Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice-2

Ng tree: The unrooted tree, constructed using ClustalX (1.83), summarizes the evolutionary relationship among the 68 members of CCCH families. The neighbor-joining tree was constructed using aligned full-length amino acid sequences. The proteins are named according to their gene name (see Table 2) with the CCCH zinc finger number of each protein. The tree shows the 11 major phylogenetic subfamilies (left column, numbered I to XI and marked with different alternating tones of a gray background to make subfamily identification easier) with high predictive value. The numbers beside the branches represent bootstrap values (≥500) based on 1000 replications that were used to class the major 11 subfamilies. Gene structure: The gene structure is presented by black exon(s) and spaces between the black boxes correspond to introns. The sizes of exons and introns can be estimated using the horizontal lines. Protein structure: Each black box represents the motif in the protein, as indicated in the table on the left side. The conserved motifs outside CCCH motif are highlighted with an arranged number, and the same number referred to the same motif. The length of the motif can be estimated using the scale at top. aa, amino acids.<p><b>Copyright information:</b></p><p>Taken from "Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice"</p><p>http://www.biomedcentral.com/1471-2164/9/44</p><p>BMC Genomics 2008;9():44-44.</p><p>Published online 27 Jan 2008</p><p>PMCID:PMC2267713.</p><p></p

Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice-0

residues, respectively. The three cysteine and one histidine residues putatively responsible for the zinc-finger structure are indicated.<p><b>Copyright information:</b></p><p>Taken from "Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice"</p><p>http://www.biomedcentral.com/1471-2164/9/44</p><p>BMC Genomics 2008;9():44-44.</p><p>Published online 27 Jan 2008</p><p>PMCID:PMC2267713.</p><p></p

Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice-1

Al MySQL database. The whole program is available in additional file (see Additional file and ).<p><b>Copyright information:</b></p><p>Taken from "Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice"</p><p>http://www.biomedcentral.com/1471-2164/9/44</p><p>BMC Genomics 2008;9():44-44.</p><p>Published online 27 Jan 2008</p><p>PMCID:PMC2267713.</p><p></p

The Mitochondrial Phosphate Transporters Modulate Plant Responses to Salt Stress via Affecting ATP and Gibberellin Metabolism in <em>Arabidopsis thaliana</em>

<div><p>The mitochondrial phosphate transporter (MPT) plays crucial roles in ATP production in plant cells. Three <em>MPT</em> genes have been identified in <em>Arabidopsis thaliana</em>. Here we report that the mRNA accumulations of <em>AtMPTs</em> were up-regulated by high salinity stress in <em>A. thaliana</em> seedlings. And the transgenic lines overexpressing <em>AtMPTs</em> displayed increased sensitivity to salt stress compared with the wild-type plants during seed germination and seedling establishment stages. ATP content and energy charge was higher in overexpressing plants than those in wild-type <em>A. thaliana</em> under salt stress. Accordingly, the salt-sensitive phenotype of overexpressing plants was recovered after the exogenous application of atractyloside due to the change of ATP content. Interestingly, Genevestigator survey and qRT-PCR analysis indicated a large number of genes, including those related to gibberellin synthesis could be regulated by the energy availability change under stress conditions in <em>A. thaliana</em>. Moreover, the exogenous application of uniconazole to overexpressing lines showed that gibberellin homeostasis was disturbed in the overexpressors. Our studies reveal a possible link between the ATP content mediated by AtMPTs and gibberellin metabolism in responses to high salinity stress in <em>A. thaliana</em>.</p> </div

Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice-3

Een boxes indicate the duplicated segmental regions resulting from the most recent polyploidy. Only the duplicated regions containing CCCH genes are shown. Blue lines connect corresponding sister gene pairs in duplicated blocks. AtC3H1 and AtC3H51, AtC3H8 and AtC3H60, AtC3H12 and AtC3H28, AtC3H14 and AtC3H15, AtC3H30 and AtC3H56, AtC3H46 and AtC3H55, AtC3H59 and AtC3H62 are potential duplicated gene pairs which are marked with the same color rectangle, as described in the text.<p><b>Copyright information:</b></p><p>Taken from "Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice"</p><p>http://www.biomedcentral.com/1471-2164/9/44</p><p>BMC Genomics 2008;9():44-44.</p><p>Published online 27 Jan 2008</p><p>PMCID:PMC2267713.</p><p></p

The roles of AtMPT in salt stress response.

<p>(<b>A</b>) qRT-PCR analysis of <i>AtMPT</i> transcripts in wild-type plants and transgenic plants overexpressing <i>AtMPTs</i> under control and salt stress conditions. Ten-day-old seedlings grown on 1/2 MS agar media were transferred onto filter paper soaked with water and 150 mM NaCl for 24 h. The transcript level in the wild-type sample for <i>AtMPT1</i> under control conditions was set to 1, and the other levels were calculated relative to the corresponding value. Values are means±SEM of three replicates. (<b>B</b>) Photographs of wild-type and overexpression lines were taken 10 days after germination on 1/2 MS agar media and 1/2 MS agar media with 150 mM NaCl. (<b>C</b>) Mean fresh weights (FW) of 10-day-old plants. (<b>D</b>) Mean radius of rosettes of 10-day-old plants. The overexpression lines for <i>AtMPT3</i> under salt stress were damaged and had no normal rosette leaves to measure. Error bars represent±SEM. (<b>E</b>) Mean primary root lengths of 10-day-old plants. Error bars represent±SEM. Measurements shown in Figure C–E were made 10 days post-germination under control and high salinity stress conditions (n = 30). Samples with different letters are significantly different: P<0.01. OEMPTs, the <i>AtMPT</i> overexpressors.</p

AtMPT mediates salt stress tolerance through an ATP-dependent pathway.

<p>(<b>A</b>) ATP content in 10-day-old wild-type plants and the overexpression lines under control and 150 mM NaCl conditions. Values represent the average of three replicates±SEM. (<b>B</b>) Energy charge of 10-day-old wild-type plants and overexpression lines under control and salt stress. Values represent the average of three replicates±SEM. (<b>C</b>) Wild type and overexpressing seedlings germinated and grown under control and 150 mM NaCl together with 10 µM atractyloside. The pictures were taken 10 days post-germination. Samples with different letters are significantly different: P<0.05 (a and b, b and c). OEMPTs, the <i>AtMPT</i> overexpressors.</p

AtMPT structure prediction.

<p>(<b>A</b>) Transmembrane topology prediction for AtMPT1, AtMPT2, and AtMPT3. Hydropathy values were analyzed by TMPred prediction (<a href="http://www.ch.embnet.org/software/TMPRED_form.html" target="_blank">http://www.ch.embnet.org/software/TMPRED_form.html</a>). (<b>B</b>) Three- dimensional structures were predicted using their pdb coordinates and the Swiss-Model program (<a href="http://swissmodel.expasy.org" target="_blank">http://swissmodel.expasy.org</a>).</p

Additional file 1: Figure S1. of Graphene Oxide Hybridized nHAC/PLGA Scaffolds Facilitate the Proliferation of MC3T3-E1 Cells

a Surface morphology of the nHAC. b EDS spectra of the nHAC. Figure S2 SEM images of a nHAC/PLGA; b nHAC/PLGA/GO (0.5 wt%). c nHAC/PLGA/GO (1.0 wt%); d nHAC/PLGA/GO (1.5 wt%) scaffolds. (DOCX 2689 kb

RNA-Seq Characterization of Spinal Cord Injury Transcriptome in Acute/Subacute Phases: A Resource for Understanding the Pathology at the Systems Level

<div><p>Spinal cord injury (SCI) is a devastating neurological disease without effective treatment. To generate a comprehensive view of the mechanisms involved in SCI pathology, we applied RNA-Sequencing (RNA-Seq) technology to characterize the temporal changes in global gene expression after contusive SCI in mice. We sequenced tissue samples from acute and subacute phases (2 days and 7 days after injury) and systematically characterized the transcriptomes with the goal of identifying pathways and genes critical in SCI pathology. The top enriched functional categories include “inflammation response,” “neurological disease,” “cell death and survival” and “nervous system development.” The top enriched pathways include LXR/RXR Activation and Atherosclerosis Signaling, etc. Furthermore, we developed a systems-based analysis framework in order to identify key determinants in the global gene networks of the acute and sub-acute phases. Some candidate genes that we identified have been shown to play important roles in SCI, which demonstrates the validity of our approach. There are also many genes whose functions in SCI have not been well studied and can be further investigated by future experiments. We have also incorporated pharmacogenomic information into our analyses. Among the genes identified, the ones with existing drug information can be readily tested in SCI animal models. Therefore, in this study we have described an example of how global gene profiling can be translated to identifying genes of interest for functional tests in the future and generating new hypotheses. Additionally, the RNA-Seq enables splicing isoform identification and the estimation of expression levels, thus providing useful information for increasing the specificity of drug design and reducing potential side effect. In summary, these results provide a valuable reference data resource for a better understanding of the SCI process in the acute and sub-acute phases.</p> </div