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vegetative function [keywords]
- Genome-Wide Identification, Phylogenetic and Co-Expression Analysis of OsSET Gene Family in Rice. [Journal Article]
- PLoS One 2013; 8(6):e65426.
SET domain is responsible for the catalytic activity of histone lysine methyltransferases (HKMTs) during developmental process. Histone lysine methylation plays a crucial and diverse regulatory function in chromatin organization and genome function. Although several SET genes have been identified and characterized in plants, the understanding of OsSET gene family in rice is still very limited. METHODOLOGYPRINCIPAL FINDINGS: In this study, a systematic analysis was performed and revealed the presence of at least 43 SET genes in rice genome. Phylogenetic and structural analysis grouped SET proteins into five classes, and supposed that the domains out of SET domain were significant for the specific of histone lysine methylation, as well as the recognition of methylated histone lysine. Based on the global microarray, gene expression profile revealed that the transcripts of OsSET genes were accumulated differentially during vegetative and reproductive developmental stages and preferentially up or down-regulated in different tissues. Cis-elements identification, co-expression analysis and GO analysis of expression correlation of 12 OsSET genes suggested that OsSET genes might be involved in cell cycle regulation and feedback. CONCLUSIONSSIGNIFICANCE: This study will facilitate further studies on OsSET family and provide useful clues for functional validation of OsSETs.
- Tools of our trade. [EDITORIAL]
- Acta Physiol (Oxf) 2013 Jun 7.
The compartmentalization of living cells and the generation of chemical and electrical gradients are a prerequisite for life as we know it. A multitude of physiological processes critically depends on ion gradients and selective, regulated permeabilities, which in turn are based on the controlled flow of small inorganic ions over lipophilic membranes. Therefore, ion channels, exchangers and pumps have become to be considered tools of the trade of the physiologist per se. This article is protected by copyright. All rights reserved.
- DNA Binding of the Cell Cycle Transcriptional Regulator GcrA Depends on N6-Adenosine Methylation in Caulobacter crescentus and Other Alphaproteobacteria. [Journal Article]
- PLoS Genet 2013 May; 9(5):e1003541.
Several regulators are involved in the control of cell cycle progression in the bacterial model system Caulobacter crescentus, which divides asymmetrically into a vegetative G1-phase (swarmer) cell and a replicative S-phase (stalked) cell. Here we report a novel functional interaction between the enigmatic cell cycle regulator GcrA and the N6-adenosine methyltransferase CcrM, both highly conserved proteins among Alphaproteobacteria, that are activated early and at the end of S-phase, respectively. As no direct biochemical and regulatory relationship between GcrA and CcrM were known, we used a combination of ChIP (chromatin-immunoprecipitation), biochemical and biophysical experimentation, and genetics to show that GcrA is a dimeric DNA-binding protein that preferentially targets promoters harbouring CcrM methylation sites. After tracing CcrM-dependent N6-methyl-adenosine promoter marks at a genome-wide scale, we show that these marks recruit GcrA in vitro and in vivo. Moreover, we found that, in the presence of a methylated target, GcrA recruits the RNA polymerase to the promoter, consistent with its role in transcriptional activation. Since methylation-dependent DNA binding is also observed with GcrA orthologs from other Alphaproteobacteria, we conclude that GcrA is the founding member of a new and conserved class of transcriptional regulators that function as molecular effectors of a methylation-dependent (non-heritable) epigenetic switch that regulates gene expression during the cell cycle.
- Chromatin Alterations during Pollen Development in Hordeum vulgare. [JOURNAL ARTICLE]
- Cytogenet Genome Res 2013 May 30.
The dynamics of posttranslational histone modifications in relation to nuclear architecture has been analyzed during pollen development in Hordeum vulgare L. cv. Igri. Notwithstanding the asymmetry of cytokinesis associated with pollen mitosis I, immunolabeling revealed that the vegetative and generative nuclei initially display identical chromatin modification patterns. Yet, differential chromatin modification patterns between vegetative and generative nuclei emerge with the development of conspicuous differences in nuclear morphology as visualized by 4',6-diamidino-2-phenylindole staining. The temporal and spatial distribution of most histone modifications observed is in agreement with reduced gene activity in the generative nucleus and increased expression in the vegetative nucleus as indicated by immunolabeling of active RNA polymerase II. Signals of trimethylation of histone H3 lysine 27 proved to be particularly enriched in euchromatic domains of subtelomeric regions. In the context of nuclear differentiation in bicellular pollen, this modification became restricted to the vegetative nucleus, indicating a role in activating rather than suppressing gene expression. The presence of acetylated histone H3 at lysine 9 in the cytoplasm of the generative cell is indicative of a more complex, still unknown function of this particular modification.
- Unconventional pathways of secretory plant proteins from the endoplasmic reticulum to the vacuole bypassing the Golgi complex. [JOURNAL ARTICLE]
- Plant Signal Behav 2013 Jun 3; 8(8)
Studies on the basic mechanisms that regulate vacuolar delivering of proteins synthesized in the endoplasmic reticulum (ER) have a great importance in plant cell biology. Indeed, many aspects of plant physiology are affected by this intracellular traffic, for example, germination or reaction to biotic stresses due to the accumulation of storage proteins in seeds or enzymes in vegetative tissues, respectively. Up to now, the Golgi complex has been considered the main hub in the sorting of vacuolar secretory proteins; those polypeptides able to reach their final destination without the aid of this organelle are regarded as exceptions to an established route. This mini-review aims to emphasize the existence of several Golgi-independent pathways involved in the trafficking of different types of vacuolar proteins.
'Purple Rain', a purple cultivar of Betula pendula, has dark purple leaves throughout the vegetative period. In this study, B. pendula 'Purple Rain' was found to have a higher anthocyanidin level compared with B. pendula, Transcriptome analysis revealed numerous changes in gene expression that could be attributed to color change, including the upregulation of 2467 unigenes and the downregulation of 2299 unigenes in 'Purple Rain'. Furthermore, anthocyanidin synthesis and transcriptional regulation were altered in 'Purple Rain', which may have contributed to phenotypic changes. These results provide unique molecular insights into the biochemical pathways and regulatory networks that function in a purple variety of B. pendula.
- Specialized Early Treatment for Persons with Disorders of Consciousness: Program Components and Outcomes. [JOURNAL ARTICLE]
- Arch Phys Med Rehabil 2013 May 31.
OBJECTIVE:To describe a specialized early treatment program for persons with disorders of consciousness (DOC) that includes family education; to identify rates of secondary conditions, imaging used and selected interventions; and to evaluate outcomes.
DESIGN:A single center, retrospective, pre-post design using electronic medical record data.
SETTING:A CARF-accredited, long-term acute care hospital that provides acute medical and inpatient rehabilitation levels of care for people with catastrophic injuries.
PARTICIPANTS:210 persons aged 14 to 69 with DOC of primarily traumatic etiology admitted at a mean of 41.0 (SD=27.2) days post-injury; 2% were in coma, 41% were in the vegetative state and 57% were in the minimally conscious state.
INTERVENTIONS:An acute medical level of care with 90+ minutes of daily interdisciplinary rehabilitation and didactic and hands-on caretaking education for families.
MAIN OUTCOME MEASURES:Coma Recovery Scale-Revised, Modified Ashworth Scale, and discharge disposition.
RESULTS:Program admission medical acuity included dysautonomia - 15%, airway modifications - 79%, infections (e.g., pneumonia - 16%, urinary tract infection - 14%, and blood - 11%), deep vein thrombosis - 17%, pressure ulcers - 14%, and marked hypertonia - 30% in each limb. There were 168 program interruptions (i.e., 139 surgeries, 29 non-surgical intensive care unit transfers). Mean length of stay was 39.1±29.4 (range 6-204 days). Patients showed improved consciousness and respiratory function and reduced pressure ulcers and upper extremity hypertonia. At discharge, 54% showed sufficient emergence to transition to mainstream inpatient rehabilitation and 29% did not emerge but were discharged home to family with on-going programmatic support; only 13% did not emerge and were institutionalized.
CONCLUSIONS:Persons with DOC due primarily to traumatic etiology who receive specialized early treatment that includes acute medical care and 90+ minutes of daily rehabilitation are likely to show improved consciousness and body function; more than half may transition to mainstream inpatient rehabilitation. Families who receive comprehensive education and hands on training with on-going follow-up support may be twice as likely to provide care for medically stable persons with DOC in their homes v. nursing facility placement.
- Accumulation and distribution of Zn in the shoots and reproductive structures of the halophyte plant species Kosteletzkya virginica as a function of salinity. [JOURNAL ARTICLE]
- Planta 2013 Jun 2.
Kosteletzkya virginica is a wetland halophyte that is a good candidate for rehabilitation of degraded salt marshes and production of oil as biodiesel. Salt marshes are frequently contaminated by heavy metals. The distribution of Zn in vegetative and reproductive organs of adult plants, and the NaCl influence on this distribution remain unknown and were thus explored in the present study. Plants were cultivated in a nutrient film technique system, from seedling stage until seed maturation in a control, Zn (100 μM), NaCl (50 mM) or Zn + NaCl medium. Photosynthesis, ion nutrition, malondialdehyde and non-protein thiol concentrations were quantified. Zinc distribution in reproductive organs was estimated by a laser ablation-inductively coupled plasma-mass spectrometry procedure (LA-ICP-MS). Adult plants accumulated up to 2 mg g(-1) DW Zn in the shoots. Zinc reduced plant growth, inhibited photosynthesis and reduced seed yield. Zinc accumulation in the seeds was only two times higher in Zn-treated plants than in controls. Exogenous NaCl neutralized the damaging action of Zn and modified the Zn distribution through a preferential accumulation of toxic ions in older leaves. Zinc was present in seed testa, endosperm and, to a lower extent, in embryo. Additional NaCl induced a chalazal retention of Zn during seed maturation and reduced final Zn seed content. It is concluded that NaCl 50 mM had a positive impact on the response of K. virginica to Zn toxicity and acts through a modification in Zn distribution rather than a decrease in Zn absorption.
- Extraplastidial Cytidinediphosphate Diacylglycerol Synthase Activity is Required for Vegetative Development in Arabidopsis thaliana. [JOURNAL ARTICLE]
- Plant J 2013 May 25.
Cytidinediphosphate diacylglycerol synthase (CDS) catalyzes the activation of phosphatidic acid to CDP-diacylglycerol, a central intermediate in glycerolipid biosynthesis of prokaryotic and eukaryotic organisms. CDP-diacylglycerol is the precursor to phosphatidylinositol, phosphatidylglycerol and cardiolipin of eukaryotic phospholipids that are essential for various cellular functions. CDS isoforms are located in plastids, mitochondria and the endomembrane system of plants and are encoded by five genes in Arabidopsis. Two genes have previously been shown to code for the plastidial isoforms which are indispensable for the biosynthesis of plastidial PG and, thus, biogenesis and function of thylakoid membranes. Here we have focused on the extraplastidial CDS isoforms, encoded by CDS1 and CDS2 which are constitutively expressed contrary to CDS3. We provided evidence that these closely related CDS genes code for membrane proteins located in the ER and possess very similar enzymatic properties. Development and analysis of Arabidopsis mutants lacking either one or both CDS1 and CDS2 genes clearly showed that these two genes have redundant functions. As reflected in the seedling lethal phenotype of the cds1cds2 double mutant, plant cells require at least one catalytically active microsomal CDS isoform for cell division and expansion. According to the altered glycerolipid composition of the double mutant in comparison to wild type seedlings, it is likely that the drastic decrease in the level of phosphatidylinositol and the increase in phosphatidic acid cause defects in cell division and expansion. This article is protected by copyright. All rights reserved.
- The role of auxin in shaping shoot architecture. [Journal Article]
- J Exp Bot 2013 Jun; 64(9):2593-608.
The variety of plant architectures observed in nature is predominantly determined by vegetative and reproductive branching patterns, the positioning of lateral organs, and differential stem elongation. Branches, lateral organs, and stems are the final products of the activity of meristems, groups of stem cells whose function is genetically determined and environmentally influenced. Several decades of studies in different plant species have shed light on the essential role of the hormone auxin in plant growth and development. Auxin influences stem elongation and regulates the formation, activity, and fate of meristems, and has therefore been recognized as a major hormone shaping plant architecture. Increasing our knowledge of the molecular mechanisms that regulate auxin function is necessary to understand how different plant species integrate a genetically determined developmental programme, the establishment of a body plan, with constant inputs from the surrounding environment. This information will allow us to develop the molecular tools needed to modify plant architecture in several crop species and in rapidly changing environments.