A prospective study on rapid exome sequencing as a diagnostic test for multiple congenital anomalies on fetal ultrasound

Objective

Conventional genetic tests (quantitative fluorescent-PCR [QF-PCR] and single nucleotide polymorphism-array) only diagnose ~40% of fetuses showing ultrasound abnormalities. Rapid exome sequencing (rES) may improve this diagnostic yield, but includes challenges such as uncertainties in fetal phenotyping, variant interpretation, incidental unsolicited findings, and rapid turnaround times. In this study, we implemented rES in prenatal care to increase diagnostic yield.

Methods

We prospectively studied 55 fetuses. Inclusion criteria were: (a) two or more independent major fetal anomalies, (b) hydrops fetalis or bilateral renal cysts alone, or (c) one major fetal anomaly and a first-degree relative with the same anomaly. In addition to conventional genetic tests, we performed trio rES analysis using a custom virtual gene panel of ~3850 Online Mendelian Inheritance in Man (OMIM) genes.

Results

We established a genetic rES-based diagnosis in 8 out of 23 fetuses (35%) without QF-PCR or array abnormalities. Diagnoses included MIRAGE (SAMD9), Zellweger (PEX1), Walker-Warburg (POMGNT1), Noonan (PTNP11), Kabuki (KMT2D), and CHARGE (CHD7) syndrome and two cases of Osteogenesis Imperfecta type 2 (COL1A1). In six cases, rES diagnosis aided perinatal management. The median turnaround time was 14 (range 8-20) days.

Conclusion

Implementing rES as a routine test in the prenatal setting is challenging but technically feasible, with a promising diagnostic yield and significant clinical relevance.     

Inactivation of Viruses and Bacteriophages as Models for Swine Hepatitis E Virus in Food Matrices

Hepatitis E virus has been recognised as a food-borne virus hazard in pork products, due to its zoonotic properties. This risk can be reduced by adequate treatment of the food to inactivate food-borne viruses. We used a spectrum of viruses and bacteriophages to evaluate the effect of three food treatments: high pressure processing (HPP), lactic acid (LA) and intense light pulse (ILP) treatments. On swine liver at 400 MPa for 10 min, HPP gave log₁₀ reductions of ≥4.2, ≥5.0 and 3.4 for feline calicivirus (FCV) 2280, FCV wildtype (wt) and murine norovirus 1 (MNV 1), respectively. Escherichia coli coliphage ?X174 displayed a lower reduction of 1.1, while Escherichia coli coliphage MS2 was unaffected. For ham at 600 MPa, the corresponding reductions were 4.1, 4.4, 2.9, 1.7 and 1.3 log₁₀. LA treatment at 2.2 M gave log₁₀ reductions in the viral spectrum of 0.29–2.1 for swine liver and 0.87–3.1 for ham, with ?X174 and MNV 1, respectively, as the most stable microorganisms. The ILP treatment gave log₁₀ reductions of 1.6–2.8 for swine liver, 0.97–2.2 for ham and 1.3–2.3 for sausage, at 15–60 J cm^?2, with MS2 as the most stable microorganism. The HPP treatment gave significantly (p < 0.05) greater virus reduction on swine liver than ham for the viruses at equivalent pressure/time combinations. For ILP treatment, reductions on swine liver were significantly (p < 0.05) greater than on ham for all microorganisms. The results presented here could be used in assessments of different strategies to protect consumers against virus contamination and in advice to food producers. Conservative model indicators for the pathogenic viruses could be suggested.     

Factors influencing local ecological knowledge maintenance in Mediterranean watersheds: Insights for environmental policies

Local ecological knowledge (LEK) has been found to be one of the main bridges to manage biocultural diversity. We analyzed the factors affecting LEK maintenance and transmission in a Mediterranean watershed. We used a mixed methods approach to evaluate the agricultural LEK in three different dimensions: biological, soil and water management, and forecasting. We found that the main factors for its maintenance were the respondent''s time living in the area and the social relationships established among farmers, which involved partner collaboration and farmer information exchanges. Protected areas also played a key role for maintaining the LEK associated with soil and water management. Finally, we found that outmigration and mechanization were the most important indirect drivers of change underlying LEK erosion. We suggest that environmental policies should focus on promoting this experiential knowledge, considering both intergenerational renewal and the gendered aspects of this knowledge.

Electronic supplementary material

The online version of this article (doi:10.1007/s13280-014-0556-1) contains supplementary material, which is available to authorized users.     

Source, concentration, and distribution of elemental mercury in the atmosphere in Toronto, Canada

Atmospheric gaseous elemental mercury [GEM] at 1.8, 4, and 59 m above ground, in parking lots, and in indoor and outdoor air was measured in Toronto City, Canada from May 2008-July 2009. The average GEM value at 1.8 m was 1.89 ± 0.62 ng m(-3). The GEM values increased with elevation. The average GEM in underground parking lots ranged from 1.37 to 7.86 ng m(-3) and was higher than those observed from the surface parking lots. The GEM in the indoor air ranged from 1.21 to 28.50 ng m(-3), was higher in the laboratories than in the offices, and was much higher than that in the outdoor air. All these indicate that buildings serve as sources of mercury to the urban atmosphere. More studies are needed to estimate the contribution of urban areas to the atmospheric mercury budget and the impact of indoor air on outdoor air quality and human health.     

The effects of organic environmental chemicals on the growth of the alga Scenedesmus subspicatus: A contribution to environmental biology

The effective concentrations of 15 chemicals, inhibiting the cell growth of the alga $\text{Scenedesmus subspicatus}$ by 10 % and 50 % during 96 hours, have been investigated in a static test under controlled laboratory conditions.     

Bioconcentration of superlipophilic persistent chemicals

According to present understanding, persistent superlipophilic chemicals — such as octachlorodibenzo-p-dioxin, octachlorodibenzofuran, Mirex etc — with log K_ow > 6 and cross sections > 9.5 Å, bioconcentrate in aquatic organisms only little from ambient water. The most convincing argument against it is that in bioconcentration experiments with superlipophilic chemicals amounts applied exceeded water solubility by several orders of magnitude. This paper describes various methods for determining bioconcentration factors (BCF) of superlipophilic compounds. As exemplified with octachlorodibenzo-p-dioxin, BCF values evaluated by these methods match well with those calculated by QSARs for fish and mussels based on log K_ow and water solubility. As expected, these BCF values exceed previous values by several orders of magnitude. For BCF evaluation of superlipophilic chemicals in aquatic organisms we recommend:

1. flow-through systems, kinetic method (OECD guideline No. 305 E)
2. ambient concentrations < water solubility
3. during the uptake and especially during the elimination phase no toxic effects of the test organisms should occur.

     

Oxyanion flux characterization using passive flux meters: development and field testing of surfactant-modified granular activated carbon

We report here on the extension of Passive Flux Meter (PFM) applications for measuring fluxes of oxyanions in groundwater, and present results for laboratory and field studies. Granular activated carbon, with and without impregnated silver (GAC and SI-GAC, respectively), was modified with a cationic surfactant, hexadecyltrimethylammonium (HDTMA), to enhance the anion exchange capacity (AEC). Langmuir isotherm sorption maxima for oxyanions measured in batch experiments were in the following order: perchlorate>chromate>selenate, consistent with their selectivity. Linear sorption isotherms for several alcohols suggest that surfactant modification of GAC and SI-GAC reduced (approximately 30-45%) sorption of alcohols by GAC. Water and oxyanion fluxes (perchlorate and chromate) measured by deploying PFMs packed with surfactant-modified GAC (SM-GAC) or surfactant-modified, silver-impregnated GAC (SM-SI-GAC) in laboratory flow chambers were in close agreement with the imposed fluxes. The use of SM-SI-GAC as a PFM sorbent was evaluated at a field site with perchlorate contamination of a shallow unconfined aquifer. PFMs packed with SM-SI-GAC were deployed in three existing monitoring wells with a perchlorate concentration range of approximately 2.5 to 190 mg/L. PFM-measured, depth-averaged, groundwater fluxes ranged from 1.8 to 7.6 cm/day, while depth-averaged perchlorate fluxes varied from 0.22 to 1.7 g/m2/day. Groundwater and perchlorate flux distributions measured in two PFM deployments closely matched each other. Depth-averaged Darcy fluxes measured with PFMs were in line with an estimate from a borehole dilution test, but much smaller than those based on hydraulic conductivity and head gradients; this is likely due to flow divergence caused by well-screen clogging. Flux-averaged perchlorate concentrations measured with PFM deployments matched concentrations in groundwater samples taken from one well, but not in two other wells, pointing to the need for additional field testing. Use of the surfactant-modified GACs for measuring fluxes of other anions of environmental interest is discussed.