Towards Establishment of a Rice Stress Response Interactome

Rice (Oryza sativa) is a staple food for more than half the world and a model for studies of monocotyledonous species, which include cereal crops and candidate bioenergy grasses. A major limitation of crop production is imposed by a suite of abiotic and biotic stresses resulting in 30%–60% yield losses globally each year. To elucidate stress response signaling networks, we constructed an interactome of 100 proteins by yeast two-hybrid (Y2H) assays around key regulators of the rice biotic and abiotic stress responses. We validated the interactome using protein–protein interaction (PPI) assays, co-expression of transcripts, and phenotypic analyses. Using this interactome-guided prediction and phenotype validation, we identified ten novel regulators of stress tolerance, including two from protein classes not previously known to function in stress responses. Several lines of evidence support cross-talk between biotic and abiotic stress responses. The combination of focused interactome and systems analyses described here represents significant progress toward elucidating the molecular basis of traits of agronomic importance

Refinement of Light-Responsive Transcript Lists Using Rice Oligonucleotide Arrays: Evaluation of Gene-Redundancy

Studies of gene function are often hampered by gene-redundancy, especially in organisms with large genomes such as rice (Oryza sativa). We present an approach for using transcriptomics data to focus functional studies and address redundancy. To this end, we have constructed and validated an inexpensive and publicly available rice oligonucleotide near-whole genome array, called the rice NSF45K array. We generated expression profiles for light- vs. dark-grown rice leaf tissue and validated the biological significance of the data by analyzing sources of variation and confirming expression trends with reverse transcription polymerase chain reaction. We examined trends in the data by evaluating enrichment of gene ontology terms at multiple false discovery rate thresholds. To compare data generated with the NSF45K array with published results, we developed publicly available, web-based tools (www.ricearray.org). The Oligo and EST Anatomy Viewer enables visualization of EST-based expression profiling data for all genes on the array. The Rice Multi-platform Microarray Search Tool facilitates comparison of gene expression profiles across multiple rice microarray platforms. Finally, we incorporated gene expression and biochemical pathway data to reduce the number of candidate gene products putatively participating in the eight steps of the photorespiration pathway from 52 to 10, based on expression levels of putatively functionally redundant genes. We confirmed the efficacy of this method to cope with redundancy by correctly predicting participation in photorespiration of a gene with five paralogs. Applying these methods will accelerate rice functional genomics

Circ_0088036 facilitates the proliferation and inflammation and inhibits the apoptosis of fibroblast-like synoviocytes through targeting miR-326/FZD4 axis in rheumatoid arthritis

Background The function and pathological significance of circular RNAs (circRNAs) in autoimmune diseases, such as rheumatoid arthritis (RA), are barely known. Here, we explored the role of circ_0088036 in RA progression and its associated mechanism. Methods The synovial lining layer tissues of RA patients and non-RA control patients were collected for clinical study in vivo, and tumour necrosis factor α (TNF-α)-induced RA-fibroblast-like synoviocytes (RA-FLSs) were used for the experiments in vitro. Cell proliferation was assessed by Cell Counting Kit 8 (CCK8) assay and flow cytometry. Cell apoptosis was analyzed by flow cytometry. Enzyme-linked immunosorbent assay (ELISA) was conducted to analyze the release of pro-inflammatory cytokines. Dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay were performed to verify the target interaction between microRNA-326 (miR-326) and circ_0088036 or frizzled class receptor 4 (FZD4). Results Circ_0088036 expression was elevated in the synovial lining layer tissues of RA patients and TNF-α-treated RA-FLSs. Circ_0088036 interference largely reversed TNF-α-induced proliferation and inflammation in RA-FLSs. The interaction between circ_0088036 and miR-326 was verified, and miR-326 silencing largely reversed circ_0088036 knockdown-mediated effects in TNF-α-treated RA-FLSs. MiR-326 bound to the 3’ untranslated region (3’UTR) of FZD4 in RA-FLSs. FZD4 overexpression largely diminished miR-326 accumulation-mediated influences in TNF-α-treated RA-FLSs. Circ_0088036 could up-regulate FZD4 by sponging miR-326 in RA-FLSs. Conclusion Circ_0088036 contributed to TNF-α-induced RA progression partly by targeting miR-326/FZD4 signalling

Comparison of Leaf Shape between a <i>Photinia</i> Hybrid and One of Its Parents

Leaf shape and size can vary between hybrids and their parents. However, this has seldom been quantitatively tested. Photinia × fraseri is an important landscaping plant in East Asia as a hybrid between evergreen shrubs P. glabra and P. serratifolia. Its leaf shape looks like that of P. serratifolia. To investigate leaf shape, we used a general equation for calculating the leaf area (A) of broad-leaved plants, which assumes a proportional relationship between A and product of lamina length (L) and width (W). The proportionality coefficient (which is referred to as the Montgomery parameter) serves as a quantitative indicator of leaf shape, because it reflects the proportion of leaf area A to the area of a rectangle with L and W as its side lengths. The ratio of L to W, and the ellipticalness index were also used to quantify the complexity of leaf shape for elliptical leaves. A total of >4000 leaves from P. × fraseri and P. serratifolia (with >2000 leaves for each taxon) collected on a monthly basis was used to examine: (i) whether there is a significant difference in leaf shape between the two taxa, and (ii) whether there is a monotonic or parabolic trend in leaf shape across leaf ages. There was a significant difference in leaf shape between the two taxa (p P. serratifolia, which has wider and more elliptical leaves than the hybrid. This work demonstrates that variations in leaf shape resulting from hybridization can be rigorously quantified and compared among species and their hybrids. In addition, this work shows that leaf shape does not changes as a function of age either before or after the full expansion of the lamina

The Relationship between Seven Common Polymorphisms from Five DNA Repair Genes and the Risk for Breast Cancer in Northern Chinese Women

<div><p>Background</p><p>Converging evidence supports the central role of DNA damage in progression to breast cancer. We therefore in this study aimed to assess the potential interactions of seven common polymorphisms from five DNA repair genes (XRCC1, XRCC2, XRCC3, XPA and APEX1) in association with breast cancer among Han Chinese women.</p><p>Methodology/Principal Findings</p><p>This was a case-control study involving 606 patients diagnosed with sporadic breast cancer and 633 age- and ethnicity-matched cancer-free controls. The polymerase chain reaction - ligase detection reaction method was used to determine genotypes. All seven polymorphisms were in accordance with Hardy-Weinberg equilibrium in controls. Differences in the genotypes and alleles of XRCC1 gene rs25487 and XPA gene rs1800975 were statistically significant between patients and controls, even after the Bonferroni correction (P<0.05/7). Accordingly, the risk for breast cancer was remarkably increased for rs25487 (OR = 1.28; 95% CI: 1.07–1.51; P = 0.006), but decreased for rs1800975 (OR = 0.77; 95% CI: 0.67–0.90; P = 0.001) under an additive model at a Bonferroni corrected alpha of 0.05/7. Allele combination analysis showed higher frequencies of the most common combination C-G-G-C-G-G-G (alleles in order of rs1799782, rs25487, rs3218536, rs861539, rs1800975, rs1760944 and rs1130409) in controls than in patients (P_Sim = 0.002). In further interaction analysis, two-locus model including rs1800975 and rs25487 was deemed as the overall best model with the maximal testing accuracy of 0.654 and the cross-validation consistency of 10 out of 10 (P = 0.001).</p><p>Conclusion</p><p>Our findings provide clear evidence that XRCC1 gene rs25487 and XPA gene rs1800975 might exert both independent and interactive effects on the development of breast cancer among northern Chinese women.</p></div

Summary of multifactor dimensionality reduction (MDR) analysis.

<p><i>Abbreviations</i>: CVC, cross-validation consistency. *The overall best MDR model.</p

The allele combinations of seven polymorphisms under study between breast cancer patients and controls.

<p>*Alleles were arranged according to rs1799782, rs25487, rs3218536, rs861539, rs1800975, rs1760944 and rs1130409.</p