Hi-Plex targeted sequencing is effective using DNA derived from archival dried blood spots

Many genetic epidemiology resources have collected dried blood spots (predominantly as Guthrie Cards) as an economical and efficient means of archiving sources of DNA, conferring great value to genetic screening methods that are compatible with this medium. We applied Hi-Plex to screen the breast cancer predisposition gene PALB2 in 93 Guthrie Card-derived DNA specimens previously characterized for PALB2 genetic variants via DNA derived from lymphoblastoid cell lines, whole blood, and buffy coat. Of the 93 archival Guthrie Card-derived DNAs, 92 (99%) were processed successfully and sequenced using approximately half of a MiSeq run. From these 92 DNAs, all 59 known variants were detected and no false-positive variant calls were yielded. Fully 98.13% of amplicons (5417/5520) were represented within 15-fold of the median coverage (2786 reads), and 99.98% of amplicons (5519/5520) were represented at a depth of 10 read-pairs or greater. With Hi-Plex, we show for the first time that a High-Plex amplicon-based massively parallel sequencing (MPS) system can be applied effectively to DNA prepared from dried blood spot archival specimens and, as such, can dramatically increase the scopes of both method and resource.

Scaling of near-wall flows in quasi-two-dimensional turbulent channels

The law of the wall and the log law rule the near-wall mean velocity profile of three-dimensional turbulent flows. These well-known laws, which are validated by legions of experiments and simulations, may be universal. Here, using a soap-film channel, we report the first experimental test of these laws in quasi-two-dimensional turbulent channel flows under two disparate turbulent spectra. We find that despite the differences with three-dimensional flows, the laws prevail, albeit with notable distinctions: the two parameters of the log law are markedly distinct from their three-dimensional counterpart; further, one parameter (the von Kármán constant) is independent of the spectrum whereas the other (the offset of the log law) depends on the spectrum. Our results suggest that the classical theory of scaling in wall-bounded turbulence is incomplete wherein a key missing element is the link with the turbulent spectrum.

Enhanced glucocorticoid-induced leucine zipper in dendritic cells induces allergen-specific regulatory CD4(+) T-cells in respiratory allergies

BACKGROUND

Respiratory allergies rely on a defect of IL-10-secreting regulatory CD4(+) T-cells (IL-10-Tregs ) leading to excessive Th2-biased immune responses to allergens. According to clinical data, the restoration of allergen-specific IL-10-Tregs is required to control respiratory allergies and cure patients. The discovery of mechanisms involved in the generation of IL-10-Tregs will thus help to provide effective treatments. We previously demonstrated that dendritic cells (DCs) expressing high levels of the glucocorticoid-induced leucine zipper protein (GILZ) generate antigen-specific IL-10-Tregs .

OBJECTIVE

We suspect a defective expression of GILZ in the DCs of respiratory allergic patients and speculate that increasing its expression might restore immune tolerance against allergens through the induction of IL-10-Tregs .

METHODS

We assessed GILZ expression in blood DCs of patients and healthy nonallergic donors by qPCR. We compared the ability of patients' DCs to induce allergen-specific IL-10-Tregs before and after an in vivo up-regulation of GILZ expression by steroid administration, steroids being inducers of GILZ.

RESULTS

We report lower levels of GILZ in DCs of respiratory allergic patients that return to normal levels after steroid administration. We show that patients' DCs with increased levels of GILZ generate allergen-specific IL-10-Tregs again. We further confirm unequivocally that GILZ is required in patients' DCs to activate these IL-10-Tregs .

CONCLUSION

This proof of concept study shows that the re-establishment of GILZ expression in patients' DCs to normal levels restores their capacity to activate allergen-specific IL-10-Tregs . We thus highlight the up-regulation of GILZ in DCs as a new interventional approach to restore the immune tolerance to allergens.

Perinatal management of trisomy 18: a survey of obstetricians in Australia, New Zealand and the UK

OBJECTIVE

The objective of this study was to explore the attitudes of obstetricians in Australia, New Zealand and the UK towards prenatally diagnosed trisomy 18 (T18).

METHOD

Obstetricians were contacted by email and invited to participate in an anonymous electronic survey.

RESULTS

Survey responses were obtained from 1018/3717 (27%) practicing obstetricians/gynaecologists. Most (60%) had managed a case of T18 in the last 2 years. Eighty-five per cent believed that T18 was a 'lethal malformation', although 38% expected at least half of liveborn infants to survive for more than 1 week. Twenty-one per cent indicated that a vegetative existence was the best developmental outcome for surviving children. In a case of antenatally diagnosed T18, 95% of obstetricians would provide a mother with the option of termination. If requested, 99% would provide maternal-focused obstetric care (aimed at maternal wellbeing rather than fetal survival), whereas 80% would provide fetal-oriented obstetric care (to maximise fetal survival). Twenty-eight per cent would never discuss the option of caesarean; 21% would always discuss this option. Management options, attitudes and knowledge of T18 were associated with location, practice type, gender and religion of obstetricians.

CONCLUSION

There is variability in obstetricians' attitudes towards T18, with significant implications for management of affected pregnancies.

Renal cell carcinoma metastases to the spermatic cord: review of the literature and case presentation

We present a case of clear cell renal cell carcinoma with metachronous metastasis to the ipsilateral spermatic cord. We also review the literature of the rare instance of renal cell carcinoma metastasising to the spermatic cord.

The potential role for acupuncture in treating symptoms in patients with lung cancer: an observational longitudinal study

BACKGROUND

Most lung cancer patients experience multiple symptoms related either to the disease or its treatment. The commonly reported symptoms are pain, depression, anxiety, nausea, and poor well-being. The aim of the present study was to evaluate the effect of acupuncture as a potential treatment modality in symptomatic lung cancer patients.

METHODS

This prospective observational study enrolled 33 lung cancer patients from the Peter Brojde Lung Cancer Centre between August 2010 and May 2012. All patients received 45-minute sessions of acupuncture, 1-2 times weekly for a minimum of 4 sessions. Symptom severity was assessed using the Edmonton Symptom Assessment System (esas) before and after completion of acupuncture.

RESULTS

The study cohort included 30 patients with non-small- cell lung cancer and 3 with small-cell lung cancer. Mean age was 62 years (range: 36-88 years); 17 of the patients were women. Most of the patients had advanced-stage cancer (73%) and good performance status (Eastern Cooperative Oncology Group 0-1: 88%). Of these patients, 67% received anticancer treatment (chemotherapy or radiotherapy, or both) with acupuncture. Of the remaining 10 patients, 8 received acupuncture after a complete surgical resection of their tumour, and because of their advanced age, 2 received acupuncture and best supportive care. The median number of acupuncture sessions was 7 (interquartile range: 4-13 sessions). Statistically significant improvements in pain, appetite, nausea, nervousness, and well-being were observed. A clinically important improvement (2 points on the esas) was reported by 61% of patients for pain and by 33% for well-being. A significant positive correlation between improved well-being and the number of acupuncture sessions was observed. This correlation remained significant even after controlling for treatment and narcotic use. Receiver operating characteristic analysis demonstrated that a minimum of 6 acupuncture sessions are required for a 70% chance of a clinically important improvement in well-being.

CONCLUSIONS

The present study is the first to demonstrate that acupuncture may be an effective approach for improving symptoms-in particular, pain and well-being-in lung cancer patients. Acupuncture is a safe and minimally invasive procedure, and it is potentially useful even in patients undergoing anticancer treatment.

Spontaneous regression of metastatic melanoma after inoculation with tetanus-diphtheria-pertussis vaccine

Spontaneous regression of metastatic melanoma is an exceedingly rare event, with only 76 well-documented cases in the literature since 1866. Here, we present the case of a patient who developed metastatic melanoma despite interferon therapy and who then achieved spontaneous regression shortly after a reaction to tetanus-diphtheria-pertussis vaccination. A common theme among these cases is the development of febrile illness before remission of the malignant disease. A brief overview of proposed mechanisms for these miraculous recoveries is presented, including a highlight on the potential role of the herv-k-mel viral marker, a nona- or decapeptide that appears in most melanomas, with homologies to peptides in pathogenic microorganisms.

Recombinant expression of trypanosome surface glycoproteins in Pichia pastoris for the diagnosis of Trypanosoma evansi infection

Serodiagnosis of surra, which causes vast economic losses in livestock, is still based on native antigens purified from bloodstream form Trypanosoma (T.) evansi grown in rodents. To avoid the use of laboratory rodents in antigen preparation we expressed fragments of the invariant surface glycoprotein (ISG) 75, cloned from T. brucei gambiense cDNA, and the variant surface glycoprotein (VSG) RoTat 1.2, cloned from T. evansi gDNA, recombinantly in Pichia (P.) pastoris. The M5 strain of this yeast has an engineered N-glycosylation pathway resulting in homogenous Man5GlcNAc2 N-glycosylation which resembles the predominant Man9-5GlcNAc2 oligomannose structures in T. brucei. The secreted recombinant antigens were affinity purified with yields of up to 10mg and 20mg per liter cell culture of rISG 7529-465-E and rRoTat 1.223-385-H respectively. In ELISA, both recombinant proteins discriminated between pre-immune and immune serum samples of 25 goats experimentally infected with T. evansi. The diagnostic potential of rRoTat 1.223-385-H but not of rISG 7529-465-E was confirmed with sera of naturally infected and control dromedary camels. The results suggest that rRoTat 1.223-385-H expressed in P. pastoris requires further evaluation before it could replace native RoTat 1.2 VSG for serodiagnosis of surra, thus eliminating the use of laboratory animals for antigen production.

Tumor-infiltrating regulatory T cells: phenotype, role, mechanism of expansion in situ and clinical significance

In immunocompetent individuals, the immune system initially eradicates potentially tumorigenic cells as they develop, a capacity that is progressively lost when malignant cells acquire alterations that sustain immunosubversion and/or immunoevasion. One of the major mechanisms whereby cancer cells block antitumor immune responses involves a specific class of immunosuppressive T cells that-in the vast majority of cases-express the Forkhead box P3 (FOXP3) transcription factor. Such FOXP3(+) regulatory T cells (Tregs) accumulate within neoplastic lesions as a result of several distinct mechanisms, including increased infiltration, local expansion, survival advantage and in situ development from conventional CD4(+) cells. The prognostic/predictive significance of tumor infiltration by Tregs remains a matter of debate. Indeed, high levels of intratumoral Tregs have been associated with poor disease outcome in cohorts of patients affected by multiple, but not all, tumor types. This apparent discrepancy may relate to the existence of functionally distinct Treg subsets, to the fact that Tregs near-to-invariably infiltrate neoplastic lesions together with other cells from the immune system, notably CD4(+) and CD8(+) T lymphocytes and/or to peculiar features of some oncogenic programs that involve a prominent pro-inflammatory component. In this review, we will discuss the phenotype, function and clinical significance of various Treg subsets.

Moderate influenza vaccine effectiveness in Victoria, Australia, 2011

We used a sentinel general practitioner (GP) network to conduct surveillance for laboratory-confirmed influenza amongst patients presenting with influenza-like illness (ILI) in Victoria, Australia in 2011. The test negative variation of the case control study design was used to estimate effectiveness for seasonal trivalent influenza vaccine. Cases and controls were ILI patients that tested positive and negative for influenza, respectively. Vaccination status was recorded by GPs and vaccine effectiveness (VE) was calculated as (1-adjusted odds ratio)x100%. There were 529 patients included in the study, of which 29% were influenza positive. Twelve percent of study participants were reported as vaccinated, 6% of cases and 15% of controls. Adjusted VE against all influenza was 56%, but not statistically significant. There was generally little variation in VE estimates when stratified by virus type and subtype, which is consistent with good matches between circulating strains and the vaccine strains. The VE was higher among adults of working age than among children.

Moderate influenza vaccine effectiveness in Victoria, Australia, 2011

We used a sentinel general practitioner (GP) network to conduct surveillance for laboratory-confirmed influenza amongst patients presenting with influenza-like illness (ILI) in Victoria, Australia in 2011. The test-negative variation of the case control study design was used to estimate effectiveness for seasonal trivalent influenza vaccine. Cases and controls were ILI patients that tested positive and negative for influenza, respectively. Vaccination status was recorded by GPs and vaccine effectiveness (VE) was calculated as (1-adjusted odds ratio)x100%. There were 529 patients included in the study, of which 29% were influenza-positive. Twelve percent of study participants were reported as vaccinated, 6% of cases and 15% of controls. Adjusted VE against all influenza was 56%, but not statistically significant. There was generally little variation in VE estimates when stratified by virus type and subtype, which is consistent with good matches between circulating strains and the vaccine strains. The VE was higher among adults of working age than among children.

Primary school children's knowledge of, and attitudes towards, healthy computer use

BACKGROUND

Australian children as young as five years are using computers in the home and school environments with increased frequency and longer duration as they age. Consequently, they may be exposed to risk factors for the development of physical health problems described in studies of adult computer users. To date schools have focused on providing children with the latest computer technologies; with far less attention given to appropriate workstations, ergonomics education and incorporating safe computing practices. By better understanding children's attitudes and knowledge, a directional approach to the development of an ergonomics education program may be established using a health promotion framework to encourage healthy computing behaviors.

OBJECTIVE

The purpose of this study was to identify children's knowledge of, and attitudes towards healthy computing.

METHOD

A cross-sectional inferential study of 537 Australian school children (aged 9 to 11 years) from Catholic Education Schools across Western Australia was conducted. Multiple logistic regression analyses identified that children's beliefs and attitudes about the negative health effects of computers were found to be most associated with unhealthy computing behaviors.

RESULTS

Children lacked sufficient knowledge about the importance of postural and task variation, but had sufficient knowledge about adjusting workstation furniture specific to healthy computer use.

Antimicrobial resistance and molecular subtyping of Campylobacter jejuni and Campylobacter coli from retail meats

Campylobacter isolates (n = 297; 202 C. jejuni and 95 C. coli isolates) recovered from 2,513 retail meat samples (chicken breasts, ground turkey, ground beef, and pork chops) were examined for antimicrobial susceptibility. The isolates were further analyzed for genetic relatedness by pulsed-field gel electrophoresis (PFGE) using SmaI and KpnI restriction enzymes, and a subset of isolates (n = 174) were subtyped by multilocus sequence typing (MLST). The resistance most frequently observed was that to doxycycline (27.6%), followed by ciprofloxacin (13.8%) and erythromycin (6.4%). All isolates were susceptible to gentamicin and meropenem. C. coli showed higher resistance to doxycycline than did C. jejuni (42.1 versus 20.8%) and lower resistance to ciprofloxacin than did C. jejuni (10.5 versus 15.3%). Erythromycin resistance was only observed in C. coli. PFGE using SmaI plus KpnI digestion generated 168 clusters from 297 isolates: 115 from C. jejuni and 53 from C. coli. MLST revealed 44 sequence types (STs) under 10 clonal complexes from 120 C. jejuni and 27 STs under two clonal complexes from 54 C. coli. There was a positive association between PFGE and STs; however, PFGE showed greater discriminatory power than MLST. Subtyping data did not correlate with antimicrobial resistance phenotypes.

The significance of interactions between organic compounds on low pressure membrane fouling

Fouling of hollow fibre microfiltration and ultrafiltration membranes by solutions of pure organic compounds and mixtures of these compounds was studied with a backwashable membrane filtration apparatus. Small molecular weight compounds resulted in little fouling, while their polymeric analogues resulted in more severe fouling. Neutrally charged dextran resulted in minor, irreversible fouling, that was considered to be associated with blocking of small pores. Cationically charged chitosan produced gross fouling for which the extent of reversibility increased with salt addition. Anionically charged alginic acid resulted in gross irreversible fouling, except when being filtered by a hydrophilic membrane in the absence of calcium where a high degree of flux recovery was observed. Calcium addition to the alginic acid solutions resulted in gross fouling of all membranes and calcium bridging was considered to be responsible for this behaviour. Greater fouling occurred on the hydrophilic membrane compared to the hydrophobic membranes for bovine serum albumin (BSA) solutions, and this was considered to be due to physical blocking of pores, because addition of calcium resulted in lower flux declines. Addition of BSA and calcium to alginic acid solutions resulted in lower flux recoveries for the alginic acid system, consistent with the proposition that interactions between polysaccharide and other compounds are required for irreversible fouling on hydrophilic membranes.