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 offers multi-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).

Genetic and Phenotypic Variation of Campylobacter jejuni NCTC11168 Caused by flhA Mutation during Laboratory Passage.

Objective: Campylobacter jejuni NCTC11168 is commonly used as a standard strain for flagellar biosynthesis research. In this report, two distinguished phenotypic isolates (CJ1Z, flhA mutant strain, lawn; CJ2S, flhA complemented strain, normal colony) appeared during laboratory passages for NCTC11168. Methods: Phenotypic assessments, including motility plates, transmission electron microscopy, biofilm formation assay, autoagglutination assay, and genome re-sequencing for these two isolates (CJ1Z, flhA mutant strain; CJ2S, flhA complemented strain) were carried out in this study. Results: Transmission electron microscopy revealed that the flagellum was lost in CJ1Z. Phenotypic assessments and genome sequencing of the two isolates were performed in this study. The capacity for biofilm formation, colony auto-agglutination, and isolate motility was reduced in the mutant CJ1Z. Comparative genomic analysis indicated a unique native nucleotide insertion in flhA (nt, 2154) that caused the I719Y and I720Y mutations and early truncation in flhA. Conclusion: FlhA has been found to influence the expression of flagella in C. jejuni. To the best of our knowledge, this is the first study to describe the function of the C-terminal of this protein.

Genetic Characteristics of Lipooligosaccharide and Capsular Polysaccharide of Campylobacter jejuni from Different Sources in China.

Objective: To determine the distribution of two important virulence factors [lipooligosaccharide (LOS) and capsular polysaccharide (CPS)] in Campylobacter jejuni ( C. jejuni) isolated from different sources in China and to develop a rapid screening method for Guillain-Barré syndrome (GBS)-associated strains. Methods: Whole-genome sequencing was carried out for 494 C. jejuni strains. The OrthoMCL software was used to define the LOS/CPS gene clusters. CPS genotyping was performed with serotype-specific sequence alignment using the BLAST software. Real-time Polymerase chain reaction (PCR) was developed with the unique sequences of specific CPS types. Results: Nine novel and 29 previously confirmed LOS classes were identified. LOS classes A, B, and C were the most common (48.2%, 238/494) among the 494 strains. Twenty-six capsular types were identified in 448 strains. HS2, HS4c, HS5/31, HS19, and HS8/17 were the most frequent CPS genotypes (58.7%, 263/448). Strains of 17 CPS genotypes (strain number > 5) had one or two prevalent LOS classes ( P < 0.05). Multiplex real-time PCR for rapid identification of HS2, HS19, and HS41 was developed and validated with strains of known serotypes. Conclusion: Our results describe the genetic characteristics of the important virulence factors in C. jejuni strains in China. The multiplex real-time PCR developed in this study will facilitate enhanced surveillance of GBS-associated strains in China.

The electrochemiluminescence coreactant accelerator of metal-organic frameworks grafted with N-(aminobutyl)-N-(ethylisoluminol) for the ultrasensitive detection of chloramphenicol.

In this work, metal-organic frameworks (MOFs) are utilized as effective ECL coreactant accelerator to enhance the ECL responses of N-(aminobutyl)-N-(ethylisoluminol) (ABEI). Zn-based MOFs (MOF-Zn-1) were prepared by chelating Zn ions with melamine and thiophenedicarboxylic acid (TPDA), which observably accelerated the electrocatalytic oxidation of tripropylamine (TPA). Then, ABEI-MOF-Zn-1 as a high-performance ECL emitter was synthesized via an amide reaction between ABEI and mercaptopropionic acid (MPA) modified MOF-Zn-1. Strikingly, the ABEI-MOF-Zn-1 showed the 18-fold increase in the ECL signals relative to pure ABEI by using TPA as a coreactant. Moreover, ferrocene (Fc) as a quencher was first linked with capture DNA (cDNA), and then used to modify the ABEI-MOF-Zn-1, thereby constructing a label-free ECL biosensor. After the linkage between chloramphenicol (CAP) and aptamer DNA (aptDNA), the ECL response was definitely recovered by releasing L-DNA from double-stranded DNA (dsDNA, hybridization of aptDNA and L-DNA). The resultant sensor showed a wide linear range of 1.00 nM-0.10 mM (R2 = 0.99) and a low limit of detection (LOD) down to 0.11 nM for detecting CAP. This work developed a novel pattern to design an efficient ECL enhanced emitter, coupled by expanding its potential applications in clinical diagnosis.

Genetic Characteristics and Antimicrobial Susceptibility of Arcobacter butzleri Isolates from Raw Chicken Meat and Patients with Diarrhea in China.

Arcobacter is an emerging foodborne pathogen worldwide. In this study, the prevalence, antimicrobial susceptibility and genetic characteristics of Arcobacter from different sources were investigated. Eighteen A. butzleri isolates were obtained from 60 raw chicken meat samples (16/60, 27%) and 150 patients with diarrhea (2/150, 1.3%). The resistance ratios to nalidixic acid, ciprofloxacin, clindamycin, chloramphenicol, and florfenicol were 83.33% (15/18), 38.89% (7/18), 38.89% (7/18), 33.33% (6/18) and 33.33% (6/18), respectively. We performed whole genome sequencing of the 18 isolates, and we predicted antibiotic resistance genes and virulence factors by using assembled genomes through blastx analysis. Two resistance genes, bla OXA-464 and tet(H), and the C254T mutation in gyrA, were identified in the genomes of some resistant isolates. Furthermore, virulence genes, such as flgG, flhA, flhB, fliI, fliP, motA, cadF, cjl349, ciaB, mviN, pldA and tlyA, were found in all strains, whereas hecA, hecB and iroE were found in only some strains. Phylogenetic tree analysis of A. butzleri isolates on the basis of the core-genome single nucleotide polymorphisms showed that two isolates from patients with diarrhea clustered together, separately from the isolates from raw chicken and the chicken strains. This study is the first comprehensive analysis of Arcobacter isolated in Beijing.

Highly Enhanced Electrochemiluminescence Luminophore Generated by Zeolitic Imidazole Framework-8-Linked Porphyrin and Its Application for Thrombin Detection.

Novel and distinct enhancement in electrochemiluminescence (ECL) signals of advanced organic luminophores are of importance for expanding their applications in early diagnosis. This work reported the construction of an ultrasensitive label-free ECL aptasensor for thrombin (TB) detection by grafting zinc proto-porphyrin IX (ZnP) onto an aminated zeolitic imidazole framework-8 (defined as ZnP-NH-ZIF-8 for clarity) as the luminophore. The structure and optical properties of the resulting ZnP-NH-ZIF-8 were carefully characterized. For that, there appeared to be weak ECL radiation for ZnP in dichloromethane (DCM) containing tetra-n-butylammonium perchlorate (TBAP) because of the as-formed singlet-state oxygen via the "reduction-oxidation" route. More notably, the ECL signals display 153-times enhancement for ZnP-NH-ZIF-8, thanks to the excellent catalytic kinetics for the oxygen reduction reaction (ORR). By virtue of the specific interactions of the TB aptamer (TBA) with the TB protein and the highly efficient catalysis of the ZnP-NH-ZIF-8 for ORR, the as-prepared aptasensor showed a wider linear range (0.1 fM∼1 pM) and a lower detection limit (ca. 58.6 aM). This work provides some useful guidelines for synthesis of an advanced organic luminophore with largely boosted ECL signals in ultrasensitive analysis and clinical diagnosis.

Genetic and Antibiotic Resistance Characteristics of Campylobacter jejuni Isolated from Diarrheal Patients, Poultry and Cattle in Shenzhen.

OBJECTIVE: To investigate genetic and antibiotic resistance characteristics of Campylobacter jejuni (C. jejuni) isolated from Shenzhen. METHODS: Multilocs sequence typing and agar dilution methods were used to define the genotype and antibiotic resistance of C. jejuni, respectively. RESULTS: In total, 126 C. jejuni strains were isolated. The prevalence of C. jejuni was 5.3% in diarrheal patients. The prevalence in poultry meat (36.5%) was higher than that in cattle meat (1.1%). However, the prevalence in poultry cloacal swabs (27.0%) was lower than that in cattle stool (57.3%). Sixty-two sequence types were obtained, among which 27 of the STs and 10 alleles were previously unreported. The most frequently observed clonal complexes were ST 21 (11.9%), ST-22 (10.3%), and ST-403 (7.1%). ST-21, ST-45, ST-354, ST-403, and ST-443 complexes overlapped between isolates from patients and cattle, whereas ST-45 and ST-574 complexes overlapped between isolates from patients and poultry. All C. jejuni were resistant to at least one antibiotic. The highest resistance rate was toward ciprofloxacin (89.7%), followed by tetracycline (74.6%), and nalidixic acid (69.0%). CONCLUSION: This is the first report of the genotypes and antibiotic resistance of C. jejuni in Shenzhen. Overlapping clonal complexes were found between isolates from patients and cattle, and between patients and poultry.

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/mL) was used to induce intestinal infection to develop a PI-IBS model. After evaluation of the post-infectious phase by biochemical tests, DNA 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 mRNA and protein levels were detected by real-time PCR and Western blot, respectively. RESULTS: The levels of SERT mRNA 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 mRNA level by 2.67 times compared with the control group by week 2, and SERT mRNA expression kept increasing later. Double-diluted LGG-s was similar to undiluted-LGG-s, resulting in high levels of SERT mRNA. Triple-diluted LGG-s up-regulated SERT mRNA expression level by 6.9-times compared with the control group, but SERT mRNA 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 triple-diluted 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 mRNA and protein levels in the brain had no statistical difference in the groups during the experiment. CONCLUSION: LGG-s can up-regulate SERT mRNA and protein levels in intestinal tissue but has no influence in brain tissue in rats with PI-IBS.

In vitro protein expression profile of Campylobacter jejuni strain NCTC11168 by two-dimensional gel electrophoresis and mass spectrometry.

OBJECTIVE: To investigate the protein expression profiles of the major food-borne pathogen Campylobacter jejuni NCTC11168. METHODS: Membrane and soluble cellular proteins were extracted from the genome-sequenced C. jejuni strain NCTC11168. Protein expression profiles were determined using two-dimensional gel electrophoresis (2-DE). All the detected spots on the 2-DE map were subjected to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF) analysis. RESULTS: A total of 537 and 333 spots were detected from the whole cell and membrane-associated proteins of C. jejuni NCTC11168 cultured on Columbia agar medium at 42 °C by 2-DE and Coomassie Brilliant Blue staining, respectively. Analyses of whole cell and membrane-associated proteins included 399 and 133 spots, respectively, which included 182 and 53 functional proteins identified by MALDI-TOF/TOF analysis. CONCLUSION: The comprehensive expression protein profiles of C. jeuni NCTC11168 obtained in this study will be useful for elucidating the roles of these proteins in further pathogenesis investigation.

Bacterial flora concurrent with Helicobacter pylori in the stomach of patients with upper gastrointestinal diseases.

AIM: To investigate the non-Helicobacter pylori (H. pylori) bacterial flora concurrent with H. pylori infection. METHODS: A total of 103 gastric biopsy specimens from H. pylori positive patients were selected for bacterial culture. All the non-H. pylori bacterial isolates were identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). RESULTS: A total of 201 non-H. pylori bacterial isolates were cultivated from 67 (65.0%) of the 103 gastric samples, including 153 isolates identified successfully at species level and 48 at genus level by MALDI-TOF MS. The dominant species were Streptococcus, Neisseria, Rothia and Staphylococcus, which differed from the predominantly acid resistant species reported previously in healthy volunteers. The prevalence of non-H. pylori bacteria was higher in non-ulcer dyspepsia group than in gastric ulcer group (100% vs 42.9%, P < 0.001). Six bacterial species with urease activity (Staphylococcus epidermidis, Staphylococcus warneri, Staphylococcus capitis, Staphylococcus aureus, Brevibacterium spp. and Klebsiella pneumoniae) were also isolated. CONCLUSION: There is a high prevalence of the non-H. pylori bacteria concurrent with H. pylori infection, and the non-H. pylori bacteria may also play important as-yet-undiscovered roles in the pathogenesis of stomach disorders.

Analysis of the urinary peptidome associated with Helicobacter pylori infection.

AIM: To investigate the relationship between urinary peptide changes and Helicobacter pylori (H. pylori) infection using urinary peptidome profiling. METHODS: The study was performed in volunteers (n=137) who gave informed consent. Urinary peptides were enriched by magnetic beads based weak cation exchange chromatography and spectrums acquired by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). ClinProTools bioinformatics software was used for statistical analysis and the recognition of peptide patterns. The marker peptides were identified by LTQ Obitrap XL tandem MS. RESULTS: Approximately 50 proteins or peptides which loaded onto the magnetic beads were detected by MALDI-TOF MS. By optimizing the parameters of the model, the Genetic Algorithm model had good recognition capability (97%) and positive predictive value (94%). Based on the model, 2 markers with molecular masses of 6788 and 1912 Da were found that differentiated between H. pylori positive and negative volunteers. The m/z 1912 sequence was parsed as SKQFTSSTSYNRGDSTF. The peptide was identified as isoform 1 of the fibrinogen α chain precursor, whose concentration in urine was markedly higher in H. pylori infected volunteers than in H. pylori non-infected ones. CONCLUSION: The appearance of urinary fibrinogen degradation products is caused by an active H. pylori-induced process.

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. CONCLUSIONS: 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.

Characteristics of lipo-oligosaccharide loci of Campylobacter jejuni isolates associated with Guillain-Barré Syndrome from Hebei, China.

Ganglioside mimicry by C.jejuni lipo-oligosaccharides (LOS) could induce the production of autoantibodies against gangliosides and the development of Guillain-Barré syndrome (GBS). The LOS biosynthesis region exhibits significant variation with different strains. Using PCR amplifications of genes from published LOS loci and sequencing the LOS biosynthesis loci, the eight GBS-associated C. jejuni strains from HeBei could be classified into four classes. The expression of sialylated LOS structures (class A) or non-sialylated LOS structures(class F, H and P) in the C. jejuni LOS is considered to be two different factors for the induction of GBS.

Comparative proteomic analysis of Campylobacter jejuni cultured at 37C and 42C.

Campylobacter jejuni has the potential to thrive at 37C (e.g., in the human intestinal tract) and 42C (e.g., in the poultry intestinal tract). We aimed to determine the protein expression profiles of C. jejuni cultured at 37C and 42C in vitro by two-dimensional electrophoresis (2DE). The differentially expressed spots/proteins between C. jejuni cultured at 37C and 42C were defined when their expression differed by twofold. The differently expressed spots detected from C. jejuni cultured both on agar and in broth at 37C and 42C were subjected to protein identification by MALDI-TOF/TOF. Overall, 15 and 20 differentially expressed proteins were defined for C. jejuni cultured at the two temperatures on agar and in broth, respectively. All of the identified differentially expressed proteins could be clustered as proteins involving the metabolism, regulator system, periplasmic proteins and the major antigens of C. jejuni. In conclusion, there are subsets of proteins that are optimally expressed at 37C, which may contribute to the host adaptation and/or the pathogenicity in the human intestinal tract.

[Multilocus sequence typing of methicillin-resistant Staphylococcus aureus].

OBJECTIVE: To analyze multilocus sequence typing (MLST) of methicillin-resistant Staphylococcus aureus (MRSA) strains in 2000 and 2005, and get a primary knowledge of MLST Characterization of MRSA. METHODS: Sequence analysis was conducted on seven allelic genes of 29 methicillin-resistant Staphylococcus aureus strains and 2 methicillin-sensitive Staphylococcus aureus (MSSA) strains and the allelic profiles were gained from internet database. RESULTS: All 12 MRSA strains in 2000 were sequence type (ST) 239 and 10 MRSA strains in 2005 were ST239, while 7 MRSA strains in 2005 were new types, ST5 (41.18%, 7/17). ST6 and ST630 were allelic profiles of 2 MSSA strains. ST239 was the most prevalent allelic profile (75.86%, 22/29), while ST5 was the second prevalent allelic profile (24.14%, 7/29) among all isolates. CONCLUSION: ST239 and ST5 are the most prevalent MRSA clones in this research. MRSA strains have different allelic profile from MSSA strains. MLST might provide an unambiguous method for assigning MRSA and MSSA isolates to known clones or assigning them as novel clones via the internet. Further studies need to be taken by increasing strains.

Comparative proteomic analysis of passaged Helicobacter pylori.

In order to identify the proteins associated with Helicobacter pylori colonization in mice, we used 2-dimensional gel electrophoresis (2-DE) to analyze the membrane- and soluble-cellular proteins extracted from H. pylori strain 26695 and the mouse-passaged homolog 88-3887. We defined 2- and 3-fold changes in protein expression as the threshold values for differential expression in the membrane-protein and whole-cell-protein fractions, respectively. The differentially expressed proteins were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF). A total of 29 proteins, including 16 membrane- or membrane-associated proteins (13 upregulated, 3 downregulated) and 13 cellular proteins (10 upregulated, 3 downregulated) were differentially expressed between the strains 26695 and 88-3887. Among the upregulated proteins, 10 proteins had been previously shown to be associated with the mouse colonization, and 13 upregulated proteins were shown to be associated with the adaptation of H. pylori in murine hosts for the first time in this study. The identified proteins were classified as proteins related to metabolism, stress response, virulence, or adhesion. The data presented in this report indicated that there were subsets of upregulated proteins in mouse-adapted H. pylori. In particular, the adhesins, virulence factors, and stress-response proteins are likely to contribute to colonization in mice.

[Multi-PCR identification and virulence genes detection of Campylobacter jejuni isolated from China].

OBJECTIVE: This study was to simultaneously identify Campylobacter jejuni and Campylobacter coli isolates in China by Multi-PCR assay and to study the prevalence of six virulence and toxin genes on them. METHODS: A multi-PCR method with three sets of primers specifically designed for application of a 16S rRNA as a universal control, mapA, ceuE based on the specific sequence of C. jejuni and C. coli, was applied to detect 65 Campylobacter isolates from China. Another two separately PCR Primers were directed towards the hippuricase gene (hipO) characteristic of C.jejuni and glyA gene characteristic of C. coli were performed for further confirmation. The presence of the cadF, virB11, flaA, cdtA, cdtB, cdtC genes among these 65 strains were investigated by PCR. RESULTS: From multi-PCR detection, 42 isolates belonged to C. jejuni, other 23 isolates belong to C. coli. Data showing the identification were 100% in concordance with the separated PCR for hipO and glyA amplification. The efficiency (100%) of identification by these three primers multi-PCR method was higher than the biochemical test (83.1%). The cadF and flaA genes were detected from 100% (65/65) of the isolates and the PCR product of each gene were identical with each isolate. Only 10.8% (7/65) of the isolates were positive for virB11. The cdtA gene was found in 92% (60/65) of the isolates. 97.6% (41/42) of C. jejuni had cdtB gene, whereas no PCR product with this primers for all the C. coli isolates. cdtC was presented in all the isolates but the lengths of PCR products were different. For C. jejuni, it was 555 bp, for C. coli, it was about 465 bp. CONCLUSION: This three primers simultaneous multi-PCR method seemed to be useful for the identification of C. jejuni and C. coli isolates from China since cadF and flaA genes were widely spread in Campylobacter isolates in this country. The present report on virB11 was similar to previous reports from other countries, but the distribution of cdt gene cluster in Campylobacter species isolated from China might be different.