Use of molecular probes and PCR for detection and typing of Leishmania - a mini-review

The use of molecular tools to detect and type Leishmania species in humans, reservoirs or sandflies has been pursued using different approaches. The polymerase chain reaction provided sensitivity to case this task, since the use of hybridization procedures alone employing specifics probes is hampered due to the low detection limit. In this report, we describe the different molecular targets used in our laboratory, aiming at the detection and specific typing of these protozoa. Different kits based on hybridization assays and PCR amplification using kinetoplast and nuclear targets are described and the results obtained from their use are reported.

Artificial neural network study of whole-cell bacterial bioreporter response determined using fluorescence flow cytometry.

Genetically engineered bioreporters are an excellent complement to traditional methods of chemical analysis. The application of fluorescence flow cytometry to detection of bioreporter response enables rapid and efficient characterization of bacterial bioreporter population response on a single-cell basis. In the present study, intrapopulation response variability was used to obtain higher analytical sensitivity and precision. We have analyzed flow cytometric data for an arsenic-sensitive bacterial bioreporter using an artificial neural network-based adaptive clustering approach (a single-layer perceptron model). Results for this approach are far superior to other methods that we have applied to this fluorescent bioreporter (e.g., the arsenic detection limit is 0.01 microM, substantially lower than for other detection methods/algorithms). The approach is highly efficient computationally and can be implemented on a real-time basis, thus having potential for future development of high-throughput screening applications.

Detection of Wuchereria bancrofti DNA in paired serum and urine samples using polymerase chain reaction-based systems

The Global Program for the Elimination of Lymphatic Filariasis (GPELF) aims to eliminate this disease by the year 2020. However, the development of more specific and sensitive tests is important for the success of the GPELF. The present study aimed to standardise polymerase chain reaction (PCR)-based systems for the diagnosis of filariasis in serum and urine. Twenty paired biological urine and serum samples from individuals already known to be positive for Wuchereria bancrofti were collected during the day. Conventional PCR and semi-nested PCR assays were optimised. The detection limit of the technique for purified W. bancrofti DNA extracted from adult worms was 10 fg for the internal systems (WbF/Wb2) and 0.1 fg by using semi-nested PCR. The specificity of the primers was confirmed experimentally by amplification of 1 ng of purified genomic DNA from other species of parasites. Evaluation of the paired urine and serum samples by the semi-nested PCR technique indicated only two of the 20 tested individuals were positive, whereas the simple internal PCR system (WbF/Wb2), which has highly promising performance, revealed that all the patients were positive using both samples. This study successfully demonstrated the possibility of using the PCR technique on urine for the diagnosis of W. bancrofti infection.

When zero doesn't mean it and other geomathematical mischief

There is almost not a case in exploration geology, where the studied data doesn’tincludes below detection limits and/or zero values, and since most of the geological dataresponds to lognormal distributions, these “zero data” represent a mathematicalchallenge for the interpretation.We need to start by recognizing that there are zero values in geology. For example theamount of quartz in a foyaite (nepheline syenite) is zero, since quartz cannot co-existswith nepheline. Another common essential zero is a North azimuth, however we canalways change that zero for the value of 360°. These are known as “Essential zeros”, butwhat can we do with “Rounded zeros” that are the result of below the detection limit ofthe equipment?Amalgamation, e.g. adding Na2O and K2O, as total alkalis is a solution, but sometimeswe need to differentiate between a sodic and a potassic alteration. Pre-classification intogroups requires a good knowledge of the distribution of the data and the geochemicalcharacteristics of the groups which is not always available. Considering the zero valuesequal to the limit of detection of the used equipment will generate spuriousdistributions, especially in ternary diagrams. Same situation will occur if we replace thezero values by a small amount using non-parametric or parametric techniques(imputation).The method that we are proposing takes into consideration the well known relationshipsbetween some elements. For example, in copper porphyry deposits, there is always agood direct correlation between the copper values and the molybdenum ones, but whilecopper will always be above the limit of detection, many of the molybdenum values willbe “rounded zeros”. So, we will take the lower quartile of the real molybdenum valuesand establish a regression equation with copper, and then we will estimate the“rounded” zero values of molybdenum by their corresponding copper values.The method could be applied to any type of data, provided we establish first theircorrelation dependency.One of the main advantages of this method is that we do not obtain a fixed value for the“rounded zeros”, but one that depends on the value of the other variable.Key words: compositional data analysis, treatment of zeros, essential zeros, roundedzeros, correlation dependency

Simple and fast methods based on solid-phase extraction coupled to liquid chromatography with UV detection for the monitoring of caffeine in natural and waste waters as marker of anthropogenic impact

Two concentration methods for fast and routine determination of caffeine (using HPLC-UV detection) in surface, and wastewater are evaluated. Both methods are based on solid-phase extraction (SPE) concentration with octadecyl silica sorbents. A common “offline” SPE procedure shows that quantitative recovery of caffeine is obtained with 2 mL of an elution mixture solvent methanol-water containing at least 60% methanol. The method detection limit is 0.1 μg L−1 when percolating 1 L samples through the cartridge. The development of an “online” SPE method based on a mini-SPE column, containing 100 mg of the same sorbent, directly connected to the HPLC system allows the method detection limit to be decreased to 10 ng L−1 with a sample volume of 100 mL. The “offline” SPE method is applied to the analysis of caffeine in wastewater samples, whereas the “on-line” method is used for analysis in natural waters from streams receiving significant water intakes from local wastewater treatment plants

Fluorine-19 magnetic resonance angiography of the mouse.

PURPOSE: To implement and characterize a fluorine-19 ((19)F) magnetic resonance imaging (MRI) technique and to test the hypothesis that the (19)F MRI signal in steady state after intravenous injection of a perfluoro-15-crown-5 ether (PCE) emulsion may be exploited for angiography in a pre-clinical in vivo animal study. MATERIALS AND METHODS: In vitro at 9.4T, the detection limit of the PCE emulsion at a scan time of 10 min/slice was determined, after which the T(1) and T(2) of PCE in venous blood were measured. Permission from the local animal use committee was obtained for all animal experiments. 12 µl/g of PCE emulsion was intravenously injected in 11 mice. Gradient echo (1)H and (19)F images were obtained at identical anatomical levels. Signal-to-noise (SNR) and contrast-to-noise (CNR) ratios were determined for 33 vessels in both the (19)F and (1)H images, which was followed by vessel tracking to determine the vessel conspicuity for both modalities. RESULTS: In vitro, the detection limit was ∼400 µM, while the (19)F T(1) and T(2) were 1350±40 and 25±2 ms. The (19)F MR angiograms selectively visualized the vasculature (and the liver parenchyma over time) while precisely coregistering with the (1)H images. Due to the lower SNR of (19)F compared to (1)H (17±8 vs. 83±49, p<0.001), the (19)F CNR was also lower at 15±8 vs. 52±35 (p<0.001). Vessel tracking demonstrated a significantly higher vessel sharpness in the (19)F images (66±11 vs. 56±12, p = 0.002). CONCLUSION: (19)F magnetic resonance angiography of intravenously administered perfluorocarbon emulsions is feasible for a selective and exclusive visualization of the vasculature in vivo.

The Lithium, Boron and Beryllium content of serpentinized peridotites from ODP Leg 209 (Sites 1272A and 1274A): Implications for lithium and boron budgets of oceanic lithosphere

Despite the key importance of altered oceanic mantle as a repository and carrier of light elements (B, Li, and Be) to depth, its inventory of these elements has hardly been explored and quantified. In order to constrain the systematics and budget of these elements we have studied samples of highly serpentinized (>50%) spinel harzburgite drilled at the Mid-Atlantic Ridge (Fifteen-Twenty Fracture zone, ODP Leg 209, Sites 1272A and 1274A). In-situ analysis by secondary ion mass spectrometry reveals that the B, Li and Be contents of mantle minerals (olivine, orthopyroxene, and clinopyroxene) remain unchanged during serpentinization. B and Li abundances largely correspond to those of unaltered mantle minerals whereas Be is close to the detection limit. The Li contents of clinopyroxene are slightly higher (0.44-2.8 mu g g(-1)) compared to unaltered mantle clinopyroxene, and olivine and clinopyroxene show an inverse Li partitioning compared to literature data. These findings along with textural observations and major element composition obtained from microprobe analysis suggest reaction of the peridotites with a mafic silicate melt before serpentinization. Serpentine minerals are enriched in B (most values between 10 and 100 mu g g(-1)), depleted in Li (most values below I mu g g(-1)) compared to the primary phases, with considerable variation within and between samples. Be is at the detection limit. Analysis of whole rock samples by prompt gamma activation shows that serpentinization tends to increase B (10.4-65.0 mu g g(-1)), H2O and Cl contents and to lower Li contents (0.07-3.37 mu g g(-1)) of peridotites, implying that-contrary to alteration of oceanic crust-B is fractionated from Li and that the B and Li inventory should depend essentially on rock-water ratios. Based on our results and on literature data, we calculate the inventory of B and Li contained in the oceanic lithosphere, and its partitioning between crust and mantle as a function of plate characteristics. We model four cases, an ODP Leg 209-type lithosphere with almost no igneous crust, and a Semail-type lithosphere with a thick igneous crust, both at I and 75 Ma, respectively. The results show that the Li contents of the oceanic lithosphere are highly variable (17-307 kg in a column of I m x I m x thickness of the lithosphere (kg/col)). They are controlled by the primary mantle phases and by altered crust, whereas the B contents (25-904 kg/col) depend entirely on serpentinization. In all cases, large quantities of B reside in the uppermost part of the plate and could hence be easily liberated during slab dehydration. The most prominent input of Li into subduction zones is to be expected from Semail-type lithosphere because most of the Li is stored at shallow levels in the plate. Subducting an ODP Leg 209-type lithosphere would mean only very little Li contribution from the slab. Serpentinized mantle thus plays an important role in B recycling in subduction zones, but it is of lesser importance for Li. (C) 2008 Elsevier Ltd. All rights reserved.

Measurement of biologically available naphthalene in gas and aqueous phases by use of a Pseudomonas putida biosensor.

Genetically constructed microbial biosensors for measuring organic pollutants are mostly applied in aqueous samples. Unfortunately, the detection limit of most biosensors is insufficient to detect pollutants at low but environmentally relevant concentrations. However, organic pollutants with low levels of water solubility often have significant gas-water partitioning coefficients, which in principle makes it possible to measure such compounds in the gas rather than the aqueous phase. Here we describe the first use of a microbial biosensor for measuring organic pollutants directly in the gas phase. For this purpose, we reconstructed a bioluminescent Pseudomonas putida naphthalene biosensor strain to carry the NAH7 plasmid and a chromosomally inserted gene fusion between the sal promoter and the luxAB genes. Specific calibration studies were performed with suspended and filter-immobilized biosensor cells, in aqueous solution and in the gas phase. Gas phase measurements with filter-immobilized biosensor cells in closed flasks, with a naphthalene-contaminated aqueous phase, showed that the biosensor cells can measure naphthalene effectively. The biosensor cells on the filter responded with increasing light output proportional to the naphthalene concentration added to the water phase, even though only a small proportion of the naphthalene was present in the gas phase. In fact, the biosensor cells could concentrate a larger proportion of naphthalene through the gas phase than in the aqueous suspension, probably due to faster transport of naphthalene to the cells in the gas phase. This led to a 10-fold lower detectable aqueous naphthalene concentration (50 nM instead of 0.5 micro M). Thus, the use of bacterial biosensors for measuring organic pollutants in the gas phase is a valid method for increasing the sensitivity of these valuable biological devices.

Uimahallien vedestä haihtuvat epäpuhtaudet ja niiden leviäminen allastilassa

Uimaveden klooridesinfioinnissa syntyy sivutuotteena haihtuvia ja haitallisia halogeeniyhdisteitä, kuten trihalometaaneja ja triklooriamiinia, jotka voivat heikentää allas-tilan sisäilman laatua merkittävästi. Tämän tutkimuksen tavoitteena oli kartoittaa näiden desinfioinnin sivutuotteiden pitoisuuksia suomalaisissa uimahalleissa sekä selvittää epäpuhtauksien kulkeutumista allastiloissa. Lisäksi pyrittiin löytämään merkittävimmät veden laatu- ja käsittelyparametrit sekä ilmanvaihtotekniset tekijät, jotka vaikuttavat vedestä haihtuvien epäpuhtauksien pitoisuuksiin hallitiloissa. Mittaukset tehtiin kymmenessä eri puolilla Suomea sijaitsevassa uimahallissa. Mittausten perusteella havaittiin, että allastilojen kloroformipitoisuudet vaihtelivat välillä 8,9-84,0 ¿g/m3. Terapia-allasostoilta mitatut pitoisuudet olivat pääallastiloista mitattuja pitoisuuksia suurempia ja aamulla mitattu pitoisuus alhaisempi kuin illalla mitattu. Lisäksi ilmastoiduista valvomoista mitatut pitoisuudet olivat merkittävästi allastilojen pitoisuuksia pienempiä. Triklooriamiininäytteistä suurin osa oli alle määritysrajan. Sisäilman kloroformipitoisuuden havaittiin korreloivan veden lämpötilan sekä ilman kosteuden kanssa. Triklooriamiinille tilastollista analyysiä ei voitu tehdä mm. määritys-rajan alle jääneiden näytteiden suuren osuuden vuoksi. Teknisten kyselyiden ja ilmanvaihtomittausten perusteella todettiin, että uimahallien ilmanvaihto toimii lämmitystarpeen vuoksi sekoittavana ja epäpuhtauksien leviämistä allastilassa ei voida käytännössä katsoen estää. Ilman virtausnopeudet pääaltaiden reunoilla olivat pieniä ja ilman virtauskenttien ei todettu vaikuttavan epäpuhtauksien kulkeutumiseen allastiloissa. Mittauskohteiden vähyydestä ja vedenkäsittelyn hallikohtaisista erityispiirteistä johtuen luotettavia johtopäätöksiä vedenkäsittelymenetelmien vaikutuksesta allasveden ja allastilan ilman laatuun ei pystytty tekemään.

Raman spectroscopy and microspectroscopy of reactive dyes on cotton fibres: analysis and detection limits

A collaborative study on Raman spectroscopy and microspectrophotometry (MSP) was carried out by members of the ENFSI (European Network of Forensic Science Institutes) European Fibres Group (EFG) on different dyed cotton fabrics. The detection limits of the two methods were tested on two cotton sets with a dye concentration ranging from 0.5 to 0.005% (w/w). This survey shows that it is possible to detect the presence of dye in fibres with concentrations below that detectable by the traditional methods of light microscopy and microspectrophotometry (MSP). The MSP detection limit for the dyes used in this study was found to be a concentration of 0.5% (w/w). At this concentration, the fibres appear colourless with light microscopy. Raman spectroscopy clearly shows a higher potential to detect concentrations of dyes as low as 0.05% for the yellow dye RY145 and 0.005% for the blue dye RB221. This detection limit was found to depend both on the chemical composition of the dye itself and on the analytical conditions, particularly the laser wavelength. Furthermore, analysis of binary mixtures of dyes showed that while the minor dye was detected at 1.5% (w/w) (30% of the total dye concentration) using microspectrophotometry, it was detected at a level as low as 0.05% (w/w) (10% of the total dye concentration) using Raman spectroscopy. This work also highlights the importance of a flexible Raman instrument equipped with several lasers at different wavelengths for the analysis of dyed fibres. The operator and the set up of the analytical conditions are also of prime importance in order to obtain high quality spectra. Changing the laser wavelength is important to detect different dyes in a mixture.

Label-free detection of tobramycin in serum by transmission-localized surface plasmon resonance.

In order to improve the efficacy and safety of treatments, drug dosage needs to be adjusted to the actual needs of each patient in a truly personalized medicine approach. Key for widespread dosage adjustment is the availability of point-of-care devices able to measure plasma drug concentration in a simple, automated, and cost-effective fashion. In the present work, we introduce and test a portable, palm-sized transmission-localized surface plasmon resonance (T-LSPR) setup, comprised of off-the-shelf components and coupled with DNA-based aptamers specific to the antibiotic tobramycin (467 Da). The core of the T-LSPR setup are aptamer-functionalized gold nanoislands (NIs) deposited on a glass slide covered with fluorine-doped tin oxide (FTO), which acts as a biosensor. The gold NIs exhibit localized plasmon resonance in the visible range matching the sensitivity of the complementary metal oxide semiconductor (CMOS) image sensor employed as a light detector. The combination of gold NIs on the FTO substrate, causing NIs size and pattern irregularity, might reduce the overall sensitivity but confers extremely high stability in high-ionic solutions, allowing it to withstand numerous regeneration cycles without sensing losses. With this rather simple T-LSPR setup, we show real-time label-free detection of tobramycin in buffer, measuring concentrations down to 0.5 μM. We determined an affinity constant of the aptamer-tobramycin pair consistent with the value obtained using a commercial propagating-wave based SPR. Moreover, our label-free system can detect tobramycin in filtered undiluted blood serum, measuring concentrations down to 10 μM with a theoretical detection limit of 3.4 μM. While the association signal of tobramycin onto the aptamer is masked by the serum injection, the quantification of the captured tobramycin is possible during the dissociation phase and leads to a linear calibration curve for the concentrations over the tested range (10-80 μM). The plasmon shift following surface binding is calculated in terms of both plasmon peak location and hue, with the latter allowing faster data elaboration and real-time display of the results. The presented T-LSPR system shows for the first time label-free direct detection and quantification of a small molecule in the complex matrix of filtered undiluted blood serum. Its uncomplicated construction and compact size, together with the remarkable performances, represent a leap forward toward effective point-of-care devices for therapeutic drug concentration monitoring.

Detection of Clinically Significant Prostate Cancer Using Magnetic Resonance Imaging-Ultrasound Fusion Targeted Biopsy: A Systematic Review.

CONTEXT: The current standard for diagnosing prostate cancer in men at risk relies on a transrectal ultrasound-guided biopsy test that is blind to the location of the cancer. To increase the accuracy of this diagnostic pathway, a software-based magnetic resonance imaging-ultrasound (MRI-US) fusion targeted biopsy approach has been proposed. OBJECTIVE: Our main objective was to compare the detection rate of clinically significant prostate cancer with software-based MRI-US fusion targeted biopsy against standard biopsy. The two strategies were also compared in terms of detection of all cancers, sampling utility and efficiency, and rate of serious adverse events. The outcomes of different targeted approaches were also compared. EVIDENCE ACQUISITION: We performed a systematic review of PubMed/Medline, Embase (via Ovid), and Cochrane Review databases in December 2013 following the Preferred Reported Items for Systematic reviews and Meta-analysis statement. The risk of bias was evaluated using the Quality Assessment of Diagnostic Accuracy Studies-2 tool. EVIDENCE SYNTHESIS: Fourteen papers reporting the outcomes of 15 studies (n=2293; range: 13-582) were included. We found that MRI-US fusion targeted biopsies detect more clinically significant cancers (median: 33.3% vs 23.6%; range: 13.2-50% vs 4.8-52%) using fewer cores (median: 9.2 vs 37.1) compared with standard biopsy techniques, respectively. Some studies showed a lower detection rate of all cancer (median: 50.5% vs 43.4%; range: 23.7-82.1% vs 14.3-59%). MRI-US fusion targeted biopsy was able to detect some clinically significant cancers that would have been missed by using only standard biopsy (median: 9.1%; range: 5-16.2%). It was not possible to determine which of the two biopsy approaches led most to serious adverse events because standard and targeted biopsies were performed in the same session. Software-based MRI-US fusion targeted biopsy detected more clinically significant disease than visual targeted biopsy in the only study reporting on this outcome (20.3% vs 15.1%). CONCLUSIONS: Software-based MRI-US fusion targeted biopsy seems to detect more clinically significant cancers deploying fewer cores than standard biopsy. Because there was significant study heterogeneity in patient inclusion, definition of significant cancer, and the protocol used to conduct the standard biopsy, these findings need to be confirmed by further large multicentre validating studies. PATIENT SUMMARY: We compared the ability of standard biopsy to diagnose prostate cancer against a novel approach using software to overlay the images from magnetic resonance imaging and ultrasound to guide biopsies towards the suspicious areas of the prostate. We found consistent findings showing the superiority of this novel targeted approach, although further high-quality evidence is needed to change current practice.

Post-mortem determination of insulin using chemiluminescence enzyme immunoassay: preliminary results.

Insulin determination in blood sampled during post-mortem investigation has been repeatedly asserted as being of little diagnostic value due to the rapid occurrence of decompositional changes and blood haemolysis. In this study, we assessed the feasibility of insulin determination in post-mortem serum, vitreous humour, bile, and cerebrospinal and pericardial fluids in one case of fatal insulin self-administration and a series of 40 control cases (diabetics and non-diabetics) using a chemiluminescence enzyme immunoassay. In the case of suicide by insulin self-administration, insulin concentrations in pericardial fluid and bile were higher than blood clinical reference values, though lower than post-mortem serum concentration. Insulin concentrations in vitreous (11.50 mU/L) and cerebrospinal fluid (17.30 mU/L) were lower than blood clinical reference values. Vitreous insulin concentrations in non-diabetic control cases were lower than the estimated detection limit of the method. These preliminary results tend to confirm the usefulness of insulin determination in vitreous humour in situations of suspected fatal insulin administration. Additional findings pertaining to insulin determination in bile, pericardial, and cerebrospinal fluid would suggest that analysis performed in post-mortem serum and injection sites could be complemented, in individual cases, by investigations carried out in alternative biological fluids. Lastly, these results would indicate that analysis with chemiluminescence enzyme immunoassay may provide suitable data, similar to analysis with liquid chromatography-tandem mass spectrometry (LC-MS/MS) and immunoradiometric assay, to support the hypothesis of insulin overdose. Copyright © 2015 John Wiley & Sons, Ltd.

Geração eletroquímica do hidreto de selênio em sistema de injeção em fluxo com detecção por espectrometria de absorção atômica com chama Ar-Glp

This paper presents a system for electrochemical hydride generation using flow-injection and atomic absorption spectrometry to determine selenium in biological materials. The electrolytic cell was constructed by assembling two reservoirs, one for the sample and the other for the electrolytic solution separated by a Nafion membrane. Each compartment had a Pt electrode. The sample and electrolyte flow-rates, acidic media, and applied current were adjusted to attain the best analytical performance and ensure the membrane lifetime. The atomisation system used a T quartz tube in an air-LPG flame. The composition of the flame, the observation height, and the argon flow rate used to carry the hydrides were critically investigated. The system allowed to perform thirty determinations per hour with a detection limit of 10 mug L-1 of Se. Relative standard deviations were in general lower than 1.5% for a solution containing 20.0 and 34.0 mug L-1 of Se in a typical sample digest. Accuracy was assessed analysing the certified materials: rice flour (NIST-1568) from National Institute of Standard and Technology and dried fish (MA-A-2), whole animal blood (A-2/1974) from the International Atomic Energy Agency.

Determinação espectrofotométrica de vitamina B2 (riboflavina) em formulações farmacêuticas empregando sistema de análises por injeção em fluxo

A flow injection spectrophotometric procedure exploiting merging zones is proposed for determining vitamin B2 (riboflavin) in pharmaceutical preparations. The determination is based on the red-colored complex formation between vitamin B2 and silver(I) which was measured at 520 nm. Vitamin B2 was determined in four pharmaceutical preparations in the 1.0 to 50.0 mg L-1 concentration range, with a detection limit of 0.5 mg L-1. The recovery from three samples ranged from 98.0 to 104.0 %. The analytical frequency was 42 h-1 and r.s.d. were lower than 1% for solutions containing 10.0, 30.0 and 50.0 mg L-1 vitamin B2 (n= 10). The results obtained in commercial formulations using the FIA procedure were in good agreement with those obtained by using a conventional fluorimetric procedure (r=0.9998) and also with the label values (r= 0.9997).