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Journal of Invertebrate Pathology Nov 2017Wireworms (Coleoptera: Elateridae) are serious agricultural pests, with soil-dwelling larvae attacking subterranean tissues of crop plants and their fruit when in...
Wireworms (Coleoptera: Elateridae) are serious agricultural pests, with soil-dwelling larvae attacking subterranean tissues of crop plants and their fruit when in contact with the soil surface. Researchers collect wireworms for laboratory experiments to study their behaviour and test pest control agents but frequently lose them to Metarhizium Petch (Ascomycota: Hypocreales: Clavicipitaceae) infection. We found latent M. brunneum infection in 13-100% of live, asymptomatic Agriotes obscurus and A. lineatus wireworms acquired from agricultural fields and in wireworms maintained indoors, indicating its enzootic presence. M. brunneum DNA in the wireworms maintained indoors sometimes exceeded 250pg/ug total DNA (0.025% of whole-sample DNA mass). Expressed as copies of M. brunneum DNA/g, unadulterated soil levels of M. brunneum ranged from 4037 in agricultural field soil to 721,538 in soil harbouring a wireworm collection indoors, with the prevalence of latently-infected live wireworm specimens being directly related to soil levels. M. brunneum levels in live wireworms, when regressed against relative levels of 394 bacteria species in the microbiome, were proportionally related to only four: Pantoea agglomerans, Pandoraea pnomenusa, Nocardia pseudovaccinii, and Mycobacterium frederiksbergense. All four of these bacteria have previously been reported to express antimicrobial mechanisms. Consistent with occurrences of disease immunity reported for other pathogen-insect pairs, symbiotic bacteria may be suppressing M. brunneum-induced wireworm mortality. This would help explain why wireworms commonly succumb to infection after being brought into sterilized conditions, as well as the sometimes limited efficacy of M. brunneum when using it as a pest control agent in the field.
Topics: Agriculture; Animals; Coleoptera; Larva; Metarhizium; Mycoses; Pest Control, Biological
PubMed: 28919016
DOI: 10.1016/j.jip.2017.09.012 -
Bioinformatics (Oxford, England) Sep 2018Long-reads, point-of-care and polymerase chain reaction-free are the promises brought by nanopore sequencing. Among various steps in nanopore data analysis, the...
MOTIVATION
Long-reads, point-of-care and polymerase chain reaction-free are the promises brought by nanopore sequencing. Among various steps in nanopore data analysis, the end-to-end mapping between the raw electrical current signal sequence and the reference expected signal sequence serves as the key building block to signal labeling, and the following signal visualization, variant identification and methylation detection. One of the classic algorithms to solve the signal mapping problem is the dynamic time warping (DTW). However, the ultra-long nanopore sequencing and an order of magnitude difference in the sampling speed complexify the scenario and make the classical DTW infeasible to solve the problem.
RESULTS
Here, we propose a novel multi-level DTW algorithm, continuous wavelet DTW (cwDTW), based on continuous wavelet transforms with different scales of the two signal sequences. Our algorithm starts from low-resolution wavelet transforms of the two sequences, such that the transformed sequences are short and have similar sampling rates. Then the peaks and nadirs of the transformed sequences are extracted to form feature sequences with similar lengths, which can be easily mapped by the original DTW. Our algorithm then recursively projects the warping path from a lower-resolution level to a higher-resolution one by building a context-dependent boundary and enabling a constrained search for the warping path in the latter. Comprehensive experiments on two real nanopore datasets on human and on Pandoraea pnomenusa demonstrate the efficiency and effectiveness of the proposed algorithm. In particular, cwDTW can gain remarkable acceleration with tiny loss of the alignment accuracy. On the real nanopore datasets, cwDTW can finish an alignment task in few seconds, which is about 3000 times faster than the original DTW. By successfully applying cwDTW on the tasks of signal labeling and ultra-long sequence comparison, we further demonstrate the power and applicability of cwDTW.
AVAILABILITY AND IMPLEMENTATION
Our program is available at https://github.com/realbigws/cwDTW.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Algorithms; Humans; Nanopores; Sequence Analysis; Time Factors
PubMed: 30423085
DOI: 10.1093/bioinformatics/bty555 -
Ecotoxicology and Environmental Safety Feb 2016A series of toxicity bioassays was conducted to monitor the ecotoxicity of soils in the different phases of bioremediation. Artificially oil-contaminated soil was...
A series of toxicity bioassays was conducted to monitor the ecotoxicity of soils in the different phases of bioremediation. Artificially oil-contaminated soil was inoculated with a petroleum hydrocarbon-degrading bacterial consortium containing Burkholderia cepacia GS3C, Sphingomonas GY2B and Pandoraea pnomenusa GP3B strains adapted to crude oil. Soil ecotoxicity in different phases of bioremediation was examined by monitoring total petroleum hydrocarbons, soil enzyme activities, phytotoxicity (inhibition of seed germination and plant growth), malonaldehyde content, superoxide dismutase activity and bacterial luminescence. Although the total petroleum hydrocarbon (TPH) concentration in soil was reduced by 64.4%, forty days after bioremediation, the phytotoxicity and Photobacterium phosphoreum ecotoxicity test results indicated an initial increase in ecotoxicity, suggesting the formation of intermediate metabolites characterized by high toxicity and low bioavailability during bioremediation. The ecotoxicity values are a more valid indicator for evaluating the effectiveness of bioremediation techniques compared with only using the total petroleum hydrocarbon concentrations. Among all of the potential indicators that could be used to evaluate the effectiveness of bioremediation techniques, soil enzyme activities, phytotoxicity (inhibition of plant height, shoot weight and root fresh weight), malonaldehyde content, superoxide dismutase activity and luminescence of P. phosphoreum were the most sensitive.
Topics: Bacteria; Biodegradation, Environmental; Germination; Hydrocarbons; Magnoliopsida; Malondialdehyde; Petroleum; Plant Development; Plant Roots; Seeds; Soil Microbiology; Soil Pollutants; Superoxide Dismutase
PubMed: 26491984
DOI: 10.1016/j.ecoenv.2015.10.005 -
Transplantation Dec 2021Uncontrolled donation after circulatory death (DCD) donors are an extraordinary resource to increase the number of lungs available for transplantation. However, the risk...
BACKGROUND
Uncontrolled donation after circulatory death (DCD) donors are an extraordinary resource to increase the number of lungs available for transplantation. However, the risk of the warm ischemia resulting from cardiac arrest to irreversibly damage the organs is considerable. Moreover, graft preservation issues and organizational problems often worsen the dangerous effects of warm ischemia. Ex vivo lung perfusion (EVLP) enables us to evaluate and recondition lungs whose functionality is doubtful, as well as to overcome the difficulties related to time and logistics.
METHODS
We report the case of uncontrolled DCD lungs successfully treated with an exceptionally prolonged EVLP. Because the donor's blood count and liver biopsy showed signs of possible leukemia, EVLP was protracted up to 17 h while waiting for immunohistochemical analyses to rule out this diagnosis; eventually, the results came back negative, and the lungs were judged suitable for transplantation.
RESULTS
The recipient was a 32-y-old male individual with cystic fibrosis, colonized by Pandoraea pnomenusa. Bilateral transplantation required central extracorporeal membrane oxygenation. The patient was extubated after 36 h and was discharged 21 d after the operation. Despite early recolonization by Pandoraea pnomenusa and airway complications requiring pneumatic dilatation, he is alive and has a satisfactory respiratory function 15 mo after transplantation.
CONCLUSIONS
Uncontrolled DCD represents a challenge due to both logistical issues and the complexity of graft evaluation before procurement. EVLP with cellular perfusate could be a valuable tool to overcome these limits. Nonetheless, caution should be exercised when interpreting the effects of this technique on airway healing.
Topics: Extracorporeal Circulation; Humans; Lung; Lung Transplantation; Male; Organ Preservation; Perfusion; Tissue Donors; Warm Ischemia
PubMed: 33496562
DOI: 10.1097/TP.0000000000003646 -
Archives of Biochemistry and Biophysics Dec 2011In this work we have investigated the ability of the biphenyl dioxygenase of Burkholderia xenovorans LB400 (BphAE(LB400)) and of Pandoraea pnomenusa B356 (BphAE(B356))...
In this work we have investigated the ability of the biphenyl dioxygenase of Burkholderia xenovorans LB400 (BphAE(LB400)) and of Pandoraea pnomenusa B356 (BphAE(B356)) to metabolize DDT. Data show BphAE(LB400) is unable to metabolize this substrate but BphAE(B356) metabolizes DDT to produce two stereoisomers. Structural analysis of DDT-docked BphAE(LB400) and BphAE(B356) identified residue Phe336 of BphAE(LB400) as critical to prevent productive binding of DDT to BphAE(LB400). Furthermore, the fact that residue Gly319 of BphAE(B356) is less constrained than Gly321 of BphAE(LB400) most likely contributes to the ability of BphAE(B356) to bind DDT productively. This was confirmed by examining the ability of BphAE chimeras obtained by shuffling bphA genes from strain B356 and LB400. Chimeras where residues Thr335 (which modulates the constraints on Gly321) and Phe336 (which contacts the substrate) of BphAE(LB400) were replaced by Gly and Ile respectively were able to metabolize DDT. However their stereospecificities varied depending on the presence of other segments or residues from BphAE(B356). Structural analysis suggests that either one or both of residue 267 and a segments comprised of residue 247-260 are likely involved in stereospecificity.
Topics: Amino Acid Sequence; Biphenyl Compounds; Burkholderia; Burkholderiaceae; Catalytic Domain; DDT; Dioxygenases; Insecticides; Models, Molecular; Molecular Sequence Data; Protein Binding; Sequence Alignment
PubMed: 22001737
DOI: 10.1016/j.abb.2011.09.016 -
Research in Microbiology 2008Twenty-one thiosulfate-oxidizing bacteria were isolated from rhizosphere soils and 16S rRNA analysis revealed that the isolates were affiliated with seven different...
Twenty-one thiosulfate-oxidizing bacteria were isolated from rhizosphere soils and 16S rRNA analysis revealed that the isolates were affiliated with seven different phylogenetic groups within the Beta and Gamma subclasses of Proteobacteria and Actinobacteria. Among these, five genera, including Dyella, Burkholderia, Alcaligenes, Microbacterium and Leifsonia sp., represented new sulfur oxidizers in rhizosphere soils. The thiosulfate-oxidizing Dyella, Burkholderia, Alcaligenes, Microbacterium, Leifsonia and Pandoraea were able to grow chemolithotrophically with a medium containing thiosulfate and exhibited growth coupled with thiosulfate oxidation. They accumulated intermediate products such as sulfur, sulfite and trithionate in the spent medium during the time course of thiosulfate oxidation, and these products were finally oxidized into sulfate. Furthermore, they possessed thiosulfate-metabolizing enzymes such as rhodanese, thiosulfate oxidase, sulfite oxidase and trithionate hydrolase, suggesting that these bacteria use the 'S4 intermediate' (S4I) pathway for thiosulfate oxidation. Phylogenetic analysis of the soxB gene revealed that Pandoraea sp. and Pandoraea pnomenusa strains formed a separate lineage within Betaproteobacteria.
Topics: Bacteria; Bacterial Proteins; Chemoautotrophic Growth; Crops, Agricultural; Molecular Sequence Data; Oxidation-Reduction; Phylogeny; Plant Roots; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Sulfur; Thiosulfates
PubMed: 18832027
DOI: 10.1016/j.resmic.2008.08.007 -
Journal of Hazardous Materials Sep 2010Four oil component-degrading bacteria and one oil-tolerant microalgae, Scenedesmus obliquus GH2, were used to construct an artificial microalgal-bacterial consortium for...
Four oil component-degrading bacteria and one oil-tolerant microalgae, Scenedesmus obliquus GH2, were used to construct an artificial microalgal-bacterial consortium for crude-oil degradation. The bacterial strains included Sphingomonas GY2B and Burkholderia cepacia GS3C, along with a mixed culture, named GP3, containing Pseudomonas GP3A and Pandoraea pnomenusa GP3B. GY2B could only degrade polycyclic aromatic hydrocarbons, GS3C was able to degrade aliphatic chain hydrocarbons, and GP3 could utilize both saturated and aromatic hydrocarbons. In combination with unialgal or axenic algae, the bacteria showed different effects on oil degradation. Unialgal GH2 was not suitable for the consortium construction, as it could not cooperate well with GS3C and GP3. The axenic GH2 exhibited no oil-degrading ability; however, it significantly promoted the degradation ability of the oil component-degrading bacteria, especially for degrading biorefractory polycyclic aromatic hydrocarbons. Axenic S. obliquus GH2, combined with the four bacteria mentioned above, formed an optimal algal-bacterial consortium. The artificial consortium demonstrated an elevated efficiency in degrading both aliphatic and aromatic hydrocarbons of crude oil.
Topics: Alkanes; Bacteria; Biodegradation, Environmental; Eukaryota; Hydrocarbons, Aromatic; Petroleum
PubMed: 20638971
DOI: 10.1016/j.jhazmat.2010.05.033 -
Journal of Clinical Microbiology Nov 2009The identification of microbial species from respiratory specimens and their susceptibility to antimicrobial agents are among the most important diagnostic measures of...
The identification of microbial species from respiratory specimens and their susceptibility to antimicrobial agents are among the most important diagnostic measures of care for patients with cystic fibrosis (CF). Under the umbrella of EuroCareCF, two quality assurance trials of CF microbiology were performed in 2007 and 2008. Nine formulations with CF bacterial isolates were dispatched. A total of 31/37 laboratories from 18/21 European countries participated in the 2007 and 2008 trials. The common CF pathogens Pseudomonas aeruginosa and Staphylococcus aureus were correctly identified by almost all participants in both trials, even if the strains presented uncommon phenotypes. Burkholderia cenocepacia IIIB and Burkholderia vietnamensis CF isolates, however, were correctly assigned to the species level by only 26% and 27% of the laboratories, respectively. Emerging pathogens such as Achromobacter xylosoxidans, Inquilinus limosus, and Pandoraea pnomenusa were also not detected or were misclassified by many laboratories. One participant correctly identified all CF isolates in both trials. The percentages of correct classifications (susceptible, intermediate, resistant) by antimicrobial susceptibility testing ranged from 55 to 100% (median, 96%) per isolate and drug. The shortcomings in the diagnostics of rare and emerging pathogens point to the need for continuing education in CF microbiology and suggest the establishment of CF microbiology reference laboratories.
Topics: Bacteria; Bacterial Infections; Bacteriological Techniques; Bronchopneumonia; Cystic Fibrosis; Diagnostic Errors; Europe; Health Services Research; Humans; Microbial Sensitivity Tests; Quality Control
PubMed: 19741077
DOI: 10.1128/JCM.01182-09 -
Biotechnology and Bioengineering Jan 2008We have previously reported the disappearance of a specific strain degrading chlorobenzene from a functionally stable bioreactor. In the present work, we investigated...
We have previously reported the disappearance of a specific strain degrading chlorobenzene from a functionally stable bioreactor. In the present work, we investigated this species succession and isolated a new dominant strain, identified as Pandoraea pnomenusa sp. strain MCB032. A specific 16S rRNA-targeted oligonucleotide probe was designed and validated to identify strain MCB032 using fluorescence in situ hybridisation (FISH). The results confirmed the presence of strain MCB032 in samples collected over time, and showed that it was primarily located within the biofilm. Denaturing gradient gel electrophoresis (DGGE) provided evidence that the species succession occurred early in the operating period. The application of these biomolecular tools highlighted the remarkable stability of this new strain during the 15 months of reactor operation. The succession was attributed to the competitive kinetic behaviour of strain MCB032, which exhibited faster growth (micro(max) = 0.34 h(-1)) and higher substrate affinity (K(s) = 0.35 mg L(-1)) than strain JS150. Finally, this study contributed to the characterisation of the recently established Pandoraea genus, an emerging group in the biodegradation field.
Topics: Biodegradation, Environmental; Bioreactors; Cell Differentiation; Chlorobenzenes; Computer Simulation; Models, Biological; Proteobacteria; Species Specificity
PubMed: 17680678
DOI: 10.1002/bit.21576