Identification of genomic groups in the genus Stenotrophomonas using gyrB RFLP analysis

Stenotrophomonas maltophilia isolates have been recovered from various clinical samples, including the respiratory tract of cystic fibrosis (CF) patients, but this organism is also widespread in nature. Previously it has been shown that there is a considerable genomic diversity within S. maltophilia. The aims of our study were to determine the taxonomic resolution of restriction fragment length polymorphism (RFLP) analysis of the polymerase chain reaction-amplified gyrB gene for the genus Stenotrophomonas. Subsequently, we wanted to use this technique to screen a set of S. maltophilia isolates (with emphasis on a specific subset, isolates recovered from CF patients), to assess the genomic diversity within this group. In this study we investigated 191 Stenotrophomonas sp. isolates (including 40 isolates recovered from CF patients) by means of gyrB RFLP. The taxonomic resolution of gyrB RFLP, and hence its potential as an identification tool, was confirmed by comparison with results from published and novel DNA-DNA hybridisation experiments. Our data also indicate that the majority of CF isolates grouped in two clusters. This may indicate that isolates from specific genomic groups have an increased potential for colonisation of the respiratory tract of CF patients.     

Bacillus spp.的筛选鉴定及浸矿渣效果研究

目的:研究Bacillus spp.的生长特性及浸镉渣效果。方法:采用9K培养基划线分离纯化目标菌种,利用传统的测定方法测定其生长特征,采用16S rDNA对菌株进行分子生物学鉴定,最后对该菌株浸三种矿渣浸出效果进行了分析。结果:该微生物形态为扁球形,革兰氏染色呈阳性,能运动,单生鞭毛;最适生长温度30℃,最适pH值为3;代谢类型为兼性营养型;耐受NaCl浓度为4%;微生物氧化酶为阴性,接触酶为阳性;经鉴定该菌株属于Bacillus属。以5%的接种量,培养基pH为3条件下,镉浸出效果较好,沉渣中浸出率为90.4%,其余两种渣中浸出效果最佳。结论:Bacillus spp.可应用于镉渣中镉的浸出。     

三株提高刺五加苷E 含量内生真菌的鉴定及其作用方式分析

目的:确定自刺五加分离的内生真菌P109-4、P116-1b和P312-1的分类地位,并初步分析其提高刺五加苷E含量的作用方式。方法:应用形态学及18S rDNA序列分析方法进行鉴定,将菌液回接刺五加浸出液进行发酵培养和将灭活后的菌液注射刺五加后,HPLC法分析刺五加苷含量E的变化。结果:P109-4、P116-1b和P312-1分别与尖孢镰孢菌、葡萄座腔菌和角担菌的形态学特征相符,与各对应种属真菌的18S rDNA序列同源性分别高达99.28%、99.76%和97.23%。活体的3株内生真菌能延长刺五加浸出液中刺五加苷E的存在时间,灭活后P312-1可显著提高刺五加苷E的含量,P109-4和P116-1B无显著作用。结论:P109-4为Fusarium oxysporum,P116-1b为Botryosphaeria dothidea,P312-1为Ceratobasidium spp.。P312-1的作用方式为通过菌体某种不被高温破坏的物质提高刺五加苷E的含量,P116-1b和P109-4仅能对已存在的刺五加苷E发挥作用。     

Why complexity and entropy matter: information, posttranslational modifications, and assay fidelity

Computationally aided protein identification of mass spectrometry (MS) data has been a challenge for the proteomic community since the field's inception. As the community attempts to address challenges such as computational site assignment of posttranslational modifications (PTMs), selective reaction monitoring data analysis, and the transition of proteomic assays to the clinic a robust framework with defined metrics is essential. The frameworks used for protein identification are currently score based, not hypothesis driven nor deterministic, resulting in a gradation from poor to good but without the ability to recognize when a given tandem MS spectrum has insufficient information in the context of the proteome to be identified. Means of computing deterministic and pseudodeterministic assays have been proposed by both us and others [Sherman, J., McKay, M.J., Ashman, K., Molloy, M.P., Unique ion signature mass spectrometry, a deterministic method to assign peptide identity. Mol. Cell. Proteomics 2009, 8, 2051-2062; Kiyonami, R., Schoen, A., Prakash, A., Peterman, S., et al., Increased selectivity, analytical precision, and through-put in targeted proteomics. Mol. Cell. Proteomics 2011, 10, M110.002931]. We believe it is crucial to incorporate the complexity of the proteome into the design of the experiment/data analysis upstream and that by doing so proteomic data analysis will become more robust. The seminal paper by Claude Shannon published in 1948 provides the robust mathematical framework now called Information Theory, to achieve this goal. Information Theory defines appropriate metrics for information and complexity as well as means to account for interference, all of which is directly applicable to peptide identification. We attempt to encourage the adoption of Information Theory as a means to ensure that appropriate metrics are used to measure the uncertainty in a peptide identification with or without PTM site assignment.     

糖-蛋白质相互作用在酶固定及蛋白质识别与分离中的应用

近些年来,糖-蛋白质相互作用的研究越来越受到研究人员的重视,它在生命过程中发挥着重要的作用,是生命体中信号传导、免疫应答、细胞黏附、病菌感染、受精、增殖、分化等许多细胞识别过程的基础。依据糖的类型不同对糖-蛋白质相互作用作了三个方面的应用总结:应用于酶的固定化,主要有壳聚糖,淀粉,琼脂糖,纤维素等多糖;应用于蛋白质的识别,主要是一些糖类芯片;应用于蛋白质的分离,主要有琼脂糖,肝素/硫酸类肝素,葡聚糖等。最后,对糖-蛋白质相互作用在生物化学领域的意义作了展望。     

经典植物分类学的发展与iFlora

简要介绍了经典植物分类的基础工作,即鉴定、描述、命名和分类,以及发展动向。作者认为计算机辅助鉴定（如delta intkey）将成为形态鉴定的常规手段;模式识别技术是植物图像鉴定的发展方向;突出物种遗传本质的分子鉴定将成为植物物种鉴定的核心。DELTA系统或类似的符合计算机逻辑的分类学描述语言将成为新一代植物志（iFlora）的基本语言。近20年来,一些学者逐渐表现出对现行植物命名法规的质疑和修改意愿,特别是生物法规草案（Draft BioCode）和谱系法规（PhyloCode）两个试行法规的诞生。它们促进对法规的革新与完善,并在iFlora中得以体现。以APG系统为代表的分子系统发育研究已经成为植物系统分类研究的主流,但在物种层面,物种的界定仅仅依靠分子信息显然是不够的,而必须运用综合的特征性状信息进行分析解读,真正实现物种在形态、遗传信息等综合性状的融合统一。了解和掌握这些新的技术和研究成果,无疑对于iFlora设计和编研有着重要的参考意义,而基于新技术和新理念的iFlora也将成为植物分类最新发展成果的集中体现。     

DNA条形码(ITS2)在葫芦科鉴定中应用价值的评估

探讨在纳入分析数据时,数据信息的选择对ITS2序列作为DNA条形码在葫芦科植物中鉴定能力的影响。首先,建立由葫芦科植物ITS2序列组成的3个资料组,其中Dataset1为实验样本,Dataset2由实验样本及GenBank数据库样本组合,Dataset3为从Dataset2中去除部分序列后所得。通过比较3个资料组的种间、种内的变异、Barcoding Gap及鉴定成功率,评估纳入分析的数据选择差异对ITS2鉴定能力的影响。结果显示ITS2序列在3个资料组属水平上的鉴定成功率均达到100%;种水平上,用BLAST1法鉴定成功率分别为100%、 67.8%、 90.6%,Nearest Distance法鉴定成功率分别为100%、 52.5%、 66.5%。可见纳入分析的数据选择有差异时,会导致鉴定成功率的较大变化。3个资料组中,ITS2分析仅有Dataset2的Barcoding Gap不够显著。因此对于DNA条形码分析中的数据纳入标准,值得进一步研究。     

人工哺育期腹泻婴猴奇异变形杆菌的分离与鉴定

目的对一株人工哺育期引发恒河猴婴猴腹泻的奇异变形杆菌进行了鉴定,为实验猕猴疾病检测、鉴别诊断提供参考依据。方法通过培养特性、菌落形态、染色、生化试验和血清学诊断鉴别等检查,对分离菌株进行初步鉴定,同时,对分离菌株进行致病性试验及药敏试验。结果通过表型生物学特性鉴定,并结合血清学诊断鉴别方法,确证该分离菌株为奇异变形杆菌,应用药敏试验筛选出了高度敏感的抗菌药,控制了该病的继续发生,致病性试验证明,该分离菌株对小白鼠有高致病性。结论分离到的奇异变形杆菌是导致本次婴猴腹泻死亡的病原菌,该菌为条件致病菌,对实验猕猴和研究人员均有潜在的危害,尽管该菌不是国家标准要求排除的病原菌,但该菌引发的传染病将对动物实验造成严重影响,故应引起高度重视。     

饲料乳酸菌的分离鉴定及优良菌株筛选

对从饲料玉米、高粱、麦秆及棉花中筛选出的乳酸菌进行分类鉴定和综合性分析。用MRS+CaCO3固体培养基从棉花中分离出乳酸菌18株、高粱中30株、饲料玉米中18株、麦秆中18株。经形态学、生理生化试验进行初步鉴定并按产酸试验,耐盐及耐酸试验挑选出32株产酸率强的乳酸菌对其进行16S rDNA分子鉴定。结果显示,32株菌都具有良好的耐盐、耐酸能力;经生理生化和16S rDNA基因序列鉴定可知32株乳酸菌分属于两个属,即乳杆菌属、肠球菌属,4个种,即干酪乳杆菌(Lactobacilluscasei)、肠道球菌(Entercoccus faecium)、植物乳杆菌(Lactobacillus plantarum)、海氏肠球菌(Entercoccus hirae)。4种饲料原料中肠道球菌普遍存在。除了这种乳酸菌以外,棉花有干酪乳杆菌、植物乳杆菌、海氏肠球菌,玉米和麦秆内有植物乳杆菌。从饲料中筛选出4株具有较强产酸能力的乳酸菌,可进一步研发成青贮饲料添加剂。     

大鼠肺泡Ⅱ型上皮细胞的原代分离

目的建立大鼠肺泡Ⅱ型上皮细胞(alveolar epithelial cells typeⅡ,AECⅡ)分离、纯化、原代培养及鉴定的方法。方法用4.2U/ml的弹性蛋白酶通过气管插管注入肺泡内,消化分离AECⅡ。把细胞悬液接种到包被有大鼠IgG的塑料平皿中纯化细胞。用电镜、碱性磷酸酶显色法、改良巴氏染色法、单宁酸染色法、免疫组化染色法鉴定AECⅡ。结果细胞纯度达到90%以上,倒置显微镜下可见细胞呈岛屿状生长。电镜下可见细胞内有大量板层小体,包膜上有绒毛结构。碱性磷酸酶染色法(BCIP/NBT)可见胞浆内有蓝色颗粒。改良巴氏染色法、单宁酸染色法可见胞浆内有黑色颗粒。抗大鼠肺泡表面活性蛋白A(surfactant protein A,SP-A)免疫组化染色呈阳性反应。结论弹性蛋白酶作用温和,不损伤胞膜,分离所得细胞活力好;IgG免疫粘附纯化法操作简单,纯化效率高。电镜、BCIP/NBT、巴氏染色、单宁酸染色及免疫组化染色等鉴定方法稳定可靠,特异性高。