNA in regulating different target genes and functions in specific biological contexts. There is a great demand to understand the principles of context - specific miRNA target recognition in order to design future experiments and models of normal developmental and disease states. PMID:26317116

  6. Hypothalamic miRNAs: emerging roles in energy balance control

    PubMed Central

    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. PMID:25729348

  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. 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. PMID:26527651

  9. 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

  10. Microarray and Real-Time PCR Comparisons of Tall Fescue Gene Expression in Endophyte-Infected and Endophyte-Free Plants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many grasses have mutualistic symbioses with fungi of the family Clavicipitaceae. Tall fescue [Schedonorus arundinaceus (Schreb.) Dumont. = Festuca arundinacea (Schreb.)] can harbor the obligate endophyte, Neotyphodium coenophialum, that is asexually propagated and transmitted via host seeds. In a...

  11. Does modification of tall fescue leaf texture and forage nutritive value for improved livestock performance increase suitability for a grass-feeding caterpillar

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Grass breeders are developing new forage-type tall fescue [Schedonorus arundinaceus (Schreb.) Dumort = Lolium arundinaceum (Schreb.) Darbysh., formerly known as Festuca arundinacea Schreb.] cultivars with smoother texture, improved nutritive value, and reduced fiber for improved livestock performanc...

  12. Microarray and Real-Time PCR Comparison of Endophyte-Infected and Endophyte-Free Tall Fescue Gene Expression

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many grasses have mutualistic symbioses with fungi of the family Clavicipitaceae. Tall fescue [Schedonorus arundinaceus (Schreb.) Dumont. = Festuca arundinacea (Schreb.)] can harbor the obligate endophyte, Neotyphodium coenophialum, that is asexually propagated and transmitted via host seeds. To d...

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

    PubMed

    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

  14. 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

  15. Normalization of Affymetrix miRNA Microarrays for the Analysis of Cancer Samples.

    PubMed

    Wu, Di; Gantier, Michael P

    2016-01-01

    microRNA (miRNA) microarray normalization is a critical step for the identification of truly differentially expressed miRNAs. This is particularly important when dealing with cancer samples that have a global miRNA decrease. In this chapter, we provide a simple step-by-step procedure that can be used to normalize Affymetrix miRNA microarrays, relying on robust normal-exponential background correction with cyclic loess normalization. PMID:25971910

  16. miRNA sensitivity to Drosha levels correlates with pre-miRNA secondary structure

    PubMed Central

    Sperber, Henrik; Beem, Alan; Shannon, Sandra; Jones, Ross; Banik, Pratyusha; Chen, Yu; Ku, Sherman; Varani, Gabriele; Yao, Shuyuan; Ruohola-Baker, Hannele

    2014-01-01

    microRNAs (miRNAs) are crucial for cellular development and homeostasis. In order to better understand regulation of miRNA biosynthesis, we studied cleavage of primary miRNAs by Drosha. While Drosha knockdown triggers an expected decrease of many mature miRNAs in human embryonic stem cells (hESC), a subset of miRNAs are not reduced. Statistical analysis of miRNA secondary structure and fold change of expression in response to Drosha knockdown showed that absence of mismatches in the central region of the hairpin, 5 and 9–12 nt from the Drosha cutting site conferred decreased sensitivity to Drosha knockdown. This suggests that, when limiting, Drosha processes miRNAs without mismatches more efficiently than mismatched miRNAs. This is important because Drosha expression changes over cellular development and the fold change of expression for miRNAs with mismatches in the central region correlates with Drosha levels. To examine the biochemical relationship directly, we overexpressed structural variants of miRNA-145, miRNA-137, miRNA-9, and miRNA-200b in HeLa cells with and without Drosha knockdown; for these miRNAs, elimination of mismatches in the central region increased, and addition of mismatches decreased their expression in an in vitro assay and in cells with low Drosha expression. Change in Drosha expression can be a biologically relevant mechanism by which eukaryotic cells control miRNA profiles. This phenomenon may explain the impact of point mutations outside the seed region of certain miRNAs. PMID:24677349

  17. 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

  18. Revisiting absorption of dietary plant-based miRNAs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  19. MiRNAs from cotton roots infected with Meloidogyne incognita

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  20. 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. PMID:25874226

  1. Direct sequencing and expression analysis of a large number of miRNAs in Aedes aegypti and a multi-species survey of novel mosquito miRNAs

    PubMed Central

    2009-01-01

    Background MicroRNAs (miRNAs) are a novel class of gene regulators whose biogenesis involves hairpin structures called precursor miRNAs, or pre-miRNAs. A pre-miRNA is processed to make a miRNA:miRNA* duplex, which is then separated to generate a mature miRNA and a miRNA*. The mature miRNAs play key regulatory roles during embryonic development as well as other cellular processes. They are also implicated in control of viral infection as well as innate immunity. Direct experimental evidence for mosquito miRNAs has been recently reported in anopheline mosquitoes based on small-scale cloning efforts. Results We obtained approximately 130, 000 small RNA sequences from the yellow fever mosquito, Aedes aegypti, by 454 sequencing of samples that were isolated from mixed-age embryos and midguts from sugar-fed and blood-fed females, respectively. We also performed bioinformatics analysis on the Ae. aegypti genome assembly to identify evidence for additional miRNAs. The combination of these approaches uncovered 98 different pre-miRNAs in Ae. aegypti which could produce 86 distinct miRNAs. Thirteen miRNAs, including eight novel miRNAs identified in this study, are currently only found in mosquitoes. We also identified five potential revisions to previously annotated miRNAs at the miRNA termini, two cases of highly abundant miRNA* sequences, 14 miRNA clusters, and 17 cases where more than one pre-miRNA hairpin produces the same or highly similar mature miRNAs. A number of miRNAs showed higher levels in midgut from blood-fed female than that from sugar-fed female, which was confirmed by northern blots on two of these miRNAs. Northern blots also revealed several miRNAs that showed stage-specific expression. Detailed expression analysis of eight of the 13 mosquito-specific miRNAs in four divergent mosquito genera identified cases of clearly conserved expression patterns and obvious differences. Four of the 13 miRNAs are specific to certain lineage(s) within mosquitoes. Conclusion

  2. The endophytic symbiont Epichloë festucae establishes an epiphyllous net on the surface of Lolium perenne leaves by development of an expressorium, an appressorium-like leaf exit structure.

    PubMed

    Becker, Matthias; Becker, Yvonne; Green, Kimberly; Scott, Barry

    2016-07-01

    Epichloë festucae forms a mutualistic symbiotic association with Lolium perenne. This biotrophic fungus systemically colonizes the intercellular spaces of aerial tissues to form an endophytic hyphal network. E. festucae also grows as an epiphyte, but the mechanism for leaf surface colonization is not known. Here we identify an appressorium-like structure, which we call an expressorium that allows endophytic hyphae to penetrate the cuticle from the inside of the leaf to establish an epiphytic hyphal net on the surface of the leaf. We used a combination of scanning electron, transmission electron and confocal laser scanning microscopy to characterize this novel fungal structure and determine the composition of the hyphal cell wall using aniline blue and wheat germ agglutinin labelled with Alexafluor-488. Expressoria differentiate immediately below the cuticle in the leaf blade and leaf sheath intercalary cell division zones where the hyphae grow by tip growth. Differentiation of this structure requires components of both the NoxA and NoxB NADPH oxidase complexes. Major remodelling of the hyphal cell wall occurs following exit from the leaf. These results establish that the symbiotic association of E. festucae with L. perenne involves an interconnected hyphal network of both endophytic and epiphytic hyphae. PMID:26991322

  3. [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/. PMID:26510603

  4. 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

  5. Profiling miRNA Expression in Bovine Tissues by Deep Sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    miRNA are short RNA sequences ( ~ 21 nt long) that have been recently identified and were found to play an important role in gene regulation and controlling major cellular processes. Several miRNA are found to be evolutionarily conserved among the mammalian species. Some miRNAs are even conserved be...

  6. Serum miRNAs Signature Plays an Important Role in Keloid Disease.

    PubMed

    Luan, Y; Liu, Y; Liu, C; Lin, Q; He, F; Dong, X; Xiao, Z

    2016-01-01

    The molecular mechanism underlying the pathogenesis of keloid is largely unknown. MicroRNA (miRNA) is a class of small regulatory RNA that has emerged as a group of posttranscriptional gene repressors, participating in diverse pathophysiological processes of skin diseases. We investigated the expression profiles of miRNAs in the sera of patients to decipher the complicated factors involved in the development of keloid disease. MiRNA expression profiling in the sera from 9 keloid patients and 7 normal controls were characterized using a miRNA microarray containing established human mature and precursor miRNA sequences. Quantitative real-time PCR was performed to confirm the expression of miRNAs. The putative targets of differentially expressed miRNAs were functionally annotated by bioinformatics. MiRNA microarray analysis identified 37 differentially expressed miRNAs (17 upregulated and 20 downregulated) in keloid patients, compared to the healthy controls. Functional annotations revealed that the targets of those differentially expressed miRNAs were enriched in signaling pathways essential for scar formation and wound healing. The expression profiling of miRNAs is altered in the keloid, providing a clue for the molecular mechanisms underlying its initiation and progression. MiRNAs may partly contribute to the etiology of keloids by affecting the critical signaling pathways relevant to keloid pathogenesis. PMID:27132794

  7. Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    MicroRNAs (miRNAs) are endogenous single-stranded small RNA molecules (sRNA) that are fundamental post-transcriptional regulators of gene expression. Many conserved plant miRNAs play important roles in plant growth and development, but more species-specific miRNAs remain to be identified and charact...

  8. Identification of miRNA encoded by Jatropha curcas from EST and GSS

    PubMed Central

    Vishwakarma, Nutan Prakash; Jadeja, Vasant J.

    2013-01-01

    miRNAs are endogenous approx 22 nucleotide RNA which mediates transcriptional or Post-transcriptional gene regulation and play a critical role in diverse aspects of plant development. miRNA identification in wet lab have various constraints, it is time consuming and expensive. It also faces the limitation of identifying miRNAs expressed at specific time and/or at special conditions. Due to the nature of strong conservation of miRNA in plant species, the use of comparative genomics approach for expressed sequence tags (ESTs), Genome Survey Sequence (GSS) and structural feature criteria filter has paved the way toward the identification of conserved miRNAs from the plant species whose genomes are not yet available in public domain. To identify the novel miRNA from Jatropha curcas, a total of 46862 EST sequences and 1569 GSS were searched for homology to previously known viridiplantae 2502 mature miRNA. After predicting the RNA secondary structure, 24 new potential miRNA were identified in J. curcas. Using the newly identified miRNA sequences, a total of 78 potential target genes were identified for 3 miRNA families. Most of the miRNA targeted genes were predicted to encode transcription factors that regulate cell growth and development, signaling, and metabolism. These findings considerably broaden the scope of understanding the functions of miRNA in J. curcas. PMID:23299511

  9. 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. PMID:25294817

  10. Upregulation of miRNA3195 and miRNA374b Mediates the Anti-Angiogenic Properties of Melatonin in Hypoxic PC-3 Prostate Cancer Cells

    PubMed Central

    Sohn, Eun Jung; Won, Gunho; Lee, Jihyun; Lee, Sangyoon; Kim, Sung-hoon

    2015-01-01

    Recently microRNAs (miRNAs) have been attractive targets with their key roles in biological regulation through post-transcription to control mRNA stability and protein translation. Though melatonin was known as an anti-angiogenic agent, the underlying mechanism of melatonin in PC-3 prostate cancer cells under hypoxia still remains unclear. Thus, in the current study, we elucidated the important roles of miRNAs in melatonin-induced anti-angiogenic activity in hypoxic PC-3 cells. miRNA array revealed that 33 miRNAs (>2 folds) including miRNA3195 and miRNA 374b were significantly upregulated and 16 miRNAs were downregulated in melatonin-treated PC-3 cells under hypoxia compared to untreated control. Melatonin significantly attenuated the expression of hypoxia-inducible factor (HIF)-1 alpha, HIF-2 alpha and vascular endothelial growth factor (VEGF) at mRNA level in hypoxic PC-3 cells. Consistently, melatonin enhanced the expression of miRNA3195 and miRNA 374b in hypoxic PC-3 cells by qRT-PCR analysis. Of note, overexpression of miRNA3195 and miRNA374b mimics attenuated the mRNA levels of angiogenesis related genes such as HIF-1alpha, HIF-2 alpha and VEGF in PC-3 cells under hypoxia. Furthermore, overexpression of miRNA3195 and miRNA374b suppressed typical angiogenic protein VEGF at the protein level and VEGF production induced by melatonin, while antisense oligonucleotides against miRNA 3195 or miRNA 374b did not affect VEGF production induced by melatonin. Also, overexpression of miR3195 or miR374b reduced HIF-1 alpha immunofluorescent expression in hypoxic PC-3 compared to untreated control. Overall, our findings suggest that upregulation of miRNA3195 and miRNA374b mediates anti-angiogenic property induced by melatonin in hypoxic PC-3 cells. PMID:25553085

  11. Complexity of murine cardiomyocyte miRNA biogenesis, sequence variant expression and function.

    PubMed

    Humphreys, David T; Hynes, Carly J; Patel, Hardip R; Wei, Grace H; Cannon, Leah; Fatkin, Diane; Suter, Catherine M; Clancy, Jennifer L; Preiss, Thomas

    2012-01-01

    microRNAs (miRNAs) are critical to heart development and disease. Emerging research indicates that regulated precursor processing can give rise to an unexpected diversity of miRNA variants. We subjected small RNA from murine HL-1 cardiomyocyte cells to next generation sequencing to investigate the relevance of such diversity to cardiac biology. ∼40 million tags were mapped to known miRNA hairpin sequences as deposited in miRBase version 16, calling 403 generic miRNAs as appreciably expressed. Hairpin arm bias broadly agreed with miRBase annotation, although 44 miR* were unexpectedly abundant (>20% of tags); conversely, 33 -5p/-3p annotated hairpins were asymmetrically expressed. Overall, variability was infrequent at the 5' start but common at the 3' end of miRNAs (5.2% and 52.3% of tags, respectively). Nevertheless, 105 miRNAs showed marked 5' isomiR expression (>20% of tags). Among these was miR-133a, a miRNA with important cardiac functions, and we demonstrated differential mRNA targeting by two of its prevalent 5' isomiRs. Analyses of miRNA termini and base-pairing patterns around Drosha and Dicer cleavage regions confirmed the known bias towards uridine at the 5' most position of miRNAs, as well as supporting the thermodynamic asymmetry rule for miRNA strand selection and a role for local structural distortions in fine tuning miRNA processing. We further recorded appreciable expression of 5 novel miR*, 38 extreme variants and 8 antisense miRNAs. Analysis of genome-mapped tags revealed 147 novel candidate miRNAs. In summary, we revealed pronounced sequence diversity among cardiomyocyte miRNAs, knowledge of which will underpin future research into the mechanisms involved in miRNA biogenesis and, importantly, cardiac function, disease and therapy. PMID:22319597

  12. miRNAs as biomarkers of myocardial infarction: a step forward towards personalized medicine?

    PubMed

    Goretti, Emeline; Wagner, Daniel R; Devaux, Yvan

    2014-12-01

    miRNAs are small noncoding RNAs known to post-transcriptionally regulate gene expression. miRNAs are expressed in the heart where they regulate multiple pathophysiological processes. The discovery of stable cardiac miRNAs in the bloodstream has also motivated the investigation of their potential as biomarkers. This review gathers the current knowledge on the use of miRNAs as novel biomarkers to improve risk stratification, diagnosis, and prognosis of patients with myocardial infarction. In the rapidly evolving era of biomarkers, the potential of miRNAs as promising tools to move personalized medicine a step forward is discussed. PMID:25457620

  13. The biological functions of miRNAs: lessons from in vivo studies.

    PubMed

    Vidigal, Joana A; Ventura, Andrea

    2015-03-01

    Despite their clear importance as a class of regulatory molecules, pinpointing the relevance of individual miRNAs has been challenging. Studies querying miRNA functions by overexpressing or silencing specific miRNAs have yielded data that are often at odds with those collected from loss-of-functions models. In addition, knockout studies suggest that many conserved miRNAs are dispensable for animal development or viability. In this review, we discuss these observations in the context of our current knowledge of miRNA biology and review the evidence implicating miRNA-mediated gene regulation in the mechanisms that ensure biological robustness. PMID:25484347

  14. The biological functions of miRNAs: lessons from in vivo studies

    PubMed Central

    Vidigal, Joana A.; Ventura, Andrea

    2014-01-01

    Despite their clear importance as a class of regulatory molecules, pinpointing the relevance of individual miRNAs has been challenging. Studies querying miRNA functions by overexpressing or silencing specific miRNAs have yielded data that are often at odds with those collected from loss-of-functions models. In addition, knockout studies suggest that many conserved miRNAs are dispensable for animal development or viability. In this review we discuss these observations in the context of our current knowledge of miRNA biology and review the evidence implicating miRNA-mediated gene regulation in the mechanisms that ensure biological robustness. PMID:25484347

  15. 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

  16. 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.

  17. On Measuring miRNAs after Transient Transfection of Mimics or Antisense Inhibitors

    PubMed Central

    Thomson, Daniel W.; Bracken, Cameron P.; Szubert, Jan M.; Goodall, Gregory J.

    2013-01-01

    The ability to alter microRNA (miRNA) abundance is crucial for studying miRNA function. To achieve this there is widespread use of both exogenous double-stranded miRNA mimics for transient over-expression, and single stranded antisense RNAs (antimiRs) for miRNA inhibition. The success of these manipulations is often assessed using qPCR, but this does not accurately report the level of functional miRNA. Here, we draw attention to this discrepancy, which is overlooked in many published reports. We measured the functionality of exogenous miRNA by comparing the total level of transfected miRNA in whole cell extracts to the level of miRNA bound to Argonaute following transfection and show that the supraphysiological levels of transfected miRNA frequently seen using qPCR do not represent the functional levels, because the majority of transfected RNA that is detected is vesicular and not accessible for loading into Argonaute as functionally active miRNAs. In the case of microRNA inhibition by transient transfection with antisense inhibitors, there is also the potential for discrepancy, because following cell lysis the abundant inhibitor levels from cellular vesicles can directly interfere with the PCR reaction used to measure miRNA level. PMID:23358900

  18. 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. PMID:27322812

  19. 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

  20. Microevolution of nematode miRNAs reveals diverse modes of selection.

    PubMed

    Jovelin, Richard; Cutter, Asher D

    2014-01-01

    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. PMID:25355809

  1. 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. PMID:25735537

  2. VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their targets.

    PubMed

    Qureshi, Abid; Thakur, Nishant; Monga, Isha; Thakur, Anamika; Kumar, Manoj

    2014-01-01

    Viral microRNAs (miRNAs) regulate gene expression of viral and/or host genes to benefit the virus. Hence, miRNAs play a key role in host-virus interactions and pathogenesis of viral diseases. Lately, miRNAs have also shown potential as important targets for the development of novel antiviral therapeutics. Although several miRNA and their target repositories are available for human and other organisms in literature, but a dedicated resource on viral miRNAs and their targets are lacking. Therefore, we have developed a comprehensive viral miRNA resource harboring information of 9133 entries in three subdatabases. This includes 1308 experimentally validated miRNA sequences with their isomiRs encoded by 44 viruses in viral miRNA ' VIRMIRNA: ' and 7283 of their target genes in ' VIRMIRTAR': . Additionally, there is information of 542 antiviral miRNAs encoded by the host against 24 viruses in antiviral miRNA ' AVIRMIR': . The web interface was developed using Linux-Apache-MySQL-PHP (LAMP) software bundle. User-friendly browse, search, advanced search and useful analysis tools are also provided on the web interface. VIRmiRNA is the first specialized resource of experimentally proven virus-encoded miRNAs and their associated targets. This database would enhance the understanding of viral/host gene regulation and may also prove beneficial in the development of antiviral therapeutics. Database URL: http://crdd.osdd.net/servers/virmirna. PMID:25380780

  3. miRNA Repertoires of Demosponges Stylissa carteri and Xestospongia testudinaria.

    PubMed

    Liew, Yi Jin; Ryu, Taewoo; 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

  4. 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

  5. miRNA regulation during cardiac development and remodeling in cardiomyopathy

    PubMed Central

    Chaitra, K.L.; Ulaganathan, Kayalvili; James, Anita; Ananthapur, Venkateshwari; Nallari, Pratibha

    2013-01-01

    miRNAs have been found to play a major role in cardiomyopathy, a heart muscle disorder characterized by cardiac dysfunction. Several miRNAs including those involved in heart development are found to be dysregulated in cardiomyopathy. These miRNAs act either directly or indirectly by controlling the genes involved in normal development and functioning of the heart. Indirectly it also targets modifier genes and genes involved in signaling pathways. In this review, miRNAs involved in heart development, including dysregulation of miRNA which regulate various genes, modifiers and notch signaling pathway genes leading to cardiomyopathy are discussed. A study of these miRNAs would give an insight into the mechanisms involved in the processes of heart development and disease. Apart from this, information gathered from these studies would also generate suitable therapeutic targets in the form of antagomirs which are chemically engineered oligonucleotides used for silencing miRNAs. PMID:27092038

  6. Expression Profiling of LPS Responsive miRNA in Primary Human Macrophages

    PubMed Central

    Naqvi, Afsar Raza; Zhong, Sheng; Dang, Hong; Fordham, Jezrom B; Nares, Salvador; Khan, Asma

    2016-01-01

    microRNAs (miRNAs) have emerged as important regulators of the innate and adaptive immune response. The purpose of the present study was to interrogate miRNA profiles of primary human macrophages challenged with bacterial lipopolysaccharide (LPS) with focus on expression kinetics. We employed Nanostring platform to precisely characterize the changes in miRNA expression following different doses and durations of LPS exposure. Differentially expressed miRNAs were identified in response to LPS challenge with convergent and divergent expression profiles. Pathway analysis of LPS-responsive miRNAs revealed regulation of biological processes linked to key cell signaling (including PIK3-Akt, MAP kinase, ErbB) and pathogen response pathways. Our data provide a comprehensive miRNA profiling of human primary macrophages treated with LPS. These results show that bacterial Toll like receptor (TLR) ligands can temporally modulate macrophage miRNA expression. PMID:27307950

  7. 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. PMID:24480175

  8. miRNAs and their putative roles in the development and progression of Parkinson's disease

    PubMed Central

    Wong, Garry; Nass, Richard

    2012-01-01

    Small regulatory RNAs, such as miRNAs, are increasingly being recognized not only as regulators of developmental processes but contributors to pathological states. The number of miRNAs determined experimentally to be involved in Parkinson's disease (PD) development and progression is small and includes regulators of pathologic proteins, neurotrophic factors, and xenobiotic metabolizing enzymes. PD gene-association studies have also indicated miRNAs in the pathology. In this review, we present known miRNAs and their validated targets that contribute to PD development and progression. We also incorporate data mining methods to link additional miRNAs with non-experimentally validated targets and propose additional roles of miRNAs in neurodegenerative processes. Furthermore, we present the potential contribution of next-generation-sequencing approaches to elucidate mechanisms and etiology of PD through discovery of novel miRNAs and other non-coding RNA classes. PMID:23316214

  9. Computational identification of miRNAs in medicinal plant Senecio vulgaris (Groundsel).

    PubMed

    Sahu, Sarika; Khushwaha, Anjana; Dixit, Rekha

    2011-01-01

    RNAs Interference plays a very important role in gene silencing. In vitro identification of miRNAs is a slow process as it is difficult to isolate them. Nucleotide sequences of miRNAs are highly conserved among the plants and, this form the key feature behind the identification of miRNAs in plant species by homology alignment. In silico identification of miRNAs from EST database is emerging as a novel, faster and reliable approach. Here EST sequences of Senecio vulgaris (Groundsel) were searched against known miRNA sequences by using BLASTN tool. A total of 10 miRNAs were identified from 1956 EST sequences and 115 GSS sequences. The most stable miRNA identified is svu-mir-1. This approach will accelerate advance research in regulation of gene expression in Groundsel by interfering RNAs. PMID:22347777

  10. Computational identification of miRNAs in medicinal plant Senecio vulgaris (Groundsel)

    PubMed Central

    Sahu, Sarika; Khushwaha, Anjana; Dixit, Rekha

    2011-01-01

    RNAs Interference plays a very important role in gene silencing. In vitro identification of miRNAs is a slow process as it is difficult to isolate them. Nucleotide sequences of miRNAs are highly conserved among the plants and, this form the key feature behind the identification of miRNAs in plant species by homology alignment. In silico identification of miRNAs from EST database is emerging as a novel, faster and reliable approach. Here EST sequences of Senecio vulgaris (Groundsel) were searched against known miRNA sequences by using BLASTN tool. A total of 10 miRNAs were identified from 1956 EST sequences and 115 GSS sequences. The most stable miRNA identified is svu-mir-1. This approach will accelerate advance research in regulation of gene expression in Groundsel by interfering RNAs. PMID:22347777

  11. 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

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

    PubMed Central

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

    2016-01-01

    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/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. PMID:27345473

  13. 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

  14. 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. PMID:23840875

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

    PubMed

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

    2016-01-01

    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. PMID:27345473

  16. Platelets in Patients with Premature Coronary Artery Disease Exhibit Upregulation of miRNA340* and miRNA624*

    PubMed Central

    Sondermeijer, Brigitte M.; Bakker, Annemieke; Halliani, Amalia; de Ronde, Maurice W. J.; Marquart, Arnoud A.; Tijsen, Anke J.; Mulders, Ties A.; Kok, Maayke G. M.; Battjes, Suzanne; Maiwald, Steffi; Sivapalaratnam, Suthesh; Trip, Mieke D.; Moerland, Perry D.; Meijers, Joost C. M.; Creemers, Esther E.; Pinto-Sietsma, Sara-Joan

    2011-01-01

    Background Coronary artery disease (CAD) is the leading cause of human morbidity and mortality worldwide, underscoring the need to improve diagnostic strategies. Platelets play a major role, not only in the process of acute thrombosis during plaque rupture, but also in the formation of atherosclerosis itself. MicroRNAs are endogenous small non-coding RNAs that control gene expression and are expressed in a tissue and disease-specific manner. Therefore they have been proposed to be useful biomarkers. It remains unknown whether differences in miRNA expression levels in platelets can be found between patients with premature CAD and healthy controls. Methodology/Principal Findings In this case-control study we measured relative expression levels of platelet miRNAs using microarrays from 12 patients with premature CAD and 12 age- and sex-matched healthy controls. Six platelet microRNAs were significantly upregulated (miR340*, miR451, miR454*, miR545:9.1. miR615-5p and miR624*) and one miRNA (miR1280) was significantly downregulated in patients with CAD as compared to healthy controls. To validate these results, we measured the expression levels of these candidate miRNAs by qRT-PCR in platelets of individuals from two independent cohorts; validation cohort I consisted of 40 patients with premature CAD and 40 healthy controls and validation cohort II consisted of 27 patients with artery disease and 40 healthy relatives. MiR340* and miR624* were confirmed to be upregulated in patients with CAD as compared to healthy controls in both validation cohorts. Conclusion/Significance Two miRNAs in platelets are significantly upregulated in patients with CAD as compared to healthy controls. Whether the two identified miRNAs can be used as biomarkers and whether they are cause or consequence of the disease remains to be elucidated in a larger prospective study. PMID:22022480

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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. KRAS-dependent sorting of miRNA to exosomes.

    PubMed

    Cha, Diana J; Franklin, Jeffrey L; Dou, Yongchao; Liu, Qi; Higginbotham, James N; Demory Beckler, Michelle; Weaver, Alissa M; Vickers, Kasey; Prasad, Nirpesh; Levy, Shawn; Zhang, Bing; Coffey, Robert J; Patton, James G

    2015-01-01

    Mutant KRAS colorectal cancer (CRC) cells release protein-laden exosomes that can alter the tumor microenvironment. To test whether exosomal RNAs also contribute to changes in gene expression in recipient cells, and whether mutant KRAS might regulate the composition of secreted microRNAs (miRNAs), we compared small RNAs of cells and matched exosomes from isogenic CRC cell lines differing only in KRAS status. We show that exosomal profiles are distinct from cellular profiles, and mutant exosomes cluster separately from wild-type KRAS exosomes. miR-10b was selectively increased in wild-type exosomes, while miR-100 was increased in mutant exosomes. Neutral sphingomyelinase inhibition caused accumulation of miR-100 only in mutant cells, suggesting KRAS-dependent miRNA export. In Transwell co-culture experiments, mutant donor cells conferred miR-100-mediated target repression in wild-type-recipient cells. These findings suggest that extracellular miRNAs can function in target cells and uncover a potential new mode of action for mutant KRAS in CRC. PMID:26132860

  19. Multiplexed miRNA northern blots via hybridization chain reaction

    PubMed Central

    Schwarzkopf, Maayan; Pierce, Niles A.

    2016-01-01

    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. PMID:27270083

  20. Assessing Agreement between miRNA Microarray Platforms

    PubMed Central

    Bassani, Niccolò P.; Ambrogi, Federico; Biganzoli, Elia M.

    2014-01-01

    Over the last few years, miRNA microarray platforms have provided great insights into the biological mechanisms underlying the onset and development of several diseases. However, only a few studies have evaluated the concordance between different microarray platforms using methods that took into account measurement error in the data. In this work, we propose the use of a modified version of the Bland–Altman plot to assess agreement between microarray platforms. To this aim, two samples, one renal tumor cell line and a pool of 20 different human normal tissues, were profiled using three different miRNA platforms (Affymetrix, Agilent, Illumina) on triplicate arrays. Intra-platform reliability was assessed by calculating pair-wise concordance correlation coefficients (CCC) between technical replicates and overall concordance correlation coefficient (OCCC) with bootstrap percentile confidence intervals, which revealed moderate-to-good repeatability of all platforms for both samples. Modified Bland–Altman analysis revealed good patterns of concordance for Agilent and Illumina, whereas Affymetrix showed poor-to-moderate agreement for both samples considered. The proposed method is useful to assess agreement between array platforms by modifying the original Bland–Altman plot to let it account for measurement error and bias correction and can be used to assess patterns of concordance between other kinds of arrays other than miRNA microarrays.

  1. Multiplexed miRNA northern blots via hybridization chain reaction.

    PubMed

    Schwarzkopf, Maayan; Pierce, Niles A

    2016-09-01

    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. PMID:27270083

  2. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  4. Novel endophyte-infected tall fescues

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tall fescue (Schedonorus arundinaceus (Schreb.) Dumort. = Lolium arundinaceum (Schreb.) Darbysh., formerly Festuca arundinacea Schreb. and before that, Festuca elatior L.) is a cool-season perennial grass that is well adapted in the upper transition zone between the temperate northeast and subtropic...

  5. MiRNA-20 and MiRNA-106a Regulate Spermatogonial Stem Cell Renewal at the Post-transcriptional Level via Targeting STAT3 and Ccnd1

    PubMed Central

    He, Zuping; Jiang, Jiji; Kokkinaki, Maria; Tang, Lin; Zeng, Wenxian; Gallicano, Ian; Dobrinski, Ina; Dym, Martin

    2013-01-01

    Studies onspermatogonial stem cells (SSCs) are of unusual significance because they are the unique stem cells that transmit genetic information to subsequent generations and they can acquire pluripotency to become embryonic stem-like cells that have therapeutic applications in human diseases. MicroRNAs (miRNAs) have recently emerged as critical endogenous regulators in mammalian cells. However, the function and mechanisms of individual miRNAs in regulating SSC fate remain unknown. Here we report for the first time that miRNA-20 and miRNA-106a are preferentially expressed in mouse SSCs. Functional assays in vitro and in vivo using miRNA mimics and inhibitors reveal that miRNA-20 and miRNA-106a are essential for renewal of SSCs. We further demonstrate that these two miRNAs promote renewal at the post-transcriptional level via targeting STAT3 and Ccnd1 and that knockdown of STAT3, Fos, and Ccnd1 results in renewal of SSCs. This study thus provides novel insights into molecular mechanisms regulating renewal and differentiation of SSCs and may have important implications for regulating male reproduction. PMID:23836497

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  7. Towards Clinical Applications of Blood-Borne miRNA Signatures: The Influence of the Anticoagulant EDTA on miRNA Abundance

    PubMed Central

    Leidinger, Petra; Backes, Christina; Rheinheimer, Stefanie; Keller, Andreas; Meese, Eckart

    2015-01-01

    Background Circulating microRNAs (miRNAs) from blood are increasingly recognized as biomarker candidates for human diseases. Clinical routine settings frequently include blood sampling in tubes with EDTA as anticoagulant without considering the influence of phlebotomy on the overall miRNA expression pattern. We collected blood samples from six healthy individuals each in an EDTA blood collection tube. Subsequently, the blood was transferred into PAXgeneTM tubes at three different time points, i.e. directly (0 min), 10 min, and 2 h after phlebotomy. As control blood was also directly collected in PAXgeneTM blood RNA tubes that contain a reagent to directly lyse blood cells and stabilize their content. For all six blood donors at the four conditions (24 samples) we analyzed the abundance of 1,205 miRNAs by human Agilent miRNA V16 microarrays. Results While we found generally a homogenous pattern of the miRNA abundance in all 24 samples, the duration of the EDTA treatment appears to influence the miRNA abundance of specific miRNAs. The most significant changes are observed after longer EDTA exposition. Overall, the impact of the different blood sample conditions on the miRNA pattern was substantially lower than intra-individual variations. While samples belonging to one of the six individuals mostly cluster together, there was no comparable clustering for any of the four tested blood sampling conditions. The most affected miRNA was miR-769-3p that was not detected in any of the six PAXgene blood samples, but in all EDTA 2h samples. Accordingly, hsa-miR-769-3p was also the only miRNA that showed a significantly different abundance between the 4 blood sample conditions by an ANOVA analysis (Benjamini-Hochberg adjusted p-value of 0.003). Validation by qRT-PCR confirmed this finding. Conclusion The pattern of blood-borne miRNA abundance is rather homogenous between the four tested blood sample conditions of six blood donors. There was a clustering between the miRNA

  8. 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

  9. 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

  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. PMID:27081157

  11. Quantitative analysis of miRNA expression in seven human foetal and adult organs.

    PubMed

    Tang, Yanping; Liu, Dong; Zhang, Lijie; Ingvarsson, Sigurdur; Chen, Huiping

    2011-01-01

    miRNAs have been found to repress gene expression at posttranscriptional level in cells. Studies have shown that expression of miRNAs is tissue-specific and developmental-stage-specific. The mechanism behind this could be explained by miRNA pathways. In this study, totally 54 miRNAs were analysed in 7 matched human foetal and adult organs (brain, colon, heart, kidney, liver, lung and spleen) using real-time PCR. Quantitative analysis showed that a big proportion of the 54 miRNAs have higher general expression in the organs of the foetal period than the adult period, with the exception of the heart. The miRNA gene promoter methylation level in the adult stages was higher than in the foetal stages. Moreover, there is a high general expression level of several miRNAs in both stages of brain, kidney, liver, lung and spleen, but not seen in colon and heart. Our results indicate that the miRNAs may play a bigger role in the foetal stage than the adult stage of brain, colon, kidney, liver, lung and spleen. The majority of the miRNAs analysed may play an important role in the growth and development of brain, kidney, liver, lung and spleen. However, a minority of the miRNAs may be functional in colon and heart. PMID:22194897

  12. MiRNA profiles in cerebrospinal fluid from patients with central hypersomnias.

    PubMed

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

    2014-12-15

    MicroRNAs (miRNAs) are involved in the pathogenesis of many human diseases, including some neurological disorders. Recently, we have reported dysregulated miRNAs in plasma from patients with central hypersomnias including type 1 and type 2 narcolepsy, and idiopathic hypersomnia. This study addressed whether miRNA levels are altered in the cerebrospinal fluid (CSF) of patients with central hypersomnias. We conducted high-throughput analyses of miRNAs in CSF from patients using quantitative real-time polymerase chain reaction panels. We identified 13, 9, and 11 miRNAs with a more than two-fold change in concentration in CSF from patients with type 1 and type 2 narcolepsy and idiopathic hypersomnia, respectively, compared with matched healthy controls. Most miRNAs differed in more than one of the sleep disorders. However, all miRNAs were detected at low levels in CSF and varied between individuals. None of them showed significant differences in concentrations between groups after correcting for multiple testing, and none could be validated in an independent cohort. Nevertheless, approximately 60% of the most abundant miRNAs in the profile reported here have previously been identified in the CSF of healthy individuals, showing consistency with previous miRNA profiles found in CSF. In conclusion, we were not able to demonstrate distinct levels or patterns of miRNAs in CSF from central hypersomnia patients. PMID:25451005

  13. miRNA Profiling Reveals Dysregulation of RET and RET-Regulating Pathways in Hirschsprung's Disease.

    PubMed

    Li, Shuangshuang; Wang, Shiqi; Guo, Zhenhua; Wu, Huan; Jin, Xianqing; Wang, Yi; Li, Xiaoqing; Liang, Shaoyan

    2016-01-01

    Hirschsprung's disease (HSCR), the most common congenital malformation of the gut, is regulated by multiple signal transduction pathways. Several components of these pathways are important targets for microRNAs (miRNAs). Multiple miRNAs have been associated with the pathophysiology of HSCR, and serum miRNAs profiles of HSCR patients have been reported, but miRNA expression in HSCR colon tissue is almost completely unexplored. Using microarray technology, we screened colon tissue to detect miRNAs whose expression profiles were altered in HSCR and identify targets of differentially expressed miRNAs. Following filtering of low-intensity signals, data normalization, and volcano plot filtering, we identified 168 differentially expressed miRNAs (104 up-regulated and 64 down-regulated). Fifty of these mRNAs represent major targets of dysegulated miRNAs and may thus important roles in the pathophysiology of HSCR. Pathway analysis revealed that 7 of the miRNA targets encode proteins involved in regulation of cell proliferation and migration via RET and related signaling pathways (MAPK and PI3K/AKT). Our results identify miRNAs that play key roles in the pathophysiology of the complex multi-factorial disease HSCR. PMID:26933947

  14. 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

  15. miRNA Profiling Reveals Dysregulation of RET and RET-Regulating Pathways in Hirschsprung's Disease

    PubMed Central

    Li, Shuangshuang; Wang, Shiqi; Guo, Zhenhua; Wu, Huan; Jin, Xianqing; Wang, Yi; Li, Xiaoqing; Liang, Shaoyan

    2016-01-01

    Hirschsprung’s disease (HSCR), the most common congenital malformation of the gut, is regulated by multiple signal transduction pathways. Several components of these pathways are important targets for microRNAs (miRNAs). Multiple miRNAs have been associated with the pathophysiology of HSCR, and serum miRNAs profiles of HSCR patients have been reported, but miRNA expression in HSCR colon tissue is almost completely unexplored. Using microarray technology, we screened colon tissue to detect miRNAs whose expression profiles were altered in HSCR and identify targets of differentially expressed miRNAs. Following filtering of low-intensity signals, data normalization, and volcano plot filtering, we identified 168 differentially expressed miRNAs (104 up-regulated and 64 down-regulated). Fifty of these mRNAs represent major targets of dysegulated miRNAs and may thus important roles in the pathophysiology of HSCR. Pathway analysis revealed that 7 of the miRNA targets encode proteins involved in regulation of cell proliferation and migration via RET and related signaling pathways (MAPK and PI3K/AKT). Our results identify miRNAs that play key roles in the pathophysiology of the complex multi-factorial disease HSCR. PMID:26933947

  16. Evaluation of the capability of the PCV2 genome to encode miRNAs: lack of viral miRNA expression in an experimental infection.

    PubMed

    Núñez-Hernández, Fernando; Pérez, Lester J; Vera, Gonzalo; Córdoba, Sarai; Segalés, Joaquim; Sánchez, Armand; Núñez, José I

    2015-01-01

    Porcine circovirus type 2 (PCV2) is a ssDNA virus causing PCV2-systemic disease (PCV2-SD), one of the most important diseases in swine. MicroRNAs (miRNAs) are a new class of small non-coding RNAs that regulate gene expression post-transcriptionally. Viral miRNAs have recently been described and the number of viral miRNAs has been increasing in the past few years. In this study, small RNA libraries were constructed from two tissues of subclinically PCV2 infected pigs to explore if PCV2 can encode viral miRNAs. The deep sequencing data revealed that PCV2 does not express miRNAs in an in vivo subclinical infection. PMID:25934266

  17. Annotation of primate miRNAs by high throughput sequencing of small RNA libraries

    PubMed Central

    2012-01-01

    Background In addition to genome sequencing, accurate functional annotation of genomes is required in order to carry out comparative and evolutionary analyses between species. Among primates, the human genome is the most extensively annotated. Human miRNA gene annotation is based on multiple lines of evidence including evidence for expression as well as prediction of the characteristic hairpin structure. In contrast, most miRNA genes in non-human primates are annotated based on homology without any expression evidence. We have sequenced small-RNA libraries from chimpanzee, gorilla, orangutan and rhesus macaque from multiple individuals and tissues. Using patterns of miRNA expression in conjunction with a model of miRNA biogenesis we used these high-throughput sequencing data to identify novel miRNAs in non-human primates. Results We predicted 47 new miRNAs in chimpanzee, 240 in gorilla, 55 in orangutan and 47 in rhesus macaque. The algorithm we used was able to predict 64% of the previously known miRNAs in chimpanzee, 94% in gorilla, 61% in orangutan and 71% in rhesus macaque. We therefore added evidence for expression in between one and five tissues to miRNAs that were previously annotated based only on homology to human miRNAs. We increased from 60 to 175 the number miRNAs that are located in orthologous regions in humans and the four non-human primate species studied here. Conclusions In this study we provide expression evidence for homology-based annotated miRNAs and predict de novo miRNAs in four non-human primate species. We increased the number of annotated miRNA genes and provided evidence for their expression in four non-human primates. Similar approaches using different individuals and tissues would improve annotation in non-human primates and allow for further comparative studies in the future. PMID:22453055

  18. 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

  19. 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. PMID:26799570

  20. 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

  1. 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

  2. A method for clustering of miRNA sequences using fragmented programming.

    PubMed

    Ivashchenko, Anatoly; Pyrkova, Anna; Niyazova, Raigul

    2016-01-01

    Clustering of miRNA sequences is an important problem in molecular genetics associated cellular biology. Thousands of such sequences are known today through advancement in sophisticated molecular tools, sequencing techniques, computational resources and rule based mathematical models. Analysis of such large-scale miRNA sequences for inferring patterns towards deducing cellular function is a great challenge in modern molecular biology. Therefore, it is of interest to develop mathematical models specific for miRNA sequences. The process is to group (cluster) such miRNA sequences using well-defined known features. We describe a method for clustering of miRNA sequences using fragmented programming. Subsequently, we illustrated the utility of the model using a dendrogram (a tree diagram) for publically known A.thaliana miRNA nucleotide sequences towards the inference of observed conserved patterns. PMID:27212839

  3. Circulating miRNAs in Ageing and Ageing-Related Diseases

    PubMed Central

    Jung, Hwa Jin; Suh, Yousin

    2015-01-01

    MicroRNAs (miRNAs) are small non-coding RNAs that negatively regulate gene expression at the post-transcriptional level. They are involved in important biological processes including development, homeostasis, and ageing. Recently, extracellular miRNAs have been discovered in the bloodstream and bodily fluids. These miRNAs are shown to be secreted and circulating in microvesicles (MVs), or in complex with other factors such as RNA-binding proteins and high-density lipoprotein (HDL) particles. These cell-free, circulating miRNAs can be taken into and function as negative regulators of target genes in recipient cells. Here we review the biogenesis and uptake of circulating miRNAs as well as their profiles in ageing and ageing-related diseases. We discuss the emerging role of circulating miRNAs as biomarkers and therapeutic targets. PMID:25269672

  4. New miRNA labeling method for bead-based quantification

    PubMed Central

    2010-01-01

    Background microRNAs (miRNAs) are small single-stranded non-coding RNAs that act as crucial regulators of gene expression. Different methods have been developed for miRNA expression profiling in order to better understand gene regulation in normal and pathological conditions. miRNAs expression values obtained from large scale methodologies such as microarrays still need a validation step with alternative technologies. Results Here we have applied with an innovative approach, the Luminex® xMAP™ technology validate expression data of differentially expressed miRNAs obtained from high throughput arrays. We have developed a novel labeling system of small RNA molecules (below 200 nt), optimizing the sensitive cloning method for miRNAs, termed miRNA amplification profiling (mRAP). The Luminex expression patterns of three miRNAs (miR-23a, miR-27a and miR-199a) in seven different cell lines have been validated by TaqMan miRNA assay. In all cases, bead-based meas were confirmed by the data obtained by TaqMan and microarray technologies. Conclusions We demonstrate that the measure of individual miRNA by the bead-based method is feasible, high speed, sensitive and low cost. The Luminex® xMAP™ technology also provides flexibility, since the central reaction can be scaled up with additional miRNA capturing beads, allowing validation of many differentially expressed miRNAs obtained from microarrays in a single experiment. We propose this technology as an alternative method to qRT-PCR for validating miRNAs expression data obtained with high-throughput technologies. PMID:20553585

  5. Dynamic regulation of novel and conserved miRNAs across various tissues of diverse Cucurbit spp.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  6. DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association.

    PubMed

    Maragkakis, Manolis; Vergoulis, Thanasis; Alexiou, Panagiotis; Reczko, Martin; Plomaritou, Kyriaki; Gousis, Mixail; Kourtis, Kornilios; Koziris, Nectarios; Dalamagas, Theodore; Hatzigeorgiou, Artemis G

    2011-07-01

    microRNAs (miRNAs) are small endogenous RNA molecules that are implicated in many biological processes through post-transcriptional regulation of gene expression. The DIANA-microT Web server provides a user-friendly interface for comprehensive computational analysis of miRNA targets in human and mouse. The server has now been extended to support predictions for two widely studied species: Drosophila melanogaster and Caenorhabditis elegans. In the updated version, the Web server enables the association of miRNAs to diseases through bibliographic analysis and provides insights for the potential involvement of miRNAs in biological processes. The nomenclature used to describe mature miRNAs along different miRBase versions has been extensively analyzed, and the naming history of each miRNA has been extracted. This enables the identification of miRNA publications regardless of possible nomenclature changes. User interaction has been further refined allowing users to save results that they wish to analyze further. A connection to the UCSC genome browser is now provided, enabling users to easily preview predicted binding sites in comparison to a wide array of genomic tracks, such as single nucleotide polymorphisms. The Web server is publicly accessible in www.microrna.gr/microT-v4. PMID:21551220

  7. 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. PMID:25897123

  8. Methylation of miRNA genes in the response to temperature stress in Populus simonii.

    PubMed

    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

  9. Global miRNA expression is temporally correlated with acute kidney injury in mice

    PubMed Central

    Chen, Xiao

    2016-01-01

    MicroRNAs (miRNAs) are negative regulators of gene expression and protein abundance. Current evidence shows an association of miRNAs with acute kidney injury (AKI) leading to substantially increased morbidity and mortality. Here, we investigated whether miRNAs are inductive regulators responsible for the pathological development of AKI. Microarray analysis was used to detect temporal changes in global miRNA expression within 48 h after AKI in mice. Results indicated that global miRNA expression gradually increased over 24 h from ischemia reperfusion injury after 24 h, and then decreased from 24 h to 48 h. A similar trend was observed for the index of tubulointerstitial injury and the level of serum creatinine, and there was a significant correlation between the level of total miRNA expression and the level of serum creatinine (p < 0.05). This expression-phenotype correlation was validated by quantitative reverse transcription PCR on individual miRNAs, including miR-18a, -134, -182, -210 and -214. Increased global miRNA expression may lead to widespread translational repression and reduced cellular activity. Furthermore, significant inflammatory cytokine release and peritubular capillary loss were observed, suggesting that the initiation of systematic destruction programs was due to AKI. Our findings provide new understanding of the dominant role of miRNAs in promoting the pathological development of AKI. PMID:26966664

  10. 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. PMID:25256277