Systematic investigation of Amphioxus (Branchiostoma floridae) microRNAs

Ascaris lumbricoides and Ascaris suum are parasitic nematodes living in the small intestine of humans and pigs, and can cause the disease ascariasis. For long, there has been controversy as to whether the two ascaridoid taxa represent the same species due to their significant resemblances in morphology. However, the complete mitochondrial (mt) genome data have been lacking for A. lumbricoides in spite of human and animal health significance and socio-economic impact globally of these parasites. In the present study, we sequenced the complete mt genomes of A. lumbricoides and A. suum (China isolate), which was 14,303 bp and 14,311 bp in size, respectively. The identity of the mt genomes was 98.1% between A. lumbricoides and A. suum (China isolate), and 98.5% between A. suum (China isolate) and A. suum (USA isolate). Both genomes are circular, and consist of 36 genes, including 12 genes for proteins, 2 genes for rRNA and 22 genes for tRNA, which are consistent with that of all other species of ascaridoid studied to date. All genes are transcribed in the same direction and have a nucleotide composition high in A and T (71.7% for A. lumbricoides and 71.8% for A. suum). The AT bias had a significant effect on both the codon usage pattern and amino acid composition of proteins. Phylogenetic analyses of A. lumbricoides and A. suum using concatenated amino acid sequences of 12 protein-coding genes, with three different computational algorithms (Bayesian analysis, maximum likelihood and maximum parsimony) all clustered in a clade with high statistical support, indicating that A. lumbricoides and A. suum was very closely related. These mt genome data and the results provide some additional genetic evidence that A. lumbricoides and A. suum may represent the same species. The mt genome data presented in this study are also useful novel markers for studying the molecular epidemiology and population genetics of Ascaris.     

A pseudo-likelihood method for estimating misclassification probabilities in competing-risks settings when true-event data are partially observed

Outcome misclassification occurs frequently in binary-outcome studies and can result in biased estimation of quantities such as the incidence, prevalence, cause-specific hazards, cumulative incidence functions, and so forth. A number of remedies have been proposed to address the potential misclassification of the outcomes in such data. The majority of these remedies lie in the estimation of misclassification probabilities, which are in turn used to adjust analyses for outcome misclassification. A number of authors advocate using a gold-standard procedure on a sample internal to the study to learn about the extent of the misclassification. With this type of internal validation, the problem of quantifying the misclassification also becomes a missing data problem as, by design, the true outcomes are only ascertained on a subset of the entire study sample. Although, the process of estimating misclassification probabilities appears simple conceptually, the estimation methods proposed so far have several methodological and practical shortcomings. Most methods rely on missing outcome data to be missing completely at random (MCAR), a rather stringent assumption which is unlikely to hold in practice. Some of the existing methods also tend to be computationally-intensive. To address these issues, we propose a computationally-efficient, easy-to-implement, pseudo-likelihood estimator of the misclassification probabilities under a missing at random (MAR) assumption, in studies with an available internal-validation sample. We present the estimator through the lens of studies with competing-risks outcomes, though the estimator extends beyond this setting. We describe the consistency and asymptotic distributional properties of the resulting estimator, and derive a closed-form estimator of its variance. The finite-sample performance of this estimator is evaluated via simulations. Using data from a real-world study with competing-risks outcomes, we illustrate how the proposed method can be used to estimate misclassification probabilities. We also show how the estimated misclassification probabilities can be used in an external study to adjust for possible misclassification bias when modeling cumulative incidence functions.     

Molecular Evidence for the Hybrid Origin of Bauhinia blakeana （Caesalpinioideae）

Bauhinia blakeana Dunn is the Hong Kong Special Administrative Region emblem and a popular horticultural species in many Asian countries. It was first described as a new species from Hong Kong almost a century ago. This plant is sterile and has long been considered a hybrid, possibly from two related species, B. purpurea and B. variegata. However, not much evidence based on molecular methods was available to support this hypothesis. In this study, sequences of internal transcribed spacer I （ITS1）, rbcL and atpB-rbcL intergenic spacer for five Bauhinia species and two varieties of one of the species were determined and compared. There were two types of ITS1 sequences in B. blakeana, one indistinguishable from that of B. purpurea and the other one identical to that of B. variegata. This confirmed that B. blakeana was a hybrid of these two species. Chloroplast atpB-rbcL intergenic spacer sequence of B. blakeana was identical to that of B. purpurea, indicating that B. purpurea was the female parent. The hybridization event seemed to occur only recently and was a rare incident. Its occurrence was likely facilitated by interspecific pollen competition. It appeared that human efforts played a crucial role in the preservation and ubiquity of B. blakeana.     

兔痒螨和水牛痒螨第二转录间隔区（ITS-2）基因序列分析

为了探讨水牛痒螨株和兔痒螨株的分类地位,采用 PCR 技术扩增了四川水牛痒螨株和四川兔痒螨株的第二内部转录间隔区（ITS-2）基因,并与 GenBank 中注册的 5 个国外痒螨株的同源基因进行了比较。序列分析发现：兔痒螨株和水牛痒螨株的序列长度分别为 277 bp 和 281 bp,两序列间存在多处转换、颠换和缺失。四川水牛痒螨株同四川兔痒螨株间及国外痒螨分离株间的 ITS-2 基因同源性较低（87.1%～88.0％）; 而四川兔痒螨株与国外痒螨分离株的同源性较高（95.5％～100.0％）。用痒螨 ITS-2 基因构建的 MP,NJ,ME 及 UPGM 树中,兔痒螨株和水牛痒螨株在不同的系统树中其位置比较固定,且两者相距均较远。根据痒螨 ITS-2 基因同源性分析和系统树构建结果以及其他已报道的相关证据,作者认为：兔痒螨株和水牛痒螨株可能为痒螨属 Psoroptes 中两个不同的种,兔痒螨分离株为马痒螨 P. equi ;而水牛痒螨株与来自兔、山羊、绵羊和黄牛等痒螨株亲缘关系较远,可能为痒螨属中的另一个独立有效种。     

广义青篱竹属(Arundinaria)核糖体DNA ITS序列及亲缘关系研究

利用PCR扩增产物直接测序的方法分析广义青篱竹属(Arundinaria)中有关争议类群的代表种或模式种(毛竹为外类群)等18种竹种的核糖体DNA内转录间隔区(Internal Transcribed Spacers,ITS)序列。通过最简约性分析产生的ITS系统发育树表明,供试竹种形成一个自然的单系类群,这说明广义青篱竹属中这些不同的类群归属青篱竹属是合理的。17种竹种可聚为2大分支：其中斑苦竹(A,oleosa)、仙居苦竹(A．hsienchuensis)、茶秆竹(A．amabilis)、长叶苦竹(A．chino)、苦竹(A．amara)、宜兴苦竹(A．yixingensis)、菲白竹(A．fortunei)、翠竹(A．pygmaea)为一个分支;而大明竹(A．graminea)、巴山木竹(A．fargesii)、冷箭竹(A．faberi)、凤竹(A．hupehense)、鼓节矢竹(Pseudosasa japonica cv．Tsutsumiana)、矢竹(Pseudosasa japonica)、短穗竹(Brachystachyum densiflorum)、肿节竹(A．oedogonata)、少穗竹(A．sulcata)组合在另一分支。ITS系统发育树还表明,大明竹与巴山木竹、鼓节矢竹与矢竹、少穗竹与短穗竹和肿节竹关系极为密切,均得到较高的Bootstrap(分别为99％、100％和87％)的支持;茶秆竹与仙居苦竹关系非常密切,茶秆竹可归隶到青篱竹属中;翠竹和菲白竹关系密切,且与苦竹类竹种分为两个分支。     

DIFFERENCES IN SEQUENCES OF RIBOSOMAL DNA SECOND INTERNAL TRANSCRIBED SPACER AMONG THREE MEMBERS OF ANOPHELES HYRCANUS COMPLEX FROM THE REPUBLIC OF KOREA

Abstract  Differences in sequences of ribosomal DNA second internal transcribed spacer (ITS) among Anopheles sinensis, An. lesteri and An. yatsushiroensis from Korea were compared. The PCR amplified rDNA-ITS2 fragments were sequenced directly. Three samples of each species were individually determined.
Lengths of the ITS2 regions were 468bp in An sinensis , 451bp in An lesteri and 453bp in An yatsushiroenesis and GC contents were 44.87 % 46.2 % and 45.7 % respectively. Variations of the sequences ranged from 12.16 % to 30.7 % among the three species. The differences of the rDNA-ITS2 sequences would be useful for molecular identification of the three members of Anopheles hycanus complex from Korea.     

BEVSIM: Battery electric vehicle sustainability impact assessment model

To achieve climate neutrality ambitions, greenhouse gas emissions from the transport sector need to be reduced by at least 90% by 2050. To support industry and policy makers on mitigating actions on climate goals it is important to holistically compare and reduce life cycle environmental impacts of road passenger vehicles. A web-based sustainability assessment tool named battery electric vehicle sustainability impact assessment model, BEVSIM, is developed to assess the environmental, circularity, and economic performance of the materials, sub-systems, parts, and individual components of battery electric vehicles and internal combustion engine vehicles. This tool allows to measure and compare impacts resulting from recycling technologies, end-of-life scenarios, and future scenarios resulting from changes in grid mixes. This paper explains the purpose of the tool, its functionality and design as well as the underlying assumptions.     

FTIR spectro-imaging of collagens for characterization and grading of gliomas

Collagens are a family of at least 30 protein types organized as networks. They constitute the main support material of cells under the form of extracellular matrix as well as for membranes in vessels, organs, and tissue compartments. Collagen network abnormalities are at the origin of many diseases, including myopathies and fibroses. The characterization of collagens remains an analytical challenge due to the insolubility of these molecules and the difficulty encountered in isolating given types without altering their structure or in maintaining network organization, which is critical to diagnosing related pathologies. We have proposed using a vibrational spectroscopy based imaging technique, namely Fourier-transform infrared (FTIR) imaging, for a spatially-resolved analysis of secondary structure of different collagen types in complex samples, and more specifically for characterizing gliomas. With newly developed spectral data treatments and chemometrics using secondary structure parameters of collagen proteins, FTIR imaging is now able to distinguish between several types. On this basis, gliomas have been investigated as specific collagen-rich tissues developing in a non-collagenous environment, providing high specificity to this FTIR imaging utilization. Here, we review the recent advances in this imaging approach for understanding glioma development, with FTIR imaging now being proposed as a molecular histopathology tool for clinicians.     

赤拟谷盗HSP70基因克隆和竞争定量PCR检测

为研究赤拟谷盗Tribolium castaneum受到热胁迫后高度保守的热激蛋白70（heat shock protein 70,HSP70）基因的表达变化,本研究扩增了681 bp的赤拟谷盗hsp70片段,编码227个氨基酸残基,GenBank登录号为HM345948。同源性分析表明：赤拟谷盗hsp70核苷酸序列与马铃薯甲虫Leptinotarsa decemlineata的hsp70（GenBank登录号：AF322911.1）同源性最高,为97%;其推测的蛋白序列与马铃薯甲虫、甘蓝夜蛾Mamestra brassicae、黑腹果蝇Drosophila melanogaster和美洲斑潜蝇Liriomyza sativae的HSP70蛋白均有94%以上的同源性。利用RT-PCR技术得到与赤拟谷盗hsp70进行竞争定量的内部竞争物, 以等量的目标cDNA和一系列稀释的竞争模板进行竞争PCR扩增,构建了hsp70的竞争定量PCR检测体系, 该体系标准曲线的线性方程为Y=1.032X-1.618 (r²=0.975)。这些结果为赤拟谷盗的hsp70定量检测提供了方便,并为热控技术防治害虫提供了基础资料。