刺果甘草全基因组Survey及叶绿体基因组特征分析＊

目的 基于基因组Survey分析对刺果甘草Glycyrrhiza pallidiflora Maxim.基因组大小和杂合率进行估计，并通过叶绿体基因组序列特征对其在甘草属Glycyrrhiza L.中的系统发育位置进行研究。方法 使用二代测序技术对刺果甘草进行测序，采用K-mer方法对测序reads进行分析，估算刺果甘草基因组大小和杂合率，使用生物信息学方法进行叶绿体基因组组装、注释和系统发育分析。结果 Survey分析结果显示其基因组大小约为577.82 Mb，杂合度约为0.31%，重复序列比例约为53.72%。叶绿体基因组长度为127，267 bp，不具有典型的四分体结构，总GC含量为34.32%，包含110个基因，其中76个蛋白质编码基因，30个tRNA基因和4个rRNA基因。系统发育分析表明，刺果甘草与圆果甘草G. squamulosa Franch.亲缘较接近。结论 刺果甘草存在低杂合和重复序列较多的特点，为了更好地对全基因组进行序列拼接和组装，可尝试采用三代测序结合二代测序的分析策略进行基因组组装；刺果甘草叶绿体全基因组比对和系统发育分析，为后续开展甘草属遗传多样性研究和分子鉴定标记筛选提供了重要依据。     

γ射线诱发人正常肝细胞基因组不稳定性研究

目的探讨电离辐射诱发的基因组不稳定性效应。方法采用^60Co γ射线照射人正常肝细胞，检测克隆形成率和微核发生率，利用单细胞凝胶电泳（SCGE）技术检测DNA损伤情况。照射2、4、6、8和10Gy后传代培养，在40代后各剂量组再次统一照射2Gy，进行辐射损伤的检测。结果首次照射后，克隆形成率随受照剂量的增大而降低。存活细胞经二次照射后，SCGE结果和微核发生率结果表明，首次照射剂量与子代二次照射后的损伤程度存在剂量效应关系。结论γ射线不仅在肝细胞中产生直接的生物效应，而且还可以诱发产生可遗传的基因组不稳定性，使子代细胞中的突变频率增加，表现出滞后的遗传改变。二次事件的放大作用是研究基因组不稳定性的一种较好方法。     

Methodological Studies on Genomic DNA Extraction and Purification from Plant Drug Materials

本文探讨了菊科９种植物和地胆草的４种对口商品药材基因组ＤＮＡ提取与纯化的原理、方法通过对３种常用植物基因组ＤＮＡ提取方法（ＣｓＣｌ梯度超速离心法、ＣＴＡＢＣｓＣｌ梯度超速离心法和ＣＴＡＢ微量提取法）的条件摸索在ＤＮＡ产率、纯度以及提取纯化过程中影响ＰＣＲ扩增因子方面进行比较，认为ＣＴＡＢ微量提取法是植物类药材基因组ＤＮＡ一种比较省时、有效、经济的提取方法     

Genomic imprinting and its relevance to genetic diseases

Summary Genomic imprinting is a biological phenomenon determined by an evolutionally acquired, underlying system that may control harmonious development and growth in mammals. It is also relevant to some genetic disorders in man. In this article, lines of biological evidence of imprinting, characteristics of the mouse and human imprinted genes, and findings and mechanisms on the occurrence of several human imprinting disorders are reviewed.     

A modified approach to identification of the sickle cell anemia mutation by means of allele-specific polymerase chain reaction.

The allele-specific PCR approach has been modified by introducing a second mismatch at the 3'-penultimate link of the primer and used to identify the sickle cell anemia mutation (A-->T transversion in the sixth codon of the human beta-globin gene causing Glu-->Val substitution in the protein), thus obviating the problem of an interpretationally ambiguous 3'-terminal mismatch including T residue.     

DNA聚合酶β可能参与了更广泛的细胞反应并引起遗传不稳定

近年来有关真核细胞中ＤＮＡ聚合酶的研究迅速增多。 1985年前 ,确认的ＤＮＡ聚合酶只有 3种 :聚合酶α、β以及线粒体聚合酶γ。时至今日已至少发现了 14种ＤＮＡ聚合酶 ,包括聚合酶α、β、γ、δ、ε、ζ、η、θ、ι、κ、λ、μ、ＲＥＶ1及ＭＵＳ30 8,在真核细胞ＤＮＡ的复制、修复、跨损伤合成、ＤＮＡ重组以及细胞周期调控等多种重要的生物代谢过程中发挥重要作用[1] 。在一定程度上 ,细胞内的各种聚合酶均有其独特的功能和作用领域。如具有引物酶活性的聚合酶α的作用是启动ＤＮＡ复制并合成ＲＮＡ -ＤＮＡ引物 ;聚合酶δ和ε是主要…     

Worldwide genomic diversity of the human papillomaviruses-53, 56, and 66, a group of high-risk HPVs unrelated to HPV-16 and HPV-18

Among more than 200 human papillomavirus (HPV) types presumed to exist, 18 "high-risk" HPV types are frequently found in anogenital cancer. The best studied types are HPV-16 and 18, which are only distantly related to one another and form two separate phylogenetic branches, each including six closely related types. HPV-30, 53, 56, and 66 form a third phylogenetic branch unrelated to HPV-16 and 18. Worldwide comparison of HPV-16 and 18 isolates revealed a distribution of variant genomes that correlated with the geographic origin and the ethnicity of the infected cohort and led to the concept of unique African, European, Asian, and Native American HPV-16 and 18 variants. Here, we address the question whether similar phylogenies are found for HPV-53, 56, and 66 by determining the sequence of the long control regions (LCR) of these HPVs in samples from Europe, Asia, and Africa, and from immigrant societies in North and South America. Phylogenetic trees calculated from point mutations and a few insertions/deletions affecting 2-4.2% of the nucleotide sequences were distinct for each of the three HPVs and divergent from HPV-16 and 18. In contrast to the "star-phylogenies" formed by HPV-16 and 18 variants, 44 HPV-53 isolates represented nine variants, which formed two deep dichotomic branches reminiscent of the beginning split into two new taxa, as recently observed for subtypes of HPV-44 and 68. A total of 66 HPV-56 isolates represented 17 variants, which formed three branches preferentially containing European, Asian, and African variants. Variants of a fourth branch, deeply separated from the other three, were characterized by a 25 bp insertion and created a dichotomy rather than star-like phylogeny. As it contained isolates from cohorts in all continents, it may have evolved before the spread of humans into all continents. 18 of 31 HPV-66 isolates represented the prototype clone, which was found in all parts of the world, while the remaining 13 clones formed 11 branches without any geographic association. Our findings confirm the notion of a quantitatively limited genomic diversity of each HPV type with some correlation to the geographic origin of the sample. In addition, we observed in some variants of these three HPV types mutations that affect the amino acid sequence of the E6 oncoproteins and the L1 capsid protein, supporting the possibility of immunogenic and oncogenic diversity between variants of any HPV type.     

Sources of behavioral deviation modeled by early color preferences in quail. III. Developmental stability and normative canalization

Successful artificial selection of quail (C. coturnix japonica) for divergent early approach preferences for, and imprintabilities to, the wavelength characteristics of otherwise identical visual stimuli decreased the trait's developmental stability. The developmental error that resulted from selecting for extreme initial preferences was associated with enhanced imprintabilities. Conversely, the developmental error that resulted from selecting for extreme imprintabilities was associated with enhanced expression of directional gene effects in extreme initial preferences. The data are attributed to selectively relaxed normative canalization of trait development, and to related enhanced expression of genetic, environmental, and stochastic influences in trait deviations.     

Differentiating molecular etiologies of Angelman syndrome through facial phenotyping using deep learning

Angelman syndrome (AS) is caused by several genetic mechanisms that impair the expression of maternally‐inherited UBE3A through deletions, paternal uniparental disomy (UPD), UBE3A pathogenic variants, or imprinting defects. Current methods of differentiating the etiology require molecular testing, which is sometimes difficult to obtain. Recently, computer‐based facial analysis systems have been used to assist in identifying genetic conditions based on facial phenotypes. We sought to understand if the facial‐recognition system DeepGestalt could find differences in phenotype between molecular subtypes of AS. Images and molecular data on 261 individuals with AS ranging from 10 months through 32 years were analyzed by DeepGestalt in a cross‐validation model with receiver operating characteristic (ROC) curves generated. The area under the curve (AUC) of the ROC for each molecular subtype was compared and ranked from least to greatest differentiable phenotype. We determined that DeepGestalt demonstrated a high degree of discrimination between the deletion subtype and UPD or imprinting defects, and a lower degree of discrimination with the UBE3A pathogenic variants subtype. Our findings suggest that DeepGestalt can recognize subclinical differences in phenotype based on etiology and may provide decision support for testing.     

Expression enhancement of the Tn5 neomycin-resistance gene by removal of upstream ATG sequences and its use for probing heterologous upstream activating sequences in yeast

We have constructed a series of promoter or upstream activating sequence (UAS)-probe plasmids carrying the Tn5-derived neomycin resistance gene whose seven additional ATG codons in the 5-untranslated region were completely or partially removed. When the deleted version of the neo sequence retaining only one additional ATG (NeoD) was expressed under the control of a TDH3 promoter whose UAS was deleted, the transformed cells were unable to grow at a low concentration of the antibiotic G418. In contrast with this, yeast cells expressing the NeoC sequence and having no additional ATG exhibited a high level of G418-resistance. Moreover, the UAS-probe system using NeoD has been successfully applied for the identification of several E. coli DNA sequences that clearly function as UASs in yeast cells. Two of these prokaryotic sequences with UAS activity were identified as a part of the coding region of the tgt and the hydG gene, respectively.