Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design

Background  

In moderate-throughput SNP genotyping there was a gap in the workflow, between choosing a set of SNPs and submitting their sequences to proprietary assay design software, which was not met by existing software. Retrieval and formatting of sequences flanking each SNP, prior to assay design, becomes rate-limiting for more than about ten SNPs, especially if annotated for repetitive regions and adjacent variations. We routinely process up to 50 SNPs at once.     

华西雨屏带及其对我国生物多样性保育的意义

华西雨屏带为四川盆地西部边缘独特的自然地理区域。东西宽50-70km,南北长400－450km,总面积约2.5万km^2,仅占我国国土总面积的0.26%左右。本区以自然风景优美、天然植被类型丰富、动植物资源种类多样而享誉中外。迄今为止,尚未将华西雨屏带作为相对独立的自然地理单元来研究其生物多样性。本文从当地剧烈的地形、地貌变化,特殊的气候、植被类型与动物栖息环境以及邻近人类聚居区的特点入手,扼要阐述了本区生态系统与环境的多样性状况。进一步通过对当地动植物种类,尤其是种子植物、兽类、鸟类、鱼类物种多样性与珍、稀、特保护物种的数量比重分析,提出了本带作为我国乃至世界上研究与保护生物多样性的热点区域的立论依据。华西雨屏带是一个大尺度、复合性的生态过渡带（ccotone),是我国西部地区以阴湿为主要特征的罕见的气候地理单元,是我国西部生态保护与建设的一道绿色屏障,是我国生物多样性保护与研究不可替代的关键地区之一。     

Estimation of divergence time between two sibling species of the <Emphasis Type="Italic">Anopheles (Kerteszia) cruzii</Emphasis>complex using a multilocus approach

Background  

Anopheles cruzii is the primary human Plasmodium vector in southern and southeastern Brazil. The distribution of this mosquito follows the coast of the Brazilian Atlantic Forest. Previous studies indicated that An. cruzii is a complex of cryptic species.     

A fluorescent coagulation assay for thrombin using a fibre optic evanescent wave sensor

A fibre optic evanescent wave sensor is used for the rapid detection of thrombin. Coagulation of solution phase fluorescently labelled fibrinogen to unlabelled fibrinogen bound to the surface of the fibre optic is observed in real time by the evanescent wave sensor. Thrombin concentrations down to 0.01 NIHml(-1) are detectable within 5 min. The potential application of this technique for rapid amplified immunosensing is discussed.     

Comparative susceptibility of turbot Scophthalmus maximus to different genotypes of viral haemorrhagic septicaemia virus

Viral haemorrhagic septicaemia (VHS) disease has exerted a significant impact on the development of turbot aquaculture in the British Isles. The source of such outbreaks is believed to be naturally occurring marine isolates of viral haemorrhagic septicaemia virus (VHSV), which are endemic in the marine environment of Northern Europe. Genetic studies have classified these marine VHSV isolates into genotypes based on their geographic rather than host-species origin. This study set out to explore the hypothesis that susceptibility of turbot to VHSV might be genotype specific. Immersion infection of turbot with a range of isolates, selected according to genotype, identified significant differences between susceptibility and genotype. Viruses belonging to Genotypes Ib (Baltic marine isolates) and III (North Sea/E. Atlantic marine isolates) caused significantly higher mortality than isolates from Genotypes Ia (isolates associated with rainbow trout aquaculture) and II (Baltic marine isolates). This study serves to highlight the importance of thoroughly investigating the susceptibility of any given species to the range of pathogens to which they might be exposed prior to considering them resistant to any disease. Furthermore, it highlights different risk factors that might be associated with turbot aquaculture undertaken in different environments. Finally, an increased knowledge of the relative virulence of different isolates in turbot will assist in understanding virulence determinants, which could lead to advances in disease control.     

Management into the Development Strategies of Urbanizing Regions in Asia: Implications of Urban Function, Form, and Role

The way urbanization unfolds over the next few decades in the developing countries of Asia will have profound implications for sustainability. One of the more important opportunities is to guide urbanization along pathways that begin to uncouple these gains in well-being from rising levels of energy use. Increasing energy use for transport, construction, climate control in houses and offices, and industrial processes is often accompanied by increasing levels of atmospheric emissions that impact human health, ecosystem functions, and the climate system. Agriculture, forestry, and animal husbandry alter carbon stocks and fluxes as carbon dioxide, methane, and black carbon. In this article we explore how carbon management could be integrated into the development strategies of cities and urbanizing regions. In particular, we explore how changes in urban form, functions, and roles might alter the timing, aggregation, spatial distribution, and composition of carbon emissions. Our emphasis is on identifying system linkages and points of leverage. The study draws primarily on emission inventories and regional development histories carried out in the regions around the cities of Manila, Jakarta, Ho Chi Minh City, New Delhi, and Chiang Mai. We find that how urban functions, such as mobility, shelter, and food, are provided has major implications for carbon emissions, and that each function is influenced by urban form and role in distinct ways. Our case studies highlight the need for major "U-turns" in urban policy.     

Effects of solar ultraviolet radiation on the potential efficiency of photosystem II in leaves of tropical plants

The effects of solar ultraviolet (UV)-B and UV-A radiation on the potential efficiency of photosystem II (PSII) in leaves of tropical plants were investigated in Panama (9°N). Shade-grown tree seedlings or detached sun leaves from the outer crown of mature trees were exposed for short periods (up to 75 min) to direct sunlight filtered through plastic or glass filters that absorbed either UV-B or UV-A+B radiation, or transmitted the complete solar spectrum. Persistent changes in potential PSII efficiency were monitored by means of the dark-adapted ratio of variable to maximum chlorophyll a fluorescence. In leaves of shade-grown tree seedlings, exposure to the complete solar spectrum resulted in a strong decrease in potential PSII efficiency, probably involving protein damage. A substantially smaller decline in the dark-adapted ratio of variable to maximum chlorophyll a fluorescence was observed when UV-B irradiation was excluded. The loss in PSII efficiency was further reduced by excluding both UV-B and UV-A light. The photoinactivation of PSII was reversible under shade conditions, but restoration of nearly full activity required at least 10 d. Repeated exposure to direct sunlight induced an increase in the pool size of xanthophyll cycle pigments and in the content of UV-absorbing vacuolar compounds. In sun leaves of mature trees, which contained high levels of UV-absorbing compounds, effects of UV-B on PSII efficiency were observed in several cases and varied with developmental age and acclimation state of the leaves. The results show that natural UV-B and UV-A radiation in the tropics may significantly contribute to photoinhibition of PSII during sun exposure in situ, particularly in shade leaves exposed to full sunlight.     

Effect of major liver resection on hepatic ureagenesis in humans

Changes in hepatic ureagenesis following major hepatectomy are not well characterized. We studied the relation between urea synthesis and liver mass before and after major hepatectomy in humans. Fifteen patients scheduled for resection of malignancies in otherwise healthy livers were studied. Pre- and postoperative liver volume was assessed by computerized tomography-volumetry. During surgery, a primed, continuous infusion of [(13)C]urea was administered intravenously, and arterial blood samples were obtained hourly. Indocyanine green clearance was determined before and after resection. Seven patients underwent major hepatectomy, and eight patients underwent minor [<5% functional liver volume (total volume -- tumor volume)] or no resection, serving as controls. Resected functional liver volume in the major hepatectomy group averaged 60%. Urea synthesis per gram of functional liver tissue increased 2.6-fold following major hepatectomy, maintaining whole body urea synthesis. Arterial ammonia remained unchanged throughout the study, whereas following hepatectomy a hyperaminoacidemia occurred. In conclusion, immediately following major hepatectomy, urea synthesis per gram of functional liver tissue increases rapidly and proportionately to the amount of liver tissue resected, maintaining whole body urea synthesis at preoperative levels. This rapid and complete adaptation suggests that the capacity of urea synthesis is not limiting the maximum resectable volume in otherwise healthy livers.     

Gene regulatory divergence among species estimated by altered developmental patterns in interspecific hybrids

Disturbances in the schedules of gene expression in developing interspecific fish hybrids have been used to draw inferences about the extent of gene regulatory divergence between species and about the degree to which this gene regulatory divergence is correlated with structural gene divergence, as estimated by genetic distance. Sperm from each of 10 different species representing six genera within the family Centrarchidae was used to fertilize eggs of the Florida largemouth bass (Micropterus salmoides floridanus). The genetic distances (D; Nei 1978) between the parental species used to form the hybrids ranged from 0.133 to 0.974. The developmental success and temporal patterns of gene expression of each of the hybrids were compared with those of the Florida largemouth bass. As the genetic distance between the paternal species and the Florida largemouth bass increased, there was a general decline in developmental success in the hybrid embryos as demonstrated by the observed reductions in the percentage of hatching and by progressively earlier and more extensive morphological abnormalities. Concomitantly, progressively more marked alterations in developmental schedules of expression of 15 enzyme loci occurred in the hybrids as the genetic distance between parental species increased. However, observed deviations from this trend for a few species may represent an uncoupling of the rates and modes of evolution of structural genes from those for genes regulating developmental processes.