A novel homozygous 10 nucleotide deletion in BBS10 causes Bardet–Biedl syndrome in a Pakistani family

Bardet–Biedl Syndrome is a multisystem autosomal recessive disorder characterized by central obesity, polydactyly, hypogonadism, learning difficulties, rod-cone dystrophy and renal dysplasia. Bardet–Biedl Syndrome has a prevalence rate ranging from 1 in 100,000 to 1 in 160,000 births although there are communities where Bardet–Biedl Syndrome is found at a higher frequency due to consanguinity. We report here a Pakistani consanguineous family with two affected sons with typical clinical features of Bardet–Biedl Syndrome, in addition to abnormal liver functioning and bilateral basal ganglia calcification, the latter feature being typical of Fahr's disease. Homozygous regions obtained from SNP array depicted three known genes BBS10, BBS14 and BBS2. Bidirectional sequencing of all coding exons by traditional sequencing of all these three genes showed a homozygous deletion of 10 nucleotides (c.1958_1967del), in BBS10 in both affected brothers. The segregation analysis revealed that the parents, paternal grandfather, maternal grandmother and an unaffected sister were heterozygous for the deletion. Such a large deletion in BBS10 has not been reported previously in any population and is likely to be contributing to the phenotype of Bardet–Biedl Syndrome in this family.     

起始密码子下游区域AT含量优化工具BestAT的开发与应用

基因的表达水平受到起始密码子下游区域AT含量的影响,从巨大的序列集中筛选出具有特定AT含量和密码子用法特征的同义序列是一个繁琐的工作。本文研发AT含量优化工具"BestAT",初步解决了自动获取海量同义序列和充分展示同义序列的密码子用法特性两个关键问题,并且实现了与密码子用法数据库(CUD)的无缝结合,采用了密码子参数的原位标示和AT含量曲线等直观方式展示序列特性,为这类实验设计提供有力的支持。     

城市生态智慧管理系统的生态系统服务评估功能与应用

开展生态系统服务评估已经成为国土空间功能管治、城市治理、生态产品价值实现等工作中的先行基础动作。生态系统服务的类型和模型方法多,数据需求复杂,传统基于多学科软件开展生态系统服务评估的工作模式知识和技术门槛较高、效率低。当前专业的生态系统服务评估软件多为美国从业人员开发,对我国的数据构成和本地化参数适应性有限。介绍了我国自主开发的生态系统分析软件（城市生态智慧管理系统,IUEMS）的主要功能和应用情况,并将其的生态系统服务评估功能与InVEST、ARIES等国外主流软件在操作逻辑、评估模型、数据取得、空间精度、界面交互五个方面进行了对比。     

hw‐quickcheck: an easy‐to‐use computer program for checking genotypes for agreement with Hardy–Weinberg expectations

Deviations from Hardy–Weinberg expectations are frequently a sign of genotyping error. hw‐quickcheck is an easy‐to‐use computer program for detecting departures from Hardy–Weinberg equilibrium. hw‐quickcheck uses exact tests for all of its calculations. These tests include a global test for heterozygote excess/deficiency and genotype‐specific tests.     

burnr: Fire history analysis and graphics in R

We developed a new software package, burnr, for fire history analysis and plotting in the R statistical programming environment. It was developed for tree-ring fire-scar analysis, but is broadly applicable to other event analyses (e.g., avalanches, frost rings, or culturally modified trees). Our new package can read, write, and manipulate standard tree-ring fire history FHX files, produce fire—demography charts, calculate fire frequency and seasonality statistics, and run superposed epoch analysis (SEA). A key benefit of burnr is that it enables automation of analyses and plotting, especially for large data sets. The package also facilitates creative plotting, mapping, and analyses when combined with the thousands of packages available in R. In this paper, we describe the basic functionality of burnr and introduce users to fire history analyses in R.     

The Blue Water Footprint of Primary Copper Production in Northern Chile

Water consumption related to the life cycle of metals is seldom reported, even though mines are often situated in very dry regions. In this study we quantified the life cycle consumption of groundwater and fresh surface water (blue water footprint [WF_blue]) for the extraction and production of high‐grade copper refined from both a copper sulfide ore and a copper oxide ore in the Atacama Desert of northern Chile. Where possible, we used company‐specific data. The processes for extracting copper from the two types of ore are quite different from each other, and the WF_blue of the sulfide ore refining process is 2.4 times higher than that of the oxide ore refining process (i.e., 96 cubic meters per metric ton [tonne] of copper versus 40 cubic meters per tonne of copper). Most of the water consumption (59% of WF_blue) in the sulfide ore process occurred at the concentrator plant, via seepage, accumulation, and also by evaporation. In the oxide ore process, the main user of water is the heap‐leaching process, with 45% of WF_blue. The crushing and agglomeration operations, electrowinning cells, and solution pools are also significant contributors to the total consumption of water in the oxide ore process. Most of the water consumed in the oxide ore process was lost to evaporation. The WF_blue of the oxide ore process can be reduced by preventing water evaporation and using more sophisticated devices during irrigation of the leaching heaps. The WF_blue of the sulfide ore refining process can be reduced by improving water recovery (i.e., reducing seepage, accumulation, and evaporation) from the tailings dam at the concentrator plant. Using seawater in the production of copper is also a promising option to reduce the WF_blue by up to 62%.     

MultiGWAS: An integrative tool for Genome Wide Association Studies in tetraploid organisms

The genome‐wide association studies (GWASs) are essential to determine the genetic bases of either ecological or economic phenotypic variation across individuals within populations of the model and nonmodel organisms. For this research question, the GWAS replication testing different parameters and models to validate the results'' reproducibility is common. However, straightforward methodologies that manage both replication and tetraploid data are still missing. To solve this problem, we designed the MultiGWAS, a tool that does GWAS for diploid and tetraploid organisms by executing in parallel four software packages, two designed for polyploid data (GWASpoly and SHEsis) and two designed for diploid data (GAPIT and TASSEL). MultiGWAS has several advantages. It runs either in the command line or in a graphical interface; it manages different genotype formats, including VCF. Moreover, it allows control for population structure, relatedness, and several quality control checks on genotype data. Besides, MultiGWAS can test for additive and dominant gene action models, and, through a proprietary scoring function, select the best model to report its associations. Finally, it generates several reports that facilitate identifying false associations from both the significant and the best‐ranked association Single Nucleotide Polymorphisms (SNPs) among the four software packages. We tested MultiGWAS with public tetraploid potato data for tuber shape and several simulated data under both additive and dominant models. These tests demonstrated that MultiGWAS is better at detecting reliable associations than using each of the four software packages individually. Moreover, the parallel analysis of polyploid and diploid software that only offers MultiGWAS demonstrates its utility in understanding the best genetic model behind the SNP association in tetraploid organisms. Therefore, MultiGWAS probed to be an excellent alternative for wrapping GWAS replication in diploid and tetraploid organisms in a single analysis environment.     

Investigations of the kinetic energy parameters of irradiated (La)‐doped phosphate glass

The current study characterizes and analyzes glow curves obtained from phosphate glass doped with different concentrations of lanthanum. Kinetic parameters of the glow curves obtained from beta‐irradiated phosphate glass samples doped with lanthanum were determined using a newly designed deconvoluted software. The obtained results from the analyses indicated that the glow curves of the phosphate glass samples were composed of five overlapping peaks. The activation energies of the five electron traps were located between 0.622 and 1.133 eV. The obtained kinetic parameters were evaluated using the designed software and another two methods and all revealed good agreement. The first three traps displayed non‐first‐order behaviour, while the two deep traps obeyed nearly first‐order kinetics.     

Review of impact categories and environmental indicators for life cycle assessment of geotechnical systems

Life cycle assessment (LCA) has only had limited application in the geotechnical engineering discipline, though it has been widely applied to civil engineering systems such as pavements and roadways. A review of previous geotechnical LCAs showed that most studies have tracked a small set of impact categories, such as energy and global warming potential. Accordingly, currently reported environmental indicators may not effectively or fully capture important environmental impacts and tradeoffs associated with geotechnical systems, including those associated with land and soil resources. This research reviewed previous studies, methods, and models for assessment of land use and soil‐related impacts to understand their applicability to geotechnical LCA. The results of this review show that critical gaps remain in current knowledge and practice. In particular, further development or refinement of environmental indicators, impact categories, and cause–effect pathways is needed as they pertain to geotechnical applications—specifically those related to soil quality, soil functions, and the ecosystem services soils provide. In addition, many existing methods emerge from research on land use and land use change related to other disciplines (e.g., agriculture). For applicability to geotechnical projects, the resolution of many of these methods and resulting indicators need to be downscaled from the landscape/macro scale to the project scale. In the near term, practitioners of geotechnical LCA should begin tracking changes to soil properties and report impacts to land and soil resources qualitatively.     

Life cycle assessment of emerging technologies at the lab scale: The case of nanowire‐based solar cells

Nanomaterials are expected to play an important role in the development of sustainable products. The use of nanomaterials in solar cells has the potential to increase their conversion efficiency. In this study, we performed a life cycle assessment (LCA) for an emerging nanowire‐based solar technology. Two lab‐scale manufacturing routes for the production of nanowire‐based solar cells have been compared—the direct growth of GaInP nanowires on silicon substrate and the growth of InP nanowires on native substrate, peel off, and transfer to silicon substrate. The analysis revealed critical raw materials and processes of the current lab‐scale manufacturing routes such as the use of trifluoromethane (CHF₃), gold, and an InP wafer and a stamp, which are used and discarded. The environmental performance of the two production routes under different scenarios has been assessed. The scenarios include the use of an alternative process to reduce the gold requirements—electroplating instead of metallization, recovery of gold, and reuse of the InP wafer and the stamp. A number of suggestions, based on the LCA results—including minimization of the use of gold and further exploration for upscaling of the electroplating process, the increase in the lifetimes of the wafer and the stamp, and the use of fluorine‐free etching materials—have been communicated to the researchers in order to improve the environmental performance of the technology. Finally, the usefulness and limitations of lab‐scale LCA as a tool to guide the sustainable development of emerging technologies are discussed.