RNA uridylation and decay in plants

RNA uridylation consists of the untemplated addition of uridines at the 3' extremity of an RNA molecule. RNA uridylation is catalysed by terminal uridylyltransferases (TUTases), which form a subgroup of the terminal nucleotidyltransferase family, to which poly(A) polymerases also belong. The key role of RNA uridylation is to regulate RNA degradation in a variety of eukaryotes, including fission yeast, plants and animals. In plants, RNA uridylation has been mostly studied in two model species, the green algae Chlamydomonas reinhardtii and the flowering plant Arabidopsis thaliana Plant TUTases target a variety of RNA substrates, differing in size and function. These RNA substrates include microRNAs (miRNAs), small interfering silencing RNAs (siRNAs), ribosomal RNAs (rRNAs), messenger RNAs (mRNAs) and mRNA fragments generated during post-transcriptional gene silencing. Viral RNAs can also get uridylated during plant infection. We describe here the evolutionary history of plant TUTases and we summarize the diverse molecular functions of uridylation during RNA degradation processes in plants. We also outline key points of future research.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.

Metabolic Profiling and Post-harvest Behavior of "Dottato" Fig (Ficus carica L.) Fruit Covered With an Edible Coating From O. ficus-indica

Fig fruits are usually highly sensitive to some physiopathological disorders during post-harvest life, such as softening and skin cracking. Indeed, the use of edible coating (EC) has been evaluated in several fruit crops to reduce fruit post-harvest transpiration and to maintain fruit visual quality. The aim of this study was to determine the post-harvest metabolic response of breba figs treated with mucilage extract from O puntia ficus-indica cladodes, using an untargeted metabolomic approach. Coated and non-coated (control) fruit were sealed in plastic bags, and stored at 4°C for 7 days. The effect of the ECs on their quality fruit during cold storage and qualitative attributes were evaluated by analyzing the fruit primary metabolism and other qualitative parameters such as total soluble solids (TSS) content, titratable acidity (TA), fresh weight loss and firmness. Results underlined that EC was effective in maintaining fruit fresh weight, and fruit firmness. Stepwise discriminant analysis was able to discriminate fruit conditions. Alanine, xylulose, aspartic acid, glutamic, acid and 2,5-dihydroxypyrazine showed a significant role on discriminating edible coated fruit from untreated ones. Principal component analysis (PCA) was able to highlight clear differences in the overall metabolism changes between untreated and treated fruit. The application of EC significantly mitigated the decrease of most of the aminoacid content during cold storage. EC treatment caused the changes of several organic acids in comparison to untreated control, increasing the amount of carbohydrates and other key metabolites, such as beta-sitosterol, glycerol, and uracil. These results clearly showed the drastic effects of EC on fig metabolism during post-harvest and shed light on the beneficial mechanisms of this treatment.

Identification of miRNAs linked with the drought response of tef [Eragrostis tef (Zucc.) Trotter]

Tef [Eragrostis tef (Zucc.) Trotter], a staple food crop in the Horn of Africa and particularly in Ethiopia, has several beneficial agronomical and nutritional properties, including waterlogging and drought tolerance. In this study, we performed microRNA profiling of tef using the Illumina HiSeq 2500 platform, analyzing both shoots and roots of two tef genotypes, one drought-tolerant (Tsedey) and one drought-susceptible (Alba). We obtained more than 10 million filtered reads for each of the 24 sequenced small cDNA libraries. Reads mapping to known miRNAs were more abundant in the root than shoot tissues. Thirteen and 35 miRNAs were significantly modulated in response to drought, in Alba and Tsedey roots, respectively. One miRNA was upregulated under drought conditions in both genotypes. In shoots, nine miRNAs were modulated in common between the two genotypes and all showed similar trends of expression. One-hundred and forty-seven new miRNA mature sequences were identified in silico, 22 of these were detected in all relevant samples and seven were differentially regulated when comparing drought with normal watering. Putative targets of the miRNA regulated under drought in root and shoot tissues were predicted. Among the targets were transcription factors such as CCAAT-HAP2, MADS and NAC. Verification with qRT-PCR revealed that five of six potential targets showed a pattern of expression that was consistent with the correspondent miRNA amount measured by RNA-Seq. In general, candidate miRNAs involved in the post-transcriptional regulation of the tef response to drought could be included in next-generation breeding programs.

The size, shape, density and ring of the dwarf planet Haumea from a stellar occultation

Haumea-one of the four known trans-Neptunian dwarf planets-is a very elongated and rapidly rotating body. In contrast to other dwarf planets, its size, shape, albedo and density are not well constrained. The Centaur Chariklo was the first body other than a giant planet known to have a ring system, and the Centaur Chiron was later found to possess something similar to Chariklo's rings. Here we report observations from multiple Earth-based observatories of Haumea passing in front of a distant star (a multi-chord stellar occultation). Secondary events observed around the main body of Haumea are consistent with the presence of a ring with an opacity of 0.5, width of 70 kilometres and radius of about 2,287 kilometres. The ring is coplanar with both Haumea's equator and the orbit of its satellite Hi'iaka. The radius of the ring places it close to the 3:1 mean-motion resonance with Haumea's spin period-that is, Haumea rotates three times on its axis in the time that a ring particle completes one revolution. The occultation by the main body provides an instantaneous elliptical projected shape with axes of about 1,704 kilometres and 1,138 kilometres. Combined with rotational light curves, the occultation constrains the three-dimensional orientation of Haumea and its triaxial shape, which is inconsistent with a homogeneous body in hydrostatic equilibrium. Haumea's largest axis is at least 2,322 kilometres, larger than previously thought, implying an upper limit for its density of 1,885 kilograms per cubic metre and a geometric albedo of 0.51, both smaller than previous estimates. In addition, this estimate of the density of Haumea is closer to that of Pluto than are previous estimates, in line with expectations. No global nitrogen- or methane-dominated atmosphere was detected.

Preferential myofibroblast differentiation of cardiac mesenchymal progenitor cells in the presence of atrial fibrillation

Atrial fibrillation (AF) is characterized by electrical, contractile, and structural remodeling mediated by interstitial fibrosis. It has been shown that human cardiac mesenchymal progenitor cells (CMPCs) can be differentiated into endothelial, smooth muscle, and fibroblast cells. Here, we have investigated, for the first time, the contribution of CMPCs in the fibrotic process occurring in AF. As expected, right auricolae samples displayed significantly higher fibrosis in AF vs control (CTR) patients. In tissue samples of AF patients only, double staining for c-kit and the myofibroblast marker α-smooth muscle actin (α-SMA) was detected. The number of c-kit-positive CMPC was higher in atrial subepicardial regions of CTR than AF cells. AF-derived CMPC (AF-CMPC) and CTR-derived CMPC (Ctr-CMPC) were phenotypically similar, except for CD90 and c-kit, which were significantly more present in AF and CTR cells, respectively. Moreover, AF showed a lower rate of population doubling and fold enrichment vs Ctr-CMPC. When exogenously challenged with the profibrotic transforming growth factor-β1 (TGF-β1), AF-CMPC showed a significantly higher nuclear translocation of SMAD2 than Ctr-CMPC. In addition, TGF-β1 treatment induced the upregulation of COL1A1 and COL1A2 in AF-CMPC only. Further, both a marked production of soluble collagen and α-SMA upregulation have been observed in AF-CMPC only. Finally, electrophysiological studies showed that the inwardly rectifying potassium current (I_K1) was evenly present in AF- and Ctr-CMPC in basal conditions and similarly disappeared after TGF-β1 exposure. All together, these data suggest that AF steers the resident atrial CMPC compartment toward an electrically inert profibrotic phenotype.

PSA Doubling Time as a Predictor of the Outcome of Random Prostate Biopsies Prompted by Isolated PSA Elevation in Subjects Referred to an Outpatient Biopsy Facility in a Routine Clinical Scenario

Aim

To assess the validity of PSA doubling time (PSADT) as a predictor of prostate sextant biopsy outcome in patients with PSA levels in the 4–10 ng/mL range.

Material and methods

A consecutive series of 355 sextant biopsies performed during 2001–2007 in subjects with negative digital rectal examination and transrectal ultrasonography was considered. Variables tested as possible predictors were age, total and free/total PSA value, PSA velocity and PSA doubling time. While PSA at time of biopsy and free/total PSA were determined with a standardized method undergoing strict quality control, previous PSA values used to assess velocity/doubling time came from other labs using different assays over widely varying intervals of time. The association with biopsy outcome (cancer vs non-cancer) was investigated by univariate and multivariate analysis.

Results

Apart from free/total PSA ratio, no other studied variable showed a statistically significant and independent association with biopsy outcome, either at univariate or multivariate analysis. No studied variable had a good performance as a biopsy indicator. Depending on the variable considered, 1.17 to 1.97 cancers would be missed to spare 10 benign biopsies.

Conclusion

When based on PSA data determined with different assays over widely varying intervals and in the absence of an underlying protocol for PSA surveillance, PSA velocity and doubling time should never discount a biopsy prompted by total PSA elevation.

Identifying Host Molecular Features Strongly Linked With Responses to Huanglongbing Disease in Citrus Leaves

A bioinformatic analysis of previously published RNA-Seq studies on Huanglongbing (HLB) response and tolerance in leaf tissues was performed. The aim was to identify genes commonly modulated between studies and genes, pathways and gene set categories strongly associated with this devastating Citrus disease. Bioinformatic analysis of expression data of four datasets present in NCBI provided 46-68 million reads with an alignment percentage of 72.95-86.76%. Only 16 HLB-regulated genes were commonly identified between the three leaf datasets. Among them were key genes encoding proteins involved in cell wall modification such as CESA8, pectinesterase, expansin8, expansin beta 3.1, and a pectate lyase. Fourteen HLB-regulated genes were in common between all four datasets. Gene set enrichment analysis showed some different gene categories affected by HLB disease. Although sucrose and starch metabolism was highly linked with disease symptoms, different genes were significantly regulated depending on leaf growth and infection stages and experimental conditions. Histone-related transcription factors were highly affected by HLB in the analyzed RNA-Seq datasets. HLB tolerance was linked with induction of proteins involved in detoxification. Protein-protein interaction (PPI) network analysis confirmed a possible role for heat shock proteins in curbing disease progression.

Effects of transgenic expression of Brevibacterium linens methionine gamma lyase (MGL) on accumulation of Tylenchulus semipenetrans and key aminoacid contents in Carrizo citrange

Carrizo transgenic plants overexpressing methionine-gamma-lyase produced dimethyl sulfide. The transgenic plants displayed more resistance to nematode attacks (Tylenculus semipenetrans) and may represent an innovative strategy for nematode control. Tylenchulus semipenetrans is a nematode pest of many citrus varieties that causes extensive damage to commercial crops worldwide. Carrizo citrange vr. (Citrus sinensis L. Usb × Poncirus trifoliate L. Raf) plants overexpressing Brevibacterium linens methionine-gamma-lyase (BlMGL) produced the sulfur volatile compound dimethyl sulfide (DMS). The aim of this work was to determine if transgenic citrus plants expressing BlMGL showed increased tolerance to T. semipenetrans infestation and to determine the effect on the content of key amino acids. While transgenic lines emitted dimethyl sulfide from leaves and roots, no sulfur-containing volatiles were detectable in wild-type Carrizo in the same tissues. Significant changes detected some key amino acids from leaves of transgenic plants such as aspartate, lysine, glycine, leucine and threonine with no changes in the amounts of methionine and α-ketobutyrate. In roots only glycine showed significant changes across all transgenic lines in comparison to wild-type plants. Transgenic plants expressing BlMGL and emitting DMS had less T. semipenetrans aggregation and more biomass than infected WT control plants, indicating that they may represent an innovative management alternative to pesticide/nematicide-based remedies.

Arbuscular mycorrhizal symbiosis mitigates the negative effects of salinity on durum wheat

Arbuscular mycorrhizal (AM) symbiosis is generally considered to be effective in ameliorating the plant tolerance to salt stress. Unfortunately, the comprehension of the mechanisms implicated in salinity stress alleviation by AM symbiosis is far from being complete. Thus, an experiment was performed by growing durum wheat (Triticum durum Desf.) plants under salt-stress conditions to evaluate the influence of AM symbiosis on both the plant growth and the regulation of a number of genes related to salt stress and nutrient uptake. Durum wheat plants were grown outdoors in pots in absence or in presence of salt stress and with or without AM fungi inoculation. The inoculum consisted of a mixture of spores of Rhizophagus irregularis (formerly Glomus intraradices) and Funneliformis mosseae (formerly G. mosseae). Results indicate that AM symbiosis can alleviate the detrimental effects of salt stress on the growth of durum wheat plants. In fact, under salt stress conditions mycorrhizal plants produced more aboveground and root biomass, had higher N uptake and aboveground N concentration, and showed greater stability of plasma membranes compared to non-mycorrhizal plants. Inoculation with AM fungi had no effect on the expression of the N transporter genes AMT1.1, AMT1.2, and NAR2.2, either under no-stress or salt stress conditions, probably due to the fact that plants were grown under optimal N conditions; on the contrary, NRT1.1 was always upregulated by AM symbiosis. Moreover, the level of expression of the drought stress-related genes AQP1, AQP4, PIP1, DREB5, and DHN15.3 observed in the mycorrhizal stressed plants was markedly lower than that observed in the non-mycorrhizal stressed plants and very close to that observed in the non-stressed plants. Our hypothesis is that, in the present study, AM symbiosis did not increase the plant tolerance to salt stress but instead generated a condition in which plants were subjected to a level of salt stress lower than that of non-mycorrhizal plants.

Left atrial ball thrombus after edge-to-edge mitral valve repair

A thrombus can develop in the left atrium during atrial fibrillation because the loss of contractile function leads to blood flow stasis. Anticoagulation therapy is indicated for prevention of systemic embolism, usually maintaining an international normalized ratio between 2 and 3. Rarely a massive thrombosis develops in the atrium resulting in a peduncolated ball valve thrombus or in a free-floating thrombus. These two conditions are characterized by variables in the physical findings. Such masses are hazardous and upon discovery surgical treatment, often in emergency, is mandatory. We present here the case of a patient who developed an unnoticed huge left atrial ball thrombus despite warfarin therapy after previous mitral valve surgery. <Learning objective: Risk of atrial thrombosis threatens patients suffering from atrial fibrillation. The presence of a ring and a modified valve anatomy following a surgical repair could represent an additional drive in the thrombus formation pathway. A free-floating ball thrombus in the left atrium is an unusual occurrence that may cause fatal systemic emboli or left ventricular inflow obstruction, often resulting in sudden death. In such cases, even in the absence of symptoms, prompt surgical excision is recommended.>.

Gaining Insight into Exclusive and Common Transcriptomic Features Linked with Biotic Stress Responses in Malus

Identifying key information in transcriptomic data is very important, especially when the "omic" study deals with plant responses to stresses in field conditions where a high number of variables and disturbing factors may affect the analysis. In this meta-analysis we collected 12 transcriptomic works in Malus in order to identify which key genes, proteins, gene categories are involved in general plant pathological conditions and those features linked with exclusive biotic stress responses. Those genes that are only related with molecular responses to pathogen attacks and those linked with other plant physiological processes were identified. A pipeline composed by pathway and gene set enrichment analysis, protein-protein interaction networks and gene visualization tools was employed. A total of 13,230 genes of the 12 studies were analyzed with functional data mining tools: 5,215 were upregulated, 8,015 were downregulated. Gene set enrichment analysis pointed out that photosynthesis was inhibited by Erwinia amylovora and fungal pathogens. Different hormonal crosstalk was linked with responses to different pathogens. Gibberellin-related pathways, ABA-related were mostly repressed by fungal pathogens. Relating to transcription factors, genes encoding MYBs and WRKY2 were downregulated by fungal pathogens and 12 WRKYs were commonly regulated by different biotic stresses The protein-protein interaction analysis discovered the presence of several proteins affected by more than one biotic stress including a WRKY40 and some highly interactive proteins such as heat shock proteins. This study represents a first preliminary curated meta-analysis of apple transcriptomic responses to biotic stresses.