Vesicle trafficking in rice: too little is known

The vesicle trafficking apparatus is a fundamental machinery to maintain the homeostasis of membrane-enclosed organelles in eukaryotic cells. Thus, it is broadly conserved in eukaryotes including plants. Intensive studies in the model organisms have produced a comprehensive picture of vesicle trafficking in yeast and human. However, with respect to the vesicle trafficking of plants including rice, our understanding of the components and their coordinated regulation is very limited. At present, several vesicle trafficking apparatus components and cargo proteins have been identified and characterized in rice, but there still remain large unknowns concerning the organization and function of the rice vesicle trafficking system. In this review, we outline the main vesicle trafficking pathways of rice based on knowledge obtained in model organisms, and summarize current advances of rice vesicle trafficking. We also propose to develop methodologies applicable to rice and even other crops for further exploring the mysteries of vesicle trafficking in plants

Correction: Analysis of Cytoplasmic Effects and Fine-Mapping of a Genic Male Sterile Line in Rice.

[This corrects the article DOI: 10.1371/journal.pone.0061719.]

Implications of false negative and false positive diagnosis in lymph node staging of NSCLC by means of ¹⁸F-FDG PET/CT.

BACKGROUND:Integrated ¹⁸F-fluorodeoxyglucose positron emission tomography/computed tomography (¹⁸F-FDG PET/CT) is widely performed in hilar and mediastinal lymph node (HMLN) staging of non-small cell lung cancer (NSCLC). However, the diagnostic efficiency of PET/CT remains controversial. This retrospective study is to evaluate the accuracy of PET/CT and the characteristics of false negatives and false positives to improve specificity and sensitivity. METHODS:219 NSCLC patients with systematic lymph node dissection or sampling underwent preoperative PET/CT scan. Nodal uptake with a maximum standardized uptake value (SUV(max)) >2.5 was interpreted as PET/CT positive. The results of PET/CT were compared with the histopathological findings. The receiver operating characteristic (ROC) curve was generated to determine the diagnostic efficiency of PET/CT. Univariate and multivariate analysis were conducted to detect risk factors of false negatives and false positives. RESULTS:The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy of PET/CT in detecting HMLN metastases were 74.2% (49/66), 73.2% (112/153), 54.4% (49/90), 86.8% (112/129), and 73.5% (161/219). The ROC curve had an area under curve (AUC) of 0.791 (95% CI 0.723-0.860). The incidence of false negative HMLN metastases was 13.2% (17 of 129 patients). Factors that are significantly associated with false negatives are: concurrent lung disease or diabetes (p<0.001), non-adenocarcinoma (p<0.001), and SUV(max) of primary tumor >4.0 (p=0.009). Postoperatively, 45.5% (41/90) patients were confirmed as false positive cases. The univariate analysis indicated age > 65 years old (p=0.009), well differentiation (p=0.002), and SUV(max) of primary tumor ≦4.0 (p=0.007) as risk factors for false positive uptake. CONCLUSION:The SUV(max) of HMLN is a predictor of malignancy. Lymph node staging using PET/CT is far from equal to pathological staging account of some risk factors. This study may provide some aids to pre-therapy evaluation and decision-making

Analysis of Cytoplasmic Effects and Fine-Mapping of a Genic Male Sterile Line in Rice

<div><p>Cytoplasm has substantial genetic effects on progeny and is important for yield improvement in rice breeding. Studies on the cytoplasmic effects of cytoplasmic male sterility (CMS) show that most types of CMS have negative effects on yield-related traits and that these negative effects vary among CMS. Some types of genic male sterility (GMS), including photo-thermo sensitive male sterility (PTMS), have been widely used in rice breeding, but the cytoplasmic effects of GMS remain unknown. Here, we identified a GMS mutant line, <i>h₂s</i>, which exhibited small, white anthers and failed to produce mature pollen. Unlike CMS, the <i>h₂s</i> had significant positive cytoplasmic effects on the seed set rate, weight per panicle, yield, and general combining ability (GCA) for plant height, seed set rate, weight per panicle, and yield. These effects indicated that <i>h₂s</i> cytoplasm may show promise for the improvement of rice yield. Genetic analysis suggested that the phenotype of <i>h₂s</i> was controlled by a single recessive locus. We mapped <i>h₂s</i> to a 152 kb region on chromosome 6, where 22 candidate genes were predicted. None of the 22 genes had previously been reported to be responsible for the phenotypes of <i>h₂s</i>. Sequencing analysis showed a 12 bp deletion in the sixth exon of <i>Loc_Os06g40550</i> in <i>h₂s</i> in comparison to wild type, suggesting that <i>Loc_Os06g40550</i> is the best candidate gene. These results lay a strong foundation for cloning of the <i>H₂S</i> gene to elucidate the molecular mechanism of male reproduction.</p> </div

Down-Regulation of OsEMF2b Caused Semi-sterility Due to Anther and Pollen Development Defects in Rice

Anther and pollen development are crucial processes of plant male reproduction. Although a number of genes involved in these processes have been identified, the regulatory networks of pollen and anther development are still unclear. EMBRYONIC FLOWER 2b (OsEMF2b) is important for rice development. Its biological function in floral organ, flowering time and meristem determinacy have been well-studied, but its role, if only, on male reproduction is still unknown, because null mutants of OsEMF2b barely have anthers. In this study, we identified a weak allele of OsEMF2b, osemf2b-4. The T-DNA insertion was located in the promoter region of OsEMF2b, and OsEMF2b expression was significantly decreased in osemf2b-4. The osemf2b-4 mutant exhibited much more normal anthers than null mutants of OsEMF2b, and also showed defective floret development similar to null mutants. Cytological analysis showed various defects of anther wall and pollen development in osemf2b-4, such as slightly or extremely enlarged tapetum, irregular or normal morphology microspores, and partial or complete sterility. OsEMF2b was highly expressed in tapetum and microspores, and the protein was localized in the nucleus. The expression of 15 genes essential for anther and pollen development was investigated in both WT and osemf2b-4. Fourteen genes including GAMYB was up-regulated, and only PTC1 was down-regulated in osemf2b-4. This suggests that up-regulated GAMYB and down-regulated PTC1 might contribute to the defective anther and pollen development in osemf2b-4. Overall, our work suggests that OsEMF2b plays an essential role during post-meiotic anther and pollen development

<i>h₂s</i> cytoplasmic effects on seed set rate, weight/panicle and yield in comparison with Zhenshan97A (A2), D702A (A3), G46A (A4), K18A (A5) and XieqingzaoA (A6).

<p>The numbers separated by slashes represent data from different years, 2006 (left) and 2008 (right). *and **Significant at 0.05 and 0.01 probability level, respectively.</p

GCA effects on seed set rate, weight per panicle and yield among cytoplasms of <i>h₂s</i> (A1), Zhenshan97A (A2), D702A (A3), G46A (A4), K18A (A5) and XieqingzaoA (A6).

<p>The numbers separated by slashes represent the data from different years, 2006 (left) and 2008 (right). Values followed by the same letter in a column within a year are not significantly different at α = 0.05.</p

DAPI staining analysis for the meiosis of microspore mother cells and mitosis of young microspores between the wild type (WT) and <i>h₂s</i>.

<p>(A–I) and (K–S) for WT, (B–J) and (L–T) for <i>h₂s</i>; (A) and (B) Pachytene, (C) and (D) diakinesis, (E) and (F) metaphase I, (G) and (H) anaphase I, (I) and (J) telophase I, (K) and (L) prophase II, (M) and (N) metaphase II, (O) and (P) tetrad, (Q) and (R) young microspore stage, and (S) and (T) vacuolated pollen stage. No difference in the process of meiosis was observed between WT and <i>h2s</i>. Bars = 10 µm.</p

Candidate genes in the 154 kb region on chromosome 6 where <i>h₂s</i> locus was fine mapped.

*<p>expressed in inflorescence.</p