Experimental investigation of a line plume in a filling box

Environmental Fluid Mechanics - A series of experiments were conducted to quantify the dynamics of a filling box driven by a line plume that spans the full width of the enclosure. Three...     

Noninvasive screening by cell-free DNA for 22q11.2 deletion: Benefits,limitations, and challenges

Cell-free DNA (cfDNA) testing for fetal aneuploidy is one of the most important technical advances in prenatal care. Additional chromosome targets beyond common aneuploidies, including the 22q11.2 microdeletion, are now available because of this clinical testing technology. While there are numerous potential benefits, 22q11.2 microdeletion screening using cfDNA testing also presents significant limitations and pitfalls. Practitioners who are offering this test should provide comprehensive pretest and posttest prenatal counselling. The discussion should include the possibility of an absence of a result, as well as the risk of possible discordance between cfDNA screening results and the actual fetal genetic chromosomal constitution. The goal of this review is to provide an overview of the cfDNA testing technologies for 22q11.2 microdeletions screening, describe the current state of test validation and clinical experience, review “no results” and discordant findings based on differing technologies, and discuss management options.     

Non-invasive prenatal testing (NIPT): Combination of copy number variant and gene analyses using an “in-house” target enrichment next generation sequencing—Solution for non-centralized NIPT laboratory?

Objective

Recent studies have integrated copy number variant (CNV) and gene analysis using target enrichment. Here, we transferred this concept to our routine genetics laboratory, which is not linked to centralized non-invasive prenatal testing (NIPT) facilities.

Method

From a cohort of 100 pregnant women, 22 were selected for the analysis of maternal genomic DNA (gDNA) along with fetal cell-free DNA. Using targeted enrichment, 135 genes were analyzed, combined with aberrations of chromosomes 21, 18, 13, X, and Y. The data were subjected to specificity and sensitivity analyses, and correlated with the results from invasive testing methods.

Results

The sensitivity/specificity was determined for the CNV analysis of chromosomes: 21 (80%/75%), 18 (-/82%), 13 (100%/67%), and Y (100%/100%). The gene detection was valid for maternal gDNA. However, for cell-free fetal DNA, it was not possible to determine the boundary between an artifact and a real sequence variant.

Conclusion

The target enrichment method combining CNV and gene detection seems feasible in a regular laboratory. However, this method can only be responsibly optimized with a sufficient number of controls and further validation on a strong bioinformatic background. The present results showed that NIPT should be performed in specialized centers, and that its introduction to isolated laboratories may not provide valid data.     

Genotoxicity evaluation of water soil leachates by Ames test, comet assay, and preliminary Tradescantia micronucleus assay

Combining genotoxicity/mutagenicity tests and physico-chemical methodologies can be useful for determining the potential genotoxic contaminants in soil samples. The aim of our study was to evaluate the genotoxicity of soil by applying an integrated physico-chemical-biological approach. Soil samples were collected at six sampling points in a Slovenian industrial and agricultural region where contamination by heavy metals and sulphur dioxide (SO₂) are primarily caused by a nearby power plant. The in vitro alkaline version of the comet assay on water soil leachates was performed with Caco-2 and HepG2 cells. A parallel genotoxicity evaluation of the samples was performed by Ames test using Salmonella typhimurium and the Tradescantia micronucleus test. Pedological analyses, heavy metal content determination, and different physico-chemical analyses, were also performed utilizing standard methodology. Water leachates of soil samples were prepared according to standard methods. Since only a battery of biotests with prokaryotic and eukaryotic organisms or cells can accurately estimate the effects of (geno)toxicants in soil samples and water soil leachates, a combination of three bioassays, with cells or organisms belonging to different trophic levels, was used. Genotoxicity of all six water soil leachates was proven by the comet assay on both human cell lines, however no positive results were detected by bacterial assay, Ames test. The Tradescantia micronucleus assay showed increase in micronuclei formation for three samples. According to these results we can assume that the comet assay was the most sensitive assay, followed by the micronucleus test. The Ames test does not appear to be sensitive enough for water soil leachates genotoxicity evaluations where heavy metal contamination is anticipated.     

Effects assessment: boron compounds in the aquatic environment

In previous studies, boron compounds were considered to be of comparatively low toxicity in the aquatic environment, with predicted no effect concentration (PNEC) values ranging around 1 mg B/L (expressed as boron equivalent). In the present study, we describe an evaluation of toxicity data for boron available for the aquatic environment by different methods.For substances with rich datasets, it is often possible to perform a species sensitivity distribution (SSD). The typical outcome of an SSD is the Hazardous Concentration 5% (HC₅), the concentration at which 95% of all species are protected with a probability of 95%. The data set currently available on the toxic effects of boron compounds to aquatic organisms is comprehensive, but a careful evaluation of these data revealed that chronic data for aquatic insects and plants are missing. In the present study both the standard assessment factor approach as well as the SSD approach were applied. The standard approach led to a PNEC of 0.18 mg B/L (equivalent to 1.03 mg boric acid/L), while the SSD approach resulted in a PNEC of 0.34 mg B/L (equivalent to 1.94 mg boric acid/L). These evaluations indicate that boron compounds could be hazardous to aquatic organisms at concentrations close to the natural environmental background in some European regions. This suggests a possible high sensitivity of some ecosystems for anthropogenic input of boron compounds. Another concern is that the anthropogenic input of boron could lead to toxic effects in organisms adapted to low boron concentration.     

Accumulation of organochlorine contaminants in loggerhead sea turtles, Caretta caretta, from the eastern Adriatic Sea

We analyzed 15 polychlorinated biphenyls (PCBs) and five organochlorine pesticides (OCPs) in fat tissue of 27 loggerhead sea turtles (Caretta caretta) from eastern Adriatic Sea with the curved carapace length ranging from 25.0 to 84.5 cm. The PCB profile was dominated by hexa- and hepta-chlorinated congeners, with PCB-153 (median: 114.9 ng g⁻¹ wet mass), PCB-138 (80.0 ng g⁻¹ w.m.), and PCB-180 (26.7 ng g⁻¹ w.m.) detected with the highest levels. Toxic mono-ortho congeners PCB-118, PCB-105 and PCB-180 with dioxin-like toxicity were found in >70% samples. 4,4′-DDE (81.0 ng g⁻¹ w.m.) prevailed the OCP signature, accounting for 80% of the total DDTs. A significant increasing trend in accumulation with size was found for PCB-52 (r_s = 0.512, p < 0.01) and PCB-114 (r_s = 0.421, p < 0.05). Comparison of our results with organochlorine contaminant (OC) pattern in some prey taxa suggest that contamination occurs primarily through the food web, with biomagnification factors of 0.14-6.99 which were positively correlated with the octanol-water partition coefficient (log K_ow; p < 0.05). This study, based upon a fairly large sample size collected mostly from incidentally captured animals over a short time period (June 2001-November 2002), present a temporal snapshot of OC contamination in wild, free-ranging loggerheads from Adriatic feeding grounds and provide a baseline for monitoring the regional OC trends in this endangered species.