乳头状甲状腺癌差异表达基因的筛选及生存分析

目的利用生物信息学方法筛选乳头状甲状腺癌（PTC）的关键基因及其所在信号通路，探讨其致癌机制。方法 从基因表达综合数据库（GEO）的两个测序平台的7个GSE芯片中获得PTC和癌旁组织样本的数据。首先利用R语言分别筛选出两个测序平台样本的差异基因，然后通过Metascape和STRING对差异基因进行生物学功能、信号通路分析和蛋白质-蛋白质相互作用分析,最后利用Cytoscape 3.5.1软件筛选出关键基因。结果 两个测序平台的样本求交集共获得302个差异表达基因，其中149个基因上调，153个基因下调，利用Cytoscape 3.5.1软件筛选出15个关键基因，其中12个关键基因位于细胞外基质受体相互作用信号通路中。利用UALCAN数据库对15个关键基因进行生存分析，其中4个基因的表达水平变化与患者的生存时间紧密相关。结论 利用生物信息学技术对来自7个PTC基因芯片数据集的信息进行分析，弥补了小样本结果的不一致性，提高了结果的可靠性和稳定性，并且筛选出了15个关键基因，发现了细胞外基质受体相互作用信号通路在甲状腺癌的发生发展中的重要作用。     

大鼠C6胶质瘤细胞的基因表达谱

目的:筛选比较大鼠C6胶质瘤细胞与正常星型胶质细胞中的差异表达基因。方法:利用Illumina Hi Seq4000技术对大鼠C6胶质瘤细胞和正常星形胶质细胞进行转录组测序并对测序结果进行功能注释。以|log2 Fold Change|≥1和q值0.05为标准筛选差异表达基因,并通过GO和KEGG数据库分析其功能和参与的信号通路。结果:较之正常星形胶质细胞,大鼠C6胶质瘤细胞中共筛选得到4363个差异表达基因,其中1603个基因表达上调,2760个基因表达下调;GO富集结果表明:4109个差异表达基因共映射到906个GO term,主要与GTP酶活性正性调节、基因表达正性调节、蛋白结合和钙离子结合等功能相关;KEGG富集结果表明:1535个差异表达基因共参与106条通路,富集最多的是PI3K-Akt信号通路和癌症发生通路。结论:成功获取大鼠C6胶质瘤细胞与正常胶质细胞的基因表达谱,并对其差异基因进行GO和KEGG注释,结果有助于胶质瘤发生发展的研究。     

大鼠骨髓基质细胞分化为施万细胞样细胞过程中的基因表达变化

目的:利用转录组测序技术(RNA-seq)检测骨髓基质细胞(BMSCs)分化为施万细胞(SCs)样细胞过程中基因表达谱的变化,筛选与分化相关的差异表达基因,并分析与分化相关的信号通路.方法:体外培养大鼠BMSCs,用三步诱导法对其进行诱导,在复合生长因子诱导第12 h和7 d收集样本.经Illumina测序平台对BMS...     

大鼠C6脑胶质瘤模型的基因表达谱分析

目的:筛选和分析大鼠胶质瘤模型与正常星型胶质细胞中的差异表达基因。方法:构建大鼠C6颅内胶质瘤模型,利用Illumina Hi Seq 4000技术对大鼠胶质瘤模型的胶质细胞和正常星形胶质细胞进行转录组测序并对测序结果进行功能注释。以q值0. 05为标准筛选差异表达基因,并通过GO和KEGG数据库分析其功能和参与的信号通路。结果:较之正常星形胶质细胞,大鼠胶质瘤模型组细胞共筛选得到9221个差异表达基因,其中4604个基因表达上调,4617个基因表达下调; GO富集结果表明:这些差异表达基因共映射到575个GO term,与各类结合相关的分子如蛋白结合、离子结合、小分子结合、核苷酸结合等功能富集显著; KEGG富集结果表明:差异表达基因共参与22条通路,富集最多的是癌症发生通路、MAPK通路、胞吞通路和黏着斑通路。结论:成功获取大鼠胶质瘤模型细胞与正常胶质细胞的基因表达谱,差异表达基因富集在癌症发生通路、MAPK通路、胞吞作用通路和黏着斑等生物学通路,这些信号通路可能在胶质瘤发生发展过程中发挥重要作用,对其进一步分析将为临床治疗胶质瘤提供新的靶点。     

慢性移植肾肾病患者外周血差异表达基因的分析

分析慢性移植肾肾病(CAN)患者与移植物功能稳定肾移植受者外周血基因表达差异,探索CAN免疫致病机制。从GEO数据库获取GSE12187和GSE22229两个肾移植受者外周血的基因芯片表达谱数据集,选取其中13个CAN样本为实验组,15个移植物功能稳定的样本为对照组。以SAM筛选两组样本的差异表达基因。应用DAVID及GENECODIS网络工具对差异基因进行功能富集分析。通过Cytoscape软件的MiMI插件进行差异基因的蛋白质-蛋白质相互作用(PPI)网络分析。SAM筛选出上调基因168个,下调基因141个。基因富集结果显示,上调基因主要为调控转录和翻译过程的基因,而下调基因参与广泛信号传导通路以及基因表达的调控。Cytoscape软件的PPI分析筛选出19个CAN相关核心基因。CAN患者与移植肾功能稳定受者的免疫功能状态存在显著差异;CAN致病机制涉及免疫细胞复杂的基因表达调控及细胞增值、凋亡、迁移等广泛的信号传导通路变化;免疫细胞在基因的转录、RNA加工、翻译及蛋白质代谢等环节的改变可能在CAN的致病中发挥了关键作用;TAGAP、EIF3F、NUDT21、PAPOLA、RPL等CAN核心基因的免疫调控机制需要深入探索。     

人呼吸道合胞病毒北京地区A亚型ON1基因型地方株感染A549细胞转录组学分析

目的应用转录组测序方法, 分析北京地区人呼吸道合胞病毒(respiratory syncytial virus, RSV)A亚型优势流行基因型ON1地方株感染A549细胞后差异表达基因, 为RSV防治提供潜在靶点。方法选用已经过全基因组测序确定为RSV A亚型ON1基因型的地方株(61397-ON1)感染A549细胞, 提取总mRNA, 通过转录组测序筛选出与未感染的A549细胞为对照的差异表达基因, 对其进行GO分析、KEGG通路分析, 同时随机选择6个差异表达倍数大于2倍的基因进行qRT-PCR验证。结果以未感染的A549细胞为对照, 筛选出1 632个差异表达基因, 其中807个基因表达上调, 825个基因表达下调。差异基因主要参与细胞因子反应以及MAPK级联反应正向调控等免疫应答相关生物过程, 并在MAPK信号通路、NOD样受体信号通路、p53信号通路、TNF信号通路、IL-17信号通路及NF-κB信号通路发生了富集。选择的6个差异表达基因qRT-PCR验证结果与转录组数据趋势一致。结论 RSV A亚型ON1基因型毒株感染A549细胞后的差异表达基因主要参与细胞因子应答及免疫相...     

妊娠期乳腺癌相关基因的生物信息学分析

目的通过生物信息分析途径对妊娠期乳腺癌患者与正常人群的差异基因进行分析,从分子水平探讨妊娠期乳腺癌的发病机制。方法从公共数据库基因表达数据库(GEO)中下载妊娠期乳腺癌相关数据集,采用Qlucore Omics Explore(QOE)筛选差异表达基因,用DAIVID、STRING等在线分析工具对差异表达基因进行功能富集分析,信号转导通路分析以及预测蛋白质之间的关系。结果共筛选出148个差异表达基因,其中表达上调24个,下调124个,对其进行生物信息学分析发现,TAGLN、ACTG2、TPM2、TPM3、MYLK、ACTA2、MTH11等基因以及MAPK信号通路、黏着斑信号通路、血管平滑肌细胞收缩信号通路等在妊娠期乳腺癌的发生发展中可能起着重要作用。通过STRING分析发现,20个基因处于核心节点位置。结论利用生物信息学的方法能有效分析基因芯片数据并获取生物内在信息。     

人正常宫颈上皮细胞感染沙眼衣原体的基因表达谱分析

目的分析人正常宫颈上皮细胞(HcerEpic)感染沙眼衣原体(Chlamydia trachomatis, Ct)前后基因表达谱差异。方法 HcerEpic细胞经DEAE-D预处理后加入E型Ct标准株, 培养44 h后收集HcerEpic细胞(感染组), 并以未感染Ct的HcerEpic细胞作为对照组, 提取两组总RNA后反转录并构建cDNA文库。通过高通量测序分析两组基因表达谱差异, 并选择代表性基因通过实时荧光定量PCR(qPCR)验证。结果共检测23 997个基因, 差异基因125个, 其中上调基因119个, 下调基因6个;GO分析显示差异基因富集于对病毒防御反应、Ⅰ型干扰素(interferon, IFN)信号通路、对Ⅰ型IFN的细胞反应等条目;KEGG富集通路为甲型流感、单纯疱疹病毒感染、EB病毒感染、HPV感染、NOD样受体通路等相关通路。结论人正常宫颈上皮细胞感染Ct前后转录组存在差异, 差异基因主要富集于IFN通路, 与细胞抗病毒过程密切相关。qPCR验证了ISG15、IFIT2、OASL、UBE2L6等差异显著且与IFN通路密切相关的基因。     

基于SMART-seq2测序分析结直肠癌外周血DNT细胞转录组的表达差异及功能初探北大核心CSCD

目的 探讨结直肠癌患者外周血中双阴性T细胞差异基因及功能。方法 选取2例结直肠癌患者和2例健康体检者,首先采用流式细胞术分选外周血双阴性T细胞,然后利用单细胞全长转录组（SMART-seq2）测序技术获得测序数据,筛选差异表达基因,并对筛选出的差异表达基因进行基因本体富集分析(GO)和京都基因与基因组百科全书(KEGG)途径富集分析。利用STRING数据库构建蛋白质互作网络,并通过Cytoscape软件鉴定关键基因。采用RT-qPCR验证差异表达基因。结果 与健康体检者相比,结直肠癌患者外周血双阴性T细胞差异基因共有1 276个,其中141个上调基因,1 135个下调基因。GO分析显示差异基因主要参与甲基化、代谢过程以及转移酶活性等生物学功能。KEGG通路分析显示差异基因主要涉及自噬、P53信号通路和磷酸肌醇代谢等信号通路。蛋白质互作网络包含1 154个节点和1 022条边,并鉴定出10个Hub基因：PIK3C3、WIPI1、ATG101、PIK3R4、DDX10、RBM28、SDAD1、ATG16L1、UVRAG、ATG7。RT-qPCR验证10个差异表达基因,其中7个差异基因表达变化趋势与测序结果一致,3个基因表达与测序结果不符。结论 DNT细胞可能通过甲基化、P53信号通路和自噬等作用参与了结直肠癌的发生发展,同时,DNT细胞可能通过对基因的调控抑制结直肠癌的发生发展。本研究为进一步探讨DNT细胞在恶性肿瘤中的功能提供理论依据。     

果糖诱导斑马鱼肝脏脂肪变性的转录组学分析

目的非酒精性脂肪肝(NAFLD)的发病呈低龄化趋势,本研究旨在建立一种模拟低龄人群的高糖诱导的NAFLD模型,揭示其基因表达谱特征,为疾病的机制研究和药物筛选提供基础。方法采用高果糖饮食诱导斑马鱼产生肝脏脂肪变性,油红O染色分析肝脏脂肪变性率,组织病理学方法观察肝脏脂质堆积,并分析肝脏生化指标变化。利用转录组测序观察基因表达谱变化,通过基因与基因组百科全书(KEGG)和基因本体(GO)数据库进行差异基因功能富集,分析其可能影响的信号通路与生物过程。结果斑马鱼幼鱼高果糖喂养10 d后发生肝脏脂肪变性,肝脏切片HE染色和油红O染色结果发现,果糖喂饲的幼鱼肝脏出现微小脂质空泡,呈大面积红色着色。肝脏甘油三酯、葡萄糖含量显著高于正常对照组。经转录组测序发现果糖喂饲的幼鱼肝脏表达谱发生明显改变,共发现485个差异表达基因(变化倍数 3,P 0.05)。差异基因KEGG分析表明,PPAR信号通路为显著富集通路,real-time PCR结果确认PPAR通路中fads2、fabp7b、plin2、adipoqa基因水平显著上调。下调基因的GO分析结果显示,病毒防御为显著富集的生物学过程。结论建立了一种果糖诱导的斑马鱼NAFLD模型,可应用于斑马鱼幼体肝脏脂肪变性的机制研究和药物筛选。能量代谢相关基因表达的变化可为果糖致NAFLD的作用机制研究提供依据。     

Schizophrenia in a North Swedish geographical isolate, 1900–1977. Epidemiology, genetics and biochemistry

Over 200 schizophrenic patients belonging to three major and interrelated pedigree complexes have been investigated over the past 30 years in a North Swedish geographically isolated population, presently numbering about 6,000. An intensive investigation of a number of biochemical correlates and genetic markers in a few selected families belonging to one of the major pedigrees has indicated new strategies for the current research program.
Schizophrenia, as defined operationally, is significantly associated with decreased activities of two enzymes (1) blood platelet monoamine oxidase, (2) plasma dopamine-β-hydroxylase, and (3) with the genetic marker Gc² (group specific antigen). Both enzymes are subject to genetic variation. A positive score for linkage between schizophrenia and low plasma DBH activity has been calculated, but, so far, available data are insufficient for discrimination between linkage and partial contribution of genetically controlled low plasma DBH to the pathogenesis of the disease. Alternatively, both mechanisms could be involved.
As a model for continued research, schizophrenia is explained as based on a double dominant-recessive genotype (Aabb), representing a vulnerability which in about 50 % of cases develops into clinical schizophrenia. It is suggested that the dominant mutation (A) operates on or affects MAO activity, and that the recessive genotype (bb) is instrumental in low variates of DBH activity and very likely such variates within the normal range of physiological variation. Moreover, it is suggested that the combined effects of MAO- and DBH-reduced efficiency on the metabolism of e.g. dopamine could be an essential pathogenic mechanism for the schizophrenic illness which is segregating in this population.     

Renal dysplasia and asplenia in two sibs

A family is reported in which two sibs, one male and the other female, both died within 24 hours of birth with enlarged polycystic kidneys. Postmortem histology in the second child showed gross renal dysplasia. In both children the pancreas was enlarged, nodular and cystic but the liver appeared macroscopically normal. In the second child, histological examination confirmed pancreatic fibrosis with cystic dilation of ducts, but showed portal fibrosis with bile duct proliferation in the liver.
This combination of findings is very reminiscent of those in a girl and her brother reported by Ivemark et al. (1959). The children reported here also showed absence or hypoplasia of the spleen, cardiac anomalies and other features of the Ivemark syndrome (Ivemark 1955), a quite different, usually sporadic, congenital disorder. It is suggested that the children described here have a distinct lethal congenital disorder, probably inherited in an autosomal recessive manner.     

The dominant diseases of modernized societies as omega-3 essential fatty acid deficiency syndrome: Substrate beriberi

About 1900, modern food selection and processing caused widespread $\text{epidemics}$ of the B vitamin deficiency diseases of beriberi and pellagra which, for genetic reasons, often expressed as different diseases ranging from bowel and heart disease to dermatoses and psychoses. But the B vitamins merely help convert essential fatty acids (EFA) into the prostaglandin (PG) tissue regulators and it now turns out that, through hydrogenation, milling and selection of w3-poor southern foods, we have also been systematically depleting, by as much as 90%, a newly discovered trace Nordic EFA (w3) of special importance to primates and sole precursor of the PG3(4) series, even as a concurrent fiber deficiency increases body demand for EFA. Since substrate EFA is processed by many B vitamin catalysts, an EFA deficiency will mimic a $\text{panh}$ypovitaminosis B, i.e., a mixture of $\text{substrate}$ beriberi and $\text{substrate}$ pellagra resembling vitamin beriberi and pellagra but exhibiting as even more diverse $\text{endemic}$ disease. This would consitute a second stage of the Modern Malnutrition and explain why some workers now hold the dominant diseases of modermized societies to be new, nutritionally based, pellagraform yet lipid-related and to range, once again, from heart disease to psychosis. It is an assumption that our dominant diseases are unrelated to each other or are merely revealed by our diagnostic acumen and therapeutic success; and that hydrogenating millions of tons of food oils annually, to destroy the rancidity producing w3-EFA, is safe for $\text{primates}$. Extensive beriberiform disease is reported here in 32 typical cases taken from medical practice which responds strikingly to linseed oil supplements (60% w3-EFA) in confirmation of identical results in Capuchins.     

'Very sore nights and days': the child's experience of illness in early modern England, c.1580-1720

Sick children were ubiquitous in early modern England, and yet they have received very little attention from historians. Taking the elusive perspective of the child, this article explores the physical, emotional, and spiritual experience of illness in England between approximately 1580 and 1720. What was it like being ill and suffering pain? How did the young respond emotionally to the anticipation of death? It is argued that children’s experiences were characterised by profound ambivalence: illness could be terrifying and distressing, but also a source of emotional and spiritual fulfilment and joy. This interpretation challenges the common assumption amongst medical historians that the experiences of early modern patients were utterly miserable. It also sheds light on children’s emotional feelings for their parents, a subject often overlooked in the historiography of childhood. The primary sources used in this article include diaries, autobiographies, letters, the biographies of pious children, printed possession cases, doctors’ casebooks, and theological treatises concerning the afterlife.     

Guidelines for the Validation and Use of Immunoassays for Determination of Introduced Proteins in Biotechnology Enhanced Crops and Derived Food Ingredients

Recent advancements in agricultural biotechnology have created a need for analytical techniques to determine introduced proteins in crops enhanced through modern biotechnology techniques. These proteins are expressed in plant tissues and may be present in food ingredients. Immunoassays are ideally suited for protein detection and may be used as both quantitative and threshold methods. Microplate ELISA and lateral flow devices are two of the most commonly used immunoassay formats for agricultural biotechnology applications. This paper provides general background information and a discussion of criteria for the validation and application of immunochemical methods to the analysis of proteins introduced into plants and food ingredients using biotechnology methods. It is the result of a collaborative effort of members of the Analytical Environmental Immunochemical Consortium. This collaborative effort represents the combined expertise of several organizations to reach consensus on establishing guidelines for the validation and use of immunoassays. Further, the paper offers developers and users a consistent approach to adopting the technology as well as aid in producing accurate and meaningful results.     

HLA in North Colombia Chimila Amerindians

HLA-A,-B,-C,-DRB1 and -DQB1 alleles have been studied in Chimila Amerindians from Sabana de San Angel (North Colombian Coast) by using high resolution molecular typing. A frequent extended haplotype was found:HLA-A*24:02-B*51:10-C*15:02-BRB1*04:07-DQB1*03:02 (28.7%) which has also been described in Amerinndian Mayos Mexican population (Mexico, California Gulf, Pacific Ocean). Other haplotypes had already been found in Amerindians from Mexico (Pacific and Atlantic Coast), Peru (highlands and Amazon Basin), Bolivia and North USA. A geographic pattern according to HLA allele or haplotype frequencies is lacking in Amerindians, as already known. Also, five new extended haplotypes were found in Chimila Amerindians. Their HLA-A*24:02 high frequencies characteristic is shared with aboriginal populations of Taiwan; also, HLA-C*01:02 high frequencies are found in New Zealand Maoris, New Caledonians and Kimberly Aborigines from Australia. Finally, this study may show a model of evolutionary factors acting and rising one HLA allele frequency (-A*24:02), but not in others that belong to the same or different HLA loci.     

Ultracryotomy: development and application (with examples from the yeast cytology) (author's transl)

The preparation steps usually necessary for obtaining ultrathin frozen sections of biological material (chemical prefixation, enclosing, cryoprotective treatment, freezing, sectioning, and post-staining the sections for transmission electron microscopy) are submitted to a critical analysis. The application of cryo-ultramicrotomy, in particularly for cytochemical purposes, is reviewed. Fundamental considerations of chemical prefixation and poststaining are supported by examples from yeast cytology. Furthermore, the efficiency of the cryo-ultramicrotomy (electron optical resolution of ultrastructural details) is demonstrated on yeast cells and protoplasts.     

The universal muscular chamber. A basic unit of the genitourinary, cardiovascular, gastro-intestinal, skeletal, cutaneous, respiratory and other systems, endocameral hypertension; and spasm, the key to their idiopathic diseases and arthropathies

Starting with the integument, we see many organs are contractile sacs or multiples thereof, which tubes or bags constitute the major part of the entire body. Recognition of this basic unit and its characteristics sheds new light, individually and collectively, on many disorders previously considered unrelated. Muscular tears and perforations develop in the walls of these chambers, being no way peculiar to those organs, wherein, hydrochloric acid occurs. So, it is not necessary to explain the absence of excessive acid from patients who exhibit holes in the gastric, uterine, aortic, duodenal, rectal, pulmonary, retina, and other walls. Muscle, not acid is the great common factor relating idiopathic disorders in the gastrointestinal tract to each other and to similar diseases in other systems. When the units are linked together, the lesions tend to appear as arthropathies, i.e. at the joints. Rephrasing common-place observations, frees us from conventional, conceptual cul-de-sacs. An observation is only as good as its interpretation, so all possibilities must be considered, otherwise, we will remain blinded by our misconceptions.     

Der Einfluß von Nahrungsmitteln und Rauchen auf die klinisch-chemische Diagnostik von Phäochromozytom,Neuroblastom und Karzinoid-Syndrom

Zusammenfassung Der Einfluß von verschiedenen Nahrungsmitteln auf Methoden zur Bestimmung von Adrenalin (AD), Noradrenalin (NA), Vanillinmandelsäure (VMS), Metanephrinen (MN), Homovanillinsäure (HVS) und 5-Hydroxyindolessigsäure (5-HIE) im 24 h-Harn zur Diagnose des Phäochromozytoms bzw. Karzinoid-Syndroms wurde untersucht. Die in die Untersuchung einbezogenen Nahrungsmittel waren: Tee, Kaffee, Mandeln, Ananas, Käse, Walnüsse, Vanillepudding, Bananen, Tomaten und Milchschokolade. Außerdem wurde der Einfluß des Zigarettenrauchens auf die Bestimmung von AD, NA, VMS und MN untersucht.Walnüsse führten zu einer starken Erhöhung der 5-HIE-Ausscheidung. Bananen erhöhten die Ausscheidung von AD, NA, VMS, MN und 5-HIE. Kaffee und Ananas bewirkten eine geringe Zunahme der MN-Werte. Rauchen von 20–30 Zigaretten/Tag beeinflußte keine der vier Variablen.Wenn die beschriebenen Methoden benutzt werden, sollte lediglich auf den Verzehr von Bananen und Walnüssen vor und während der Harnsammelperioden verzichtet werden, da die oberen Normgrenzen im Harn überschritten werden könnten. Ein Verzicht auf Kaffee und Ananas in normalen Mengen ist nicht erforderlich. Es besteht kein Anlaß, weiterhin die bisherigen umfangreichen Restriktionen der übrigen Nahrungsmittel beizubehalten.