scholarly journals Electrochemical profiles of bacteria isolated from crude oil on simple benzene compounds detection

2021 ◽  
Vol 948 (1) ◽  
pp. 012026
Author(s):  
A A Ghozali ◽  
D Iswantini ◽  
C Kusmana ◽  
N Nurhidayat
Keyword(s):  
Crude Oil ◽  
Polyaromatic Hydrocarbons ◽  
Bacterial Species ◽  
Media Culture ◽  
Bacterial Dna ◽  
Growth Assay ◽  
Cyclic Voltammetry Method ◽  
Benzene Toluene ◽  
Positive Results ◽  
Benzene Compounds

Abstract Five polyaromatic hydrocarbons (PAHs) degrading bacterial species had been isolated from crude oil samples. All bacteria were positive Gram-stained, except one; and had positive results on the catalase test. After sequencing bacterial DNA, three bacterial genera were obtained with 99-100% certainty, namely: Pseudomonas sp., Staphylococcus sp., and Bacillus sp. All bacteria were known strongly to form a biofilm, thus can be applied for biosensing and/or bioremediation techniques. Using minimal mineral media growth assay as media culture, all bacteria were able to degrade naphthalene and anthracene, Staphylococcus sp. shown the strong degradation affinity. Meanwhile, Bacillus sp. tended to form strong biofilm. Electrochemical data were obtained with the cyclic voltammetry method, with a scan rate of 100 mV/s. Voltammogram profiles of all bacteria against simple benzene compounds (benzene, toluene, and xylene; concentration for each compound 1μL/mL) showed irreversible oxidation peaks at 0.20-0.40 V ppm of the analyte, producing current 50-100 μA. The measurements were taken when the solution was more stable (±10 seconds) after vigorous shaking to homogenize benzene compounds and introducing O2 into the solution. The peaks were decreasing over the next cycles, indicating the lower bioavailability of benzene compounds to be degraded with O2.

Absence of Yersinia pestis-specific DNA in human teeth from five European excavations of putative plague victims

Microbiology ◽  
2004 ◽  
Vol 150 (2) ◽  
pp. 341-354 ◽  
Author(s):  
M. Thomas P. Gilbert ◽  
Jon Cuccui ◽  
William White ◽  
Niels Lynnerup ◽  
Richard W. Titball ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
Ancient Dna ◽  
Dna Sequences ◽  
Bacterial Species ◽  
Collaborative Study ◽  
Independent Research ◽  
Human Teeth ◽  
Bacterial Dna ◽  
Embedding Technique ◽  
Positive Results

This study reports the results of a collaborative study undertaken by two independent research groups to (a) confirm recent PCR-based detection of Yersinia pestis DNA in human teeth from medieval plague victims in France, and (b) to extend these observations over five different European burial sites believed to contain plague victims dating from the late 13th to 17th centuries. Several different sets of primers were used, including those previously documented to yield positive results on ancient DNA extracts. No Y. pestis DNA could be amplified from DNA extracted from 108 teeth belonging to 61 individuals, despite the amplification of numerous other bacterial DNA sequences. Several methods of extracting dentine prior to the DNA extraction were also compared. PCR for bacterial 16S rDNA indicated the presence of multiple bacterial species in 23 out of 27 teeth DNA extracts where dentine was extracted using previously described methods. In comparison, positive results were obtained from only five out of 44 teeth DNA extracts for which a novel contamination-minimizing embedding technique was used. Therefore, high levels of environmental bacterial DNA are present in DNA extracts where previously described methods of tooth manipulation are used. To conclude, the absence of Y. pestis-specific DNA in an exhaustive search using specimens from multiple putative European plague burial sites does not allow us to confirm the identification of Y. pestis as the aetiological agent of the Black Death and subsequent plagues. In addition, the utility of the published tooth-based ancient DNA technique used to diagnose fatal bacteraemias in historical epidemics still awaits independent corroboration.

scholarly journals Energy and Resource Utilization of Refining Industry Oil Sludge by Microwave Treatment

2020 ◽  
Vol 12 (17) ◽  
pp. 6862
Author(s):  
Chien Li Lee ◽  
Cheng-Hsien Tsai ◽  
Chih-Ju G. Jou
Keyword(s):  
Crude Oil ◽  
Microwave Power ◽  
Petroleum Refining ◽  
Microwave Treatment ◽  
Field Energy ◽  
Oily Sludge ◽  
Sludge Sample ◽  
Volatile Hydrocarbons ◽  
Benzene Toluene ◽  
Oil Tank

The oily sludge from crude oil contains hazardous BTEX (benzene, toluene, ethylbenzene, xylene) found in the bottom sediment of the crude oil tank in the petroleum refining plant. This study uses microwave treatment of the oily sludge to remove BTEX by utilizing the heat energy generated by the microwave. The results show that when the oily sludge sample was treated for 60 s under microwave power from 200 to 300 W, the electric field energy absorbed by the sample increased from 0.17 to 0.31 V/m and the temperature at the center of the sludge sample increased from 66.5 °C to 96.5 °C. In addition, when the oily sludge was treated for 900 s under microwave power 300 W, the removal rates were 98.5% for benzene, 62.8% for toluene, 51.6% for ethylbenzene, and 29.9% for xylene. Meanwhile, the highest recovery rates of light volatile hydrocarbons in sludge reached 71.9% for C3, 71.3% for C4, 71.0% for C5, and 78.2% for C6.

scholarly journals Rapid Identification of Bacterial Species with Bacterial DNA Microarray in Cirrhotic Patients with Spontaneous Bacterial Peritonitis

2009 ◽  
Vol 48 (1) ◽  
pp. 3-10 ◽  
Author(s):  
Takaaki Sugihara ◽  
Masahiko Koda ◽  
Yoshiko Maeda ◽  
Tomomitsu Matono ◽  
Takakazu Nagahara ◽  
...  
Keyword(s):  
Dna Microarray ◽  
Spontaneous Bacterial Peritonitis ◽  
Bacterial Species ◽  
Rapid Identification ◽  
Bacterial Dna ◽  
Bacterial Peritonitis ◽  
Cirrhotic Patients

scholarly journals Oral Dextran Sulfate Sodium Administration Induces Peripheral Spondyloarthritis Features in SKG Mice Accompanied by Intestinal Bacterial Translocation and Systemic Th1 and Th17 Cell Activation.

2021 ◽  
Author(s):  
Yuya Tabuchi ◽  
Masao Katsushima ◽  
Yuri Nishida ◽  
Mirei Shirakashi ◽  
Hideaki Tsuji ◽  
...  
Keyword(s):  
Bacterial Translocation ◽  
Whole Blood ◽  
Th17 Cell ◽  
Cell Activation ◽  
Dextran Sulfate ◽  
Dextran Sulfate Sodium ◽  
Quantitative Polymerase Chain Reaction ◽  
Bacterial Species ◽  
Bacterial Dna ◽  
Anti Fungal

Abstract Background: Spondyloarthritis (SpA) is an autoimmune and autoinflammatory musculoskeletal disease characterised by systemic enthesitis. Recent research has focused on subclinical inflammatory bowel disease (IBD) in SpA pathogenesis. SKG mice, harbouring the Zap70 W163C mutation, increase autoreactive Th17 cells intrinsically, and show SpA features, including enteritis, after peritoneal injection of β-1,3- glucan under SPF conditions. In a conventional environment, they exhibit spontaneous arthritis with fungal factors. This study aimed to clarify whether oral dextran sulfate sodium (DSS) administration, utilised in IBD model mice, can provoke SpA features in SKG mice under SPF conditions, focusing on the relationship between gut microorganisms and SpA pathogenesis.Methods: SKG and BALB/c mice were administered oral DSS, and their body weights, arthritis, and enthesitis scores were recorded. In another cohorts, antibiotics (meropenem and vancomycin) or an anti-fungal agent (amphotericin B) were administered orally before DSS administration. The splenic Th1 and Th17 cell populations were examined before and after DSS administration using flow cytometry. Furthermore, the amount of circulating bacterial DNA in whole blood was measured by absolute quantitative polymerase chain reaction (qPCR), and the number and characteristics of bacterial species corresponding to these circulating DNA were analised by next-generation sequencing (NGS).Results: Ankle enthesitis as a peripheral SpA feature was elicited in half of DSS-administered SKG mice, and none of the BALB/c mice. Pre-administration of antibiotics suppressed enthesitis, whilst an anti-fungal agent could not. Th1 and Th17 cell levels in the spleen increased after DSS administration, and this was suppressed by pre-administration of antibiotics. SKG mice have a larger amount of bacterial DNA in whole blood than BALB/c mice before and one day after the initiation of DSS administration. The number of bacterial species in whole blood increased after DSS administration in SKG and BALB/c mice. Some genera and species significantly specific to the DSS-treated SKG mice group were also detected. Conclusion: Oral DSS administration alone elicited peripheral enthesitis in SKG mice with bacterial translocation accompanied by increased splenic Th1 and Th17 cell levels. Pre-administration of antibiotics ameliorated these DSS-induced SpA features. These findings suggest that intestinal bacterial leakage plays a pivotal role in SpA pathogenesis.

scholarly journals Evaluating Flinders Technology Associates card for transporting bacterial isolates and retrieval of bacterial DNA after various storage conditions

2020 ◽  
Vol 13 (10) ◽  
pp. 2243-2251
Author(s):  
Azhar G. Shalaby ◽  
Neveen R. Bakry ◽  
Abeer A. E. Mohamed ◽  
Ashraf A. Khalil
Keyword(s):  
Nucleic Acid ◽  
Bacterial Species ◽  
Storage Conditions ◽  
Animal Origin ◽  
Cell Detection ◽  
Bacterial Cells ◽  
Gram Positive ◽  
Bacterial Dna ◽  
Gram Negative ◽  
Fta Cards

Background and Aim: Flinders Technology Associates (FTA) cards simplify sample storage, transport, and extraction by reducing cost and time for diagnosis. This study evaluated the FTA suitability for safe transport and storage of Gram-positive and Gram-negative bacterial cells of animal origin on its liquid culture form and from organ impression smears (tissues) under the same routine condition of microbiological laboratory along with detecting their nucleic acid over different storage conditions. Materials and Methods: Increase in bacterial count from 104 to 107 (colony-forming units/mL) of 78 isolates representing seven bacterial species was applied onto cards. FTA cards were grouped and inoculated by these bacteria and then stored at different conditions of 24-27°C, 4°C, and –20°C for 24 h, for 2 weeks, for 1 and 3 month storage, respectively. Bacteriological examination was done, after which bacterial DNA was identified using specific primers for each bacterial type and detected by polymerase chain reaction (PCR). Results: The total percentage of recovered bacteria from FTA cards was 66.7% at 24-27–C for 24 h, the detection limit was 100% in Gram-positive species, while it was 57.4% in Gram-negative ones. Regarding viable cell detection from organ impression smears, it was successful under the previous conditions. No live bacterial cells were observed by bacteriological isolation rather than only at 24-27°C for 24 h storage. All bacterial DNA were sufficiently confirmed by the PCR technique at different conditions. Conclusion: Overall, the FTA card method was observed to be a valid tool for nucleic acid purification for bacteria of animal origin in the form of culture or organ smears regardless of its Gram type and is used for a short time only 24 h for storage and transport of live bacteria specifically Gram-positive type. Moreover, the bacterial nucleic acid was intact after storage in –20°C for 3 months and was PCR amplifiable.

scholarly journals Activation of Toll-Like Receptor 9 by DNA from Different Bacterial Species

2006 ◽  
Vol 74 (2) ◽  
pp. 940-946 ◽  
Author(s):  
Alexander Dalpke ◽  
Jutta Frank ◽  
Mirjam Peter ◽  
Klaus Heeg
Keyword(s):  
Bacterial Species ◽  
Bacterial Genome ◽  
Hek293 Cells ◽  
Toll Like Receptor ◽  
Bacterial Dna ◽  
Cpg Dinucleotides ◽  
Genome Data ◽  
Efficient Delivery ◽  
The Individual ◽  
Cg Dinucleotides

ABSTRACT Toll-like receptor 9 (TLR-9) recognizes unmethylated CpG dinucleotides which are abundant in prokaryotic DNA and yet are rare in eukaryotic DNA. Little is known about the significance of TLR-9 in terms of recognition of different bacterial DNA species. In this study HEK293 cells stably transfected with human TLR-9 were used to analyze the immunostimulatory properties of 15 bacterial DNA preparations. In addition, bacterial genome data were analyzed for the frequency of unmethylated cytosine-guanosine ([CG]) dinucleotides. We observed that DNA samples of different bacteria showed considerable differences in their potential to stimulate TLR-9. This correlated with the frequency of [CG] dinucleotides. Based upon data from our experiments the estimate of immunostimulatory bacterial DNA concentrations translated to as high as 109 bacteria/ml. Application of the transfection reagent DOTAP resulted in a more efficient delivery of DNA into the cell, and this went along with increased TLR-9 activation. The data indicate that bacterial DNA preparations from different species differ in their capacity to activate TLR-9, which is dependent on the individual [CG] content. Moreover, increased intracellular delivery results in a marked enhancement of immunostimulation.

scholarly journals Assessment of Campylobacter fetus subsp. venerealis molecular diagnosis using clinical samples of bulls

2020 ◽  
Vol 16 (1) ◽  
Author(s):  
Marta Filipa Silva ◽  
Ana Duarte ◽  
Gonçalo Pereira ◽  
Luísa Mateus ◽  
Luís Lopes-da-Costa ◽  
...  
Keyword(s):  
False Positive ◽  
Bacterial Species ◽  
Venereal Disease ◽  
High Rate ◽  
Clinical Samples ◽  
Campylobacter Fetus ◽  
Subspecies Level ◽  
Geographical Regions ◽  
Pcr Assays ◽  
Positive Results

Abstract Background Campylobacter fetus subsp. venerealis (Cfv) is the pathogen responsible for Bovine Genital Campylobacteriosis (BGC), a venereal disease of cattle associated with impaired reproductive performance. Although several PCR assays were developed to identify this pathogen, most of them are still poorly evaluated in clinical samples. This study evaluated real-time PCR assays for Cfv detection in preputial samples of bulls (n = 308). Results The detection at the subspecies level (Cfv) compared four assays: two targeting ISCfe1 and two targeting parA gene. The detection at the species level (C. fetus) considered an assay targeting the nahE gene and a commercial kit for C. fetus identification. At the subspecies level, assays directed either to different targets (parA and ISCfe1), or to the same target (ISCfe1 or parA), showed a high percentage of disagreeing results. All samples positive at the subspecies level (n = 169) were negative in C. fetus detection assays, which strongly suggests the horizontal gene transfer of ISCfe1 and parA to other bacterial species. This was confirmed by microbiological isolation of three Campylobacter portucalensis strains responsible for false positive results. Sequences with a high level of identity with ISCfe1 and parA gene of Cfv were identified in C. portucalensis genome. Conclusions Overall, this study reveals that PCR assays solely directed to a subspecies target originate a high rate of false positive results, due to the presence of parA and ISCfe1 homologous sequences in other bacterial species, namely of the genus Campylobacter. Although the specificity of these methods may be higher if applied to bulls from herds with clinical features of BGC or in other geographical regions, current PCR diagnosis should couple subspecies and species targets, and further research must be envisaged to identify Cfv specific molecular targets.

scholarly journals The architects of bacterial DNA bridges: a structurally and functionally conserved family of proteins

Open Biology ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 190223 ◽  
Author(s):  
L. Qin ◽  
A. M. Erkelens ◽  
F. Ben Bdira ◽  
R. T. Dame
Keyword(s):  
Environmental Changes ◽  
Bacterial Species ◽  
Dna Duplexes ◽  
New Members ◽  
Bacterial Dna ◽  
Architectural Proteins ◽  
Bacterial Chromosomes ◽  
Associated Proteins ◽  
Chromatin Proteins ◽  
Dna Binding Properties

Every organism across the tree of life compacts and organizes its genome with architectural chromatin proteins. While eukaryotes and archaea express histone proteins, the organization of bacterial chromosomes is dependent on nucleoid-associated proteins. In Escherichia coli and other proteobacteria, the histone-like nucleoid structuring protein (H-NS) acts as a global genome organizer and gene regulator. Functional analogues of H-NS have been found in other bacterial species: MvaT in Pseudomonas species, Lsr2 in actinomycetes and Rok in Bacillus species. These proteins complement hns − phenotypes and have similar DNA-binding properties, despite their lack of sequence homology. In this review, we focus on the structural and functional characteristics of these four architectural proteins. They are able to bridge DNA duplexes, which is key to genome compaction, gene regulation and their response to changing conditions in the environment. Structurally the domain organization and charge distribution of these proteins are conserved, which we suggest is at the basis of their conserved environment responsive behaviour. These observations could be used to find and validate new members of this protein family and to predict their response to environmental changes.

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