Chromosomal microarray analysis of consecutive individuals with autism spectrum disorders or learning disability presenting for genetic services

Chromosomal microarray analysis is now commonly used in clinical practice to identify copy number variants (CNVs) in the human genome. We report our experience with the use of the 105 K and 180 K oligonucleotide microarrays in 215 consecutive patients referred with either autism or autism spectrum disorders (ASD) or developmental delay/learning disability for genetic services at the University of Kansas Medical Center during the past 4 years (2009–2012). Of the 215 patients [140 males and 75 females (male/female ratio = 1.87); 65 with ASD and 150 with learning disability], abnormal microarray results were seen in 45 individuals (21%) with a total of 49 CNVs. Of these findings, 32 represented a known diagnostic CNV contributing to the clinical presentation and 17 represented non-diagnostic CNVs (variants of unknown significance). Thirteen patients with ASD had a total of 14 CNVs, 6 CNVs recognized as diagnostic and 8 as non-diagnostic. The most common chromosome involved in the ASD group was chromosome 15. For those with a learning disability, 32 patients had a total of 35 CNVs. Twenty-six of the 35 CNVs were classified as a known diagnostic CNV, usually a deletion (n = 20). Nine CNVs were classified as an unknown non-diagnostic CNV, usually a duplication (n = 8). For the learning disability subgroup, chromosomes 2 and 22 were most involved. Thirteen out of 65 patients (20%) with ASD had a CNV compared with 32 out of 150 patients (21%) with a learning disability. The frequency of chromosomal microarray abnormalities compared by subject group or gender was not statistically different. A higher percentage of individuals with a learning disability had clinical findings of seizures, dysmorphic features and microcephaly, but not statistically significant. While both groups contained more males than females, a significantly higher percentage of males were present in the ASD group.     

孤独症谱系障碍儿童听觉脑干反应特征分析

摘要 目的：探讨孤独症谱系障碍(autism spectrum disorder,ASD)儿童听觉脑干反应(auditory brainstem response,ABR)各波潜伏期和波间期特征与ASD行为表型间的关联。方法：对2019年7月-2020年12月来我科就诊的26例明确诊断的2~6岁ASD儿童的患儿进行声导抗,听性脑干反应,畸变产物耳声发射及多频稳态听觉诱发电位测试,以38例正常儿童为对照组,进行同样的测试,并对其测试结果进行统计分析。分析ASD儿童左右耳各波潜伏期,波间期特征及与ASD临床表型的关联。结果：ASD儿童左右耳Ⅰ,Ⅲ,Ⅴ波潜伏期分别为(1.42±0.09)ms,(3.67±0.09)ms,(5.65±0.13)ms;(1.45±0.11)ms,(3.69±0.08)ms,(5.62±0.15)ms。ASD组的右耳I,III波的潜伏期均值大于正常组 (P 值均＜0.05);ASD儿童两组间左耳III-V,右耳III-V,右耳I-V的波间期分别是(1.97±0.07)ms,(1.93±0.10)ms,(4.15±0.14)ms;ASD组的左耳III-V,右耳III-V,右耳I-V波间期均小于正常组(P 值均＜0.05);ASD组中小于等于3岁组与大于3岁组间ABR波间期差异不具有统计学意义。关联性分析发现,ASD儿童语言能力与右耳III波潜伏期,右耳最小阈值V波潜伏期负相关;社会行为能力与右耳I-III波间期负相关;社会生活能力与左耳最小阈值V波潜伏期负相关;而ABC评分与ASD儿童右耳III波潜伏期,左耳I-III波间期,右耳I-III波间期正相关。结论：ASD儿童存在异常的听觉脑干反应特征,且异常程度与 ASD 儿童语言,社会行为能力,社会生活能力的严重程度存在明显关联。     

The joint allele frequency spectrum of multiple populations: a coalescent theory approach

The allele frequency spectrum is a series of statistics that describe genetic polymorphism, and is commonly used for inferring population genetic parameters and detecting natural selection. Population genetic theory on the allele frequency spectrum for a single population has been well studied using both coalescent theory and diffusion equations. Recently, the theory was extended to the joint allele frequency spectrum (JAFS) for three populations using diffusion equations and was shown to be very useful in inferring human demographic history. In this paper, I show that the JAFS can be analytically derived with coalescent theory for a basic model of two isolated populations and then extended to multiple populations and various complex scenarios, such as those involving population growth and bottleneck, migration, and positive selection. Simulation study is used to demonstrate the accuracy and applicability of the theoretical model. The coalescent theory-based approach for the JAFS can characterize the demographic history with comprehensive statistical models as the diffusion approach does, and in addition gains several novel advantages: the computational complexity of calculating the JAFS with coalescent theory is reduced, and thus it is feasible to analytically obtain the JAFS for multiple populations; the hitchhiking effect can be efficiently modeled in coalescent theory, enabling the development of methodologies for detecting selection via multi-population polymorphism data. As an alternative to the diffusion approximation approach, the coalescent theory for the JAFS also provides a foundation for population genetic inference with the advent of large-scale genomic polymorphism data.     

SIMSI-Transfer: Software-Assisted Reduction of Missing Values in Phosphoproteomic and Proteomic Isobaric Labeling Data Using Tandem Mass Spectrum Clustering

Isobaric stable isotope labeling techniques such as tandem mass tags (TMTs) have become popular in proteomics because they enable the relative quantification of proteins with high precision from up to 18 samples in a single experiment. While missing values in peptide quantification are rare in a single TMT experiment, they rapidly increase when combining multiple TMT experiments. As the field moves toward analyzing ever higher numbers of samples, tools that reduce missing values also become more important for analyzing TMT datasets. To this end, we developed SIMSI-Transfer (Similarity-based Isobaric Mass Spectra 2 [MS2] Identification Transfer), a software tool that extends our previously developed software MaRaCluster (© Matthew The) by clustering similar tandem MS2 from multiple TMT experiments. SIMSI-Transfer is based on the assumption that similarity-clustered MS2 spectra represent the same peptide. Therefore, peptide identifications made by database searching in one TMT batch can be transferred to another TMT batch in which the same peptide was fragmented but not identified. To assess the validity of this approach, we tested SIMSI-Transfer on masked search engine identification results and recovered >80% of the masked identifications while controlling errors in the transfer procedure to below 1% false discovery rate. Applying SIMSI-Transfer to six published full proteome and phosphoproteome datasets from the Clinical Proteomic Tumor Analysis Consortium led to an increase of 26 to 45% of identified MS2 spectra with TMT quantifications. This significantly decreased the number of missing values across batches and, in turn, increased the number of peptides and proteins identified in all TMT batches by 43 to 56% and 13 to 16%, respectively.     

疮痂链霉菌拮抗菌株BU396的分离鉴定与抗菌性质分析

【背景】随着马铃薯种植面积的扩大,疮痂病的发生也日益严重,且化学防治存在环境污染等诸多弊端,因此利用安全和高效的生物防治手段对该病害进行防治成为研究热点。【目的】对疮痂链霉菌(Streptomyces scabies)拮抗菌株进行分离、鉴定和功能基因分析,对抗菌物进行分离及抗菌特性的研究。【方法】从马铃薯疮痂病的病害土壤中分离、筛选并鉴定得到拮抗菌株,采用PCR法对菌株进行抗菌物合成基因检测。通过硫酸铵沉淀法分离得到抗菌物,进行抗菌谱和稳定性检测,并通过盆栽试验进一步验证该菌株的生防效果。【结果】通过抗菌试验筛选得到拮抗细菌BU396,根据形态学、生理生化性质和分子生物学鉴定结果,确定其为贝莱斯芽孢杆菌(Bacillus velezensis)。功能基因分析表明BU396中含有表面活性素等4种抗菌物的合成相关基因。采用硫酸铵沉淀法对其培养液上清进行分离,当硫酸铵的饱和度为75%时,抗菌物在沉淀中析出。抗菌谱试验结果显示该抗菌物对多种动植物病原菌均具有抗菌效果。稳定性试验表明该抗菌物耐热,不易被酶解,对多种金属离子不敏感,具有宽泛的pH活性范围,盆栽试验结果显示菌株BU396处理能够明显降低马铃薯疮痂病的发病率。【结论】分离并鉴定了一株对疮痂链霉菌具有显著拮抗作用的贝莱斯芽孢杆菌BU396。该菌株含有多种抗菌物合成的相关基因,其抗菌物具有广谱的抗菌活性和良好的稳定性,对马铃薯疮痂病的生防效果显著。本研究为马铃薯疮痂病的生物防治及后续抗菌物质的深入研究奠定了基础。     

微波法提取鼠尾藻多糖的工艺研究

研究采用了微波法提取鼠尾藻多糖,考查了微波辐照时间、微波功率、料液比、超声预处理时间四个因素的影响,并采用正交实验法确定微波提取的最佳工艺。结果表明微波法提取多糖产率为6.5%,其优化工艺条件为:微波辐照时间8 min,微波功率540 W,料液比1∶30,超声时间3 min。经红外光谱得知鼠尾藻多糖的主要组成单糖为吡喃糖。微波法提取鼠尾藻多糖可行,工艺简单,产率令人满意。     

氮添加对山西太岳山天然油松林主要植物叶片性状的影响

为探讨植物性状对大气氮沉降的响应与适应机制, 该文以中国特有的、在北方温性针叶林中广泛分布的天然油松(Pinus tabuliformis)林为研究对象, 在2009-2013年开展了氮添加对植物叶片性状影响的野外控制试验, 4个氮添加浓度分别为0 kg·hm^-2·a^-1 (CK)、50 kg·hm^-2·a^-1 (低氮)、100 kg·hm^-2·a^-1 (中氮)和150 kg·hm^-2·a^-1 (高氮)。试验过程中分别测定了油松、蒙古栎(Quercus mongolica)、茶条槭(Acer ginnala)、毛榛(Corylus mandshurica)、沙梾(Cornus bretschneideri)、绣线菊(Spiraea salicifolia)、金银忍冬(Lonicera maackii)、羊须草(Carex callitrichos)、龙常草(Diarrhena mandshurica)、大火草(Anemone tomentosa)和玉竹(Polygonatum odoratum)等11种主要植物的9种叶片性状, 包括叶厚度(LT)、比叶面积(SLA)、干物质含量(LDMC)、叶氮含量(LNC)、叶磷含量(LPC)等。结果表明: 1)在氮添加影响下, 玉竹等个别物种的LT和SLA、绣线菊等部分物种的叶面积(LA)和LDMC差异显著, 上述所有物种的LNC与大多数物种的叶绿素含量(CC)、LPC显著增加, 油松等9种植物叶片N:P发生显著变化, 不同年龄、不同类型的植物叶片对氮添加的响应不同。2)叶性状之间普遍存在显著相关性, 如SLA与LNC和LPC极显著正相关, LT与LNC和LPC极显著负相关, 且相关性随氮添加强度变化。3) 11种植物的叶片特征空间分布规律与叶经济谱的描述一致, 氮添加使植物在特征空间中的位置向叶片薄、生长快、叶寿命短的“快速投资-收益型”一端发生移动; 在垂直方向上, 阔叶乔木、灌木及草本的位置与针叶乔木的移动方向相反。当环境改变时, 植物会改变生存策略, 调整资源分配, 从而保证物种间相对位置和群落整体结构的稳定性。叶经济谱的形成不依赖于环境的变化, 而是植物一种固有的属性。     

Ultraviolet radiation,ozone depletion,and marine photosynthesis

Concerns about stratospheric ozone depletion have stimulated interest in the effects of UVB radiation (280–320 nm) on marine phytoplankton. Research has shown that phytoplankton photosynthesis can be severely inhibited by surface irradiance and that much of the effect is due to UV radiation. Quantitative generalization of these results requires a biological weighting function (BWF) to quantify UV exposure appropriately. Different methods have been employed to infer the general shape of the BWF for photoinhibition in natural phytoplankton, and recently, detailed BWFs have been determined for phytoplankton cultures and natural samples. Results show that although UVB photons are more damaging than UVA (320–400 nm), the greater fluxes of UVA in the ocean cause more UV inhibition. Models can be used to analyze the sensitivity of water column productivity to UVB and ozone depletion. Assumptions about linearity and time-dependence strongly influence the extrapolation of results. Laboratory measurements suggest that UV inhibition can reach a steady-state consistent with a balance between damage and recovery processes, leading to a non-linear relationship between weighted fluence rate and inhibition. More testing for natural phytoplankton is required, however. The relationship between photoinhibition of photosynthesis and decreases in growth rate is poorly understood, so long-term effects of ozone depletion are hard to predict. However, the wide variety of sensitivities between species suggests that some changes in species composition are likely. Predicted effects of ozone depletion on marine photosynthesis cannot be equated to changes in carbon flux between the atmosphere and ocean. Nonetheless, properly designed studies on the effects of UVB can help identify which physiological and ecological processes are most likely to dominate the responses of marine ecosystems to ozone depletion.Abbreviations BWF biological weighting function - BWF/P-I photosynthesis versus photosynthetically available irradiance as influenced by biologically-weighted UV - Chl chlorophyll a - DOM dissolved organic matter - E _PAR irradiance in energy units (PAR) - E _s saturation parameter for PAR in the BWF/P-I model - E _inh ^* biologically-weighted dimensionless fluence rate for photoinhibition of photosynthesis by UV and PAR - biological weighting coefficient - % MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGafqyTduMbae% baaaa!37AC!\[\bar \varepsilon \]_PAR biological weighting coefficient for damage to photosynthesis by E _PAR - k() diffuse attenuation coefficient for wavelength - MAAs mycosporine-like amino acids - PAR photosynthetically available radiation - P ^B rate of photosynthesis normalized to Chl - P _s ^B maximum attainable rate of photosynthesis in the absence of photoinhibition - UVA ultraviolet A (320–400 nm) - UVB ultraviolet B (280–320 nm)     

一个可能与T细胞发育相关的新的C2H2型锌指蛋白基因的克隆(英)

一些在组织和细胞分化中起重要作用的蛋白质包含锌指结构域.为了克隆分离和研究与造血细胞分化和发育成熟相关的蛋白基因,利用编码C2H2型锌指蛋白结构域中部分保守氨基酸序列设计简并引物,以骨髓cDNA为模板,进行PCR扩增,得到若干新的锌指蛋白基因EST.用其中一条为探针筛选人骨髓cDNA文库,获得了一个新的锌指蛋白基因全长cDNA,GenBank收录号为AF246126,长3 888 bp,包括一个完整阅读框,编码686个氨基酸,包括17个典型的和2个非典型的C2H2模体,命名为HZF2. RNA印迹、人多组织mRNA斑点杂交分析结果显示, 其在T淋巴细胞发育和定居的器官组织胸腺、淋巴结中有较高表达,在脾脏、胎肝有中度表达,在B淋巴细胞发育的骨髓中表达很低,在外周血几个淋巴细胞系中仅有极微量的表达,提示HZF2可能对于T淋巴细胞发育和增殖有重要功能.该基因也在脑组织的若干部位、胎盘及肾上腺有较高表达,在多种其他组织细胞有微量表达,说明其可能对维持这些组织细胞的生理功能也起一定作用.将编码HZF2读框的DNA顺序克隆到pEGFP-N1载体中,转染3T3细胞,证明表达的HZF2-GFP融合蛋白定位于细胞核,这与根据HZF2蛋白结构推测其可能作为DNA结合蛋白行使调节基因转录的功能是一致的.