When rice gets the chills: comparative transcriptome profiling at germination shows WRKY transcription factor responses

Rice is vital for food security. Due to its tropical origin, rice suffers from cold temperatures that affect its entire life cycle. Key genes have been identified involved in cold tolerance. WRKYs are generally downstream of the MAPK cascade and can act together with VQ proteins to regulate stress-responsive genes. Chilling treatment was applied at germination to two rice genotypes (tolerant and sensitive). Shoots at S3 stage were collected for RNA-seq to identify OsWRKY, OsMAPKs and OsVQs expression. Relationships among MAPKs, WRKYs and VQs were predicted through correlation analysis. OsWRKY transcriptional regulation was predicted by in silico analysis of cis-regulatory elements. A total of 39 OsWRKYs were differentially expressed. OsWRKY21, OsWRK24 and OsWRKY69 are potential positive regulators, while OsWRKY10, OsWRK47, OsWRKY62, OsWRKY72 and OsWRKY77 are potential negative regulators, of chilling tolerance. 12 OsMAPKs were differentially expressed. OsMAPKs were downregulated and negatively correlated with the upregulated OsWRKYs in the tolerant genotype. 19 OsVQs were differentially expressed, three and six OsVQs were positively correlated with OsWRKYs in the tolerant and sensitive genotypes, respectively. Seven differentially expressed OsWRKYs have cold-responsive elements in their promoters and five upregulated OsWRKYs in the tolerant genotype contained the W-box motif. Chilling causes changes in OsWRKY, OsMAPK and OsVQ gene expression at germination. OsWRKYs may not act downstream of the MAPK cascade to coordinate chilling tolerance, but OsWRKYs may act with VQs to regulate chilling tolerance. Candidate OsWRKYs are correlated and have a W-box in the promoter, suggesting an auto-regulation mechanism.

Iron excess in rice: from phenotypic changes to functional genomics of WRKY transcription factors

Iron (Fe) is an essential microelement for all living organisms playing important roles in several metabolic reactions. Rice (Oryza sativa L.) is commonly cultivated in paddy fields, where Fe goes through a reduction reaction from Fe³⁺ to Fe²⁺. Since Fe²⁺ is more soluble, it can reach toxic levels inside plant cells, constituting an important target for studies. Here we aimed to verify morphological changes of different rice genotypes focusing on deciphering the underlying molecular network induced upon Fe excess treatments with special emphasis on the role of four WRKY transcription factors. The transcriptional response peak of these WRKY transcription factors in rice seedlings occurs at 4 days of exposition to iron excess. OsWRKY55-like, OsWRKY46, OsWRKY64, and OsWRKY113 are up-regulated in BR IRGA 409, an iron-sensitive genotype, while in cultivars Nipponbare (moderately resistant) and EPAGRI 108 (resistant) the expression profiles of these transcription factors show similar behaviors. Here is also shown that some cis-regulatory elements known to be involved in other different stress responses can be linked to conditions of iron excess. Overall, here we support the role of WRKY transcription factors in iron stress tolerance with other important steps toward finding why some rice genotypes are more tolerant than others.

Identification and characterization of the bZIP transcription factor involved in zinc homeostasis in cereals

Members of the basic leucine zipper family, as bZIP19, are considered to be essential regulators of the adaptation to zinc deficiency. Knowing that this gene as well as its targets are conserved in the plant kingdom, we followed an in silico approach to identify and characterize the bzip19 gene in cereals. Through BLASTp in Phytozome database, 33 bzip19 genes were identified on the genomes of Oryza sativa, Sorghum bicolor, Zea mays, Glycine max, Triticum aestivum, and Brachypodium distachyon. The analysis of conserved motifs and bZIP domains was performed using MEME and PFAM databases. In 25 of these genes, CysHis-motifs at the basic N-terminal region were found. This motif is conserved in group bZIP and suggested to play a role as a Zn-sensor. Regarding their phylogeny, it was possible to infer orthologous groups and explore the evolutionary relationship between these BZIP19 proteins. Data mining allowed us to select eight putative orthologous whose expression profile was analyzed under stress conditions in the Genevestigator platform. The comparison between the expression profiles of these eight putative orthologous and the original Arabidopsis bzip19 also seems to indicate conserved transcriptional regulation. Thus, considering that modified expression of bZIP19 genes has already been confirmed as an efficient tool to improve Arabidopsis tolerance to Zn deficiency, and that these new bZIP orthologous have a high level of conservation when compared to the original bZIP19 sequence, they can be useful for the development of tolerant crops enabling plants to grow in areas of low zinc bioavailability.

Relationships between four measures of genetic distance and breeding behavior in spring wheat

We estimated the genetic distances among 10 spring wheat genotypes based on pedigree data, morphological traits and AFLP markers, used individually and combined with morphological traits, to find the best predictors of general- and specific-combining abilities among parental genotypes. Ten wheat parents were crossed in a diallel form, disregarding reciprocal hybrids, totaling 45 combinations. The F₁ hybrids, F₂ populations and parents were evaluated in the field in 2007. The experimental plots consisted of 20 plants for F₁ hybrids and 40 plants for parental and F₂ populations. All methods (pedigree data, AFLP markers and morphological traits, used individually and combined) were found to be useful for the assessment of genetic diversity. The significant coefficient correlations ranged from low (0.45) to moderate (0.67) between the distance measures and hybrid performance. There was significant agreement between the distance measures based on AFLP markers vs morphological traits + AFLP markers (r = 0.47) and between pedigree data vs morphological traits + AFLP markers (r = 0.43). The pedigree distance was positively associated with traits 100-kernel weight and grain yield per plant in F₁ (correlations of 0.67 and 0.62, respectively) and F₂ (correlations of 0.62 and 0.59, respectively) generations. These correlation values indicate that the genetic distance, based on pedigree data, could replace diallel crosses for the selection of parents with higher combining ability and with moderate reliability.

Short-term effect of leflunomide in patients with Takayasu arteritis: an observational study

OBJECTIVES

To evaluate the efficacy of leflunomide in controlling disease activity in patients with Takayasu arteritis (TA) refractory or intolerant to conventional treatment.

METHODS

We conducted a prospective open-label study of 15 TA patients (mean age 36.2 years) with active disease based on clinical assessment, erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), and magnetic resonance angiography (MRA). Patients received leflunomide 20 mg/day for at least 6 months and were followed up for a mean of 9.1 months. Adverse events attributable to leflunomide were recorded.

RESULTS

At baseline, 14 TA patients had active disease despite therapy with corticosteroids and immunosuppressive agents, while one patient had intolerance to current treatment. In the follow-up visit, we found a significant decrease in the frequency of patients with active TA (93% vs. 20%, p = 0.002), in the mean daily dose of prednisone (34.2 vs. 13.9 mg, p < 0.001) and in the median values of ESR (29.0 vs. 27.0 mm/h, p = 0.012) and CRP (10.3 vs. 5.3 mg/L, p = 0.012). Two patients (13.3%) developed new angiographic lesions in the follow-up MRA. Three patients (20%) experienced mild adverse events during the study and none discontinued therapy.

CONCLUSIONS

This is the first open-label study to demonstrate improvement in disease activity and acute phase reactants with 20 mg/day of leflunomide in TA patients who were refractory or intolerant to conventional therapy with corticosteroids and immunosuppressive agents. Leflunomide was safe and a steroid-sparing effect was observed. A double-blind controlled study is desirable to confirm this finding.

Virulence Variability of Puccinia coronata f. sp. avenae Isolates Collected in Three Counties from Rio Grande do Sul State, Brazil

Using isolates collected in three counties of Rio Grande do Sul State, Brazil, the goals of this work were to determine (i) the pattern of virulence or avirulence of the isolates to 25 Pc resistance genes, (ii) the similarity in virulence among Puccinia coronata f. sp. avenae isolates considering their pattern of virulence or avirulence, (iii) the race code for each isolate by the North American system of nomenclature, and (iv) the supplemental Pc genes potentially useful as local differentials for P. coronata f. sp. avenae races. The results indicate that the southern Brazilian rust isolates presented a high level of virulence, because 66% of inoculations manifested the high infection type. Only the Pc 68 gene was effective against all tested isolates. In general, each isolate presented a different pattern of virulence or avirulence, which indicates the high variability for virulence that the fungus presents at the sampled sites. However, the North American system of nomenclature was not completely sufficient in distinguishing southern Brazilian races. Thus, the genes Pc 36, Pc 53, Pc 55, and Pc 63 represent a possible gene combination to be incorporated into the North American system of nomenclature.

The Hybaid Lecture. Microcollinearity and segmental duplication in the evolution of grass nuclear genomes

Recent studies have shown that grass genomes have very similar gene compositions and regions of conserved gene order, as exemplified by collinear genetic maps of DNA markers. We have begun the detailed study of sequence organization in large (100-500 kb) segments of the nuclear genomes of maize, sorghum and rice. Our results indicate collinearity of genes in the regions homoeologous to the maize adh1 and sh2-a1 genes. Comparable genes were found to be physically closer to each other in grasses with small genomes (rice and sorghum) than they are in maize. In several instances, we have found evidence of tandem and 'distantly tandem' duplications of segments containing maize and sorghum genes. These duplications complicate characterizations of microcollinearity and could also interfere with some map-based approaches to gene isolation.

Effect of diets containing dry beans (Phaseolus vulgaris, L.) on the rat excretion of endogenous nitrogen

Wistar rats of 60.5 +/- 5.0 g fasted for 24 h were injected intraperitoneally with 10 microCi of [14C]glycine. One to two hours after injection the rats were fed a diet containing 10.53 +/- 0.75% protein provided by dry beans or casein, or a protein-free diet and submitted to a 4-d nitrogen balance. Radioactivity in the feces of rats fed casein, cooked beans and raw beans was roughly 2, 5 and 10 times greater, respectively, than in the feces of those fed the protein-free diet. Apparent protein digestibility showed a strong negative linear correlation (r = -0.9805, P less than or equal to 0.01) with radioactivity in the feces. Positive correlation (P less than or equal to 0.01) was demonstrated between radioactivity and either total carbon or total nitrogen in the feces of rats injected with [14C]glycine. Mean value for the radioactivity in the urine of rats fed the different diets did not differ significantly (P less than or equal to 0.05). Endogenous nitrogen excretion of rats on bean diets was estimated by the ratio of total endogenous N to marker N, based on the protein-free diet. The results indicated that rats fed bean-containing diets excreted significantly more endogenous nitrogen than those fed the casein diet, even though the casein diet had stimulated twice as much endogenous excretion than the protein-free diet. As a consequence, apparent digestibility and biological value of bean protein are generally underestimated, although the "real" biological value was not affected by the endogenous nitrogen excretion of the rat.