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1.
Ye Mun Low Ivan Kok Seng Yap Kartini Abdul Jabar Mohd Yasim Md Yusof Chun Wie Chong Cindy Shuan Ju Teh 《Metabolomics : Official journal of the Metabolomic Society》2017,13(5):65
Introduction
Genotype and metabolomic variation are important for bacterial survival and adaptation to environmental changes.Objectives
In this study, we compared the relationship among Klebsiella pneumoniae strains based on their genotypic and metabolic profiles. In addition, we also evaluated the association of the relationship with beta-lactamase production.Methods
A total of 53 K. pneumoniae strains isolated in 2013–2014 from a tertiary teaching hospital in Malaysia were subjected to antimicrobial susceptibility testing (AST) via disk diffusion method and beta-lactamase production confirmation. The bacterial strains were also typed genotypically and metabolically via REP-PCR and 1H-NMR spectroscopy respectively. The concordance of the matrices derived based on genotypic and metabolic characterization was measured based on Spearman’s rank correlation.Results
Spearman’s correlation rank showed that there is a weak but significant negative correlation between the genetic fingerprints and metabolic profiles of K. pneumoniae. Specifically, K. pneumoniae strains were clustered into five major clusters based on REP-PCR where most of the carbapenem resistant K. pneumoniae (CRKP) strains made up the major cluster. In contrast, metabolic patterns of the three groups (i.e. CRKP, extended spectrum beta-lactamase producing K. pneumoniae (ESBL), susceptible) of K. pneumoniae were clearly differentiated on PLS-DA score plots derived from 1H-NMR spectroscopy.Conclusion
Overall, this study showed that metabolomic profiling using 1H-NMR spectroscopy is able to discriminate K. pneumoniae strains based on their beta-lactamase production status.2.
Masato Tashiro Kiyohide Fushimi Kei Kawano Takahiro Takazono Tomomi Saijo Kazuko Yamamoto Shintaro Kurihara Yoshifumi Imamura Taiga Miyazaki Katsunori Yanagihara Hiroshi Mukae Koichi Izumikawa 《BMC pulmonary medicine》2017,17(1):219
Background
There is conflicting evidence regarding the benefit of adjunctive corticosteroid therapy in patients with Mycoplasma pneumoniae pneumonia. We hypothesised that corticosteroid therapy could reduce mortality and length of stay (LOS) in such patients.Methods
Adult patients with M. pneumoniae pneumonia from January 2010 to December 2013 were identified from the Japanese Diagnosis Procedure Combination inpatient database. The effects of low-dose and high-dose corticosteroid therapies on mortality, LOS, drug costs and hyperglycaemia requiring insulin treatment were evaluated using propensity score analyses.Results
Eligible patients (n?=?2228) from 630 hospitals were divided into no-corticosteroid (n?=?1829), low-dose corticosteroid (n?=?267) and high-dose corticosteroid (n?=?132) groups. The propensity score-matched pairs were generated from no-corticoid and low-dose corticoid groups (251 pairs), or no-corticoid and high-dose corticosteroid groups (120 pairs). Adjunctive corticosteroid therapy did not decrease 30-day mortality. In addition, both low-dose and high-dose corticosteroid therapies were associated with increases in LOS. Furthermore, hyperglycaemia requiring insulin treatment and drug cost increased with corticosteroid use.Conclusions
Adjunctive treatment with low-dose or high-dose corticosteroids may not be beneficial in M. pneumoniae pneumonia.3.
Christiaan A. Rees Katherine V. Nordick Flavio A. Franchina Alexa E. Lewis Elizabeth B. Hirsch Jane E. Hill 《Metabolomics : Official journal of the Metabolomic Society》2017,13(2):18
Introduction
Microorganisms catabolize carbon-containing compounds in their environment during growth, releasing a subset of metabolic byproducts as volatile compounds. However, the relationship between growth media and the production of volatile compounds has been largely unexplored to-date.Objectives
To assess the core and media-specific components of the Klebsiella pneumoniae volatile metabolome via growth in four in vitro culture media.Methods
Headspace volatiles produced by cultures of K. pneumoniae after growth to stationary phase in four rich media (brain heart infusion broth, lysogeny broth, Mueller-Hinton broth, and tryptic soy broth) were analyzed using comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC-TOFMS). Differences in the composition of headspace volatiles as a function of growth media were assessed using hierarchical clustering analysis (HCA) and principal component analysis (PCA).Results
A total of 365 volatile compounds were associated with the growth of K. pneumoniae across all media, of which 36 (10%) were common to all growth media, and 148 (41%) were specific to a single medium. In addition, utilizing all K. pneumoniae-associated volatile compounds, strains clustered as a function of growth media, demonstrating the importance of media in determining the metabolic profile of this organism.Conclusion
K. pneumoniae produces a core suite of volatile compounds across all growth media studied, although the volatile metabolic signature of this organism is fundamentally media-dependent.4.
Chih-Yueh Liu Chang-Ching Weng Chih-Hsiang Lin Chiou-Ying Yang Kwok-Kong Tony Mong Yaw-Kuen Li 《Biotechnology letters》2017,39(3):407-413
Objectives
A Neissaria bacterial pilus sugar, bacillosamine, was synthesized and, for the first time, used as a probe to screen a single-chain variable fragment (scFv).Results
Four Neisseria, Neisseria gonorrhoeae, Neisseria meningitidis, Neisseria sicca and Neisseria subflava, and two negative controls, Streptococcus pneumoniae and Escherichia coli, were tested through ELISA, immunostaining and gold nanoparticle immunological assay. All results indicated that the selected scFv is feasible for the specific detection of Neisseria species via the recognition of bacillosamine.Conclusions
The recombinant scFv could detect Neisseria strains at 106 CFU/ml.5.
Chengqian Zhu Xiao Jiang Yongqiang Zhang Jie Lin Shuilin Fu Heng Gong 《Biotechnology letters》2015,37(9):1783-1790
Objective
To improve 1,3-propanediol production in Klebsiella pneumoniae, the effects of puuC expression in lactate- and lactate/2,3-butanediol-deficient strains were assessed.Results
Overexpression of puuC (encoding an aldehyde dehydrogenase) inhibited 1,3-propanediol production and increased 3-hydroxypropionic acid formation in both lactate- and lactate/2,3-butanediol-deficient strains. An improvement in 1,3-propanediol production was only achieved in a lactate-deficient strain via moderate expression of puuC; at the end of the fermentation, 1,3-propanediol productivity increased by 14 % compared with the control. Further comparative analysis of the metabolic flux distributions in different strains indicated that 3-hydroxypropionic acid formation could play a considerable role in cell metabolism in K. pneumoniae.Conclusion
An improvement in 3-hydroxypropionic acid formation would be beneficial for cell metabolism, which can be accomplished by enhancing 1,3-propanediol productivity in a lactate-deficient strain via moderate expression of puuC.6.
Xiaohong Chen Junjun Chen Yuanxing Zhang Ping Zhu Yong Deng Qin Liu 《Biotechnology letters》2016,38(6):959-967
Objective
To achieve secreted expression of the truncated capsid protein from porcine circovirus type 2 (PCV2) in Pichia pastoris.Results
A truncated cap gene (tcap) with a deleted N-terminal nuclear localization signal was optimized and synthesized. Effective secreted expression was achieved in P. pastoris GS115. The high-productive recombinant strain for tCap was grown in a 5 l bioreactor and the productivity of tCap in supernatant reached 250 μg/ml. Furthermore, serum antibody test demonstrated that adjuvant-assisting tCap induced a significant increase of specific PCV2-Cap antibody over time in mice and a similar antibody level in pigs compared with a commercial Cap-based subunit vaccine.Conclusion
This work establishes a secreted expression strategy in P. pastoris for the production of PCV2 Cap with superior bioactivity, and this strategy might provide potential uses in developing Cap-based subunit vaccine in the future.7.
Objective
Concatenation of two NdeI–XhoI gene fragments via an oligonucleotide linker on a plasmid vector with an SfiI site was performed to evaluate success rates in construction of polycistronic genes expressible in Escherichia coli.Results
A series of plasmids with an SfiI site between the selection marker and the replication origin were constructed. The three wheat eEF1B subunit genes inserted between the NdeI and XhoI sites of pET-22b were transferred to the SfiI-containing plasmid with a spectinomycin-resistance gene. Then, the marker gene in the resultant plasmids was substituted with the ampicillin-resistance gene. These plasmids were used for concatenation of two different genes via a linker oligonucleotide containing a ribosome-binding site. During these operations, 42 clones were picked up out of which 41 had the intended product plasmid.Conclusion
This method, named as the SfiNX method, is useful for trial-and-error based testing of different combinations of fusion and co-expression partners for optimization of recombinant protein production.8.
Thijs Welle Anna T. Hoekstra Ineke A. J. J. M. Daemen Celia R. Berkers Matheus O. Costa 《Metabolomics : Official journal of the Metabolomic Society》2017,13(7):83
Introduction
Swine dysentery caused by Brachyspira hyodysenteriae is a production limiting disease in pig farming. Currently antimicrobial therapy is the only treatment and control method available.Objective
The aim of this study was to characterize the metabolic response of porcine colon explants to infection by B. hyodysenteriae.Methods
Porcine colon explants exposed to B. hyodysenteriae were analyzed for histopathological, metabolic and pro-inflammatory gene expression changes.Results
Significant epithelial necrosis, increased levels of l-citrulline and IL-1α were observed on explants infected with B. hyodysenteriae.Conclusions
The spirochete induces necrosis in vitro likely through an inflammatory process mediated by IL-1α and NO.9.
Nicholas J. Bond Albert Koulman Julian L. Griffin Zoe Hall 《Metabolomics : Official journal of the Metabolomic Society》2017,13(11):128
Introduction
Mass spectrometry imaging (MSI) experiments result in complex multi-dimensional datasets, which require specialist data analysis tools.Objectives
We have developed massPix—an R package for analysing and interpreting data from MSI of lipids in tissue.Methods
massPix produces single ion images, performs multivariate statistics and provides putative lipid annotations based on accurate mass matching against generated lipid libraries.Results
Classification of tissue regions with high spectral similarly can be carried out by principal components analysis (PCA) or k-means clustering.Conclusion
massPix is an open-source tool for the analysis and statistical interpretation of MSI data, and is particularly useful for lipidomics applications.10.
Korey J. Brownstein Mahmoud Gargouri William R. Folk David R. Gang 《Metabolomics : Official journal of the Metabolomic Society》2017,13(11):133
Introduction
Botanicals containing iridoid and phenylethanoid/phenylpropanoid glycosides are used worldwide for the treatment of inflammatory musculoskeletal conditions that are primary causes of human years lived with disability, such as arthritis and lower back pain.Objectives
We report the analysis of candidate anti-inflammatory metabolites of several endemic Scrophularia species and Verbascum thapsus used medicinally by peoples of North America.Methods
Leaves, stems, and roots were analyzed by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) and partial least squares-discriminant analysis (PLS-DA) was performed in MetaboAnalyst 3.0 after processing the datasets in Progenesis QI.Results
Comparison of the datasets revealed significant and differential accumulation of iridoid and phenylethanoid/phenylpropanoid glycosides in the tissues of the endemic Scrophularia species and Verbascum thapsus.Conclusions
Our investigation identified several species of pharmacological interest as good sources for harpagoside and other important anti-inflammatory metabolites.11.
Ying-ge Wang Jin-mei Cheng Hai-bo Ding Xi Lin Guo-hao Chen Mei Zhou Sheng-nan Ye 《Mycopathologia》2018,183(3):551-558
Objective
To improve the diagnosis and treatment of Penicilliosis marneffei without human immunodeficiency virus infection.Methods
Analyze and review the clinical features, diagnosis and treatment of six cases of P. marneffei without human immunodeficiency virus infection at The First Affiliated Hospital of Fujian Medical University.Results
Two cases were diagnosed in the ENT Department, three cases in the respiratory department and one case in the dermatological department. Penicillium marneffei infection was confirmed by sputum culture, blood culture and tissue biopsy. After definite diagnosis, one refused further treatment, and others showed significant improvement.Conclusion
Penicilliosis marneffei is insidious onset and easy to be escaped and misdiagnosed. To achieve early diagnosis and appropriate treatment, doubtful cases should be alerted for the diagnoses as P. marneffei.12.
Chelladurai Rathnasingh Jong Myoung Park Duk-ki Kim Hyohak Song Yong Keun Chang 《Biotechnology letters》2016,38(6):975-982
Objectives
To improve the production of 2,3-butanediol (2,3-BD) in Klebsiella pneumoniae, the genes related to the formation of lactic acid, ethanol, and acetic acid were eliminated.Results
Although the cell growth and 2,3-BD production rates of the K. pneumoniae ΔldhA ΔadhE Δpta-ackA strain were lower than those of the wild-type strain, the mutant produced a higher titer of 2,3-BD and a higher yield in batch fermentation: 91 g 2,3-BD/l with a yield of 0.45 g per g glucose and a productivity of 1.62 g/l.h in fed-batch fermentation. The metabolic characteristics of the mutants were consistent with the results of in silico simulation.Conclusions
K. pneumoniae knockout mutants developed with an aid of in silico investigation could produce higher amounts of 2,3-BD with increased titer, yield, and productivity.13.
Charles Eugenio McCafferty Marra Jai Aghajani David Abi-Hanna Iain Bruce Gosbell Slade Owen Jensen 《Annals of clinical microbiology and antimicrobials》2018,17(1):36
Introduction
During clinical use, gastrointestinal endoscopes are grossly contaminated with patient’s native flora. These endoscopes undergo reprocessing to prevent infectious transmission upon future use. Endoscopy-associated infections and outbreaks have been reported, with a recent focus on the transmission of multi-drug resistant organisms. This review aims to provide an update on endoscopy-associated infections, and the factors contributing to their occurrence.Methods
PubMed, ScienceDirect, and CINAHL were searched for articles describing gastrointestinal endoscopy-associated infections and outbreaks published from 2008 to 2018. Factors contributing to their occurrence, and the outcomes of each outbreak were also examined.Results
This review found 18 articles, 16 of which described duodenoscope-associated infections, and the remaining two described colonoscope- and gastroscope-associated infection respectively. Outbreaks were reported from the United States, France, China, Germany, the Netherlands and the United Kingdom. The causative organisms reported were Klebsiella pneumoniae, Pseudomonas aeruginosa, Escherichia coli and Salmonella enteritidis.Conclusions
A number of factors, including lapses in reprocessing, biofilm formation, endoscope design issues and endoscope damage, contribute to gastrointestinal endoscopy associated infection. Methods of improving endoscope reprocessing, screening for contamination and evaluating endoscope damage may be vital to preventing future infections and outbreaks.14.
Background and aims
The changes in the characteristics of Panicum virgatum, an exotic invasive species, after invading various plant communities on the Loess Plateau in China and the main soil nutrient factors in these communities closely associated with invasion remain unclear.Methods
A pot culture experiment was carried out to simulate the changes in photosynthesis, biomass, and biomass allocation in P. virgatum and to identify the main soil nutrient factors in various soils collected from local plant communities. P. virgatum was grown in soils collected from communities of P. virgatum (PS treatment), Setaria viridis (SS treatment), Bothriochloa ischaemum (BS treatment), and Artemisia sacrorum (AS treatment) and in a mixed soil from the communities of S. viridis, B. ischaemum, and A. sacrorum (MS treatment).Results
Photosynthesis in P. virgatum differed significantly among the soil treatments. Net photosynthetic rate, stomatal conductance, and photochemical efficiency (Fv/Fm) were highest in PS, whereas single-photon avalanche diode values were highest in PS and SS. The variation of biomass differed significantly in different tissues of P. virgatum in the treatments. Leaf and stem biomasses were highest in PS and SS, and root biomass was highest in PS and MS. Total biomass differed significantly among the treatments, except between BS and MS. Both the leaf to total and stem to total biomass ratios were highest in AS and SS, but the root to total biomass ratio was lowest in these two treatments. A constrained redundancy analysis and a path analysis suggested that the water-soluble nitrate-nitrogen (W-NN) concentration of the soil could significantly affect photosynthesis, biomass, and biomass allocation in P. virgatum.Conclusions
Photosynthesis, biomass, and biomass allocation in P. virgatum differed significantly when grown in soils from different local plant communities on the Loess Plateau. The soil W-NN concentration in these local plant communities likely has a large impact on the invasive success of P. virgatum.15.
Maximilian Ginders Michael Leschnik Frank Künzel Doris Kampner Claudia Mikula Georg Steindl Inga Eichhorn Andrea T. Feßler Stefan Schwarz Joachim Spergser Igor Loncaric 《Acta veterinaria Scandinavica》2017,59(1):79
Background
The aim of the present study was to investigate the genetic relatedness and the antimicrobial resistance profiles of a collection of Austrian Streptococcus pneumoniae isolates from companion animals and horses. A total of 12 non-repetitive isolates presumptively identified as S. pneumoniae were obtained during routinely diagnostic activities between March 2009 and January 2017.Results
Isolates were confirmed as S. pneumoniae by bile solubility and optochin susceptibility testing, matrix-assisted laser desorption-ionization-time of flight (MALDI-TOF) mass spectrometry and sequence analysis of a part recA and the 16S rRNA genes. Isolates were further characterized by pneumolysin polymerase chain reaction (PCR) and genotyped by multilocus sequence typing (MLST). Antimicrobial susceptibility testing was performed and resistance genes were detected by specific PCR assays. All isolates were serotyped. Four sequence types (ST) (ST36, ST3546, ST6934 and ST6937) and four serotypes (3, 19A, 19F and 23F) were detected. Two isolates from twelve displayed a multidrug-resistance pheno- and genotype.Conclusions
This study represents the first comprehensive investigation on characteristics of S. pneumoniae isolates recovered from Austrian companion animals and horses. The obtained results indicate that common human sero- (23F) and sequence type (ST36) implicated in causing invasive pneumococcal disease (IPD) may circulate in dogs. Isolates obtained from other examined animals seem to be host-adapted.16.
Yun Kong Yajun Qu Shengjun Wang Peng George Wang Min Chen 《Biotechnology letters》2018,40(8):1219-1226
Objective
To heterologously produce the Shigella dysenteriae serotype 1 O-polysaccharide (O-PS, O-antigen) in Escherichia coli by transferring the minimum number of genes instead of the entire O-PS gene cluster.Results
The three glycosyltransferase genes (rfbR, rfbQ and rfp) responsible for the formation of the O-repeat unit were introduced into E. coli K-12 W3110 to synthesize S. dysenteriae 1 O-PS. The specific O-antigen ladder type with different chain lengths of O-repeat units was observed in the recombinant E. coli strain by SDS-PAGE silver staining and western blotting using S. dysenteriae 1 lipopolysaccharide antiserum. Analysis by mass spectrometry and ion chromatography suggested generation of the specific S. dysenteriae 1 O-repeat unit structure with an extra glucose residue attached.Conclusions
Recombinant E. coli expressing specific glycosyltransferase genes can generate the O-PS of S. dysenteriae 1 and might be able to synthesize heterologous O-antigens of various pathogenic bacteria for vaccine preparation.17.
Zeinab Panahi Asghar Abdoli Ghasem Mosayebi Mehdi Mahdavi Fariborz Bahrami 《Biotechnology letters》2018,40(3):527-533
Objective
To evaluate the combined effects of CpG oligodeoxynucleotides (CpG-ODNs) adjuvant and subcutaneous injection route on efficacy of a HIV-1-tat DNA vaccine candidate using BALB/c mice as an animal model.Results
Evaluation of cellular and humoral immunity of mice injected subcutaneously with HIV-1-tat gene cloned into a pcDNA3.1 vector indicated that significant levels of IFN-γ cytokine secretion (900 pg/ml), lymphocyte proliferation (2.5 stimulation index) and IgG2a (1.45 absorbance 450 nm) production could be achieved. These indicators of stimulated cellular immunity were elicited 2 weeks after the last injection (P < 0.05).Conclusions
Formulation of HIV-1-tat DNA vaccine candidate with CpG-ODNs as an adjuvant while administrated subcutaneously are a promising approach to induce effective cellular immunity responses against HIV-1 infection.18.
Qiong Xu Chun-yang Li Yi Wang Hui-ping Li Bing-bing Wu Yong-hui Jiang 《BMC medical genomics》2018,11(1):92
Background
Verheij syndrome is a rare microdeletion syndrome of chromosome 8q24.3 that harbors PUF60, SCRIB, and NRBP2 genes. Subsequently, loss of function mutations in PUF60 have been found in children with clinical features significantly overlapping with Verheij.Case presentation
Here we present the first Chinese Han patient with a de novo nonsense variant (c.1357C?>?T, p.Gln453*) in PUF60 by clinical whole exome sequencing. The 5-year-old boy presents with dysmorphic facial features, intellectual disability, and growth retardation but without apparent cardiac, renal, ocular, and spinal anomalies.Conclusions
Our finding contributes to the understanding of the genotype and phenotype in PUF60 related disorder.19.
Arshid Yousefi-Avarvand Mohsen Tafaghodi Saman Soleimanpour Farzad Khademi 《生物学前沿》2018,13(4):293-296