Looking beyond the exome: a phenotype-first approach to molecular diagnostic resolution in rare and undiagnosed diseases.

PurposeTo describe examples of missed pathogenic variants on whole-exome sequencing (WES) and the importance of deep phenotyping for further diagnostic testing.MethodsGuided by phenotypic information, three children with negative WES underwent targeted single-gene testing.ResultsIndividual 1 had a clinical diagnosis consistent with infantile systemic hyalinosis, although WES and a next-generation sequencing (NGS)-based ANTXR2 test were negative. Sanger sequencing of ANTXR2 revealed a homozygous single base pair insertion, previously missed by the WES variant caller software. Individual 2 had neurodevelopmental regression and cerebellar atrophy, with no diagnosis on WES. New clinical findings prompted Sanger sequencing and copy number testing of PLA2G6. A novel homozygous deletion of the noncoding exon 1 (not included in the WES capture kit) was detected, with extension into the promoter, confirming the clinical suspicion of infantile neuroaxonal dystrophy. Individual 3 had progressive ataxia, spasticity, and magnetic resonance image changes of vanishing white matter leukoencephalopathy. An NGS leukodystrophy gene panel and WES showed a heterozygous pathogenic variant in EIF2B5; no deletions/duplications were detected. Sanger sequencing of EIF2B5 showed a frameshift indel, probably missed owing to failure of alignment.ConclusionThese cases illustrate potential pitfalls of WES/NGS testing and the importance of phenotype-guided molecular testing in yielding diagnoses.

Multiplex real-time RT-qPCR for the detection of Norovirus in bottled and tap water using murine norovirus as a process control.

AIMS: To provide a rapid and sensitive method for detecting NoV GI and NoV GII in water and to evaluate the use of the murine norovirus (MNV-1) as a process control. METHODS AND RESULTS: The method is based on viral concentration by filtration on electropositive filters and direct lysis of adsorbed viruses from filters before RNA extraction and RT-qPCR amplification. An one-step multiplex RT-qPCR assay was developed for the simultaneous detection of NoV GI, NoV GII and MNV-1. Then, water samples were artificially contaminated to determine mean virus recoveries and method sensitivity. The method showed a higher sensitivity for detecting NoV GII (10(3) genome copies per 0·5 l) than for NoV GI (10(4) genome copies per 0·5 l) in the presence of MNV-1 regardless of the type of water. The data also showed that MNV-1 is a robust option as process control. CONCLUSIONS: The method described provides a valuable tool for the monitoring of potential public health risks associated with NoV contamination in drinkable water. SIGNIFICANCE AND IMPACT OF STUDY: Given the increasing evidence for NoV involvement in food outbreaks, the one-step multiplex RT-qPCR assay we used in this study would be a very useful tool to investigate NoV contamination in other food products.

Molecular biological effects of selective neuronal nitric oxide synthase inhibition in ovine lung injury.

Neuronal nitric oxide synthase is critically involved in the pathogenesis of acute lung injury resulting from combined burn and smoke inhalation injury. We hypothesized that 7-nitroindazole, a selective neuronal nitric oxide synthase inhibitor, blocks central molecular mechanisms involved in the pathophysiology of this double-hit insult. Twenty-five adult ewes were surgically prepared and randomly allocated to 1) an uninjured, untreated sham group (n = 7), 2) an injured control group with no treatment (n = 7), 3) an injury group treated with 7-nitroindazole from 1-h postinjury to the remainder of the 24-h study period (n = 7), or 4) a sham-operated group subjected only to 7-nitroindazole to judge the effects in health. The combination injury was associated with twofold increased activity of neuronal nitric oxide synthase and oxidative/nitrosative stress, as indicated by significant increases in plasma nitrate/nitrite concentrations, 3-nitrotyrosine (an indicator of peroxynitrite formation), and malondialdehyde lung tissue content. The presence of systemic inflammation was evidenced by twofold, sixfold, and threefold increases in poly(ADP-ribose) polymerase, IL-8, and myeloperoxidase lung tissue concentrations, respectively (each P < 0.05 vs. sham). These molecular changes were linked to tissue damage, airway obstruction, and pulmonary shunting with deteriorated gas exchange. 7-Nitroindazole blocked, or at least attenuated, all these pathological changes. Our findings suggest 1) that nitric oxide formation derived from increased neuronal nitric oxide synthase activity represents a pivotal reactive agent in the patho-physiology of combined burn and smoke inhalation injury and 2) that selective neuronal nitric oxide synthase inhibition represents a goal-directed approach to attenuate the degree of injury.

L-carnitine, a diet component and organic cation transporter OCTN ligand, displays immunosuppressive properties and abrogates intestinal inflammation.

Allele variants in the L-carnitine (LCAR) transporters OCTN1 (SLC22A4, 1672 C --> T) and OCTN2 (SLC22A5, -207 G --> C) have been implicated in susceptibility to Crohn's disease (CD). LCAR is consumed in the diet and transported actively from the intestinal lumen via the organic cation transporter OCTN2. While recognized mainly for its role in fatty acid metabolism, several lines of evidence suggest that LCAR may also display immunosuppressive properties. This study sought to investigate the immunomodulatory capacity of LCAR on antigen-presenting cell (APC) and CD4+ T cell function by examining cytokine production and the expression of activation markers in LCAR-supplemented and deficient cell culture systems. The therapeutic efficacy of its systemic administration was then evaluated during the establishment of colonic inflammation in vivo. LCAR treatment significantly inhibited both APC and CD4+ T cell function, as assessed by the expression of classical activation markers, proliferation and cytokine production. Carnitine deficiency resulted in the hyperactivation of CD4+ T cells and enhanced cytokine production. In vivo, protection from trinitrobenzene sulphonic acid colitis was observed in LCAR-treated mice and was attributed to the abrogation of both innate [interleukin (IL)-1beta and IL-6 production] and adaptive (T cell proliferation in draining lymph nodes) immune responses. LCAR therapy may therefore represent a novel alternative therapeutic strategy and highlights the role of diet in CD.

Pulmonary vascular permeability changes in an ovine model of methicillin-resistant Staphylococcus aureus sepsis.

INTRODUCTION: Endothelial dysfunction is a hallmark of sepsis, associated with lung transvascular fluid flux and pulmonary dysfunction in septic patients. We tested the hypothesis that methicillin-resistant Staphylococcus aureus (MRSA) sepsis following smoke inhalation increases pulmonary transvascular fluid flux via excessive nitric oxide (NO) production. METHODS: Ewes were chronically instrumented, and randomised into either a control or MRSA sepsis (MRSA and smoke inhalation) group. RESULTS: Pulmonary function remained stable in the control group, whereas the MRSA sepsis group developed impaired gas exchange and significantly increased lung lymph flow, permeability index and bloodless wet-to-dry weight-ratio (W/D ratio). The plasma nitrate/nitrite (NOx) levels, lung inducible nitric oxide synthases (iNOS) and endothelial nitric oxide synthases (eNOS), vascular endothelial growth factor (VEGF) protein expressions and poly-(ADP)-ribose (PAR) were significantly increased by MRSA challenge. CONCLUSIONS: These results provide evidence that excessive NO production may mediate pulmonary vascular hyperpermeability in MRSA sepsis via up regulation of reactive radicals and VEGF.

A waterborne outbreak of gastroenteritis with multiple etiologies among resort island visitors and residents: Ohio, 2004.

BACKGROUND: The implementation of treated municipal water systems in the 20th century led to a dramatic decrease in waterborne disease in the United States. However, communities with deficient water systems still experience waterborne outbreaks. In August 2004, we investigated an outbreak of gastroenteritis on South Bass Island, Ohio, an island of 900 residents that is visited by >500,000 persons each year. METHODS: To identify the source of illness, we conducted a case-control study and an environmental investigation. A case was defined as diarrhea in a person who traveled to the island during the period from May 1 through 30 September 2004 and became ill within 2 weeks after the visit. Healthy travel companions served as matched control subjects. We also performed an environmental assessment and extensive testing of island water sources. RESULTS: Among the 1450 persons reporting illness, Campylobacter jejuni, norovirus, Giardia intestinalis, and Salmonella enterica serotype Typhimurium were identified in 16, 9, 3, and 1 persons, respectively. We interviewed 100 case patients and 117 matched control subjects. Case patients were more likely to drink water on the island than control subjects (68% vs. 35%; matched odds ratio, 4.3; 95% confidence interval, 2.2-9.3). Sampling of ground water wells indicated contamination with multiple fecal microbes, including Escherichia coli, C. jejuni, Salmonella species, and Giardia species. Irregularities in sewage disposal practices that could have contaminated the underground aquifer were noted. CONCLUSIONS: The combined epidemiological and environmental investigation indicated that sewage-contaminated ground water was the likely source of this large outbreak. Long-term changes to the island's water supply and sewage management infrastructure are needed.

Effects of the bradykinin B2 receptor antagonist icatibant on microvascular permeability after thermal injury in sheep.

Peptide kinins are potent vasoactive agents in the microcirculation that might be released after burn injury. The present study was designed to test the hypothesis that Icatibant (JE 049), a potent, selective peptidomimetic bradykinin-B2 receptor antagonist, would reduce the cardiovascular pathology occurring in sheep exposed to 40% total body surface area (TBSA), third-degree burn. Female sheep were surgically prepared for chronic study. After 5 to 7 days' recovery from the operative procedure, they were randomized to five groups: sham (n = 6, noninjured, nontreated), medicated sham (n = 4, noninjured, treated with 20 microg kg h Icatibant), control (n = 7, 40% TBSA third-degree burn, nontreated), Icatibant-4 (n = 6, 40% TBSA third-degree burn, treated with 4 microg kg h Icatibant [low dose]), Icatibant-20 (n = 8, 40% TBSA third-degree burn, treated with 20 microg kg h Icatibant [high dose]). Prefemoral lymph flow (milliliters per hour) remained constant in the sham and medicated sham groups but increased after injury: control (0 h, 3.9 +/- 0.5; 24 h, 28 +/- 4.2; 48 h, 33.0 +/- 8.1). The increased fluid flux was associated with enhanced protein flux. Both low and high doses of Icatibant significantly reduced the microvascular fluid flux: Icatibant-4 (0 h, 5.3 +/- 0.6; 24 h, 17.5 +/- 3.5; 48 h, 20.3 +/- 3.4); Icatibant-20 (0 h, 5.3 +/- 1.1; 24 h, 15.2 +/- 2; 48 h, 17.6 +/- 4.1). Total prefemoral protein leak was reduced in all treatment groups. The low dose of Icatibant significantly reduced prefemoral lymph flow without adversely affecting the hemodynamic changes observed after burn injury in sheep, suggesting that the bradykinin antagonist would reduce edema formation and improve fluid management of thermally injured patients.

[Bone densitometry for the diagnosis of osteoporosis: the Belgian reimbursement paradox]. / L'ostéodensitométrie dans le dépistage de l'ostéoporose: le paradoxe Belge.

Osteoporosis is considered as a major Public Health issue, in most developed countries. Bone mineral density assessment is the single best predictor of the future fracture risk for an individual. Belgium has the highest number of bone densitometers, per million habitants, in Europe. However, densitometry is not yet reimbursed in Belgium. This situation is rather paradoxical since the demonstration of a prevalent vertebral fracture or of a low bone mineral density is requested to obtain the reimbursement of drugs to be used for the management of osteoporosis. Hopefully, Belgium will soon be online with the requirement s of the European Commission, suggesting to make bone densitometry accessible, through reimbursement.

Evaluation of a breast cancer screening programme--the DOM project.

In several studies it has been shown that breast cancer screening by means of mammography reduces breast cancer mortality. To ensure that when organising a service screening programme the aim is reached, it is necessary to control and monitor the process. This is possible by several methods. In this study, disease-free intervals and survival rates were used as monitoring tools. The DOM project, a breast cancer screening programme for women aged 50-64 years old at intake, started at the end of 1974. All breast cancer cases diagnosed between 1973 and 1989 were followed up to 1991. It is clear that disease-free interval and survival rates are proper predictors of the effects of screening on breast cancer mortality.

Breast cancer after a negative screen: follow-up of women participating in the DOM Screening Programme.

First-round screening results for women participating in the DOM project (a screening programme for early detection of breast cancer) are described for the age groups 40-49 and 50-64 at entry. In the younger age group, a low pick-up rate (1.96 per 1000) in proportion to the expected incidence rate in the absence of screening (1.46 per 1000) was found. For the older age group, these rates were 4.25 and 2.03, respectively, per 1000. Interval cancers occurred (relatively) more frequently in younger women. After 2 years the ratio between interval-cancers and screen-detected tumours was about 1:1 in the younger age group and 1:2.5 in the older age group. These different results can be caused by too low a sensitivity of mammography and/or a higher tumour growth rate at a young age. The sensitivity of the screen at various periods of follow-up, was compared: a rapidly decreasing sensitivity of mammography was seen for women under the age of 50, in contrast to a slower decrease for women over this age. This rapid decrease may be caused by a relatively high tumour growth rate in younger women.

Comparison of the effects of auranofin and retinoic acid on plasminogen activator activity of peritoneal macrophages and Lewis lung carcinoma cells.

Urokinase-type plasminogen activator, a neutral proteinase, seems to play a central role in the degradation of the extracellular matrix that accompanies a number of biological phenomena including inflammatory reactions and neoplasia. The effect of auranofin and retinoic acid on the plasminogen activator activity expressed by two cell types, i.e. murine macrophages and Lewis lung carcinoma cells, has been investigated. Low concentrations of both drugs (10(-6)-10(-7) M) can inhibit in vitro the induction of plasminogen activator in macrophages stimulated by phorbol 12-myristate 13-acetate. This action occurs rapidly (15 min), is irreversible and is independent of a global cytotoxic effect. Auranofin and retinoic acid remain without effect in macrophages when added after stimulation by the phorbol ester. Both drugs are thus potent inhibitors of the induction of plasminogen activator activity in macrophages, possibly through an interaction with the protein kinase C system. The plasminogen activator activity of Lewis lung carcinoma cells, which is apparently not dependent on a protein kinase C pathway, is not influenced by auranofin or retinoic acid. These observations may contribute to explain: (1) the activity of auranofin and retinoic acid in rheumatoid arthritis, and (2) the antitumor promoting activity of retinoic acid. It would be relevant to assess whether auranofin may exhibit, like retinoic acid, an antitumor-promoting activity.

Plasminogen activator activity of normal and retinoic acid-treated post-implantation embryos.

Urokinase-type plasminogen activator (uPA) has been implicated in cellular migration accompanying different biological phenomena including organogenesis. An increase in uPA activity was observed in mouse post-implantation embryos during the early organogenesis period. Since we have previously shown that all-trans retinoic acid (RA) prevented the induction of uPA in mouse peritoneal macrophages, we have now assessed whether teratogenic doses of this agent could also interfere with uPA activity in mouse embryo in vitro and in vivo. Post-implantation embryos (8.5 days) were incubated for up to 24 hr with micromolar concentration of RA resulting in the occurrence of malformations. No significant difference in uPA activity was found between control and treated embryos. Likewise, uPA activity was not altered in embryos explanted on day 9.5 from dams treated 24 hr before with a teratogenic dose of RA. This study indicates that the teratogenic activity of RA is not caused by an inhibition of the induction of uPA in embryos.

Qualitative comparison between the quantum calculations and electrospray mass spectra of complexes of polyammonium macrotricyclic ligands with dicarboxylic acids.

The host-guest interactions play a very important role in chemical and biological processes. It is therefore important to be able to characterize these complexes. Electrospray mass spectrometry can be used to characterize the complex formation. It provides information on the mass and the charge of these ionic complexes. In this article, we show that the use of ab initio and semiempirical calculations, in addition to the results obtained by electrospray mass spectrometry, reveal to be a promising tool for the study of these noncovalent complexes. In this article, host-guest complexes formed by macropolycyclic polyammonium host molecules and dicarboxylic acids are studied.

Further evidence of benefits of a (non-randomised) breast cancer screening programme: the DOM project.

STUDY OBJECTIVE: The aim was to demonstrate the benefits of breast cancer screening on mortality. DESIGN: The study was an evaluation of a breast cancer screening programme by means of different approaches: (1) a case-control study, breast cancer deaths being the cases; (2) comparing the numbers of breast cancer deaths in screened and unscreened women; (3) comparing breast cancer mortality before and after start of the programme; (4) comparing breast cancer mortality in different large cities; (5) comparing screening activity with mortality reduction. SETTING: The setting was a breast cancer screening programme in the city of Utrecht, the DOM project, for women aged 50-64 years old at intake, birth cohort 1911-1925. The programme started in 1974, and there were five screening rounds up to 1984. Participation rate in the first round was 72% (14,697 women). MAIN RESULTS: (1) Screening was protective against dying from breast cancer, odds ratio 0.52, with a stronger effect in older women and no evidence of confounding; (2) risk ratio of dying from breast cancer for women in the response group was the same as the odds ratio, 0.52; (3) breast cancer death rate after the start of the project was nearly 20% lower than before the project started; after correcting for women who could not have benefited from screening the reduction was 33%; (4) a rise in breast cancer mortality in birth cohort 1911-1925 seen in other large cities without a screening programme due to aging of the cohort was not seen in the city of Utrecht; (5) mortality reduction followed the screening activity with a time lag of approximately 5 years. CONCLUSIONS: Early diagnosis of breast cancer by mammography reduces breast cancer mortality in women 50-64 years old at intake; different approaches to the evaluation of the project give different estimates of the screening effect, making clear that the effect depends on the intensity of the programme.

[Pathogenic organisms in milk and milk products: the situation in France and in Europe]. / Les germes pathogènes dans le lait et les produits laitiers: situation en France et en Europe.

Milk and dairy products harbour a natural microbial flora and/or other micro-organisms, which vary within the wide range of products available on the French market. The origin of contamination by pathogenic bacteria varies with the type of product and the mode of production and processing. Contamination of milk and dairy products by pathogenic micro-organisms can be of endogenous origin, following excretion from the udder of an infected animal. Contamination may also be of exogenous origin, through direct contact with infected herds or through the environment (e.g. water, personnel). Treatment and processing of milk can inhibit or encourage the multiplication of micro-organisms. The authors describe the relevant aspects of bacterial physiology and ecology, the occurrence of bacteria in dairy products, and the public health significance for each of the principal micro-organisms found in such products. Bacteria most frequently involved are mycobacteria, Brucella sp., Listeria monocytogenes, Staphylococcus aureus and enterobacteria (including toxigenic Escherichia coli and Salmonella). At present, systems of testing and surveillance are required for the control of pathogenic bacteria in milk and dairy products, as specified by regulations currently being developed for all countries in the European Union. Preventive measures should take into account the well-established facts concerning the potential microbiological impact of pathogenic bacteria on milk and dairy products. There should be increased recourse to risk analysis methods to assess the threat to the consumer with regard to the presence of pathogenic bacteria in food.

Predictive microbiology of dairy products: influence of biological factors affecting growth of Listeria monocytogenes.

The growth potential of Listeria monocytogenes was evaluated at low temperature in sterilized milk and raw dairy products. Sterilized and raw milk were inoculated with different strains of L. monocytogenes in 2 physiological states and at various contamination levels. Raw cheese was naturally contaminated with Listeria spp. The results suggest that some biological factors influence the growth capacity of L monocytogenes in dairy products. Significant strain effect was observed at low temperature whatever the growth medium. By contrast, no inoculum effect was observed in the 3 dairy products. In raw matrixes, growth of L. monocytogenes was influenced greatly by bacterial interactions and physiological state of inoculum cells.

A multidisciplinary approach to breast biopsy.

The explosion in technological advances has provided physicians and patients more options in the diagnostic breast biopsy arena. Successful collaborative relationships between nurses, physicians, and all health care workers and detailed patient education are essential to provide optimum patient care. Survival in health care today mandates that perioperative nurses and their colleagues move outside traditional environments to provide quality, cost-effective care to patients and their family members. The aim of this collaborative approach to breast biopsy is to provide patients with the most expedient, accurate, cost-effective diagnoses with the least amount of physical and psychological trauma.

Understanding patients' needs is the foundation of perioperative nursing.

As I reflected on Mrs L's procedure, I realized the importance of my role. I coordinated the efforts of the radiologist, radiological technologist, surgeon, pathologist, and nurses to provide Mrs L with a positive surgical experience, and I collaborated with Mrs L and her husband to make them as comfortable and relaxed as possible. I connected with Mrs L and her husband--they knew I would help them in any way to make this a positive experience. In addition, I collected data about Mrs L's perception and satisfaction with her experience to explore her response to her stereotactic surgical biopsy procedure experience. Perioperative nurses are important to patients and their family members. By listening to patients' needs, planning for their individual care, and being present, perioperative nurses help patients through difficult situations. I use my experience and knowledge to serve as a role model for breast imaging personnel, nurses, and other coworkers, and to improve each patient's perioperative experience.

Conceptual design and scaled experimental validation of an actively damped carbon tie rods support system for the stabilization of future particle collider superstructures.

This paper presents a simple solution to increase the stability of the large superstructures supporting the final electromagnets of future linear particle collider. It consists of active carbon fiber tie rods, fixed at one end on the structure and at the other end to the detector through active tendons. In the first part of the paper, the solution has been tested on a finite element model of one half of the CLIC_ILD final focus structure. With a reasonable design, it is shown numerically that the compliance can be decreased by at least a factor 4, i.e., that the structure is 4 times more robust to technical noise at low frequency. Two additional features of the active rods are that they can also actively damp the structural resonances and realign the superstructures. The second part of the paper presents a successful experimental validation of the concept, applied to a scaled test bench, especially designed to contain the same modal characteristics as the full scale superstructure.

Pseudomonas aeruginosa is associated with increased lung cytokines and asymmetric dimethylarginine compared with methicillin-resistant Staphylococcus aureus.

The objective of the study was to investigate pulmonary responses to Pseudomonas aeruginosa and methicillin-resistant Staphylococcus aureus (MRSA) using ovine and mice models of sepsis with emphasis on lung cytokine expression, asymmetric dimethylarginine (ADMA) concentration, and the arginase pathway. Sheep were instilled with either MRSA, P. aeruginosa, or saline under deep anesthesia; mechanically ventilated; resuscitated with fluid; and killed after 24 h. Mice were instilled with either MRSA, P. aeruginosa, or saline under deep anesthesia and killed after 8 h. Lungs were assessed for ADMA concentration, arginase activity, oxidative stress, and cytokine expression, and plasma was assessed for nitrate/nitrite concentrations. The severity of lung injury was more pronounced in P. aeruginosa sepsis compared with MRSA. The significant changes in sheep lung function after P. aeruginosa sepsis were associated with significantly increased ADMA concentrations and arginase activity compared with MRSA. However, the plasma concentration of nitrites and nitrates were significantly increased in MRSA sepsis compared with P. aeruginosa sepsis. In the mice model, P. aeruginosa significantly increased lung cytokine expression (IL-1 and IL-13), protein oxidation, and arginase activity compared with MRSA. Our data suggest that the greater expression of cytokines and ADMA concentrations may be responsible for severity of acute lung injury in P. aeruginosa sepsis. The lack of arginase activity may explain the greater nitric oxide production in MRSA sepsis.