新一代测序技术在植物转录组研究中的应用

随着DNA测序技术的发展,新一代测序技术以其高通量、低成本的特点,成为越来越多的生物学研究者在开展工作时的首选。在所有的新一代测序技术中,454测序系统是最早实现商业化且发展相对成熟的一种,目前被广泛的应用于各个领域的生物学研究中。文章以454测序系统为例,综述了新一代测序系统的原理、优缺点,及其在植物转录组研究中的应用,并对其在植物研究领域中可能的发展应用方向进行了展望。     

Western印迹中蛋白质定量分析的替代方法

Western印迹广泛采用显像密度计法对特异性蛋白质表达进行定量,但是仍然存在敏感性的问题尚未解决。同时,昂贵的试剂与复杂的设备限制了其应用。建立了一种改良定量检测法,使用碱性磷酸酶标记的第二抗体,以萘酚磷酸盐和快红作反应底物。吸附膜上的终末显色用有机溶剂洗脱,通过测定光吸收值定量。结果显示该法更简便、快速、经济而不失其敏感性。     

电转移中蛋白质的透膜现象及其对蛋白质印迹结果的影响

探讨了电转移中蛋白质的透膜现象及其对蛋白质印迹结果的影响.采用抗凋亡抑制蛋白-Survivin的抗体,对细胞裂解液进行蛋白质印迹.与常规操作方法不同之处是：在电转移的凝胶“三明治”中,重叠放置两张硝酸纤维素膜.电转移后,对两张膜同时进行免疫印迹.在特定的转移条件下,两张膜的免疫印迹都出现了Survivin蛋白的特异印迹带,证实了电转移中存在着蛋白质的透膜现象.转移时间、电流强度和蛋白质的分子质量,都是影响蛋白质透膜的相关因素.电转移中蛋白质的透膜,可以产生“印迹复制失真”的效应,从而最终影响蛋白质印迹定性和定量的结果.所得实验结果和结论,揭示了蛋白质印迹技术方法学中一个需要加以充分关注的问题,对于科学掌握和应用该技术具有积极作用.     

Protein blotting: principles and applications

Extensive studies on the DNA tumor virus Simian Virus 40 (SV40) have provided a wealth of information regarding the genome organization, regulation of viral gene expression, and the mechanism of DNA replication. SV40 can grow lytically in permissive monkey cells or the viral DNA can integrate into the host genome of nonpermissive rodent cells causing morphological transformation. The viral DNA exists as a minichromosome within the nuclei of lytically infected cells and, as a consequence of DNA replication, there is a significant amplification of the viral genome during infection. These properties suggested that SV40 could be developed as a transducing vector to introduce exogenous DNA into mammalian cells and to express this foreign DNA during the SV40 infectious cycle. In this article the properties of SV40 virus vectors and SV40 hybrid plasmid vectors are described and contrasted.     

Determining protein stability in cell lysates by pulse proteolysis and Western blotting

Proteins require proper conformational energetics to fold and to function correctly. Despite the importance of having information on conformational energetics, the investigation of thermodynamic stability has been limited to proteins, which can be easily expressed and purified. Many biologically important proteins are not suitable for conventional biophysical investigation because of the difficulty of expression and purification. As an effort to overcome this limitation, we have developed a method to determine the thermodynamic stability of low abundant proteins in cell lysates. Previously, it was demonstrated that protein stability can be determined quantitatively by measuring the fraction of folded proteins with a pulse of proteolysis (Pulse proteolysis). Here, we show that thermodynamic stability of low abundant proteins can be determined reliably in cell lysates by combining pulse proteolysis with quantitative Western blotting (Pulse and Western). To demonstrate the reliability of this method, we determined the thermodynamic stability of recombinant human H‐ras added to lysates of E. coli and human Jurkat T cells. Comparison with the thermodynamic stability determined with pure H‐ras revealed that Pulse and Western is a reliable way to monitor protein stability in cell lysates and the stability of H‐ras is not affected by other proteins present in cell lysates. This method allows the investigation of conformational energetics of proteins in cell lysates without cloning, purification, or labeling.     

Echinococcus multilocularis: Two-dimensional Western blotting method for the identification and expression analysis of immunogenic proteins in infected dogs

Domesticated dogs are an important potential source of Echinococcus multilocularis infection in humans; therefore, new molecular approaches for the prevention of the parasite infection in dogs need to be developed. Here, we identified and characterized an immunogenic protein of the parasite by using a proteome-based approach. The total protein extracted from protoscoleces was subjected to two-dimensional Western blotting with sera from dogs experimentally infected with E. multilocularis. Two protein spots showed major reactivity to the sera from infected dogs. The N-terminal amino acid sequences of these spots were identical to the deduced amino acid sequence of the product of the putative hsp20 gene. RT-PCR and Western blot analyses revealed that the putative hsp20 gene and its products were expressed in almost all stages of the parasite life cycle. Furthermore, recombinant hsp20 showed specific reactivity to the sera from infected dogs, suggesting that this molecule may facilitate the development of a practical vaccine.     

Negative incorporation,the next generation and involvement in transnational organizations

ABSTRACT

Can the negative aspects of incorporation – discrimination, marginalization, and frustration with life in a country of settlement – help us to understand next generation transnationalism? This question is applied to a small, non-representative sample of next generation individuals involved in Mexican and Salvadoran transnational political and philanthropic organizations operating in California and Washington, DC. The findings suggest that negative incorporation had some explanatory potential for the transnational mobilization of some respondents. However, the study also suggests the multiple trajectories and contexts that give rise to next generation transnationalism. Involvement in cross-border organizations appears not only to be a refuge for those who perceive the country of settlement negatively or a means through which individuals can respond to negative experiences; it can also be pursued by individuals that positively identify with the country of settlement and perceive its values favourably, indicating the need for a more synthetic understanding of this phenomenon.     

棉花咖啡酸-O-甲基转移酶基因的原核表达及蛋白纯化鉴定

为获得大量高纯度的GhCOMT2蛋白以便研究其功能和性质,以pMD18-GhCOMT2质粒为模板,PCR扩增GhCOMT2基因的cDNA编码区,构建原核表达载体pET-28a-GhCOMT2,经酶切鉴定并测序后转化到大肠杆菌BL21 (DE3)中进行诱导表达,并采用Western blotting方法鉴定表达产物.结果表明:在大肠杆菌BL21(DE3)菌株中成功表达了与标签蛋白融合的GhCOMT2蛋白,大小约为40.062 kD,浓度为0.62 mg/mL.重组蛋白的最佳诱导条件为:0.2 mmol/L IPTG在16℃诱导12 h.重组蛋白以可溶形式高效表达,用蛋白标签亲和层析柱(His TrapTM HP)获得纯化重组蛋白,Western blotting分析表明其能与His多克隆抗体起特异性反应.     

Cy5 total protein normalization in Western blot analysis

Western blotting is a widely used method for analyzing specific target proteins in complex protein samples. Housekeeping proteins are often used for normalization to correct for uneven sample loads, but these require careful validation since expression levels may vary with cell type and treatment. We present a new, more reliable method for normalization using Cy5-prelabeled total protein as a loading control. We used a prelabeling protocol based on Cy5 N-hydroxysuccinimide ester labeling that produces a linear signal response. We obtained a low coefficient of variation (CV) of 7% between the ratio of extracellular signal-regulated kinase (ERK1/2) target to Cy5 total protein control signals over the whole loading range from 2.5 to 20.0 μg of Chinese hamster ovary cell lysate protein. Corresponding experiments using actin or tubulin as controls for normalization resulted in CVs of 13 and 18%, respectively. Glyceraldehyde-3-phosphate dehydrogenase did not produce a proportional signal and was not suitable for normalization in these cells. A comparison of ERK1/2 signals from labeled and unlabeled samples showed that Cy5 prelabeling did not affect antibody binding. By using total protein normalization we analyzed PP2A and Smad2/3 levels with high confidence.     

新一代测序技术在遗传性耳聋基因研究及诊断中的应用

超过50%的耳聋由遗传基因缺陷所致,伴随着基因组学技术的发展,耳聋分子遗传学研究逐渐成为耳科学研究的前沿领域。新一代高通量测序技术的出现,提供了以数据为导向的新的遗传性疾病研究模式,革新了人们对遗传性疾病的认识过程,使得对遗传性疾病的研究策略也发生了重大转变。近年来新一代测序技术(Next generation sequencing,NGS)在耳聋研究中的应用,大大加快了耳聋基因发现的速度,并逐渐向临床应用方向转化。文章总结了遗传性耳聋的特点和研究现状,以及新一代测序技术在耳聋研究中的应用和前景,以及基于NGS技术的耳聋基因研究和临床耳聋基因诊断的发展方向。     

Immunodiagnosis of tuberculous meningitis: rapid detection of mycobacterial antigens in cerebrospinal fluid by reverse passive hemagglutination assay and their characterization by Western blotting

Tuberculous meningitis (TBM) is one of the commonest chronic infections of the central nervous system (CNS). Diagnosis of TBM has been a problem as it causes various clinical manifestations which can be confused with those of other chronic infections of the CNS such as neurocysticercosis (NCC), neurobrucellosis and cryptococcal meningitis, that are prevalent in many underdeveloped and developing countries. Differential diagnosis of TBM can be made by detecting circulating mycobacterial antigens in CSF by immunoassays. In this study, a reverse passive hemagglutination (RPHA) has been developed using rabbit antimycobacterial IgG for detection of circulating mycobacterial antigens in CSFs from chronic infections of the CNS in order to develop a rapid, simple, sensitive and cost-effective method. Circulating mycobacterial antigens were characterized by immunoblot assay. The sensitivity limit of RPHA was 400 ng ml(-1). RPHA was specific as antimycobacterial IgG did not show any reaction with porcine Cysticercus cellulosae which was used as a control antigen. RPHA could detect mycobacterial antigens in CSF at a sensitivity level of 94.11% with a specificity of 99.0%. Immunoblot analysis of RPHA positive CSFs revealed predominantly 30-32 kDa and 71 kDa antigens whilst 6, 86, 120, 96 and 110 kDa showed varied degree of reactivity. Antigens of masses 30-32 and 71 kDa were absent in culture filtrate of Mycobacterium tuberculosis H37Rv grown in Proskeur-Beck liquid medium. RPHA is a rapid, simple and sensitive immunological method with a long shelf life of 6-8 weeks if stabilized coated erythrocytes are stored at +4 degrees C. RPHA could be used as an additional immunodiagnostic tool in both differential diagnosis and prognosis of TBM. Immunoblot results indicate that 30-32 kDa and 71 kDa antigens are cell wall derived.     

Use of a sensitive EnVision +-based detection system for Western blotting: avoidance of streptavidin binding to endogenous biotin and biotin-containing proteins in kidney and other tissues

Western blotting remains a central technique in confirming identities of proteins, their quantitation and analysis of various isoforms. The biotin-avidin/streptavidin system is often used as an amplification step to increase sensitivity but in some tissues such as kidney, "nonspecific" interactions may be a problem due to high levels of endogenous biotin-containing proteins. The EnVision system, developed for immunohistochemical applications, relies on binding of a polymeric conjugate consisting of up to 100 peroxidase molecules and 20 secondary antibody molecules linked directly to an activated dextran backbone, to the primary antibody. This study demonstrates that it is also a viable and sensitive alternative detection system in Western blotting applications.     

The association on SDS-polyacrylamide gels of lipopolysaccharide and outer membrane proteins of Pseudomonas aeruginosa as revealed by monoclonal antibodies and Western blotting

Abstract Monoclonal antibodies raised against single serotype components of a Pseudomonas aeruginosa vaccine have been shown to bind to the O antigen region of lipopolysaccharide (LPS). Outer membrane (OM) proteins, prepared by detergent treatment of envelope fractions and by EDTA/sonication treatment of whole cells, were separated on sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE), electrophoretically transferred to nitrocellulose membrane and reacted with LPS-specific monoclonal antibodies. The patterns produced revealed that many of the protein bands were in fact protein-LPS complexes.     

Utilizing field collected insects for next generation sequencing: Effects of sampling,storage, and DNA extraction methods

DNA sequencing technologies continue to advance the biological sciences, expanding opportunities for genomic studies of non‐model organisms for basic and applied questions. Despite these opportunities, many next generation sequencing protocols have been developed assuming a substantial quantity of high molecular weight DNA (>100 ng), which can be difficult to obtain for many study systems. In particular, the ability to sequence field‐collected specimens that exhibit varying levels of DNA degradation remains largely unexplored. In this study we investigate the influence of five traditional insect capture and curation methods on Double‐Digest Restriction Enzyme Associated DNA (ddRAD) sequencing success for three wild bee species. We sequenced a total of 105 specimens (between 7–13 specimens per species and treatment). We additionally investigated how different DNA quality metrics (including pre‐sequence concentration and contamination) predicted downstream sequencing success, and also compared two DNA extraction methods. We report successful library preparation for all specimens, with all treatments and extraction methods producing enough highly reliable loci for population genetic analyses. Although results varied between species, we found that specimens collected by net sampling directly into 100% EtOH, or by passive trapping followed by 100% EtOH storage before pinning tended to produce higher quality ddRAD assemblies, likely as a result of rapid specimen desiccation. Surprisingly, we found that specimens preserved in propylene glycol during field sampling exhibited lower‐quality assemblies. We provide recommendations for each treatment, extraction method, and DNA quality assessment, and further encourage researchers to consider utilizing a wider variety of specimens for genomic analyses.     

拟南芥HyPRP蛋白AZI1在大肠杆菌中的表达及其抗真菌活性分析

AZI1(AZELAIC ACID INDUCED 1)基因位于拟南芥4号染色体上,编码产物是脂质转移蛋白(lipid transfer protein, LTP)家族的一个成员。该基因在系统获得抗性(systemic acquired resistance, SAR)中具有重要功能,名称来自它可以被壬二酸(azelaic acid, AzA)诱导。已有的研究结果显示,在拟南芥中由AzA和甘油-3-磷酸(glycerol-3-phosphate, G3P)诱导的SAR反应需要AZI1和DIR1,这两个脂质转移蛋白有助于G3P的积累。为了确定AZI1蛋白是否具有抗真菌活性,本工作构建了原核表达载体pET28a-AZI1,利用大肠杆菌BL21(DE3)受体细胞制备了没有信号肽的AZI1重组蛋白。Western免疫印迹分析发现通过半乳糖苷类似物IPTG诱导表达的AZI1重组蛋白主要以包涵体的形式存在。体外抑菌实验以及激光共聚焦显微观察结果表明,用镍离子亲和层析树脂纯化的AZI1重组蛋白对灰霉菌、赤霉菌、棉花枯萎病菌和酿酒酵母细胞的生长/分裂均具有抑制作用。     

Membrane‐Based SDS Depletion Ahead of Peptide and Protein Analysis by Mass Spectrometry

SDS interferes with both bottom‐up and top‐down MS analysis, requiring removal prior to detection. Filter‐aided sample preparation (FASP) is favored for bottom‐up proteomics (BUP) while acetone precipitation is popular for top‐down proteomics (TDP). We recently demonstrated acetone precipitation in a membrane filter cartridge. Alternatively, our automated electrophoretic device, termed transmembrane electrophoresis (TME), depletes SDS for both TDP and BUP studies. Here TME is compared to these two alternative methods of SDS depletion in both BUP and TDP workflows. To do so, a modified FASP method is described applicable to the SDS purification and recovery of intact proteins, suitable for LC/MS. All three methods reliably deplete >99.8% SDS. TME provide higher sample yields (average 90%) than FASP (55%) or acetone precipitation (57%), translating into higher total protein identifications (973 vs 877 FASP or 890 acetone) and higher spectral matches (2.5 times) per protein. In a top down workflow, each SDS‐depletion method yields high‐quality MS spectra for intact proteins. These results show each of these membrane‐based strategies is capable of depleting SDS with high sample recovery and high spectra quality for both BUP and TDP studies.     

The human pituitary nitroproteome: detection of nitrotyrosyl-proteins with two-dimensional Western blotting, and amino acid sequence determination with mass spectrometry

Nitric oxide is an important mediator that participates in reduction-oxidation (redox) mechanisms and in cellular signal transduction pathways. Two types of post-translational modifications are induced by nitric oxide: S-nitrosylation of cysteine residues and nitration of tyrosine residues. Two-dimensional gel electrophoresis-based Western blotting was used to detect, and liquid chromatography (LC)-tandem mass spectrometry (MS/MS) to determine the amino acid sequence of, several different nitrated proteins in the human pituitary. Proteins from several 2D gel spots, which corresponded to the strongly positive anti-nitrotyrosine Western blot spots, were subjected to in-gel trypsin-digestion and LC-MS/MS analysis. MS/MS, SEQUEST analysis, and de novo sequencing were used to determine the nitration site of each nitrated peptide. A total of four different nitrated peptides were characterized and were matched to four different proteins: synaptosomal-associated protein, actin, immunoglobulin alpha Fc receptor, and cGMP-dependent protein kinase 2. Those nitrotyrosyl-proteins participate in neurotransmission, cellular immunity, and cellular structure and mobility.     

Trends in solventless sample preparation techniques for environmental analysis

The paper presents recent trends in solventless sample preparation techniques for environmental analysis. First, a general classification of solventless methods is given. Next, three of them, treated as preferable techniques, i.e. SPME, SDME and HS, are presented in detail, with respect to their usability and effectiveness for environmental samples. Examples of all discussed techniques are given in the tables.