Rapid whole exome sequencing in pregnancies to identify the underlying genetic cause in fetuses with congenital anomalies detected by ultrasound imaging

Objective

The purpose of this study was to explore the diagnostic yield and clinical utility of trio-based rapid whole exome sequencing (rWES) in pregnancies of fetuses with a wide range of congenital anomalies detected by ultrasound imaging.

Methods

In this observational study, we analyzed the first 54 cases referred to our laboratory for prenatal rWES to support clinical decision making, after the sonographic detection of fetal congenital anomalies. The most common identified congenital anomalies were skeletal dysplasia (n = 20), multiple major fetal congenital anomalies (n = 17) and intracerebral structural anomalies (n = 7).

Results

A conclusive diagnosis was identified in 18 of the 54 cases (33%). Pathogenic variants were detected most often in fetuses with skeletal dysplasia (n = 11) followed by fetuses with multiple major fetal congenital anomalies (n = 4) and intracerebral structural anomalies (n = 3). A survey, completed by the physicians for 37 of 54 cases, indicated that the rWES results impacted clinical decision making in 68% of cases.

Conclusions

These results suggest that rWES improves prenatal diagnosis of fetuses with congenital anomalies, and has an important impact on prenatal and peripartum parental and clinical decision making.     

Assessing Ecological Water Quality with Macroinvertebrates and Fish: A Case Study from a Small Mediterranean River

Biological elements, such as benthic macroinvertebrates and fish, have been used in assessing the ecological quality of rivers according to the requirements of the Water Framework Directive. However, the concurrent use of multiple organism groups provides a broader perspective for such evaluations, since each biological element may respond differently to certain environmental variables. In the present study, we assessed the ecological quality of a Greek river (RM4 type), during autumn 2003 and spring 2004 at 10 sites, with benthic macroinvertebrates and fish. Hydromorphological and physicochemical parameters, habitat structure, and riparian vegetation were also considered. Pollution sensitive macroinvertebrate taxa were more abundant at headwaters, which had good/excellent water quality according to the Hellenic Evaluation System (HES). The main river reaches possessed moderate water quality, while downstream sites were mainly characterised as having bad or poor water quality, dominated by pollution-tolerant macroinvertebrate taxa. Macroinvertebrates related strongly to local stressors as chemical degradation (ordination analysis CCA) and riparian quality impairment (bivariate analysis) while fish did not. Fish were absent from the severely impacted lower river reaches. Furthermore, external pathological signs were observed in fish caught at certain sites. A combined use of both macroinvertebrates and fish in biomonitoring programs is proposed for providing a safer assessment of local and regional habitat impairment.     

Photocatalytic degradation of the fungicide Fenhexamid in aqueous TiO(2) suspensions: identification of intermediates products and reaction pathways

Liquid-chromatography interfaced with time-of-flight mass spectrometry (LC-TOF/MS) was used to separate and characterize the transformation products arising from TiO₂-photocatalytic degradation of the fungicide Fenhexamid (FEX) in aqueous solution under simulated solar irradiation. Prior to identification, irradiated solutions of FEX (10 mg L⁻¹) were concentrated by solid-phase extraction. Assignments of the mass spectra ions were aided by elemental composition calculations, comparison of structural analogues and available literature, and acquired knowledge regarding mass spectrometry of related heterocyclic compounds. The primary transformation intermediates identified were hydroxyl and/or keto-derivatives. Several positional isomers are typically produced as a consequence of the non-selectivity of the OH radical attack. Moreover, products resulted from the cleavage of the amide and NHdichlorophenol bonds were formed. Finally, cyclic - benzo[d]oxazole intermediates are also formed through an intramolecular photocyclization process and cleavage of halogen - carbon bond. In the case of the hydroxy and/or keto-derivatives, the generic fragmentation scheme obtained from the interpretation of the ESI-TOF-MS data cannot be diagnostic to precisely localize the position of the entering substituent on the FEX molecule, and thus to characterize all its possible oxygenated derivatives by assigning a plausible structure with confidence. On the basis of identified products different pathways of photocatalytic degradation of FEX were proposed and discussed.     

Seasonal variation of fish abundance and biomass in gillnet catches of an East Mediterranean lake: Lake Doirani

The seasonal variation of fish species composition and abundance in gillnet catches (14-90 mm knot-to-knot) from the Greek part of the transboundary Lake Doirani was studied during the period 2006-2007. A total of 8,419 specimens weighing 182.3 kg and belonging to 9 species were caught. Catch composition differed with season. Thus, Rhodeus meridionalis dominated in terms of NPUE the spring, Perca fluviatilis the summer and Albumus macedonicus the autumn and winter catches. Cyprinids were generally the most abundant, with the cyprinids:percids biomass ratio ranging from 1.7 in summer to 14.8 in winter, supporting the eutrophic character of the lake. Richness and Shannon-Wiener diversity and evenness indices differed seasonally (ANOVA; p < 0.05). The abundance-biomass comparative (ABC) curves showed that fish communities were dominated by one or a few opportunistic species (e.g. Rhodeus meridionalis, Albumus macedonicus), which while dominated in number did not dominate in biomass, being small bodied.     

Using Various Guidelines and Approaches for the Assessment of Marine Sediment Quality

The aim of the present study is to explore the implications of using different quality guidelines and approaches for marine sediment characterization. As a case study, the sediments of Souda Port, Crete, Greece, were examined in order to assess heavy metal contamination and to estimate anthropogenic contribution and potential adverse effects to aquatic environment, as well as to indicate feasible future management options. The concentration of six heavy metals (Co, Cr, Cu, Ni, Pb, and Zn) was determined and compared with different sediment quality guidelines (SQGs) and regional/national criteria established for dredged material characterization and management. In addition, the geo-accumulation index (I_geo) was calculated and the sediments toxicity and heavy metals bioavailability were determined. Based on the experimental data, it is deduced that Souda sediments are characterized as moderately polluted only in terms of Co, Ni, and Pb.     

Nutrient dynamics in shallow lakes of northern greece

GOAL, SCOPE, BACKGROUND: Shallow lakes display a number of features that set them apart from the more frequently studied deeper systems. The majority of lakes in Northern Greece are small to moderate in size with a relatively low depth and are considered as sites of high value of the wetland habitat. However, the water quality of these lakes has only been evaluated segmentally and occasionally. OBJECTIVE: The objectives of this study were to thoroughly investigate nitrogen and phosphorus speciation in lakes of a high ecological significance located in N. Greece, in order to evaluate their eutrophication status and possible nutrient limitation factors, and to investigate the main factors/sources that affect the water quality of these systems. METHODS: An extensive survey was carried out during the period from 1998-1999. Water samples were collected on a monthly basis from lakes Koronia, Volvi, Doirani, Mikri Prespa and Megali Prespa located in N. Greece. Water quality parameters (temperature, dissolved oxygen, pH and conductivity), organic indices (COD, BOD5), and N- and P-species (NO3(-), NO2(-), NH4(+), and PO4(3-), Kieldahl nitrogen and acid-hydrolysable phosphorus) were determined according to standard methods for surface water. Statistical treatment of the data was employed. RESULTS AND CONCLUSIONS: The physicochemical parameters determined in the lakes studied revealed a high temporal variation. The trophic state of the lakes ranged from meso- to hypertrophic. The nutrient limiting factor varied among lakes suggesting either P-limitation conditions or mixed conditions changing from P- to N-limitation throughout the year. Urban/industrial activities and agricultural runoff are the major factors affecting all lakes, although with a varying contribution. RECOMMENDATION AND OUTLOOK: This lake-specific research offers valuable information about water quality and nutrient dynamics in lakes of significant ecological value located in N. Greece that can be useful for an effective pollution control/management of these systems. Due to the large intra-annual variability of certain physicochemical parameters, a properly designed monitoring program of lake water is recommended.     

Endocrine disrupting compounds in municipal and industrial wastewater treatment plants in Northern Greece

The occurrence and fate of endocrine disrupting compounds (EDCs) in a sewage treatment plant and two industrial wastewater treatment plants from textile and tannery factories were investigated. EDCs of interest are 4-nonylphenol, 4-octylphenol, their ethoxylate oligomers (mono- and di-ethoxylates of nonylphenol and octylphenol), bisphenol A, triclosan and steroid estrogens. Target compounds were determined in dissolved fraction, total suspended solids and sludge by employing solid phase extraction and ultrasonication followed by gas chromatography–mass spectrometry.Nonylphenols and oligomers with one or two ethoxy groups were the most abundant compounds in raw wastewater as well as in effluents from all the treatment stages of sewage treatment plant, followed by triclosan and bisphenol A. Steroids were found at very low concentrations. Almost all phenolic EDCs compounds were predominantly associated to suspended solids in influents whereas the dissolved fraction dominated the treated effluents. High removal rates, ranging from 86% to 99%, were observed throughout the whole treatment process. Biodegradation was the main removal pathway of EDCs. Tannery wastewaters exhibited high concentrations of nonylphenolic compounds. This type of wastewaters could pose a significant risk to the aquatic and terrestrial environment.     

Photocatalytic degradation of molinate in aqueous solutions

In this study, the degradation of molinate through heterogeneous photocatalysis, using two different types of the semiconductor TiO₂ as photocatalyst, as well as through homogeneous treatment, applying the photo-Fenton reaction, has been investigated. As far as heterogeneous photocatalysis is concerned, the degradation of the pesticide follows apparent first-order kinetics, while the type of the catalyst and the pH value of the solution affect the degradation rate. The effect of the addition of electron scavengers (H₂O₂ and K₂S₂O₈) was also studied. In the case of photo-Fenton-assisted system, the degradation also follows pseudo-first-order kinetics. Parameters such as iron’s and electron scavenger’s concentration and inorganic ions strongly affect the degradation rate. The extent of pesticide mineralization was investigated using dissolved organic carbon (DOC) measurements. The toxicity of the treated solution was evaluated using the Microtox test based on the luminescent bacteria Vibrio fischeri. The detoxification and mineralization efficiency was found to be dependent on the system studied, and although it did not follow the rate of pesticide disappearance, it took place in considerable extent. The study of the photodegradation treatment was completed by the determination of the intermediate by-products formed during the process, which was carried out using LC-MS/MS technique and led to similar compounds with both processes.