Transcriptome analysis of different life-history stages and screening of male-biased genes in Daphnia sinensis.

BACKGROUND: In the life history of Daphnia, the reproductive mode of parthenogenesis and sexual reproduction alternate in aquatic ecosystem, which are often affected by environmental and genetic factors. Recently, the sex-biased genes are of great significance for clarifying the origin and evolution of reproductive transformation and the molecular regulation mechanism of sex determination in Daphnia. Although some genes on reproductive transition of Daphnia had been researched, molecular mechanism on the maintenance of sexually dimorphic phenotypes of Daphnia are still not well known, including differentially expressed genes in different life-history stages. RESULTS: In this study, four life-history stages of Daphnia sinensis, juvenile female (JF), parthenogenetic female (PF), sexual female (SF) and male (M), were performed for transcriptome, and male-biased genes were screened. A total of 110437 transcripts were obtained and assembled into 22996 unigenes. In the four life-history stages (JF, PF, SF and M), the number of unique unigenes is respectively 2863, 445, 437 and 586, and the number of common unigenes is 9708. The differentially expressed genes (DEGs) between male and other three female stages (M vs JF, M vs PF and M vs SF) were 4570, 4358 and 2855, respectively. GO gene enrichment analysis showed that the up-regulated genes in male were mainly enriched in hydrolase activity and peptidase activity. Thirty-six genes in male were significantly higher expression than in the three female stages, including one Doublesex (Dsx) gene, one laminin gene, five trypsin genes and one serine protease genes, and one chitin synthase gene and two chitinase genes. CONCLUSIONS: Our results showed that thirty-six candidate genes may be as the male-biased genes involving in the maintenance of sexually dimorphic phenotypes. This work will provide a reference for further exploring the functional genes related to sex differentiation in Daphnia species. Moreover, according to previous investigations, we thought that the expression level of functional genes may be related to the life-history stages of organisms, and may be also affected by different Daphnia species.

Curcumin promotes osteogenic differentiation of human periodontal ligament stem cells by inducting EGR1 expression.

OBJECTIVE: Human periodontal ligament stem cells (hPDLSCs) attract attention for the periodontal regeneration therapy. Curcumin may promote osteogenic differentiation of hPDLSCs. This research aims to elucidate whether Curcumin displays promoting osteogenic differentiation and its mechanism. METHODS: The hPDLSCs were isolated from human periodontal ligament by immunomagnetic beads, identified with immumofluorescence. hPDLSCs were treated with 0, 5, 10, 20, 50, 100 µmol/L Curcumin. The early growth response gene 1 (EGR1) siRNA or plasmind were tranfected into the hPDLSCs. The viability, Alkaline Phosphatase (ALP) activity and mineralizaiton level of hPDLSCs were measured with 3-(4,5)-dimethylthiahiazo(-z-y1)-3,5-di-phenytetrazoliumromide (MTT) assay, ALP Assay Kit or Alizarin Red staining. The expression of EGR1, RUNX family transcription factor 2 (Runx2), bone gamma-carboxyglutamate protein (OC), secreted phosphoprotein 1 (OPN) and collagen type I alpha 1 chain (Collagen I), in hPDLSC were determined by Western blotting and quantitative reverse transcription-polymerase chain reaction. RESULTS: The isolated hPDLSCs were spindle or irregular, arranged in radial shape and shown positive expression of STRO-1, CD146 and Vimentin. Curcumin 10 µmol/L treatment maximal promoting the cells viability, ALP activities, mineralization, and levels of Runx2, OC, OPN, Collagen I and EGR-1 in hPDLSCs. EGR-1 siRNA transfection inversed Curcumin's promoting effect on ALP activities, mineralization, and levels of Runx2, OC, OPN, Collagen I and EGR-1 in hPDLSCs. While the EGR-1 plasmid transfection enhanced Curcumin's promoting effect on these parameters of hPDLSCs. CONCLUSION: Curcumin promotes the osteogenic differentiation of hPDLSCs, which may work through the EGR1. Curcumin may be a promising medicine for periodontitis treatment and periodontal regeneration.

[Spatial distribution characteristics of the physical and chemical properties of water in the Kunes River after the supply of snowmelt during spring].

Eight physical and chemical indicators related to water quality were monitored from nineteen sampling sites along the Kunes River at the end of snowmelt season in spring. To investigate the spatial distribution characteristics of water physical and chemical properties, cluster analysis (CA), discriminant analysis (DA) and principal component analysis (PCA) are employed. The result of cluster analysis showed that the Kunes River could be divided into three reaches according to the similarities of water physical and chemical properties among sampling sites, representing the upstream, midstream and downstream of the river, respectively; The result of discriminant analysis demonstrated that the reliability of such a classification was high, and DO, Cl- and BOD5 were the significant indexes leading to this classification; Three principal components were extracted on the basis of the principal component analysis, in which accumulative variance contribution could reach 86.90%. The result of principal component analysis also indicated that water physical and chemical properties were mostly affected by EC, ORP, NO3(-) -N, NH4(+) -N, Cl- and BOD5. The sorted results of principal component scores in each sampling sites showed that the water quality was mainly influenced by DO in upstream, by pH in midstream, and by the rest of indicators in downstream. The order of comprehensive scores for principal components revealed that the water quality degraded from the upstream to downstream, i.e., the upstream had the best water quality, followed by the midstream, while the water quality at downstream was the worst. This result corresponded exactly to the three reaches classified using cluster analysis. Anthropogenic activity and the accumulation of pollutants along the river were probably the main reasons leading to this spatial difference.

Identification of a novel nuclear-localized adenylate kinase 6 from Arabidopsis thaliana as an essential stem growth factor.

Adenylate kinase (AK; EC 2.7.4.3) is highly conserved across a wide range of organisms, including Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, and Homo sapiens. While AK6 orthologs play important roles in the growth of yeast and worms, the physiological function of AK6 in A. thaliana is still unknown. In this study, we first cloned and expressed Arabidopsis adenylate kinase 6 (AAK6). Enzyme assays revealed that AAK6 has characteristic adenylate kinase properties, with ATP as the preferred phosphate donor and AMP as the best phosphate acceptor. A subcellular localization assay demonstrated that AAK6 had a predominant nuclear localization. Through biochemical purification and mass spectrometry analysis, a putative homolog of the S. cerevisiae Rps14 protein was identified as a partner of AAK6. Most importantly, we observed that aak6 T-DNA insertion mutants had decreased stem growth compared with wild-type plants. These data indicate that AAK6 exhibits adenylate kinase activity and is an essential growth factor in Arabidopsis.

Protein expression, crystallization and preliminary X-ray crystallographic studies of LidA from Legionella pneumophila.

LidA, a translocated substrate of the Legionella pneumophila Dot/Icm type IV secretion system, is associated with maintenance of bacterial integrity and interferes with the early secretory pathway. However, the precise mechanism of LidA in these processes remains elusive. To further investigate the structure and function of LidA, the full-length protein was successfully expressed in Escherichia coli and purified. LidA was crystallized using sitting-drop vapour diffusion and diffracted to a resolution of 2.75 Å. The crystal belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 57.5, b = 64.5, c = 167.3 Å, α = ß = γ = 90°. There is one molecule per asymmetric unit.

Depletion of hCINAP by RNA interference causes defects in Cajal body formation, histone transcription, and cell viability.

hCINAP is a highly conserved and ubiquitously expressed protein in eukaryotic organisms and its overexpression decreases the average number of Cajal bodies (CBs) with diverse nuclear functions. Here, we report that hCINAP is associated with important components of CBs. Depletion of hCINAP by RNA interference causes defects in CB formation and disrupts subcellular localizations of its components including coilin, survival motor neurons protein, spliceosomal small nuclear ribonucleoproteins, and nuclear protein ataxia-telangiectasia. Moreover, knockdown of hCINAP expression results in marked reduction of histone transcription, lower levels of U small nuclear RNAs (U1, U2, U4, and U5), and a loss of cell viability. Detection of increased caspase-3 activities in hCINAP-depleted cells indicate that apoptosis is one of the reasons for the loss of viability. Altogether, these data suggest that hCINAP is essential for the formation of canonical CBs, histone transcription, and cell viability.

Dyadobacter beijingensis sp. nov., isolated from the rhizosphere of turf grasses in China.

Strain A54(T) was isolated from rhizospheric soil of turf grasses irrigated with reclaimed water in Taoranting Park, Beijing, China. Phenotypic, chemotaxonomic and polygenetic analyses established the affiliation of the isolate to the genus Dyadobacter. Strain A54(T) possessed 97.7, 94.4 and 94.7 % 16S rRNA gene sequence similarity with respect to the type strains of Dyadobacter fermentans, D. hamtensis and D. crusticola, respectively. Furthermore, DNA-DNA hybridization did not show significant relatedness (<25 % hybridization) between strain A54(T) and D. fermentans ATCC 700827(T). Therefore, these results indicate that strain A54(T) belongs to a novel species of the genus Dyadobacter, for which the name Dyadobacter beijingensis sp. nov. is proposed. The type strain is strain A54(T) (=CGMCC 1.6375(T)=JCM 14200(T)).

Complete Nucleotide Sequence of Ryegrass Mottle Virus : A New Species of the Genus Sobemovirus.

The genome of Ryegrass mottle virus (RGMoV) comprises 4210 nucleotides. The genomic RNA contains four open reading frames (ORFs). The largest ORF 2 encodes a polyprotein of 947 amino acids (103.6 kDa), which codes for a serine protease and an RNA-dependent RNA polymerase. The viral coat protein is encoded on ORF 4 present at the 3'-proximal region. Other ORFs 1 and 3 encode the predicted 14.6 kDa and 19.8 kDa proteins of unknown function. The consensus signal for frameshifting, heptanucleotide UUUAAAC and a stem-loop structure just downstream is in front of the AUG codon of ORF 3. Analysis of the in vitro translation products of RGMoV RNA suggests that the 68 kDa protein may represent a fusion protein of ORF 2-ORF 3 produced by frameshifting. The protease region of the polyprotein and coat protein have a low similarity with that of the sobemoviruses (approximately 25% amino acid identity), while the RNA-dependent RNA polymerase region has particularly strong similarity (54 to 60% of more than 350 amino acid residues). The sequence similarities of RGMoV to the sobemoviruses, together with the characteristic genome organization indicate that RGMoV is a new species of the genus Sobemovirus.