Transcriptome and Functional Analysis of Fiber-related Gene Expression in Cotton

Fiber cell initiation is a complex process involving many pathways,including phytohormones and components for transcriptional and posttranscriptional regulation.Here we report expression

Three Genes Related to Trehalose Metabolism Affect Sclerotial Development of Rhizoctonia solani AG-1 IA,Causal Agent of Rice Sheath Blight

Trehalose metabolism is related to the sclerotial development of Rhizoctonia solani AG-1 IA,the causal agent of rice sheath blight(RSB).Here,we further elucidated the functions of three genes Rstre,Rstps1 and Rstpp that encode three key enzymes trehalase(TRE),alpha,alpha-trehalosephosphate synthase(TPS1)and trehalose 6-phosphate phosphatase(TPP)in the sclerotial development of R.solani AG-1 IA.Due to the lack of a stable genetic transformation system for R.solani,the heterologous expression of these three genes in Pichia pastoris GS115 was performed.The results showed that reactive oxygen species(ROS)contents and enzyme activities in R.solani decreased significantly in the treatments of the fermentation broths of Rstps1 and Rstpp transformants,and that in the treatment of the fermentation broth of Rstre transformant visibly increased.Furthermore,the fermentation broths of the transformants of all the three genes were added to potato dextrose agar(PDA)medium for the cultivation of R.solani,as a result,the dry weight of sclerotia in each PDA plate containing the fermentation broths of Rstps1 and Rstpp transformants significantly increased compared with the control,and that of Rstre transformant obviously decreased.Finally,178 proteins were found to interact with RSTPS1,and 16 of them were associated with ROS.Taken together,the findings suggest that all these three genes related to trehalose metabolism play important roles in the sclerotial development of R.solani AG-1 IA,and can be used as new targets for the development of novel high-efficiency fungicides for the controlling of RSB.

Association between chromosomal aberration of COX8C and tethered spinal cord syndrome:array-based comparative genomic hybridization analysis

Copy number variations have been found in patients with neural tube abnormalities.In this study,we performed genome-wide screening using high-resolution array-based comparative genomic hybridization in three children with tethered spinal cord syndrome and two healthy parents.Of eight copy number variations,four were non-polymorphic.These non-polymorphic copy number variations were associated with Angelman and Prader-Willi syndromes,and microcephaly.Gene function enrichment analysis revealed that COX8 C,a gene associated with metabolic disorders of the nervous system,was located in the copy number variation region of Patient 1.Our results indicate that array-based comparative genomic hybridization can be used to diagnose tethered spinal cord syndrome.Our results may help determine the pathogenesis of tethered spinal cord syndrome and prevent occurrence of this disease.

The Nitrogen-Cycling Network of Bacterial Symbionts in the Sponge Spheciospongia vesparium

The microbes associated with sponges play important roles in the nitrogen cycle of the coral reefs ecosystem,e.g.,nitrification,denitrification,and nitrogen fixation.However,the whole nitrogen-cycling network has remained incomplete in any individual sponge holobiont.In this study,454 pyrosequencing of the 16S rRNA genes revealed that the sponge Spheciospongia vesparium from the South China Sea has a unique bacterial community(including 12 bacterial phyla),dominated particularly by the genus Shewanella(order Alteromonadales).A total of 10 functional genes,nifH,amoA,narG,napA,nirK,norB,nosZ,ureC,nrfA,and gltB,were detected in the microbiome of the sponge S.vesparium by gene-targeted analysis,revealing an almost complete nitrogen-cycling network in this sponge.Particularly,bacterial urea utilization and the whole denitrification pathway were highlighted.MEGAN analysis suggests that Proteobacteria(e.g.,Shewanella)and Bacteroidetes(e.g.,Bizionia)are probably involved in the nitrogen cycle in the sponge S.vesparium.

Cloning and Characterization of miRNAs and Their Targets, Including a Novel miRNA-Targeted NBS-LRR Protein Class Gene in Apple （Golden Delicious）

MicroRNA （miRNA） has emerged as an important regulator of gene expression in plants. 146 miRNAs were identified from apple （Malus domestica cv. Golden Delicious） by bioinformatic analysis and RNA library sequencing. From these, 135 were conserved and 11 were novel miRNAs. Target analysis predicted one of the novel miRNAs, Md-miRLn11 （Malus domestica microRNA Ln11）, targeted an apple nucleotide-binding site （NBS）-Ieucine-rich repeat （LRR） class protein coding gene （Md-NBS）. 5/ RACE assay confirmed the ability of Md-miRLn11 to cleave Md-NBS at the 11-12-nt position. Analysis of the expression of Md-miRLn11 and Md-NBS during the optimum invasion period in 40 apple varieties showed that the expression of Md-NBS gene in resistant varieties is higher than in susceptible varieties, with an inverse pattern for Md-miRLn11. Seedlings from the resistant apple variety ＇JiGuan＇ were used to carry out an Agrobacterium infiltration assay, and then inoculated with the apple leaf spot disease. The result showed a clear decline of disease resistance in JiGuan apples. In contrast, the susceptible variety ＇FuJi＇ infiltrated with the Md-NBS gene showed a significant increase in disease resistance. Based on the above results, we propose that Md-miRLn11 regulates Md-NBS gene expression in particular under the condition of pathogen infection, and that the Md-miRLn11 targeting P-loop site may regulate many NBS-LRR protein class genes in woody plants.

Characterization of the genes involved in nitrogen cycling in wastewater treatment plants using DNA microarray and most probable number-PCR

To improve nitrogen removal performance of wastewater treatment plants （WWTPs）, it is essential to understand the behavior of nitrogen cycling communities, which comprise various microorganisms. This study characterized the quantity and diversity of nitrogen cycling genes in various processes of municipal WWTPs by employing two molecular-based methods：most probable number-polymerase chain reaction （MPN-PCR） and DNA microarray. MPN-PCR analysis revealed that gene quantities were not statistically different among processes, suggesting that conventional actwated sludge processes （CAS） are similar to nitrogen removal processes in their ability to retain an adequate population of nitrogen cycling microorganisms. Furthermore, most processes in the WWTPs that were researched shared a pattern：the nitS and the bacterial amoA genes were more abundant than the nirK and archaeal amoA genes, respectivelv. DNA microarray analysis revealed that several kinds of nitrification and denitrification genes were detected in both CAS and anaerobic-oxic processes （AO）, whereas limited genes were detected in nitrogen removal processes. Results of this study suggest that CAS maintains a diverse community of nitrogen cycling microorganisms; moreover, the microbial communities in nitrogen removal processes may be specific.