Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: Results of a collaborative EDNAP exercise

There is increasing interest in forensic ancestry tests, which are part of a growing number of DNA analyses that can enhance routine profiling by obtaining additional genetic information about unidentified DNA donors. Nearly all ancestry tests use single nucleotide polymorphisms (SNPs), but these currently rely on SNaPshot single base extension chemistry that can fail to detect mixed DNA. Insertion-deletion polymorphism (Indel) tests have been developed using dye-labeled primers that allow direct capillary electrophoresis detection of PCR products (PCR-to-CE). PCR-to-CE maintains the direct relationship between input DNA and signal strength as each marker is detected with a single dye, so mixed DNA is more reliably detected. We report the results of a collaborative inter-laboratory exercise of 19 participants (15 from the EDNAP European DNA Profiling group) that assessed a 34-plex SNP test using SNaPshot and a 46-plex Indel test using PCR-to-CE. Laboratories were asked to type five samples with different ancestries and detect an additional mixed DNA sample. Statistical inference of ancestry was made by participants using the Snipper online Bayes analysis portal plus an optional PCA module that analyzes the genotype data alongside calculation of Bayes likelihood ratios. Exercise results indicated consistent genotyping performance from both tests, reaching a particularly high level of reliability for the Indel test. SNP genotyping gave 93.5% concordance (compared to the organizing laboratory's data) that rose to 97.3% excluding one laboratory with a large number of miscalled genotypes. Indel genotyping gave a higher concordance rate of 99.8% and a reduced no-call rate compared to SNP analysis. All participants detected the mixture from their Indel peak height data and successfully assigned the correct ancestry to the other samples using Snipper, with the exception of one laboratory with SNP miscalls that incorrectly assigned ancestry of two samples and did not obtain informative likelihood ratios for a third. Therefore, successful ancestry assignments were achieved by participants in 92 of 95 Snipper analyses. This exercise demonstrates that ancestry inference tests based on binary marker sets can be readily adopted by laboratories that already have well-established CE regimes in place. The Indel test proved to be easy to use and allowed all exercise participants to detect the DNA mixture as well as achieving complete and concordant profiles in nearly all cases. Lastly, two participants successfully ran parallel next-generation sequencing analyses (each using different systems) and achieved high levels of genotyping concordance using the exercise PCR primer mixes unmodified.

Prison prescribing practice: practitioners' perspectives on why prison is different

The current prison population in England and Wales has multiple, complex healthcare needs, presenting unique challenges to those caring for prisoners. Prison numbers have increased dramatically in the last 10 years. There are now approximately 84,000 prisoners in England and Wales and 120,000 new episodes of imprisonment each year . The authors all contribute to prison healthcare. Below, we discuss a key issue arising from first-hand experience of prisoners' health and social care needs, the prescription of psycho-active drugs by primary and secondary care practitioners. This is a core medical task, but beset with difficulties. These difficulties are not necessarily encountered in other areas of prison healthcare. However, they do illustrate how providing healthcare to prisoners is complex, often lacking a research base and can have pitfalls that are not obvious to the outsider.

Appendicitis in a Spigelian hernia: an unusual cause for a tender right iliac fossa mass

Spigelian hernias are a rare type of hernia through the Spigelian aponeurosis, whose contents commonly include omentum or small bowel. In the absence of incarceration or strangulation, they can be difficult to diagnose clinically. In the emergency setting, they can present rarely as a painful abdominal mass and computed tomography provides a reliable diagnostic imaging modality. We report an emergency presentation of a Spigelian hernia containing the appendix.

Stable low-loss optical nanofibres embedded in hydrophobic aerogel

Nanofibres, optical fibres narrower than the wavelength of light, degrade in hours on exposure to air. We show that encapsulation in hydrophobic silica aerogel (refractive index 1.05) provides protection and stability (over 2 months) without sacrificing low attenuation, strong confinement and accessible evanescent field. The measured attenuation was <0.03 dB/mm, over 10 × lower than reported with other encapsulants. This enables many nanofibre applications based on their extreme small size and strong external evanescent field, such as optical sensors, nonlinear optics, nanofibre circuits and high-Q resonators. The aerogel is more than a waterproof box, it is a completely-compatible gas-permeable material in intimate contact with the nanofibre and hydrophobic on both the macroscopic and molecular scales. Its benefits are illustrated by experiments on gas sensing (exploiting the aerogel's porosity) and supercontinuum generation (exploiting its ultra-low index).

Silica aerogel core waveguide

We have selectively filled the core of hollow photonic crystal fibre with silica aerogel. Light is guided in the aerogel core, with a measured attenuation of 0.2 dB/cm at 1540 nm comparable to that of bulk aerogel. The structure guides light by different mechanisms depending on the wavelength. At long wavelengths the effective index of the microstructured cladding is below the aerogel index of 1.045 and guidance is by total internal reflection. At short wavelengths, where the effective cladding index exceeds 1.045, a photonic bandgap can guide the light instead. There is a small region of crossover, where both index- and bandgap-guided modes were simultaneously observed.

UK and Ireland experience of cochlear implants in children with Down syndrome

OBJECTIVES

Down Syndrome (DS) is associated with a high incidence of hearing loss. The majority of hearing loss is conductive, but between 4 and 20% is sensorineural, which in the main is mild or moderate and is managed with conventional behind-the-ear hearing aids. Cochlear implantation is an elective invasive procedure, performed to provide some form of hearing rehabilitation in individuals with severe to profound sensorineural hearing loss, and initially candidacy criteria were strict--excluding patients with additional disabilities. With good results and expanding experience, more candidates with additional disabilities are now being implanted. A survey of UK and Ireland Cochlear Implant Programmes sought to identify the number of individuals with DS who have been implanted with a cochlear implant (CI) and to provide relevant information on outcomes of implantation in these individuals.

METHODS

E-mail survey of all programmes within the British Cochlear Implant Group (BCIG). Postal questionnaire to programmes identified to have implanted a child with Down Syndrome, with data collection on pre-operative assessment, surgical and post-operative outcomes. Case series review.

RESULTS

Three of 23 BCIG programmes have implanted a child with Down Syndrome. Four children have received implants. No intraoperative or post-operative surgical complications were encountered. All children had middle ear disease, but no problems with implantation were associated with their middle ear condition. All children remain implant users, 12 months to 4 years post-implantation.

CONCLUSION

Cochlear implantation is an option for a child with Down Syndrome and associated severe to profound sensorineural hearing loss. Clinicians caring for these children and their families should consider referral for assessment by a Cochlear Implant Programme.

Pleuropancreatic fistulae: specialist center management

BACKGROUND AND AIMS

Internal pancreatic fistulae are uncommon sequelae of severe acute pancreatitis. Due to their low prevalence, experience in the management of this condition remains sparse outside specialist centers and management remains controversial. We report our experience with pleuropancreatic fistulae (PPF).

PATIENTS

Six patients (three males, median age 34 years [range, 32-74 years]) with PPF were managed in our unit over a 24-month period from April 2006 to April 2008. The etiology of pancreatitis was alcohol (four), gallstones (one), and unknown cause (one). All patients had documented pleural effusions with amylase content >1,000 iu/dl.

RESULTS

All patients underwent computerized tomography (CT) and magnetic resonance imaging (MRI) cross-sectional scanning to identify the site of ductal disruption. CT alone was able to identify the disruption in four cases and a combination of CT and MRI localized the ductal disruption in all patients. Five of six patients required ERCP and placement of a pancreatic duct (PD) stent. No patient required pancreatic surgery and all patients remain well at a median follow up of 39 weeks.

CONCLUSION

Pleuropancreatic fistulae can present a challenging diagnostic dilemma. A multi-disciplinary approach addressing nutritional support and endotherapy allows successful non-operative resolution within specialist units.

Expandable metal stents for the palliation of malignant gastroduodenal obstruction

PURPOSE

Gastric outlet obstruction is a debilitating complication of upper gastrointestinal malignancy. We present our experience with insertion of self-expanding metal stents (SEMS).

METHODS

Twenty-eight patients were referred, stenting being attempted in 23. Two patients had esophageal Wallstents inserted through a gastrostomy; 21 had an endoscopic approach with enteral Wallstents.

RESULTS

One stent insertion failed, ten patients (45%) returned to a normal diet, ten patients (45%) managed semi-solid food and two patients (9%) had no significant improvement. No immediate complications were seen. One patient subsequently developed pancreatitis. Reintervention (4 stents, 1 jejunostomy, 1 gastrojejunostomy) was required in six of 22 patients (27%) for inadequate stent expansion (1), second stricture (2), stent migration (1), and tumor ingrowth (2). The mean survival was 95.4 days (SD 78.8 days, range 3-230 days). The mean follow-up time was 98.9 days (SD 86.7 days, range 3-309 days).

CONCLUSIONS

SEMS are effective in palliating malignant gastric outlet obstruction. A combined endoscopic/fluoroscopic approach allows the most complete assessment of the stricture and removes the need for gastrostomy insertion. Careful assessment of the gastrointestinal tract distal to the lesion is important.

A guaB mutant strain of Rhizobium tropici CIAT899 pleiotropically defective in thermal tolerance and symbiosis

Rhizobium tropici strain CIAT899 displays a high intrinsic thermal tolerance, and had been used in this work to study the molecular basis of bacterial responses to high temperature. We generated a collection of R. tropici CIAT899 mutants affected in thermal tolerance using TnS-luxAB mutagenesis and described the characterization of a mutant strain, CIAT899-10T, that fails to grow under conditions of high temperature. Strain CIAT899-10T carries a single transposon insertion in a gene showing a high degree of similarity with the guaB gene of Escherichia coli and other organisms, encoding the enzyme inosine monophosphate dehydrogenase. The guaB strain CIAT899-10T does not require guanine for growth due to an alternative pathway via xanthine dehydrogenase and, phenotypically, in addition to the thermal sensitivity, the mutant is also defective in symbiosis with beans, forming nodules that lack rhizobial content. Guanine and its precursors restore wild-type tolerance to grow at high temperature. Our data show that, in R. tropici, the production of guanine via inosine monophosphate dehydrogenase is essential for growth at extreme temperatures and for effective nodulation.

Stress-induced membrane association of the Streptococcus mutans GTP-binding protein, an essential G protein, and investigation of its physiological role by utilizing an antisense RNA strategy

SGP (for Streptococcus GTP-binding protein) is a Streptococcus mutans essential GTPase which has significant sequence identity to the previously identified Escherichia coli Era protein and to numerous other prokaryotic GTPase proteins of unknown function. Recent studies in our laboratory have addressed the possible role of SGP in the stress response of the oral pathogen S. mutans. Here we report that during growth in the early stationary phase, and in response to elevated temperatures or acidic pH, the distribution of SGP between the cytoplasm and the membranes of S. mutans cells varies. Immunoblot analysis of soluble and membrane protein fractions collected from the mid-log and early stationary growth phases of bacterial populations grown at normal temperature (37 degrees C) and at the elevated temperature of 43 degrees C, or at acidic pH, demonstrated that the total amount of SGP increased with the age of the bacterial culture, elevated temperature, or acidic pH. Furthermore, it was established that a substantial amount of SGP is associated with the membrane fraction under stress conditions. In order to investigate the physiological role of SGP, we constructed an S. mutans strain capable of chromosomal sgp antisense RNA expression, which interferes with the normal information processing of the sgp gene. Utilizing this strain, we determined conditions whereby the streptococcal cells can be depleted of SGP, thus avoiding the problem of constructing a conditional lethal system. From the results of measurements of the nucleotide pools extracted from the antisense strain and its isogenic counterpart, we propose that one of the physiological roles of SGP is regulation and modulation of the GTP/GDP ratio under different growth conditions. Moreover, we observed that in SGP-depleted cells the levels of glucan-binding protein A (GbpA) substantially increased, suggesting that GbpA may have stress response-related physiological functions. Finally, the potential applications of the antisense RNA approach that we employed are discussed.

Deafness and imbalance associated with inactivation of the secretory Na-K-2Cl co-transporter

Deafness can result from a variety of gene defects. Some genes involved in the physiology of hearing encode membrane transporters that regulate the ionic composition of the fluid bathing the inner ear. The endolymph is an extracellular fluid with an atypical composition that resembles the intracellular milieu, high in K+ and low in Na+. Recent studies have emphasized the prominent role of K+ channels in endolymph secretion and mechanical transduction. Coupled electroneutral transport of Na+, K+ and Cl- is mediated by two isoforms of the Na-K-2Cl co-transporter: the absorptive isoform BSC1 (also called NKCC2, encoded by Slc12a1 in mouse) that is exclusively expressed in kidney; and BSC2/NKCC1 (encoded by Slc12a2 in mouse), the secretory isoform which has a wider pattern of expression including epithelia, muscle cells, neurons and red blood cells. These co-transporters share 57% homology at the amino acid level and are pharmacologically inhibited by loop diuretics. There is functional and histochemical evidence for the presence of the secretory isoform of the Na-K-2Cl co-transporter in gerbil, rat and rabbit inner ear. We disrupted mouse Slc12a2 and report here that Slc12a2-/- mice are deaf and exhibit classic shaker/waltzer behaviour, indicative of inner-ear defects. We localized the co-transporter to key secreting epithelia of the mouse inner ear and show that absence of functional co-transporter leads to structural damages in the inner ear consistent with a decrease in endolymph secretion.

The safety sphincterotome: the device, the technique and preliminary results

BACKGROUND AND STUDY AIMS

Endoscopic sphincterotomy is a widely used and safe procedure for the management of common bile duct stones, but little attention has been paid to the design of the sphincterotome and its influence upon risk of sphincterotomy. This study was undertaken to evaluate a sphincterotome, designed to incorporate known and original aspects which may contribute to safety.

PATIENTS AND METHODS

144 patients with bile duct stones were evaluated in an open prospective study of the use of the sphincterotome in performing endoscopic sphincterotomy. Evaluation included post-sphincterotomy complications, 30-day morbidity and mortality and effective duct clearance.

RESULTS

Only one complication (0.7%) occurred in the group of 144 patients. Duct clearance of stones was ultimately achieved in 94%.

CONCLUSIONS

Whilst more experience is necessary using the sphincterotome in the manner described, the absence of significant complications in all but one patient appears to support the philosophy behind the design of the sphincterotome.

Can bedside assessment reliably exclude aspiration following acute stroke?

OBJECTIVE

To investigate the ability of a bedside swallowing assessment to reliably exclude aspiration following acute stroke.

SUBJECTS

Consecutive patients admitted within 24 h of stroke onset to two hospitals.

METHODS

A prospective study. Where possible, all patients had their ability to swallow assessed on the day of admission by both a doctor and a speech and language therapist using a standardized proforma. A videofluoroscopy examination was conducted within 3 days of admission.

RESULTS

94 patients underwent videofluoroscopy; 20 (21%) were seen to be aspirating, although this was not detected at the bedside in 10. In 18 (22%) of the patients the speech and language therapist considered the swallow to be unsafe. In the medical assessment, 39 patients (41%) had an unsafe swallow. Bedside assessment by a speech and language therapist gave a sensitivity of 47%, a specificity of 86%, positive predictive value (PPV) of 50% and a negative predictive value (NPV) of 85% for the presence of aspiration. Multiple logistic regression was used to identify the optimum elements of the bedside assessments for predicting the presence of aspiration. A weak voluntary cough and any alteration in conscious level gave a sensitivity of 75%, specificity of 72%, PPV of 41% and NPV of 91% for aspiration.

CONCLUSION

Bedside assessment of swallowing lacks the necessary sensitivity to be used as a screening instrument in acute stroke, but there are concerns about the use of videofluoroscopy as a gold standard. The relative importance of aspiration and bedside assessment in predicting complications and outcome needs to be studied.

A randomized controlled trial evaluating the use of sterile water as an irrigation fluid during transurethral electrovaporization of the prostate

OBJECTIVE

To compare the safety of sterile water and glycine when used as bladder irrigation during transurethral electrovaporization of the prostate (TUVP) in a randomized controlled trial.

PATIENTS AND METHODS

The study comprised 50 consecutive patients admitted for transurethral prostatic surgery who were randomly allocated to receive bladder irrigation with either sterile water or 1.5% glycine during TUVP. After surgery, serum electrolytes and the presence of free plasma haemoglobin (suggesting haemolysis) were determined and the patients observed for clinical evidence of the transurethral resection (TUR) syndrome.

RESULTS

There was no significant difference in the level of free plasma haemoglobin between the groups and no difference in serum sodium levels. None of the patients developed any signs of the TUR syndrome.

CONCLUSIONS

Water is a safe irrigant for use during TUVP and has several advantages over 1.5% glycine.

The role of His113 and His114 in pyruvate decarboxylase from Zymomonas mobilis

Pyruvate decarboxylase (PDC) is one of several enzymes that require thiamin diphosphate (ThDP) and a divalent cation as essential cofactors. Recently, the three-dimensional structures of the enzyme from two yeasts have been determined. While these structures shed light on the binding of the cofactors and the reaction mechanism, the interactions between the substrate pyruvate and the enzyme remain unclear. We have used PDC from Zymomonas mobilis as a model for these enzymes in order to study substrate binding. The recombinant enzyme was expressed in Escherichia coli. High yield, simplicity of purification, high stability and simple kinetics make this model well suited for these studies. Activity measurements in the pH range between 5.8 and 8.5 indicated that a His residue may be involved in substrate binding. Analysis of an alignment of all known PDC protein sequences showed two invariant His residues (His113 and His114) which, according to the crystal structure of yeast PDC, are in the vicinity of the active site. Here we demonstrate that replacement of His114 by Gln does not have a great effect on cofactor and substrate binding. However, the k(cat) is decreased indicating that His114 may assist in catalysis. In contrast, substitution of His113 by Gln renders the enzyme completely inactive. This mutant has decreased affinity for both cofactors, as revealed by measurements of tryptophan fluorescence quenching. However, this decreased affinity is insufficient to account for the complete loss of activity. Despite its inability to support overall catalysis, this [Gln113]PDC mutant is capable of releasing acetaldehyde from 2-(1-hydroxyethyl)thiamin diphosphate supplied exogenously. It is proposed that upon substrate binding, His113 is placed close to C2 of the thiazole ring. Subsequent deprotonation of this atom leads to a conformational change that allows a flexible loop (residues 105-112) that precedes His113 to close over the active site. Hence, replacement of His113 by another residue interferes with this closure of the active site and thus disrupts the catalytic process.

Aspiration following stroke: is it related to the side of the stroke?

OBJECTIVE

To investigate the relationship between the side of stroke and the presence of aspiration on videofluoroscopy.

DESIGN

Observational prospective study.

SUBJECTS

Eighty-seven patients (50% female) admitted with an acute stroke to the University Hospital of South Manchester.

METHODS

Patients admitted to the study underwent brain CT scanning and repeated videofluoroscopy.

RESULTS

CT scanning was performed within a median three days (interquartile range 2-4 days) following stroke and videofluoroscopic (VF) examination (median 2, interquartile range 1-4 days following stroke) of their swallow. Seventeen (19.5%) patients were noted to be aspirating. There were no significant relationships at this time between side or site of lesion and the presence of aspiration. A second assessment was carried out at a median time of 29 days (interquartile range 26-45) following acute stroke. Nine of 69 (13.5%) patients were noted to be aspirating, seven of whom, had right hemisphere lesions (p < 0.01).

CONCLUSIONS

Continuing aspiration may be related to the side of the cerebral lesion.