Shifts in soil microbial communities over altitudinal gradients and the driving factors are poorly studied. Their elucidation is indispensable to gain a comprehensive understanding of the response of ...ecosystems to global climate change. Here, we investigated soil archaeal, bacterial, and fungal communities at four Alpine forest sites representing a climosequence, over an altitudinal gradient from 545 to 2000 m above sea level (asl), regarding abundance and diversity by using qPCR and Illumina sequencing, respectively. Archaeal community was dominated by Thaumarchaeota, and no significant shifts were detected in abundance or community composition with altitude. The relative bacterial abundance increased at higher altitudes, which was related to increasing levels of soil organic matter and nutrients with altitude. Shifts in bacterial richness and diversity as well as community structure (comprised basically of Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes) significantly correlated with several environmental and soil chemical factors, especially soil pH. The site at the lowest altitude harbored the highest bacterial richness and diversity, although richness/diversity community properties did not show a monotonic decrease along the gradient. The relative size of fungal community also increased with altitude and its composition comprised Ascomycota, Basidiomycota, and Zygomycota. Changes in fungal richness/diversity and community structure were mainly governed by pH and C/N, respectively. The variation of the predominant bacterial and fungal classes over the altitudinal gradient was the result of the environmental and soil chemical factors prevailing at each site.
Diagnosis of gastrointestinal parasites has traditionally relied on stool microscopy, which has low diagnostic sensitivity and specificity. We have developed a novel, rapid, high-throughput ...quantitative multi-parallel real-time polymerase chain reaction (qPCR) platform. Species-specific primers/probes were used for eight common gastrointestinal parasite pathogens: Ascaris lumbricoides, Necator americanus, Ancylostoma duodenale, Giardia lamblia, Cryptosporidium spp., Entamoeba histolytica, Trichuris trichiura, and Strongyloides stercoralis. Stool samples from 400 13-month-old children in rural Ecuador were analyzed and the qPCR was compared with a standard direct wet mount slide for stool microscopy, as were 125 8-14-year-old children before and after anthelmintic treatment. The qPCR showed higher detection rates for all parasites compared with direct microscopy, Ascaris (7.0% versus 5.5%) and for Giardia (31.5% versus 5.8%). Using an enhanced DNA extraction method, we were able to detect T. trichiura DNA. These assays will be useful to refine treatment options for affected populations, ultimately leading to better health outcomes.
Emerging wastewater treatment processes such as membrane bioreactors (MBRs) have attracted a significant amount of interest internationally due to their ability to produce high quality effluent ...suitable for water recycling. It is therefore important that their efficiency in removing hazardous trace organic contaminants be assessed. Accordingly, this study investigated the removal of trace organic chemical contaminants through a full-scale, package MBR in New South Wales, Australia. This study was unique in the context of MBR research because it characterised the removal of 48 trace organic chemical contaminants, which included steroidal hormones, xenoestrogens, pesticides, caffeine, pharmaceuticals and personal care products (PPCPs). Results showed that the removal of most trace organic chemical contaminants through the MBR was high (above 90%). However, amitriptyline, carbamazepine, diazepam, diclofenac, fluoxetine, gemfibrozil, omeprazole, sulphamethoxazole and trimethoprim were only partially removed through the MBR with the removal efficiencies of 24-68%. These are potential indicators for assessing MBR performance as these chemicals are usually sensitive to changes in the treatment systems. The trace organic chemical contaminants detected in the MBR permeate were 1 to 6 orders of magnitude lower than guideline values reported in the Australian Guidelines for Water Recycling. The outcomes of this study enhanced our understanding of the levels and removal of trace organic contaminants by MBRs.
Summary Background We aimed to provide updated information about the global estimates of attributable fraction and type distribution of human papillomavirus (HPV) in head and neck squamous cell ...carcinomas by doing a systematic review and meta-analysis. Methods We did a literature search on PubMed to identify studies that used PCR for detection of HPV DNA in head and neck squamous cell carcinomas with information about HPV genotype distribution. We included studies that tested 20 or more biopsies per cancer site and were published between July 15, 1990, and Feb 29, 2012. We collected information about sex, risk factors, HPV detection methods, and biomarkers of potentially HPV-induced carcinogenesis (E6/E7 mRNA and p16INK4a ). If it was not possible to abstract the required information directly from the paper, we contacted the authors. We did a meta-analysis to produce pooled prevalence estimates including a meta-regression to explore sources of heterogeneity. Findings 148 studies were included, contributing data for 12 163 cases of head and neck squamous cell carcinoma from 44 countries. HPV DNA was detected in 3837 cases. HPV16 accounted for 82·2% (95% CI 77·7–86·4) of all HPV DNA positive cases. By cancer site, pooled HPV DNA prevalence estimates were 45·8% (95% CI 38·9–52·9) for oropharynx, 22·1% (16·4–28·3) for larynx (including hypopharynx), and 24·2% (18·7–30·2) for oral cavity. The percent positivity of p16INK4a positive cases in HPV-positive oropharyngeal cancer cases was 86·7% (95% CI 79·2–92·9) and of E6/E7 mRNA positive cases was 86·9% (73·2–96·8). The estimate of HPV attributable fraction in oropharyngeal cancer defined by expression of positive cases of E6/E7 mRNA was 39·8% and of p16INK4a was 39·7%. Of subsites, tonsils (53·9%, 95% CI 46·4–61·3) had the highest HPV DNA prevalence. HPV DNA prevalence varied significantly by anatomical site, geographic region, but not by sex or tobacco or alcohol consumption. Interpretation The contribution of HPV prevalence in head and neck squamous cell carcinoma and in particular that of HPV16 in the oropharynx shows the potential benefit of prophylactic vaccines. Funding European Commission.
Staphylococcus aureus is an extremely infectious and malignant pathogen among many bacteria species. The aim of this work is to provide a robust classification model that would be able to identify S. ...aureus independent of the culture growth stage and the variations in bacteria concentration in suspension and also one that would be able to identify the pathogen among both taxonomically close species of the same genus and taxonomically distant species of different genera, using Fourier transform infrared spectroscopy (FTIR). In total, the spectra of 141 isolates of 17 bacteria have been used. Based on a combination of principal component analysis (PCA) and linear discriminant analysis (LDA), an identification model providing 100% sensitivity and 98% specificity was built. Inherent reliability and flexibility of the model have been shown. The proposed method of analysis allows us to get closer to the diagnostic requirements in the field of clinical microbiology, and it can be utilized for typing of other pathogenic bacteria species.
European Origanum vulgare populations are either predominated by a linalool chemotype, a cymyl-chemotype or a sesquiterpene rich sabinyl-chemotype that co-occurs with a sesquiterpene-type poor in ...monoterpenes. Display omitted
•502 O. vulgare plants from 17 European countries were analysed via GC.•The content of essential oil compounds ranged between 0.03% and 4.6%.•With respect to the occurrence of main monoterpene compounds a geographical gradient was obvious.•Plants originating from the Mediterranean usually exhibited an active cymyl- and/or linalool pathway, in plants from regions with Continental climate GPP is mainly converted by the sabinyl-pathway.
This investigation focused on the qualitative and quantitative composition of essential oil compounds of European Origanum vulgare. Extracts of 502 individual O. vulgare plants from 17 countries and 51 populations were analyzed via GC. Extracts of 49 plants of 5 populations of Israeli Origanum syriacum and 30 plants from 3 populations of Turkish Origanum onites were included to exemplify essential oil characteristics of ‘high-quality’ oregano. The content of essential oil compounds of European O. vulgare ranged between 0.03% and 4.6%. The monoterpenes were primarily made up of sabinene, myrcene, p-cymene, 1,8-cineole, β-ocimene, γ-terpinene, sabinene hydrate, linalool, α-terpineol, carvacrol methyl ether, linalyl acetate, thymol and carvacrol. Among the sesquiterpenes β-caryophyllene, germacrene D, germacrene D-4-ol, spathulenol, caryophyllene oxide and oplopanone were often present in higher amounts. According to the proportions of cymyl-compounds, sabinyl-compounds and the acyclic linalool/linalyl acetate three different main monoterpene chemotypes were defined. The cymyl- and the acyclic pathway were usually active in plants from the Mediterranean climate whereas an active sabinyl-pathway was a characteristic of plants from the Continental climate.
The occurrence of fifty-five pharmaceuticals, hormones and metabolites in raw waters used for drinking water production and their removal through a drinking water treatment were studied. Thirty-five ...out of fifty-five drugs were detected in the raw water at the facility intake with concentrations up to 1200 ng/L. The behavior of the compounds was studied at each step: prechlorination, coagulation, sand filtration, ozonation, granular activated carbon filtration and post-chlorination; showing that the complete treatment accounted for the complete removal of all the compounds detected in raw waters except for five of them. Phenytoin, atenolol and hydrochlorothiazide were the three pharmaceuticals most frequently found in finished waters at concentrations about 10 ng/L. Sotalol and carbamazepine epoxide were found in less than a half of the samples at lower concentrations, above 2 ng/L. However despite their persistence, the removals of these five pharmaceuticals were higher than 95%.
► Thirty-five out of fifty-five drugs detected in raw waters. ► Drinking treatment effectively removes 30 out of 35 target pharmaceuticals. ► Phenytoin, atenolol, sotalol, hydrochlorothiazide and carbamazepine epoxide detected in finished waters.
Background and Aims The complex design of the elevator mechanism in duodenoscopes has been recognized as a challenge for disinfection and recently implicated as a potential source of persistent ...bacterial contamination. Curvilinear array (CLA) echoendoscopes also have an elevator mechanism; however, there are no recommendations or data regarding the risk of persistent bacterial contamination of echoendoscopes. Here we hoped to determine the yield of microbial growth with routine bacterial surveillance cultures of reprocessed CLA echoendoscopes. Methods Beginning in February 2015 to February 2016, CLA echoendoscopes at a single tertiary care center underwent prospective bacterial surveillance cultures after reprocessing. Any growth of gram-negative bacilli was considered to be critical. Echoendoscopes with a positive result underwent quarantine followed by repeat disinfection and culture. Results During the study period, 540 cultures were obtained; 521 (96.5%) were primary cultures obtained from 18 CLA echoendoscopes. Twenty-two primary cultures (4.2%) were positive for gram-negative bacilli after high-level disinfection reprocessing. Eleven different bacteria were isolated: Klebsiella pneumoniae , Citrobacter freundii , Escherichia coli , Pseudomonas aeruginosa , Klebsiella oxytoca , Sphingomonas paucimobilis , Acinetobacter baumanii , Enterobacter cloacae , Hafnia alvei , Pseudomonas putida , and Stenotrophomonas maltophilia . Antibiotic sensitivity data on 19 of 24 bacteria (79.2%) isolated from positive primary cultures revealed no documented cases of carbapenem-resistant enterobacteriaceae, cephalosporin-resistant- Klebsiella , or multidrug-resistant Acinetobacter. There have been no documented cases of patient-to-patient transmission. Conclusions After following standard high-level disinfection and reprocessing, CLA echoendoscopes can remain culture positive for high-concern organisms. Recommendations regarding infection risk should take into consideration elevator-containing echoendoscopes in addition to duodenoscopes to ensure patient safety and endoscope reprocessing efficacy.
In this study, dithiocarbamate(DTC)-modified magnetic reduce graphene oxide (rGO-PDTC/Fe3O4) was synthesized for the removal of heavy metal ions (Cu(II), Cd(II), Pb(II), and Hg(II)) in synthetic ...waste water. The rGO-PDTC/Fe3O4 nanocomposite was prepared via a novel synthesis route that includes GO bromination, nucleophilic substitution of polyethylenimine (PEI), the reaction with carbon disulphide (CS2) and Fe3O4 nanoparticle loading. The prepared rGO-PDTC/Fe3O4 nanocomposite was characterised by XPS, FTIR, TEM and XRD, suggesting that DTC functional groups were chemically bonded to rGO surfaces. N2 adsorption-desorption results revealed that rGO-PDTC/Fe3O4 nanocomposite exhibited high BET surface area (194.8 m2/g) and large pore volume (0.33 cm³/g) which are crucial to the function of adsorbent. Adsorption experiments showed that rGO-PDTC/Fe3O4 nanocomposite is an excellent adsorbent for heavy metal removal, which exhibits large adsorption capacities, fast kinetics and solid-liquid separation. The pseudo-second-order kinetic model and Langmuir adsorption model were used to unveil the adsorption mechanisms. The maximum adsorption capacities of the Langmuir model were 113.64, 116.28, 147.06, and 181.82 mg/g for Cu(II), Cd(II), Pb(II), and Hg(II) ions, respectively. After adsorption and desorption process, the spent rGO-PDTC/Fe3O4 nanocomposite was easily regenerated via one-step organic reaction. The regenerated rGO-PDTC/Fe3O4 composite exhibited good adsorption capacities for different metals in five adsorption-desorption-regeneration cycles.
•Dithiocarbamate (DTC) functionalized magnetic reduce graphene oxide (rGO-DTC/Fe3O4).•Efficient removal of heavy metals (Cu(II), Cd(II), Pb(II) and Hg(II)).•Excellent adsorption capacities and fast kinetics.•Easy adsorbent regeneration process.
The use of polymer inclusion membranes (PIMs) as support of 1-octanol liquid membrane in electromembrane extraction (EME) procedure is proposed. Synthesis of PIMs were optimized to a composition of ...29% (w/w) of cellulose triacetate as base polymer and 71% (w/w) of Aliquat®336 as cationic carrier. Flat PIMs of 25µm thickness and 6mm diameter were used. EME protocol was implemented for the simultaneous extraction of four non-steroidal anti-inflammatory drugs (NSAIDs) (salicylic acid, ketoprofen, naproxen and ibuprofen) and four highly polar acidic drugs (anthranilic acid, nicotinic acid, amoxicillin and hippuric acid). Posterior HPLC separation of the extracted analytes was developed with diode array detection. Recoveries in the 81–34% range were obtained. EME procedure was applied to human urine samples.
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•A PIM (cellulose triacetate and Aliquat®336) is proposed as support for EME.•PIM is used for the simultaneous extraction of NSAIDs and highly polar acidic drugs.•Optimized EME is applied to the analytes extraction in human urine samples.
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