Exome sequencing for gene discovery in lethal fetal disorders – harnessing the value of extreme phenotypes

Massively parallel sequencing has revolutionized our understanding of Mendelian disorders, and many novel genes have been discovered to cause disease phenotypes when mutant. At the same time, next-generation sequencing approaches have enabled non-invasive prenatal testing of free fetal DNA in maternal blood. However, little attention has been paid to using whole exome and genome sequencing strategies for gene identification in fetal disorders that are lethal in utero, because they can appear to be sporadic and Mendelian inheritance may be missed. We present challenges and advantages of applying next-generation sequencing approaches to gene discovery in fetal malformation phenotypes and review recent successful discovery approaches. We discuss the implication and significance of recessive inheritance and cross-species phenotyping in fetal lethal conditions. Whole exome sequencing can be used in individual families with undiagnosed lethal congenital anomaly syndromes to discover causal mutations, provided that prior to data analysis, the fetal phenotype can be correlated to a particular developmental pathway in embryogenesis. Cross-species phenotyping allows providing further evidence for causality of discovered variants in genes involved in those extremely rare phenotypes and will increase our knowledge about normal and abnormal human developmental processes. Ultimately, families will benefit from the option of early prenatal diagnosis. © 2014 John Wiley & Sons, Ltd.     

Trace elements in buried human bones: intra-population variability of Sr/Ca and Ba/Ca ratios – diet or diagenesis?

A comparative analysis of trace element data of human skeletal material from four archaeological sites is presented. We show that the state of histomorphological preservation of bone, which is a measurement for the degree of its diagenetic alteration, closely corresponds to the Sr/Ca and Ba/Ca ratios at an intra-population level. This study challenges the validity of dietary studies that are based on the presently used procedures for sample preparation and subsequent evaluation of strontium and barium concentrations.     

LCAccess – Global Directory of LCI resources

LCAccess is an EPA-sponsored web-site intended to promote the use of life cycle assessment (LCA) in business decision-making by facilitating access to data sources that are useful in developing a life cycle inventory (LCI). While LCAccess does not itself contain data, it is a searchable global directory of potential data sources. In addition to directing users to relevant data sources, LCAccess also serves as a central source for LCA information. To find the LCAccess web-site go to: http://www.epa.gov/ORD/NRMRL/lcaccess. LCAccess is soliciting organizations that have completed LCI/LCA studies to provide their data sources for reference in LCAccess.     

Health officials’ perceptions of and preparedness for the impacts of climate variability on human health in the Somali region of Ethiopia

A proactive strategy to respond effectively to health impacts related to climate variability, particularly within vulnerable populations, is of vital importance. Such a strategy can be attained if health officials have a deep understanding of how climate variability affects human health and if the resources available for the health care sector are sufficient. This study assessed the perceptions and preparedness of health officials toward climate variability and health impacts in the Somali region of Ethiopia. The resources available for the health care sector were also assessed. The results show that approximately 80% of health officials were aware of the relationship between climate variability and human health impacts, but the majority of them were unable to project the future trend of related health problems in the region. The results also show an inadequate availability of health care resources, particularly in regards to infrastructure, numbers of health professionals, and training on climate variability and health. The results further revealed problems with poor living conditions, such as access to sanitation and safe water, for the majority of people in the study area. Climate variability is thus one of the many factors exacerbating the increasing trend of human health problems in the Somali region. Besides improving training to increase health officials’ knowledge of climate variability and human health impacts, the government should also address other factors that currently hinder a successful response to increasing disease prevalence.     

Spatial variability of organochlorine pesticides （DDTs and HCHs） in surface soils from the alluvial region of Beijing, China

The spatial variability in the concentrations of 1,2,3,4,5,6-hexachlorocyclohexane (HCH) and 1,1,1-trichloro-2,2-bis-(p-chlorophenyl) ethane (DDT) in surface soils was studied on the basis of the analysis of 131 soil samples collected from the surface layer (0-20 cm depth) of the alluvial region of Beijing, China. The concentrations of total HCHs (including α-, β-, γ-, and δ-isomers) and total DDTs (i ncluding p,p'-DDT, p,p'-DDD, p,p'-DDE, and o,p'-DDT) in the surface soils tested were in the range from nondetectable to 31.72 μg/kg dry soil, with a mean value of 0.91, and from nondetectable to 5910.83 μg/kg dry soil, with a mean value of 32.13,respectively. It was observed that concentrations of HCHs in all soil samples and concentrations of DDTs in 112 soil samples were much lower than the first grade (50 μg/kg) permitted in "Environment quality standard for soils in China (GB15618-1995)". This suggests that the pollution due to organochlorine pesticides was generally not significant in the farmland soils in the Beijing alluvial region. In this study, the spatial distribution and trend of HCHs and DDTs were analyzed using Geostatistical Analyst and GS (513).Spatial distribution indicated how these pesticides had been applied in the past. Trend analysis showed that the concentrations of HCHs,DDTs, and their related metabolites followed an obvious distribution trend in the surface soils from the alluvial region of Beijing.     

Analysis of climate variability in the Manas River Valley,North-Western China (1956–2006)

This paper examines the short-run climate variability (change in the levels of temperature and precipitation) with a focus on the Manas River Valley, North-Western China, over the past 50 years (1956 to 2006) using data collected from four meteorological stations. The results show that the annual mean temperature had a positive trend, with temperature increasing at 0.4 °C per decade. Application of the Mann-Kendall test revealed that the overall positive trend became statistically significant at the p?=?0.95 level only after 1988. The increase in temperature was most marked in winter and spring (0.8 and 0.7 °C per decade, respectively), absent in summer and very small in autumn (0.1 °C per decade). Concerning precipitation, our results indicate a negative but not significant trend for the period between 1956 and 1982, while annual total precipitation tended to increase thereafter and the increase was mainly during the crop growing-season. Concerning variability in temperature and precipitation, the characteristic time scales were identified by application of wavelet analysis. For temperature the quasi-decadal variations were found on time scales between approximately 5 and 15 years, with a peak in wavelet variance on a time scale of 9 years. For precipitation, the most striking features were a precipitation increase (6.7 mm per decade) during the crop growing season. Irregularities and abrupt changes in both temperature and precipitation were more common at scales less than 10 years, indicating the complexity and uncertainty in the short-period climate variability. Possible causes of climate variability in the Manas River Valley may include anthropogenic factors such as intensive human activity and the expansion of both farmland and irrigation. Global climate variability might also have some impacts on the local climate variability; analyses of local and regional climate trends can better inform local adaptation actions for global impacts.     

Co-utilisation of CO2 and steelmaking slags for production of pure CaCO3 – legislative issues

The steel industry is characterised by large amounts of CO₂ emissions, but there is no easy means to reduce these emissions. One interesting option for the reduction of CO₂ emissions could be the utilisation of steelmaking slags for carbon dioxide mineralisation. In this option CO₂ is bound with the calcium of the slag material, producing stable carbonate as an end product. The utilisation of steelmaking slags as the raw material for carbon dioxide mineralisation will change the quality of the slags. If, however, this change degrades the slags it could prevent the use of slags in carbon dioxide mineralisation or make it very expensive.The purpose of the research presented here is to evaluate this issue with the help of a case study where the quality of the residual slag from the recently suggested carbonation method was experimentally investigated. The CO₂ mineralisation method, based on steelmaking slags and ammonium salt solutions, was found to change the quality of the slags: the calcium content was reduced, the CaO and Ca(OH)₂ phases were completely dissolved, and the solubility of the V and Cr increased notably. This residual slag would presumably have to be handled as waste. Currently, the steelmaking slag used in the case study is defined as a by-product, but if it is used for CO₂ mineralisation instead of liming its legal status will be re-evaluated. Subsequently, the CO₂ mineralisation process could possibly be defined as an end-of-waste procedure.     

Effect of bio-column composed of aged refuse on methane abatement – A novel configuration of biological oxidation in refuse landfill

An experimental bio-column composed of aged refuse was installed around the exhaust pipe as a new way to mitigate methane in refuse landfill.One of the objectives of this work was to assess the effect of aged refuse thickness in bio-column on reducing CH 4 emissions.Over the study period,methane oxidation was observed at various thicknesses,5 cm (small size),10 cm (middle size) and 15 cm (large size),representing one to three times of pipeline diameters.The middle and large size both showed over 90% methane conversion,and the highest methane conversion rate of above 95% occurred in the middle-size column cell.Michaelis-Menten equation addressed the methanotrophs diffusion in different layers of the bio-columns.Maximum methanotrophic activity (V max) measured at the three thicknesses ranged from 6.4 × 10 3 to 15.6 × 10 3 units,and the half-saturation value (K M) ranged from 0.85% to 1.67%.Both the highest V max and K M were observed at the middle-size of the bio-column,as well as the largest methanotrophs population,suggesting a significant efficiency of methane mitigation happened in the optimum zone with greatest affinity and methanotrophic bacteria activities.Therefore,bio-column is a potential style for methane abatement in landfill,and the aged refuse both naturally formed and artificially placed in the column plays a critical role in CH 4 emission.     

Adsorption behavior of ammonium by a bioadsorbent – Boston ivy leaf powder

The adsorption behaviors of ammonium ions from aqueous solution by a novel bioadsorbent, the Boston ivy (Parthenocissus tricuspidata) leaf powder (BPTL) were investigated. The SEM images and FT-IR spectra were used to characterize BPTL. The mathematical models were used to analyze the adsorption kinetics and isotherms. The optimum pH range for ammonium adsorption by BPTL was found to be 5–10. The adsorption reached equilibrium at 14 hr, and the kinetic data were well fitted by the Logistic model. The intraparticle di usion was the main rate-controlling step of the adsorption process. The high temperature was favorable to the ammonium adsorption by BPTL, indicating that the adsorption was endothermic. The adsorption equilibrium fitted well to both the Langmuir model and Freundlich model, and the maximum monolayer adsorption capacities calculated from Langmuir model were 3.37, 5.28 and 6.59 mg N/g at 15, 25 and 35°C, respectively, which were comparable to those by reported minerals. Both the separation factor (RL) from the Langmuir model and Freundlich exponent (n) suggested that the ammonium adsorption by BPTL was favorable. Therefore, the Boston ivy leaf powder could be considered a novel bioadsorbent for ammonium removal from aqueous solution.     

News – JES Symposium to celebrate 30 years of publishing environmental research

正Journal of Environmental Sciences(JES)is growing into its 30 years of continuing publication since its establishment in 1998.In celebration of the 30thanniversary of JES,Professors Chris Le(University of Alberta,Edmonton,Canada),Guibin Jiang