DNA extraction using the QIAsymphony: Evaluation of PCR inhibitor removal

The goal of this study was to compare the quantity and purity of DNA extracted from biological tracesusing the QIAsymphony robot with that of the manual QIAamp DNA mini kit currently in use in ourlaboratory. We found that the DNA yield of robot was 1.6-3.5 times lower than that of the manualprotocol. This resulted in a loss of 8% and 29% of the alleles correctly scored when analyzing 1/400 and 1/800 diluted saliva samples, respectively. Specific tests showed that the QIAsymphony was at least 2-16times more efficient at removing PCR inhibitors. The higher purity of the DNA may therefore partlycompensate for the lower DNA yield obtained. No case of cross-contamination was observed amongsamples. After purification with the robot, DNA extracts can be automatically transferred in 96-wellsplates, which is an ideal format for subsequent RT-qPCR quantification and DNA amplification. Lesshands-on time and reduced risk of operational errors represent additional advantages of the robotic platform.

Implementing statistical learning methods through Bayesian networks. Part 1: a guide to Bayesian parameter estimation using forensic science data

As a thorough aggregation of probability and graph theory, Bayesian networks currently enjoy widespread interest as a means for studying factors that affect the coherent evaluation of scientific evidence in forensic science. Paper I of this series of papers intends to contribute to the discussion of Bayesian networks as a framework that is helpful for both illustrating and implementing statistical procedures that are commonly employed for the study of uncertainties (e.g. the estimation of unknown quantities). While the respective statistical procedures are widely described in literature, the primary aim of this paper is to offer an essentially non-technical introduction on how interested readers may use these analytical approaches - with the help of Bayesian networks - for processing their own forensic science data. Attention is mainly drawn to the structure and underlying rationale of a series of basic and context-independent network fragments that users may incorporate as building blocs while constructing larger inference models. As an example of how this may be done, the proposed concepts will be used in a second paper (Part II) for specifying graphical probability networks whose purpose is to assist forensic scientists in the evaluation of scientific evidence encountered in the context of forensic document examination (i.e. results of the analysis of black toners present on printed or copied documents).

Transvaginal specimen extraction in colorectal surgery: current state of the art.

Aim  Background The expected benefit of transvaginal specimen extraction is reduced incision-related morbidity. Objectives A systematic review of transvaginal specimen extraction in colorectal surgery was carried out to assess this expectation. Method  Search strategy The following keywords, in various combinations, were searched: NOSE (natural orifices specimen extraction), colorectal, colon surgery, transvaginal, right hemicolectomy, left hemicolectomy, low anterior resection, sigmoidectomy, ileocaecal resection, proctocolectomy, colon cancer, sigmoid diverticulitis and inflammatory bowel diseases. Selection criteria Selection criteria included large bowel resection with transvaginal specimen extraction, laparoscopic approach, human studies and English language. Exclusion criteria were experimental studies and laparotomic approach or local excision. All articles published up to February 2011 were included. Results  Twenty-three articles (including a total of 130 patients) fulfilled the search criteria. The primary diagnosis was colorectal cancer in 51% (67) of patients, endometriosis in 46% (60) of patients and other conditions in the remaining patients. A concurrent gynaecological procedure was performed in 17% (22) of patients. One case of conversion to laparotomy was reported. In two patients, transvaginal extraction failed. In left- and right-sided resections, the rate of severe complications was 3.7% and 2%, respectively. Two significant complications, one of pelvic seroma and one of rectovaginal fistula, were likely to have been related to transvaginal extraction. The degree of follow up was specified in only one study. Harvested nodes and negative margins were adequate and reported in 70% of oncological cases. Conclusion  Vaginal extraction of a colorectal surgery specimen shows potential benefit, particularly when associated with a gynaecological procedure. Data from prospective randomized trials are needed to support the routine use of this technique.

Ex-PRESS R-50 miniature glaucoma implant insertion under the conjunctiva combined with cataract extraction

Rapport de synthèse : Le glaucome à angle ouvert est une neuropathie optique chronique progressive pour laquelle de nombreux traitements tant médicaux que chirurgicaux ont été proposés. La prise en charge chirurgicale s'articule principalement autour de deux chirurgies filtrantes, la trabéculectomie et la sclérectomie profonde avec implant de collagène. Cependant, les complications postopératoires de ces deux interventions étant relativement fréquentes, la recherche s'est orientée vers des traitements alternatifs dont la mise en place de micro-drains. Ces implants de drainage diminuent la pression intraoculaire en créant un court-circuit du flux d'humeur aqueuse de la chambre antérieure vers l'espace sous-conjonctival avec formation d'une bulle de filtration. L'implant Ex-PRESS R-50 est un implant miniature (2.5 mm de long pour 400 µm de diamètre) en acier inoxydable et biocompatible. La présente étude s'est proposée d'étudier l'efficacité et la sécurité de l'implant miniature Ex-Press R-50 lors d'une opération combinée cataracte-glaucome. Trente-cinq yeux de 35 patients (âge moyen: 75 ans) ont été inclus dans l'étude. Tous les patients ont bénéficié d'une opération de la cataracte par phacoemulsification et mise en place d'un implant de chambre postérieure suivie de l'implantation du micro-drain. Les pressions intraoculaires préopératoires et postopératoires, la meilleure acuité visuelle corrigée, le nombre de médicaments anti-glaucomateux ainsi que le type et le nombre de complications ont été évalués mensuellement puis tous les 6 mois pendant 4 ans. Le succès total a été défini par une pression postopératoire finale inférieure à 18mmHg sans traitement médical associé, le succès partiel par une pression postopératoire finale inférieure à 18mmHg avec ou sans traitement médical associé.. Le suivi moyen a été de 36.9 mois avec une baisse de la pression intraoculaire significative d'environ 25%. Une augmentation de l'acuité visuelle a été observée après l'opération de la cataracte et le nombre de médicaments anti-glaucomateux a été réduit de 57%. Dix patients ont bénéficié d'un traitement supplémentaire de la bulle de filtration par injection d'anti-métabolite (mitomycine C). Nous avons observé 8 complications majeures (4 érosions conjonctivales et 4 obstructions de l'orifice interne du micro-drain), toutes suivies de l'ablation de l'implant et de la réalisation d'une chirurgie classique du glaucome. En se basant sur les courbes de Kaplan-Meier à 48 mois, le taux de succès total était de 32.7% et le succès partiel de 53.7%. Nous pouvons conclure suite à ce travail que l'implant miniature Ex-PRESS R-50 est associé à un nombre trop élevé de complications, même si les cas non compliqués ont bénéficié d'une baisse significative de la pression intraoculaire. La modification de l'architecture du micro-drain ainsi que de la technique chirurgicale devrait augmenter le taux de succès.

Determination of the Enantiomers of Mianserin and its Metabolites in Plasma by Capillary Electrophoresis After Liquid-Liquid Extraction and On-Column Sample Preconcentration

Capillary electrophoresis has drawn considerable attention in the past few years, particularly in the field of chiral separations because of its high separation efficiency. However, its routine use in therapeutic drug monitoring is hampered by its low sensitivity due to a short optical path. We have developed a capillary zone electrophoresis (CZE) method using 2mM of hydroxypropyl-β-cyclodextrin as a chiral selector, which allows base-to-base separation of the enantiomers of mianserin (MIA), desmethylmianserin (DMIA), and 8-hydroxymianserin (OHMIA). Through the use of an on-column sample concentration step after liquid-liquid extraction from plasma and through the presence of an internal standard, the quantitation limits were found to be 5 ng/mL for each enantiomer of MIA and DMIA and 15 ng/mL for each enantiomer of OHMIA. To our knowledge, this is the first published CE method that allows its use for therapeutic monitoring of antidepressants due to its sensitivity down to the low nanogram range. The variability of the assays, as assessed by the coefficients of variation (CV) measured at two concentrations for each substance, ranged from 2 to 14% for the intraday (eight replicates) and from 5 to 14% for the interday (eight replicates) experiments. The deviations from the theoretical concentrations, which represent the accuracy of the method, were all within 12.5%. A linear response was obtained for all compounds within the range of concentrations used for the calibration curves (10-150 ng/mL for each enantiomer of MIA and DMIA and 20-300 ng/mL for each enantiomer of OHMIA). Good correlations were calculated between [(R) + (S)]-MIA and DMIA concentrations measured in plasma samples of 20 patients by a nonchiral gas chromatography method and CZE, and between the (R)- and (S)-concentrations of MIA and DMIA measured in plasma samples of 37 patients by a previously described chiral high-performance liquid chromatography method and CZE. Finally, no interference was noted from more than 20 other psychotropic drugs. Thus, this method, which is both sensitive and selective, can be routinely used for therapeutic monitoring of the enantiomers of MIA and its metabolites. It could be very useful due to the demonstrated interindividual variability of the stereoselective metabolism of MIA.

High-throughput and sensitive quantitation of plasma catecholamines by ultraperformance liquid chromatography-tandem mass spectrometry using a solid phase microwell extraction plate.

Plasma catecholamines provide a reliable biomarker of sympathetic activity. The low circulating concentrations of catecholamines and analytical interferences require tedious sample preparation and long chromatographic runs to ensure their accurate quantification by HPLC with electrochemical detection. Published or commercially available methods relying on solid phase extraction technology lack sensitivity or require derivatization of catecholamine by hazardous reagents prior to tandem mass spectrometry (MS) analysis. Here, we manufactured a novel 96-well microplate device specifically designed to extract plasma catecholamines prior to their quantification by a new and highly sensitive ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method. Processing time, which included sample purification on activated aluminum oxide and elution, is less than 1 h per 96-well microplate. The UPLC-MS/MS analysis run time is 2.0 min per sample. This UPLC-MS/MS method does not require a derivatization step, reduces the turnaround time by 10-fold compared to conventional methods used for routine application, and allows catecholamine quantification in reduced plasma sample volumes (50-250 μL, e.g., from children and mice).

Transrectal specimen extraction after laparoscopic left colectomy: a case-matched study.

Aim  Avoiding 'mini-laparotomy' to extract a colectomy specimen may decrease wound complications and further improve recovery after laparoscopic surgery. The aim of this study was to develop a new technique for transrectal specimen extraction (TRSE) and to compare it with conventional laparoscopy (CL) for left sided colectomy. Method  Eleven patients with benign disease requiring either sigmoid or left colon resection underwent TRSE. The unfired circular stapler was inserted transanally and used as a guide to suture-close the recto-sigmoid junction laparoscopically and as a handle to pull the sutured sigmoid through the opened rectum inside a laparoscopic camera bag. The anvil was inserted into the lumen of the intussuscepted sigmoid and pushed to the level of the anastomosis. The anastomosis was fashioned end-to-end in the first patients and side-to-end in the following patients to improve safety. Intra-operative and postoperative outcomes of patients undergoing TRSE were compared with those of a group of 20 patients undergoing CL, who were matched for type of resection, body mass index and age. Results  The procedure was successful in all but the first patient who was converted to conventional laparoscopic colectomy without any additional morbidity. Two patients in the end-to-end anastomosis group, but none in the side-to-end group, developed peri-anastomotic sepsis. Compared with CL, patients undergoing TRSE did not show any significant differences in operative time, recovery or morbidity. Conclusion  Transrectal specimen extraction after left colectomy using the circular stapler technique is feasible. A side-to-end anastomosis appears safer than an end-to-end anastomosis. Further studies are needed to explore the potential advantages of this procedure over CL.

Comparison of naphthalene bioavailability determined by whole-cell biosensing and availability determined by extraction with Tenax

A rapid biological method for the determination of the bioavailability of naphthalene was developed and its value as an alternative to extraction-based chemical approaches demonstrated. Genetically engineered whole-cell biosensors are used to determine bioavailable naphthalene and their responses compared with results from Tenax extraction and chemical analysis. Results show a 1:1 correlation between biosensor results and chemical analyses for naphthalene-contaminated model materials and sediments, but the biosensor assay is much faster. This work demonstrates that biosensor technology can perform as well as standard chemical methods, though with some advantages including the inherent biological relevance of the response, rapid response time, and potential for field deployment. A survey of results from this work and the literature shows that bioavailability under non-equilibrium conditions nonetheless correlates well with K(oc) or K(d). A rationale is provided wherein chemical resistance is speculated to be operative.

Quantitative multi-parameter mapping of R1, PD(*), MT, and R2(*) at 3T: a multi-center validation.

Multi-center studies using magnetic resonance imaging facilitate studying small effect sizes, global population variance and rare diseases. The reliability and sensitivity of these multi-center studies crucially depend on the comparability of the data generated at different sites and time points. The level of inter-site comparability is still controversial for conventional anatomical T1-weighted MRI data. Quantitative multi-parameter mapping (MPM) was designed to provide MR parameter measures that are comparable across sites and time points, i.e., 1 mm high-resolution maps of the longitudinal relaxation rate (R1 = 1/T1), effective proton density (PD(*)), magnetization transfer saturation (MT) and effective transverse relaxation rate (R2(*) = 1/T2(*)). MPM was validated at 3T for use in multi-center studies by scanning five volunteers at three different sites. We determined the inter-site bias, inter-site and intra-site coefficient of variation (CoV) for typical morphometric measures [i.e., gray matter (GM) probability maps used in voxel-based morphometry] and the four quantitative parameters. The inter-site bias and CoV were smaller than 3.1 and 8%, respectively, except for the inter-site CoV of R2(*) (<20%). The GM probability maps based on the MT parameter maps had a 14% higher inter-site reproducibility than maps based on conventional T1-weighted images. The low inter-site bias and variance in the parameters and derived GM probability maps confirm the high comparability of the quantitative maps across sites and time points. The reliability, short acquisition time, high resolution and the detailed insights into the brain microstructure provided by MPM makes it an efficient tool for multi-center imaging studies.

Spontaneous Cdc42 polarization independent of GDI-mediated extraction and actin-based trafficking.

The small Rho-family GTPase Cdc42 is critical for cell polarization and polarizes spontaneously in absence of upstream spatial cues. Spontaneous polarization is thought to require dynamic Cdc42 recycling through Guanine nucleotide Dissociation Inhibitor (GDI)-mediated membrane extraction and vesicle trafficking. Here, we describe a functional fluorescent Cdc42 allele in fission yeast, which demonstrates Cdc42 dynamics and polarization independent of these pathways. Furthermore, an engineered Cdc42 allele targeted to the membrane independently of these recycling pathways by an amphipathic helix is viable and polarizes spontaneously to multiple sites in fission and budding yeasts. We show that Cdc42 is highly mobile at the membrane and accumulates at sites of activity, where it displays slower mobility. By contrast, a near-immobile transmembrane domain-containing Cdc42 allele supports viability and polarized activity, but does not accumulate at sites of activity. We propose that Cdc42 activation, enhanced by positive feedback, leads to its local accumulation by capture of fast-diffusing inactive molecules.

More than 10 years of experience with immediate sequential bilateral cataract extraction (ISBCE) - a retrospective study

Background: To evaluate the safety of immediate sequential bilateral cataract extraction (ISBCE) with respect to indications, visual outcomes, complications, benefits and disadvantages. Methods: This is a retrospective review of all ISBCEs performed at Kantonsspital Winterthur, Switzerland, between April 2000 and September 2013. The case notes of 500 eyes of 250 patients were reviewed. Of these 500 eyes, 472 (94.4%) had a straight forward phacoemulsification with posterior chamber intraocular lens implantation; 21 (4.2%) had a planned extracapsular cataract extraction; 4 (0.8%) had an intracapsular cataract extraction and 3 (0.6%) had a combined phacoemulsification with trabeculectomy. Results: Over 66% of eyes achieved improved visual acuity (at least 3 Snellen lines) following ISBCE. Median preoperative best corrected visual acuity (BCVA) was 0.5 LogMAR; the interquartile range was [0.4, 1] LogMAR. At one week control the median BCVA was 0.3 LogMAR, IQR [0.1, 0.5] LogMAR. At one month the median BCVA was 0.15 LogMAR, IQR [0.05, 0.3] (p < 0.01). There were no sight-threatening intraoperative or postoperative complications observed. Conclusions: ISBCE is an effective and safe option with high degree of patient satisfaction. The relative benefits of ISBCE should be balanced against the theoretically enhanced risks.