Seed Coat Microsculpturing Is Related to Genomic Components in Wild Brassica juncea and Sinapis arvensis

It has been reported that wild Brassica and related species are widely distributed across Xinjiang, China, and there has been an argument for species identification. Seed coat microsculpturing (SCM) is known to be an excellent character for taxonomic and evolutionary studies. By identifying collections from Xinjiang, China, and combining SCM pattern, flow cytometry, and genome-specific DNA markers as well as sexual compatibility with known species, this study aimed to detect potential relationships between SCM and genomic types in wild Brassica and related species. Three wild collections were found to be tetraploid with a SCM reticulate pattern similar to B. juncea, and containing A and B genome-specific loci, indicating relatively high sexual compatibility with B. juncea. The others were diploid, carrying S-genome-specific DNA markers, and having relatively high sexual compatibility with Sinapis arvensis. Moreover, their SCM was in a rugose pattern similar to that of S. arvensis. It was suggested that SCM, as a morphological characteristic, can reflect genomic type, and be used to distinguish B-genome species such as B. juncea from the related S. arvensis. The relationship between SCM and genomic type can support taxonomic studies of the wild Brassica species and related species.     

Cytokinin as a Possible Component of the Floral Stimulus in Sinapis alba

Results of previous investigations indicated that one of the early and essential events occurring in the apical meristem of Sinapis alba L. during the transition to flowering is the release to mitosis of the G₂ nuclei; the trigger to mitosis is generated in the leaves and its movement out of the leaves begins around 16 hours after the start of the inductive treatment. The mitotic wave in the meristem culminates 10 hours later.     

被子植物的花器官发育和功能基因活性模式的建立

文章介绍了被子植物花器官特征属性决定的分子机制研究进展。     

Levels and Ultrastructural Localization of Calcium in Sinapis alba during the Floral Transition

Atomic absorption spectrophotometry was used to determine thetotal amount of Ca in the leaves and apical bud of the long-dayplant Sinapis alba during the floral transition induced by asingle long day. The level of Ca increased in the apical budbut did not change significantly in the leaves. Ca was furtherlocalized cytochemically and measured in the meristem cellsby X-ray microprobe analysis. In the meristem, the level ofCa was found to increase in all cellular compartments, but mainlyin the nucleolus. The results are discussed in relation to otherevents that are known to occur in the meristem during the floraltransition. (Received July 19, 1988; Accepted January 24, 1989)     

RNA-Seq Reveals Dynamic Changes of Gene Expression in Key Stages of Intestine Regeneration in the Sea Cucumber Apostichopus japonicas

Background

Sea cucumbers (Holothuroidea; Echinodermata) have the capacity to regenerate lost tissues and organs. Although the histological and cytological aspects of intestine regeneration have been extensively studied, little is known of the genetic mechanisms involved. There has, however, been a renewed effort to develop a database of Expressed Sequence Tags (ESTs) in Apostichopus japonicus, an economically-important species that occurs in China. This is important for studies on genetic breeding, molecular markers and special physiological phenomena. We have also constructed a library of ESTs obtained from the regenerative body wall and intestine of A. japonicus. The database has increased to ∼30000 ESTs.

Results

We used RNA-Seq to determine gene expression profiles associated with intestinal regeneration in A. japonicus at 3, 7, 14 and 21 days post evisceration (dpe). This was compared to profiles obtained from a normally-functioning intestine. Approximately 5 million (M) reads were sequenced in every library. Over 2400 up-regulated genes (>10%) and over 1000 down-regulated genes (∼5%) were observed at 3 and 7dpe (log₂Ratio≥1, FDR≤0.001). Specific “Go terms” revealed that the DEGs (Differentially Expressed Genes) performed an important function at every regeneration stage. Besides some expected pathways (for example, Ribosome and Spliceosome pathway term), the “Notch signaling pathway,” the “ECM-receptor interaction” and the “Cytokine-cytokine receptor interaction” were significantly enriched. We also investigated the expression profiles of developmental genes, ECM-associated genes and Cytoskeletal genes. Twenty of the most important differentially expressed genes (DEGs) were verified by Real-time PCR, which resulted in a trend concordance of almost 100% between the two techniques.

Conclusion

Our studies demonstrated dynamic changes in global gene expression during intestine regeneration and presented a series of candidate genes and enriched pathways that contribute to intestine regeneration in sea cucumbers. This provides a foundation for future studies on the genetics/molecular mechanisms associated with intestine regeneration.     

Cytokinin Fluxes during Floral Induction in the Long Day Plant Sinapis alba L

Sinapis alba is a long-day (LD) plant that can be induced to flower by a single LD. A number of changes normally occurring in the meristem of plants subjected to the LD can be produced in short day by a single application of a cytokinin to the apical bud. However, flower buds are not produced indicating that evocation by the cytokinin is only partial. In this work, the cytokinin content of root exudate, obtained under vacuum, and of leaf exudate, obtained by the EDTA-method, has been analyzed comparatively in vegetative and induced plants, using reversed-phase HPLC coupled to the Amaranthus bioassay. The results show that, as early as 16 hours after the start of the LD, there is an increase of cytokinin activity in both the root and leaf exudates of induced plants. These observations fit nicely with previous results obtained on Sinapis, and they indicate that cytokinins are part of the floral stimulus in this species.     

Transforming RNA-Seq Data to Improve the Performance of Prognostic Gene Signatures

Gene expression measurements have successfully been used for building prognostic signatures, i.e for identifying a short list of important genes that can predict patient outcome. Mostly microarray measurements have been considered, and there is little advice available for building multivariable risk prediction models from RNA-Seq data. We specifically consider penalized regression techniques, such as the lasso and componentwise boosting, which can simultaneously consider all measurements and provide both, multivariable regression models for prediction and automated variable selection. However, they might be affected by the typical skewness, mean-variance-dependency or extreme values of RNA-Seq covariates and therefore could benefit from transformations of the latter. In an analytical part, we highlight preferential selection of covariates with large variances, which is problematic due to the mean-variance dependency of RNA-Seq data. In a simulation study, we compare different transformations of RNA-Seq data for potentially improving detection of important genes. Specifically, we consider standardization, the log transformation, a variance-stabilizing transformation, the Box-Cox transformation, and rank-based transformations. In addition, the prediction performance for real data from patients with kidney cancer and acute myeloid leukemia is considered. We show that signature size, identification performance, and prediction performance critically depend on the choice of a suitable transformation. Rank-based transformations perform well in all scenarios and can even outperform complex variance-stabilizing approaches. Generally, the results illustrate that the distribution and potential transformations of RNA-Seq data need to be considered as a critical step when building risk prediction models by penalized regression techniques.     

Elevation in the Sucrose Content of the Shoot Apical Meristem of Sinapis alba at Floral Evocation

Nanogram tissue samples from apical meristems of Sinapis alba were assayed for sucrose, total soluble hexosyl equivalents ( glucose and fructose plus hexoses from sucrose hydrolysis), and total soluble glucosyl equivalents ( glucose plus glucose from sucrose hydrolysis). On dry weight basis, sucrose concentration increased by more than 50% within 10 hours after the start of either a long photoperiod or a short photoperiod displaced by 10 hours in the 24-hour cycle (`displaced short day'). (These treatments induce flower initiation) Glucose and fructose concentrations were close to zero in vegetative meristems and remained low compared to sucrose in meristems of induced plants. Within a single meristem, the peripheral and the central zones had similar concentrations of sucrose. Our results indicate that an early physiological event in floral transition is the accumulation of sucrose in the meristem.     

Changes in the Pattern of Proteins Synthesized in the Shoot Apical Meristem of Sinapis alba during Floral Transition

Because Sinapis alba can be induced to flower by a single longday (LD), we have sought for changes in gene expression in theshoot meristem during the floral transition induced by a 22h LD. To analyse the pattern of proteins synthesized in themeristem, we have used in vivo labelling of proteins, an improvedextraction procedure specifically designed for green plant tissues,two-dimensional polyacrylamide gel electrophoresis (2D-PAGE)and a strict gel comparison procedure giving a confidence levelof 3%. Following the LD, complex qualitative and quantitative changesaffected about 8% of the proteins. Twelve different patternsof changes were observed. Some quantitative changes and onequalitative change were already found 16 h after the divergenceof light regimes, other changes appeared only later. Exceptfor one protein, the qualitative changes appeared only afterthe production of flower primordia. (Received March 21, 1992; Accepted September 23, 1992)     

Dynamics of Cytokinins in Apical Shoot Meristems of a Day-Neutral Tobacco during Floral Transition and Flower Formation

This study considered cytokinin distribution in tobacco (Nicotiana tabacum L.) shoot apices in distinct phases of development using immunocytochemistry and quantitative tandem mass spectrometry. In contrast to vegetative apices and flower buds, we detected no free cytokinin bases (zeatin, dihydrozeatin, or isopentenyladenine) in prefloral transition apices. We also observed a 3-fold decrease in the content of cytokinin ribosides (zeatin riboside, dihydrozeatin riboside, and isopentenyladenosine) during this transition phase. The group concluded that organ formation (e.g. leaves and flowers) is characterized by enhanced cytokinin content, in contrast to the very low endogenous cytokinin levels found in prefloral transition apices, which showed no organogenesis. The immunocytochemical analyses revealed a differing intracellular localization of the cytokinin bases. Dihydrozeatin and isopentenyladenine were mainly cytoplasmic and perinuclear, whereas zeatin showed a clear-cut nuclear labeling. To our knowledge, this is the first time that this phenomenon has been reported. Cytokinins do not seem to act as positive effectors in the prefloral transition phase in tobacco shoot apices. Furthermore, the differences in distribution at the cellular level may be indicative of a specific physiological role of zeatin in nuclear processes.     

Cytophotometric Study of the 2C Nuclear DNA Content in the Apical Bud of Sinapis alba during Floral Transition

Feulgen cytophotometry was used to detect possible changes inthe 2C DNA content in the various parts of the apical bud ofSinapis alba during floral evocation and flower development.This study showed that there was no significant difference inthe 2C DNA content between the vegetative, evoked or reproductivemeristems. In vegetative plants, the 2C DNA content was lowerin the leaf primordia than in the meristem. This content inthe leaf exhibited a further decrease during the floral transition.In the flower primordia, the 2C value never exceeded the typicalvalue of the meristem. In the flower at anthesis, the DNA contentwas lower in the pistil and stamen than in the meristem. Apical bud, floral transition, 2C DNA content, cytophotometry, Sinapis alba L.