Small things are important: the value of singular point elements for birds in agricultural landscapes

Farmland birds belong to the most endangered group of vertebrates in Europe. They are an important component of farmland biodiversity considering the numerous functions they perform (e.g. seed dispersal, improving germination, increasing gene flow, nutrient recycling, and pest control). Therefore, their decline imposes substantial risks on agricultural ecosystems. In general, farmland bird conservation includes land-use and management alterations leading to less-intensive farming and land-sparing for breeding habitats (e.g. agri-environment-climate schemes, and organic farming). However, theoretical concepts describing farmland biodiversity maintenance and applied conservation measures usually ignore the role of singular, often very small, natural or man-made elements in an agricultural landscape. These elements play a role in the populations of certain species, their biology and in the general species richness of farmland. Furthermore, the importance of these elements has never been empirically tested, which means that conservationists and practitioners are not aware of their measurable value for birds. Herein, we define and identify singular point elements in the agricultural landscape (SPELs) which are potentially important for breeding farmland birds. We also describe each SPEL and evaluate its importance for birds in farmland based on a systematic review of the available literature. Using a horizon-scanning technique, we then polled field ornithologists about their personal observations of birds in relation to SPELs and the evaluation of the potential roles of such structures for birds. We identified 17 SPELs that vary in naturalness and age: singular trees, singular shrubs, erratic boulders, puddles, electricity pylons, wind turbines, spiritual sites, hunting platforms, fence and border posts, wells, road signs, scarecrows, piles of manure, piles of brushwood/branches, piles of stones/debris, piles of lime, and haystacks. Analysis of the literature revealed knowledge gaps, because some SPELs are frequently mentioned in ecological studies (e.g. trees, shrubs, pylons), but others such as spiritual sites, stones, hunting platforms, wells, road signs, or piles of lime are ignored. Despite the fact that some authors incorporate the effects of some SPELs in their studies, little research to date has aimed to assess the impact of various SPELs on farmland bird species numbers and distribution. Horizon scanning revealed that ornithologists often observe birds on various SPELs and thus, attribute to SPELs many functions that are important for maintaining bird populations. Horizon scanning also highlighted the importance of SPELs for many declining bird species and suggested possible mitigation of negative changes in the agricultural landscape by retaining SPELs within fields. We suggest that a better understanding of the role of SPELs for farmland birds is required. We also recommend that SPELs are considered as a potential tool for the conservation of birds, and existing conservation programs such as agri-environment-climate schemes and organic farming should be updated accordingly. Finally, we suggest that SPELs are included in predictive models that evaluate habitat suitability for farmland biodiversity.     

A novel KIT deletion variant in a German Riding Pony with white‐spotting coat colour phenotype

White spotting phenotypes in horses may be caused by developmental alterations impairing melanoblast differentiation, survival, migration and/or proliferation. Candidate genes for white‐spotting phenotypes in horses include EDNRB, KIT, MITF, PAX3 and TRPM1. We investigated a German Riding Pony with a sabino‐like phenotype involving extensive white spots on the body together with large white markings on the head and almost completely white legs. We obtained whole genome sequence data from this horse. The analysis revealed a heterozygous 1273‐bp deletion spanning parts of intron 2 and exon 3 of the equine KIT gene (Chr3: 79 579 925–79 581 197). We confirmed the breakpoints of the deletion by PCR and Sanger sequencing. Knowledge of the functional impact of similar KIT variants in horses and other species suggests that this deletion represents a plausible candidate causative variant for the white‐spotting phenotype. We propose the designation W28 for the mutant allele.     

Whole‐genome sequencing reveals a large deletion in the MITF gene in horses with white spotted coat colour and increased risk of deafness

White spotting phenotypes in horses are highly valued in some breeds. They are quite variable and may range from the common white markings up to completely white horses. EDNRB, KIT, MITF, PAX3 and TRPM1 represent known candidate genes for white spotting phenotypes in horses. For the present study, we investigated an American Paint Horse family segregating a phenotype involving white spotting and blue eyes. Six of eight horses with the white‐spotting phenotype were deaf. We obtained whole‐genome sequence data from an affected horse and specifically searched for structural variants in the known candidate genes. This analysis revealed a heterozygous ~63‐kb deletion spanning exons 6–9 of the MITF gene (chr16:21 503 211–21 566 617). We confirmed the breakpoints of the deletion by PCR and Sanger sequencing. PCR‐based genotyping revealed that all eight available affected horses from the family carried the deletion. The finding of an MITF variant fits well with the syndromic phenotype involving both depigmentation and an increased risk for deafness and corresponds to human Waardenburg syndrome type 2A. Our findings will enable more precise genetic testing for depigmentation phenotypes in horses.     

Review on chemogenomic approaches towards hepatitis C viral targets

Hepatitis C virus (HCV) is the most prevalent viral pathogen that infects more than 185 million people worldwide. HCV infection leads to chronic liver diseases such as liver cirrhosis and hepatocellular carcinoma. Direct-acting antivirals (DAAs) are the recent combination therapy for HCV infection with reduced side effects than prior therapies. Sustained virological response (SVR) acts as a gold standard marker to monitor the success of antiviral treatment. Older treatment therapies attain 50-55% of SVR compared with DAAs which attain around 90-95%. The current review emphasizes the recent chemogenomic updates that have been unfolded through structure-based drug design of HCV drug target proteins (NS3/4A, NS5A, and NS5B) and ligand-based drug design of DAAs in achieving a stable HCV viral treatment strategies.     

基于蛋白质二级结构内容的域结构类预测

运用加入竞争层的BP网络,研究了基于蛋白质二级结构内容的域结构类预测问题.在BP网络中嵌入一竞争,层显著提高了网络预测性能.仅使用了一个小的训练集和简单的网络结构,获得了很高的预测精度自支持精度97.62%,jack-knife测试精度97.62%,及平均外推精度90.74%.在建立更完备的域结构类特征向量和更有代表性的训练集的基础上,所述方法将为蛋白质域结构分类领域提供新的分类基准.     

从非同源蛋白质的一级序列预测其结构类

对基于氨基酸组成、自相关函数和自协方差函数提取特征的蛋白质结构类预测算法进行分析比较,对氨基酸组成和自相关函数相结合的方法,以及氨基酸组成和自协放差函数相结合的方法的预测算法进行了研究。结果表明：对非同源蛋白质,因氨基酸和自相关函数相结合的方法中,采用Miyazawa和Jernigan的疏水值时,训练的自检验的总精度为95．34％,其Jackknife检验的总精度为81．92％,检验加的他检验的总精工为86．61％。在氨基酸组成和自协方差函数相结合的方法中,采用Wold等的疏水值时,训练库的自检验的总精度为96．71％,其Jackknife检验的总精度为82．18％,检验加的他检验的总精工为86．88％。这说明氨基酸组成和自相关函数相结合的方法,以及氨基酸组成和自协方差函数相结合的方法可有效提高结构类预测精度,表明提取更多有效的序列信息是提高分类精度的关键。     

河南鸡公山木本植物区系的研究

鸡公山国家级自然保护区是我国北亚热带森林生态系统自然保护区之一,地处亚热带与暖温带的过渡地带,是华中、华东和华北三大植物区系的交汇区之一,木本植物种类比较丰富。据初步统计,该区有木本植物71科、181属、543种,其中裸子植物5科、5属、7种。该区木本植物区系具有下列基本特点:1)区系成分比较丰富;2)古老和孑遗成分繁多;3)区系成分过渡性明显。该区木本植物可分为14种地理成分(分布区类型),其中热带属占35.0%,温带和亚热带分布的属占65.0%。