Genomic screen identifies a role for the plasmid-borne type II
Shiga-toxigenic Escherichia coli (STEC) is often transmitted to the food through fresh products plant, where it can cause disease. To identify factors for STEC early interaction in spinach, positive system used high-throughput selection. An artificial chromosome (BAC) clone library to isolate bacteria Sakai played in four successive rounds of short-term (2 h) interaction with the roots of spinach, and enriched loci identified by microarray.
A Bayesian hierarchical model produced 115 CDS credible candidates, which consists of seven contiguous genomic region. Of the two regions selected candidates for functional assessment, pO157 two plasmid-encoded type secretion system (T2SS) interaction promoted, while fimbrial chaperone-usher gene cluster (loc6) does. The T2SS promoted spinach binds bacteria and appears to involve a protein EtpD secretin. Furthermore, the gene T2SS, etpD and etpC disclosed in the relevant crop temperature of 18 ° C, and etpD expressed in planta by E. coli in spinach plants Sakai.
During the early embryogenesis of plants, some of the most fundamental decision on the fate and identity are taken so that the process is interesting to study. It is not surprising that higher plant embryogenesis intensively analyzed during the last century, while the somatic embryogenesis probably the most studied model of regeneration. Encoded by the miRNA, short, single-stranded, non-coding miRNAs, are generally present in all eukaryotic genomes and are involved in the regulation of gene expression during critical developmental processes such as morphogenesis of plants, hormone signaling, and the transition phase of development.
Over the last few years dedicated to miRNAs, analysis methods and tools have been developed, which has been given new opportunities in functional analysis of plant miRNAs, including (i) database for in silico analysis; (Ii) detection of the expression of miRNAs and approaches; (Iii) the reporter and the line sensor for spatio-temporal analysis of the interaction of miRNA targets; (Iv) in the in situ hybridization protocol; (V) artificial miRNAs; (Vi) MIM and STTM line to inhibit miRNA activity, and (vii) of target genes that are resistant to miRNA. Here, we attempt to summarize the toolbox for functional analysis of miRNAs during plant embryogenesis. In addition to the characteristics described tools / methods, application examples have been presented.
A high-throughput genomic screen identifies a role for the plasmid-borne type II secretion system of Escherichia coli O157:H7 (Sakai) in plant-microbe interactions
functional genomics in the nodules of legume plant transporter
Over the last few decades, a combination of physiology, biochemistry, molecular and cell biology, and genetics has given us a basic understanding of some of the major transportation in the workplace in nodules legume nitrogen, especially those involved in the exchange of nutrients between the infected cells of plants and rhizobia endosymbiotic them.
However, our knowledge in this area remains uneven and scattered in many species of legume. Recent progress in the field of genomics and functional genomics of two nuts Model, Medicago truncatula and Lotus japonicus quickly fill the gaps in knowledge about the plant transporter gene is expressed constitutively in the nodules and other organs, and induced or otherwise specified in the nodule.
The last class in particular is the focus of current efforts to understand the special role of the nodule-specific transporter. This short article reviews past work on the biochemistry and molecular biology of plant transporter in nodules, before describing recent work in the field of transcriptomics and bioinformatics. Finally, we consider the functional genomics where together with a more classical approach tends to lead us in this area of research in the future.
Description: Bladder cancer with bladder tissue array, including urothelial carcinoma,squamous cell carcinoma, adenocarcinoma and normal tissue, pathololy grade, TNM and clinical stage (AJCC 8.0), 12 case/24 cores (1.5mm), replacing BL243
Description: Bladder cancer tissue array with normal bladder tissue, including pathology grade, TNM and clinical stage, 48 cases/48 cores, replaced by BL481c
Description: Bladder tissue lysate was prepared by homogenization in modified RIPA buffer (150 mM sodium chloride, 50 mM Tris-HCl, pH 7.4, 1 mM ethylenediaminetetraacetic acid, 1 mM phenylmethylsulfonyl fluoride, 1% Triton X-100, 1% sodium deoxycholic acid, 0.1% sodium dodecylsulfate, 5 μg/ml of aprotinin, 5 μg/ml of leupeptin. Tissue and cell debris was removed by centrifugation. Protein concentration was determined with Bio-Rad protein assay. The product was boiled for 5 min in 1 x SDS sample buffer (50 mM Tris-HCl pH 6.8, 12.5% glycerol, 1% sodium dodecylsulfate, 0.01% bromophenol blue) containing 50 mM DTT.
Description: Bladder tissue lysate was prepared by homogenization in modified RIPA buffer (150 mM sodium chloride, 50 mM Tris-HCl, pH 7.4, 1 mM ethylenediaminetetraacetic acid, 1 mM phenylmethylsulfonyl fluoride, 1% Triton X-100, 1% sodium deoxycholic acid, 0.1% sodium dodecylsulfate, 5 μg/ml of aprotinin, 5 μg/ml of leupeptin. Tissue and cell debris was removed by centrifugation. Protein concentration was determined with Bio-Rad protein assay. The product was boiled for 5 min in 1 x SDS sample buffer (50 mM Tris-HCl pH 6.8, 12.5% glycerol, 1% sodium dodecylsulfate, 0.01% bromophenol blue) containing 50 mM DTT.
Description: Bladder cancer with bladder tissue array (2016 WHO classification), including pathology grade, TNM and clinical stage (AJCC 7th edition), 64 cases/192 cores, replacing BL208
