Examination of Thymic Positive and Negative Selection by Flow Cytometry

A healthy immune system requires that T cells respond to foreign antigens while remaining tolerant to self-antigens. Random rearrangement of the T cell receptor (TCR) α and β loci generates a T cell repertoire with vast diversity in antigen specificity, both to self and foreign. Selection of the repertoire during development in the thymus is critical for generating safe and useful T cells. Defects in thymic selection contribute to the development of autoimmune and immunodeficiency disorders^1-4. T cell progenitors enter the thymus as double negative (DN) thymocytes that do not express CD4 or CD8 co-receptors. Expression of the αβTCR and both co-receptors occurs at the double positive (DP) stage. Interaction of the αβTCR with self-peptide-MHC (pMHC) presented by thymic cells determines the fate of the DP thymocyte. High affinity interactions lead to negative selection and elimination of self-reactive thymocytes. Low affinity interactions result in positive selection and development of CD4 or CD8 single positive (SP) T cells capable of recognizing foreign antigens presented by self-MHC⁵.Positive selection can be studied in mice with a polyclonal (wildtype) TCR repertoire by observing the generation of mature T cells. However, they are not ideal for the study of negative selection, which involves deletion of small antigen-specific populations. Many model systems have been used to study negative selection but vary in their ability to recapitulate physiological events⁶. For example, in vitro stimulation of thymocytes lacks the thymic environment that is intimately involved in selection, while administration of exogenous antigen can lead to non-specific deletion of thymocytes^7-9. Currently, the best tools for studying in vivo negative selection are mice that express a transgenic TCR specific for endogenous self-antigen. However, many classical TCR transgenic models are characterized by premature expression of the transgenic TCRα chain at the DN stage, resulting in premature negative selection. Our lab has developed the HY^cd4 model, in which the transgenic HY TCRα is conditionally expressed at the DP stage, allowing negative selection to occur during the DP to SP transition as occurs in wildtype mice¹⁰.Here, we describe a flow cytometry-based protocol to examine thymic positive and negative selection in the HY^cd4 mouse model. While negative selection in HY^cd4 mice is highly physiological, these methods can also be applied to other TCR transgenic models. We will also present general strategies for analyzing positive selection in a polyclonal repertoire applicable to any genetically manipulated mice.     

互花米草的两面性及其生态控制

互花米草是美国大西洋沿岸的本土植物,其高生产力、高繁殖率、高抗性和致密发达的地下部分等生物学特性使它能在沿海地区的抗风防浪、保滩护岸、促淤造陆、修复湿地和固定二氧化碳等方面发挥很好的正生态效应;然而,正是这与生俱来的生物学优势使该物种在引种地区侵占光滩,很快形成茂盛的单种优势群落,体现出很强的入侵性,从而也具有相当大的负生态效应。本文综述了互花米草的正负生态效应,分别从以下4个方面展开:抗风防浪的功效与改变景观的负作用,促淤造陆的功效与改变河口水文格局的负作用,固碳效应与释放温室气体的负作用,为一些物种提供营养与栖息地的同时对其他物种栖息环境的破坏性。研究证实,互花米草的本土化倾向已比较突出,如在超过100年引种历史的美国西部维拉帕湾、引种历史近40年的旧金山湾,以及引种历史近30年的我国大丰滩涂等。对于互花米草的生态控制,应结合各地的自然、社会、经济状况,因地制宜,如在一些生态脆弱(开发过度、缺乏大型植被、蚀退现象严重)的沿海地区,防灾减灾任务艰巨,根除互花米草须谨慎;在充分利用互花米草抗风防浪和促淤造陆后,可以适时围垦,以达到某些区域大面积减除的目标;此外,综合治理与利用相结合是较为科学的举措,既充分利用互花米草生物质(加工生产新食品、保健品、生物气等),又有效控制其种子飘落和扩繁,是一项生态工程,也是一种具有生态经济效益的利国利民之举。     

Multistate approaches in computational protein design

Computational protein design (CPD) is a useful tool for protein engineers. It has been successfully applied towards the creation of proteins with increased thermostability, improved binding affinity, novel enzymatic activity, and altered ligand specificity. Traditionally, CPD calculations search and rank sequences using a single fixed protein backbone template in an approach referred to as single-state design (SSD). While SSD has enjoyed considerable success, certain design objectives require the explicit consideration of multiple conformational and/or chemical states. Cases where a "multistate" approach may be advantageous over the SSD approach include designing conformational changes into proteins, using native ensembles to mimic backbone flexibility, and designing ligand or oligomeric association specificities. These design objectives can be efficiently tackled using multistate design (MSD), an emerging methodology in CPD that considers any number of protein conformational or chemical states as inputs instead of a single protein backbone template, as in SSD. In this review article, recent examples of the successful design of a desired property into proteins using MSD are described. These studies employing MSD are divided into two categories-those that utilized multiple conformational states, and those that utilized multiple chemical states. In addition, the scoring of competing states during negative design is discussed as a current challenge for MSD.     

Major role of positive selection in the evolution of conservative segments of Drosophila proteins

Slow evolution of conservative segments of coding and non-coding DNA is caused by the action of negative selection, which removes new mutations. However, the mode of selection that affects the few substitutions that do occur within such segments remains unclear. Here, we show that the fraction of allele replacements that were driven by positive selection, and the strength of this selection, is the highest within the conservative segments of Drosophila protein-coding genes. The McDonald-Kreitman test, applied to the data on variation in Drosophila melanogaster and in Drosophila simulans, indicates that within the most conservative protein segments, approximately 72 per cent (approx. 80%) of allele replacements were driven by positive selection, as opposed to only approximately 44 per cent (approx. 53%) at rapidly evolving segments. Data on multiple non-synonymous substitutions at a codon lead to the same conclusion and additionally indicate that positive selection driving allele replacements at conservative sites is the strongest, as it accelerates evolution by a factor of approximately 40, as opposed to a factor of approximately 5 at rapidly evolving sites. Thus, random drift plays only a minor role in the evolution of conservative DNA segments, and those relatively rare allele replacements that occur within such segments are mostly driven by substantial positive selection.     

带绿色荧光蛋白标签的人细胞分裂周期蛋白25同源蛋白的真核表达及其生物学功能研究

目的:构建带增强型绿色荧光蛋白(EGFP)标签的人细胞分裂周期蛋白25同源蛋白C(cdc25c)基因的真核表达载体pEGFP-cdc25c,并检测其在人胚肾293T细胞中的表达定位情况及生物学功能。方法:采用PCR技术从实验室已有质粒中扩增人cdc25c基因,并将其克隆到pEGFP-C1载体中;将重组质粒转染人胚肾293T细胞,Western印迹检测转染细胞的表达情况,荧光显微镜观察cdc25c蛋白在细胞中的定位,并利用cdc2 Tyr15位特异性抗体验证EGFP-cdc25c作为磷酸酯酶的生物学功能。结果:双酶切和测序鉴定表明,pEGFP-cdc25c真核表达质粒构建成功;转染293T细胞后获得表达,在荧光显微镜下,表达阳性的细胞呈绿色,并定位于细胞质;Western印迹结果表明,EGFP-cdc25c能增加cdc2 Tyr15位的磷酸化水平,起到拮抗内源性cdc25c的功能。结论:构建了带EGFP标签的人cdc25c基因真核表达载体,该载体能够在哺乳动物细胞293T中表达,表达产物定位于细胞质;EGFP-cdc25c能够发挥显性负性作用,为深入研究cdc25c的生物学功能奠定了重要基础。     

Escherichia coli exhibits a membrane-related response to a small arginine- and tryptophan-rich antimicrobial peptide

Since multiresistant bacterial strains are more widespread and the victim numbers steadily increase, it is very important to possess a broad bandwidth of antimicrobial substances. Antibiotics often feature membrane-associated effect mechanisms. So, we present a membrane proteomic approach to shed light on the cellular response of Escherichia coli as model organism to the hexapeptide MP196, which is arginine and tryptophan rich. Analyzing integral membrane proteins are still challenging, although various detection strategies have been developed in the past. In particular, membrane proteomics in bacteria have been conducted very little due to the special physical properties of these membrane proteins. To obtain more information on the cellular response of the new compound group of small peptides, the tryptophan- and arginine-rich hexapeptide MP196 was subject to a comprehensive quantitative membrane proteomic study on E. coli by means of metabolic labeling in combination with membrane lipid analyses. This study provides in total 767 protein identifications including 185 integral membrane proteins, from which 624 could be quantified. Among these proteins, 134 were differentially expressed. Thereby, functional groups such as amino acid and membrane biosynthesis were affected, stress response could be observed, and the lipid composition of the membrane was significantly altered. Especially, the strong upregulation of the envelope stress induced protein. Spy indicates membrane damage, as well as the downregulation of the mechano-sensitive channel MscL beside others. Finally, the exceptional downregulation of transport systems strengthens these findings.     

Erythrocyte remodeling in Plasmodium berghei infection: the contribution of SEP family members

The malaria parasite Plasmodium largely modifies the infected erythrocyte through the export of proteins to multiple sites within the host cell. This remodeling is crucial for pathology and translocation of virulence factors to the erythrocyte surface. In this study, we investigated localization and export of small exported proteins/early transcribed membrane proteins (SEP/ETRAMPs), conserved within Plasmodium genus. This protein family is characterized by a predicted signal peptide, a short lysine-rich stretch, an internal transmembrane domain and a highly charged C-terminal region of variable length. We show here that members of the rodent Plasmodium berghei family are components of the parasitophorous vacuole membrane (PVM), which surrounds the parasite throughout the erythrocytic cycle. During P. berghei development, vesicle-like structures containing these proteins detach from the PVM en route to the host cytosol. These SEP-containing vesicles remain associated with the infected erythrocyte ghosts most probably anchored to the membrane skeleton. Transgenic lines expressing the green fluorescent protein appended to different portions of sep-coding region allowed us to define motifs required for protein export. The highly charged terminal region appears to be involved in protein-protein interactions.     

Reversing mother's curse revisited

Because of maternal mtDNA inheritance, mtDNA mutations detrimental only in males are not expected to be selected against, an effect termed the "mother's curse." However, if there is positive-assortative mating, equivalent to what was called "inbreeding" by Wade and Brandvain (2009), then selection can act to reduce the frequency of these male-specific detrimental mtDNA mutants. On the other hand, as shown here negative-assortative mating, or "outbreeding, " paradoxically can result in an increase in the frequency of male-specific detrimental mtDNA mutants. The implications of these findings are briefly discussed.     

Tunable fibre‐coupled multiphoton microscopy with a negative curvature fibre

Negative curvature fibre (NCF) guides light in its core by inhibiting the coupling of core and cladding modes. In this work, an NCF was designed and fabricated to transmit ultrashort optical pulses for multiphoton microscopy with low group velocity dispersion (GVD) at 800 nm. Its attenuation was measured to be <0.3 dB m^–1 over the range 600–850 nm and the GVD was –180 ± 70 fs² m^–1 at 800 nm. Using an average fibre output power of ～20 mW and pulse repetition rate of 80 MHz, the NCF enabled pulses with a duration of <200 fs to be transmitted through a length of 1.5 m of fibre over a tuning range of 180 nm without the need for dispersion compensation. In a 4 m fibre, temporal and spectral pulse widths were maintained to within 10% of low power values up to the maximum fibre output power achievable with the laser system used of 278 mW at 700 nm, 808 mW at 800 nm and 420 mW at 860 nm. When coupled to a multiphoton microscope, it enabled imaging of ex vivo tissue using excitation wavelengths from 740 nm to 860 nm without any need for adjustments to the set‐up.