An open‐source code for Mie extinction extended multiplicative signal correction for infrared microscopy spectra of cells and tissues

Infrared spectroscopy of single cells and tissue is affected by Mie scattering. During recent years, several methods have been proposed for retrieving pure absorbance spectra from such measurements, while currently no user‐friendly version of the state‐of‐the‐art algorithm is available. In this work, an open‐source code for correcting highly scatter‐distorted absorbance spectra of cells and tissues is presented, as well as several improvements of the latest version of the Mie correction algorithm based on extended multiplicative signal correction (EMSC) published by Konevskikh et al. In order to test the stability of the code, a set of apparent absorbance spectra was simulated. To this purpose, pure absorbance spectra based on a Matrigel spectrum are simulated. Scattering contributions where obtained by mimicking the scattering features observed in a set of experimentally obtained spectra . It can be concluded that the algorithm is not depending strongly on the reference spectrum used for initializing the algorithm and retrieves well the underlying pure absorbance spectrum. The calculation time of the algorithm is considerably improved with respect to the resonant Mie scattering EMSC algorithm used by the community today.      

Comparing the preferences of three herbivore species with resistance traits of 15 perennial dicots: the effects of phylogenetic constraints

Differences in palatability between 15 perennial dicotyledonous herbaceous plant species were investigated in a multiple choice test, involving three generalist herbivores. Palatability was compared with two categories of plant traits: defence characteristics and growth properties. On theoretical grounds, we expected a positive relationship between growth rate and palatability, and a negative relationship between palatability and defence traits. The possible effect of phylogeny on the outcome of the comparisons was investigated by analysing the data using phylogenetically independent contrasts. The three herbivores showed remarkably similar preferences, which indicates that the results of the choice experiment are a good representation of leaf palatability. The significant negative correlations found in a direct comparison between herbivore preference and relative growth rate, and between herbivore preference and lignin and dry matter content, did not hold after phylogenetic correction. On the other hand, one relationship emerged only when comparing phylogenetically independent contrasts: contrary to expectation, a negative relation was noted between juvenile growth rate and plant palatability. A possible explanation for the contradictory nature of this result is the uniformly ready availability of resources in our experiment.     

CRISPR/Cas9介导的疾病模型构建与基因修复研究进展

近年来,可编程核酸酶介导的基因编辑技术迅猛发展。CRISPR/Cas9技术源于细菌和古生菌的适应性免疫系统,主要由Cas9内切酶和向导RNA（guide RNA,gRNA）组成。Cas9内切酶在gRNA的指导下造成DNA的双链断裂,从而使研究人员能够精准高效地操纵特定基因组位点。同时,该系统可以揭示基因在疾病进程中所扮演的未知角色,在临床治疗中有应用潜能。现总结了CRISPR/Cas9技术在疾病模型构建与基因修复领域应用的研究进展。     

一种基于高密度遗传标记的亲子鉴定方法及其应用

系谱是人类遗传及动植物育种研究与实践的重要信息来源之一。系谱记录错误是育种生产中普遍存在的一种记录错误,影响基因定位、遗传值及表型值预测等相关研究结果的可靠性。现有的方法软件可以利用遗传标记信息对疑似亲子进行亲子鉴定,但这些软件方法操作复杂,限制标记数量,如Cervus。针对当前高密度SNP标记在人类及动植物研究中广泛应用的现状,文章提出了一种基于全基因组高密度SNP数据的亲子鉴定新方法,命名为EasyPC。对EasyPC及Cervus的运行效率进行了对比,并用中国荷斯坦牛(n=2180)和杜洛克猪(n=191)的全基因组SNP芯片数据对EasyPC进行了验证。结果表明：EasyPC运行效率高于Cervus,牛和猪群体系谱错误率分别为20%和6%,与相关研究报道相符。通过使用全基因组SNP标记对群体孟德尔错误率的经验分布进行分析,该方法不仅可以简单、快速、准确地判别系谱的正确性,而且还可以对错误系谱进行校正。EasyPC为解决全基因组研究中基因型及系谱数据前处理过程中的系谱校正问题提供了一种新的途径。     

A new revision of the sequence of plasmid pBR322

A revised sequence in the region immediately upstream from the rop gene of pBR322 is reported. Two base pairs in the accepted sequence do not exist in the plasmid DNA. Specifically, a TA base pair is missing at sequence coordinate 1893 [Sutcliffe, Cold Spring Harbor Symp. Quant. Biol. 43 (1979) 77–90] and an AT base pair is missing at position 1915, giving a total size for pBR322 of 4361 bp. These changes are in a potential translation initiation sequence and probably reflect errors in the original sequence rather than recent evolution of the plasmid.     

黄芪复合体（豆科）核型研究补充材料

本文首次报道了民和黄芪的染色体数目及核型。发现该种与黄芪复合体其它类群的染色体数目相同,但核型有别,其核型公式为２ｎ＝１６＝８ｍ（２ＳＡＴ）＋８ｓｍ。这种核型变异与它的形态变异一致。在黄芪复合体内,每一类群的染色体至少具１对随体,且附着在最后１对染色体的短臂上（除蒙古黄芪具２对随体外）,而Ｔｏｈ（１９７１）报道采自Ｋｙｕｎｇｉ和Ｍｔ．Ｈａｒｌａ膜荚黄芪和高山膜荚黄芪（新拟）的染色体不具随体,可能观察有误。     

植物叶片解剖结构的量化及其在C4植物高粱中的应用

测量切片内所有细胞或细胞器的总周长,并乘以切片厚度和校正因子是一种量化植物叶片解剖结构的常用方法。前人在使用该方法时因忽视了细胞大小、切片厚度等影响估算精确度的因素,从而导致计数样本偏少并产生较大误差。通过分析该方法误差产生的原因及其与精确度的关系,明确了该方法在实际应用中不同精确度所要求对应的切片数量。在此基础上,将该方法用于C4植物高粱(Sorghum bicolor)叶片结构的量化,提出叶肉细胞与维管束鞘细胞接触面积(CABM)等参数,发展并完善了植物叶片解剖结构的量化方法。     

Efficient gene correction of an aberrant splice site in β‐thalassaemia iPSCs by CRISPR/Cas9 and single‐strand oligodeoxynucleotides

β‐thalassaemia is a prevalent hereditary haematological disease caused by mutations in the human haemoglobin β (HBB) gene. Among them, the HBB IVS2‐654 (C > T) mutation, which is in the intron, creates an aberrant splicing site. Bone marrow transplantation for curing β‐thalassaemia is limited due to the lack of matched donors. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR‐associated protein 9 (Cas9), as a widely used tool for gene editing, is able to target specific sequence and create double‐strand break (DSB), which can be combined with the single‐stranded oligodeoxynucleotide (ssODN) to correct mutations. In this study, according to two different strategies, the HBB IVS2‐654 mutation was seamlessly corrected in iPSCs by CRISPR/Cas9 system and ssODN. To reduce the occurrence of secondary cleavage, a more efficient strategy was adopted. The corrected iPSCs kept pluripotency and genome stability. Moreover, they could differentiate normally. Through CRISPR/Cas9 system and ssODN, our study provides improved strategies for gene correction of β‐Thalassaemia, and the expression of the HBB gene can be restored, which can be used for gene therapy in the future.     

生态系统服务价值的生态区位修正方法——以北京市为例

生态系统服务价值评估是当前生态经济学和环境经济学的研究热点和焦点,生态区位是影响生态系统服务价值的重要因子。以北京市为例,对北京市进行生态区位的划分,遵循资源稀缺性原理,将不同生态区位赋予不同的生态区位系数,并以北京市1980年、1995年和2000年土地利用图为例,以生态区位系数对北京市用地类型的生态服务价值进行修正,以体现不同生态区位单位面积生态系统服务价值的不同。研究得到了北京市3期土地利用单位面积生态系统服务价值分布图。分析发现:北京市的生态系统服务价值组成中,水田、有林地、灌木林和水体的生态系统服务价值占的比重较高;各生态区位生态系统服务总价值从城区到近郊平原区到近郊半山区到远郊山区依次增加;从1980年到1995年,北京市的生态系统服务价值减少了1.21×107元,而且各生态区位的生态系统服务价值也大都减少;从1995年到2000年,北京市的生态系统服务价值有所提高,但与1980年相比还是减少了3.07×106元。