OmicsSuite: a customized and pipelined suite for analysis and visualization of multi-omics big data

With the advancements in high-throughput sequencing technologies such as Illumina,PacBio,and 10X Genomics platforms,and gas/liquid chromatography-mass spectrometry,large volumes of biological data in multiple formats can now be obtained through multi-omics analysis.Bioinformatics is constantly evolving and seeking breakthroughs to solve multi-omics problems;however,it is challenging for most experimental biologists to analyse data using command-line interfaces,coding,and scripting.Based on experience with multi-omics,we have developed OmicsSuite,a desktop suite that comprehensively integrates statistics and multi-omics analysis and visualization.The suite has 175 sub-applications in 12 categories,including Sequence,Statistics,Algorithm,Genomics,Transcriptomics,Enrichment,Proteomics,Metabolomics,Clinical,Microorganism,Single Cell,and Table Operation.We created the user interface with Sequence View,Table View,and intelligent components based on JavaFX and the popular Shiny framework.The multi-omics analysis functions were developed based on BioJava and 300+packages provided by the R CRAN and Bioconductor communities,and it encompasses over 3000 adjustable parameter interfaces.OmicsSuite can directly read multi-omics raw data in FastA,FastQ,Mutation Annotation Format,mzML,Matrix,and HDF5 formats,and the programs emphasize data transfer directions and pipeline analysis functions.OmicsSuite can produce pre-publication images and tables,allowing users to focus on biological aspects.OmicsSuite offersmulti-omics step-by-step workflows that can be easily applied to horticultural plant breeding and molecular mechanism studies in plants.It enables researchers to freely explore the molecular information contained in multi-omics big data(Source:https://github.com/OmicsSuite/,Website:https://omicssuite.github.io,v1.3.9).

Effect of Lactobacillus rhamnosus GG supernatant on serotonin transporter expression in rats with post-infectious irritable bowel syndrome

AIM To evaluate the effect of Lactobacillus rhamnosus GG supernatant(LGG-s) on the expression of serotonin transporter(SERT) in rats with post-infectious irritable bowel syndrome(PI-IBS).METHODS Campylobacter jejuni 81-176(1010 CFU/m L) was used to induce intestinal infection to develop a PI-IBS model. After evaluation of the post-infectious phase by biochemical tests, Dn A agarose gel electrophoresis, abdominal withdrawal reflex(AWR) test, and the intestinal motility test, four PI-IBS groups received different concentrations of LGG-s for 4 wk. The treatments were maintained for 1.0, 2.0, 3.0 or 4.0 wk during the experiment, and the colons and brains were removed for later use each week. SERT m Rn A and protein levels were detected by real-time PCR and Western blot, respectively.RESULTS The levels of SERT m Rn A and protein in intestinal tissue were higher in rats treated with LGG-s than in control rats and PI-IBS rats gavaged with PBS during the whole study. Undiluted LGG-s up-regulated SERT m Rn A level by 2.67 times compared with the control group by week 2, and SERT m Rn A expression kept increasing later. Double-diluted LGG-s was similar to undiluted-LGG-s, resulting in high levels of SERT m Rn A. Triple-diluted LGG-s up-regulated SERT m Rn A expression level by 6.9-times compared with the control group, but SERT m Rn A expression decreased rapidly at the end of the second week. At the first week, SERT protein levels were basically comparable in rats treated with undiluted LGG-s, double-diluted LGG-s, and triplediluted LGG-s, which were higher than those in the control group and PBS-treated PI-IBS group. SERT protein levels in the intestine were also comparable in rats treated with undiluted LGG-s, double-diluted LGG-s, and triple-diluted LGG-s by the second and third weeks. SERT m Rn A and protein levels in the brain had no statistical difference in the groups during the experiment.CONCLUSION LGG-s can up-regulate SERT m Rn A and protein levels in intestinal tissue but has no influence in brain tissue in rats with PI-IBS.

Proteome Analysis of Neisseria meningitidis Serogroup Strains C Associated with Outbreaks in China

Objective During 2003-2005, an outbreak of meningitis due to Neisseria meningitidis serogroup C occurred in China. With the aim to find strain clues result in the final epidemics, the ancestral strain 053442, a clinical isolate, and a carrier strain 053426 with different gene type were analyzed. Methods Clinical strain 053442 and carrier strain 053426 were cultured on GC agar plates under the same condition. Two-dimensional electrophoresis was performed using the pH 3–10 nonlinear IPG strips of 24 cm length, and all the protein spots were identified by matrix-assisted laser desorption/ionization time of flight spectrometry. Results 502 and 380 protein spots were identified in 053426 and 053442 respectively, relating to 266 and 202 different genes covering a wide range of cellular functions. The express volume and number of proteins involved in energy metabolism, protein synthesis and amino acid biosynthesis in 053426 were higher than in 053442. Virulence factor Opa, Opc and a series of proteins involved in pilus assembly and retraction were identified in 053442, which appear to be of primary importance in colonization and invasion of human cells. Compared to 053442, virulence protein species were less in 053426, with lower express volumes too. No Opa and Opc were detected in 053426. Conclusion The different protein expression profiles of the clinical strain 053442 and carrier strain 053426 in the present study provide some clues of the different pathogenicity of the two strains, which may account for result in the final epidemics.