往期刊物2014
卷册: 4, 期号: 23
癌症生物学
Detection of ALT Associated Promyelocytic Leukemia Nuclear Bodies (APBs) by Immunofluorescence-FISH (IF-FISH)
免疫荧光原位杂交法（IF-FISH）检测ALT相关的前髓细胞性白血病核体（APB）
The activation of functions that counteract the physiological shortening of telomeres in rapidly proliferating cell is prerequisite for the progression of cancer cells to full malignancy (Collado et al., 2007). In most human cancers, the length of telomere is maintained through up-regulation of telomerase whereas a telomerase-independent pathway, termed Alternative Lengthening of Telomeres (ALT) is active in about 10-15% of cancers (Johnson and Broccoli, 2007; Heaphy et al., 2011). One characteristic feature of ALT is the formation of ALT-associated Promyelocytic Leukemia nuclear bodies (APBs) (Lang et al., 2010; Yeager et al., 1999). APBs contain Promyelocytic Leukemia nuclear bodies (PML-NB) components such as PML, SP100 and SUMO, telomeric DNA and telomere associated proteins including the shelterin components TRF1, TRF2, POT1, TIN2, TPP1 and Rap1 (Yeager et al., 1999). In addition, APBs contain proteins involved in DNA repair. In particular, the presence of components of the homologous recombination machinery suggests that APBs may promote telomere elongation by facilitating the homologous recombination of telomeric templates (Nabetani et al., 2004; Stavropoulos et al., 2002). This is also supported by the requirement of the homologous recombination-associated MRN complex for APB formation (Wu et al., 2000). Furthermore, APBs are suggested to be active sites of ATM and ATR dependent DNA repair (Nabetani et al., 2004). Finally, the number of APBs increases in G2 phase of the cell cycle when recombination is mainly active (Grobelny et al., 2000). We have shown that infection of normal and malignant B lymphocytes with the human oncogenic herpesvirus Epstein-Barr virus (EBV) is associated with the induction of APBs and with numerous signs of chromosomal and genomic instability (Kamranvar et al., 2007; Kamranvar and Masucci, 2011; Kamranvar et al., 2013). Here we describe a method for detection of APBs in human B-lymphocytes. The method can be applied with minor modifications to different cell types including adherent, suspension and primary cells.
细胞生物学
TGFβ Stimulation Assay
TGFβ刺激试验
TGFβ is part of a growth factor superfamily which modulates cell growth, differentiation, adhesion, migration, ECM synthesis and apoptosis (Massague, 1998; Siegel and Massague, 2003). Free TGFβ binds to its high affinity TGFβ receptor, a receptor serine/threonine kinase, inducing phosphorylation of Smad2/3 which subsequently forms a complex with Smad4 to translocate to the nucleus where it interacts with multiple co-activators and repressors generating distinct transcriptional responses.Indeed, TGFβ signaling shows a remarkable cellular context dependency and apparent multifunctionality: e.g. TGFβ is able to inhibit cell proliferation in many epithelial cells but can also enhance proliferation in fibroblasts and cell growth in endothelial cells (Guasch et al., 2007; Xiao et al., 2012); it enhances stem cell pluripotency, but promotes differentiation in other cells (Park, 2011); in cancer development it suppresses pre-malignant cell proliferation, but at the same time promotes conversion to a metastatic phenotype (Chaudhury and Howe, 2009). The TGFβ stimulation assay monitors the responsiveness of cells to TGFβ. Upon TGFβ stimulation short-term effects such as Smad2 phosphorylation and long-term effects such as cell proliferation can be analyzed. The assay will be described for murine keratinocytes, where TGFβ strongly inhibits cell proliferation, but both assays are applicable for other cell types as well.
TGFβ Release Co-culture Assay
TGFβ 释放共培养试验
TGFβ is a potent cytokine modulating various processes including proliferation, differentiation, ECM synthesis and apoptosis (Siegel and Massague, 2003). Thus in many tissues availability of TGFβ is tightly regulated. TGFβ is secreted as an inactive complex where it is encapsulated by the latency associated protein (LAP), a ligand trap protein, which inhibits TGFβ binding to its receptor and retains TGFβ in the extracellular matrix (ten Dijke and Arthur, 2007). TGFβ can be released from the matrix and converted into its biological active form by huge number of processes including heat, high and low pH, release of reactive oxygen species (ROS) or various proteases (e.g. plasmin, elastase, matrix metalloproteinase-2 and -9) (Barcellos-Hoff and Dix, 1996; Lyons et al., 1988; Taipale et al., 1994; Yu and Stamenkovic, 2000). However, under physiological conditions the interaction of αv-class integrins with the RGD tripeptide motif in the LAP protein represents the key factor for TGFβ release in vivo. The relevance of integrin mediated TGFβ release for in vivo development and homeostasis is further underlined by the observation that mice with the integrin-binding deficient LAP proteins (RGD motif mutated to RGE) recapitulate all major phenotypes of TGFβ1 null mice, including multi-organ inflammation and defects in vasculogenesis (Shull et al., 1992; Yang et al., 2007). This striking phenotype overlap with TGFβ deficient mice and phenotypes of mice lacking αv-class integrins (Aluwihare et al., 2009; Bader et al., 1998) demonstrates an essential interconnection of integrins with TGFβ signaling in vivo, while the role of non-integrin mediated release mechanisms (ROS, pH, proteolytic cleavage etc.) during development remains less clear. The TGFβ release assay measures the ability of cells to release TGFβ from a matrix. The assay was developed by (Annes et al., 2004) and we further optimized the protocol for keratinocytes. For other cell types the cell culture medium and culturing conditions would need to be adapted accordingly. In keratinocytes TGFβ release is mainly mediated by αvβ6 integrin but also integrin αvβ3, αvβ5 and αvβ8 have been shown to liberate TGFβ, while other RGD binding integrins, such as α5β1 or α8β1 cannot release TGFβ (Asano et al., 2005a, 2005b; Mu et al., 2002; Munger et al., 1999). Mechanistically, the interaction with αvβ3, αvβ5 or αvβ6 integrin induces a conformational change in the LAP-TGFβ by generating an actin cytoskeleton dependent pulling force, allowing TGFβ to access its receptors. For αvβ8 integrin mediated TGFβ release it was shown that proteolytic cleavage is involved [see (Mu et al., 2002) for blocking conditions of TGFβ release by proteolytic cleavage and αvβ8 integrin]. The following protocol is optimized for the study of αvβ6-integrin mediated TGFβ release in keratinocytes.
微生物学
Minimal Inhibitory Concentration (MIC) Assay for Acinetobacter baumannii
鲍氏不动杆菌的最小抑菌浓度（MIC）测定
Minimal inhibition concentration (MIC) is the lowest concentration of an antimicrobial agent that can inhibit the visible growth of a microorganism after overnight incubation. MIC determination is used as not only a diagnostic tool in treating bacterial infections for clinicians but also a research method in evaluating the efficacy of an antimicrobial. Multidrug resistance Acinetobacter baumannii (A. baumannii) has emerged in recent years. Accurate determination of resistance by MIC assay is important in coping with this superbug. Here we described a protocol for determining MIC for A. baumannii in hope of assisting researchers and physicians in confirming resistance of clinical isolates correctly.
Enzymatic Activity Assays in Yeast Cell Extracts
酵母细胞提取物的酶活性分析
Saccharomyces cerevisiae (S. cerevisiae) (commonly known as baker’s yeast) is a model organism that has a similar upstream base excision repair (BER) pathway for the repair of methylated bases as that in mammalian cells, and it is very easy to maintain in the laboratory environment. Here, we described a method to prepare cell extracts from yeast to investigate their enzymatic activities. This protocol is a quick and efficient way to make yeast cell extracts without using commercial kits.
Visualization of Cell Complexity in the Filamentous Cyanobacterium Mastigocladus laminosus by Transmission Electron Microscopy (TEM)
透射电镜（TEM）法观察分析丝状蓝细菌层理鞭枝藻细胞复杂度
The cyanobacterium Mastigocladus laminosus (M. laminosus) is one of the most morphologically complex prokaryotes. It forms long chains of cells that are connected via septal junction complexes; such complexes allow diffusion of metabolites and regulators between neighboring cells. Cellular division occurs in multiple planes, resulting in the formation of true branches, and cell differentiation leads to the formation of specialized cell types for nitrogen fixation (heterocysts) and culture dispersal (hormogonia and necridia). Here, we describe a detailed protocol for the preparation of M. laminosus for TEM in order to visualize the ultrastructural properties of the organism. The presented preparation method is based on adding potassium permanganate as fixative which has been shown to increases the contrast of membranes (Luft, 1956), making it suitable for studies in cyanobacteria where the visualization of the photosynthetic membranes is important.
Induction of Tigecycline Resistance in Acinetobacter baumannii
鲍氏不动杆菌中替加环素抗性的诱导
Multidrug resistance Acinetobacter baumannii (A. baumannii) (MDRAB) has emerged as a serious threat in hospitals in recent years. Currently, there are few antibiotics, including tigecycline, available to treat infections caused by MDRAB effectively. Both tigecycline-resistant and tigecycline-susceptible isogenic strains of MDRAB are valuable in understanding the mechanisms underlying tigecycline resistance. To get the isogenic strains in the laboratory, we describe a protocol for induction of tigecycline resistance in A. buamannii by serial passage to plates with tigecycline of different concentrations. The minimal inhibitory concentration of A. baumannii by tigecycline was determined according to the protocol “Minimal Inhibitory Concentration (MIC) Assay for Acinetobacter baumannii” (Lin et al., 2014b).
神经科学
Fluorescent Measurement of Synaptic Activity Using SynaptopHluorin in Isolated Hippocampal Neurons
采用SynaptopHluorin在分离海马神经元中进行突触活性荧光测量
This protocol comprises the entire process of fluorescent measurement of vesicle recycling using the probe SynaptopHluorin, a pH-dependent GFP variant whose fluorescence increases at the synapse upon vesicle release due to fluorescence quenching in acidic vesicles. This technique provides a genetic tool to monitor synaptic vesicle recycling in real time in cultured hippocampal neurons.
Creating a Rat Model of Chronic Variate Stress
大鼠慢性多种可变应激模型创建
Stress is a condition of human experience and an important factor in the onset of various diseases. There are numerous studies showing how stress can accelerate cell aging, immune senescence and some age-related diseases such as neurodegenerative disorders and osteoporosis. However, the effects of stress have different consequences depending on the type, duration or severity and predictability of the stressor applied. Although stress can be beneficial in its acute phase, repeated and severe stressful stimuli produce adverse effects. There are different models of stress depending on the exposure time; acute (when the stressor is applied for a short time, e.g. hours or days, and intensely) or chronic (when the stressor is applied for a long time, e.g. weeks or months, and less intensely. In these cases, the stressor can be repeated each time or different stressors can be used). The latter model is most frequently used to achieve similar conditions to those found in human diseases related to stress. Also, there are several different paradigms depending on the purpose of the study [development of drug therapies or modeling depressive behaviors; for the different paradigms see Dagnino-Subiabre, (2012)]. Here, we describe a 9-day variable-stressor paradigm with repeated and prolonged stimulation and a random daily stressor over days or weeks to minimize its predictability. This protocol has been adapted from other models of variable stress with significant modifications. The absence of predictability of the stressor applied is an important characteristic of this model compared to other models in which repeated stress is used. We avoid the use of a strong stressor, such as foot shock or tail pinch, and describe an easily reproducible new chronic mild stress model. Some models of chronic mild stress have been reported to lead to a wide range of behavioral disturbances and have been proposed as models of depression in animal studies (Cryan et al., 2005).
植物科学
Determination of Soluble Sugars in Arabidopsis thaliana Leaves by Anion Exchange Chromatography
阴离子交换色谱法测定拟南芥中的可溶性糖
Determination of soluble sugars is basic for the study of carbon metabolism in plants. Soluble sugar quantitation can be achieved by enzymatic methods implying different coupled reactions. Here we describe a simple method that allows rapid determination of the most abundant soluble sugars (glucose, fructose and sucrose) in Arabidopsis leaves by anion exchange chromatography. We have applied this method to study the levels of soluble sugars during the photoperiodic transition to flowering (Ortiz-Marchena et al., 2014).
Infection Assays of Tomato and Apple Fruit by the Fungal Pathogen Botrytis cinerea
真菌病原体灰葡萄孢菌对番茄和苹果果实的感染分析
Botrytis cinerea (B. cinerea) is an aggressive fungal pathogen that infects more than 200 plant species. Furthermore, the pathogen can attack fruits of some plants, such as tomato and apple. B. cinerea has become one of the model systems in molecular phytopathology because of its economic importance and sophisticated genetic operation methods. Virulence assays are very important in the study of fungal pathogenesis. This protocol details the artificial inoculation procedure of B. cinerea on tomato and apple fruits. It also can be used to analyse the virulence of postharvest fungal pathogens on other fruits, such as pear, peach, jujube and so on.
CytoTrap Two-Hybrid Screening Assay
CytoTrap双杂交筛选系统
CytoTrap two-hybrid system provides an alternate strategy to detect protein-protein interactions in yeast. In this system, bait protein is fused with human son of sevenless (hSos) protein (Li et al., 1993), and a cDNA library or prey protein is expressed by fusion with myristoylation signal which anchors the prey fusion protein to yeast cell membrane. Protein interaction between bait and prey proteins recruits the hSos protein to the cell membrane, where hSos activates the Ras signaling pathway, leading to the survival of temperature-sensitive Saccharomyces cerevisiae (S. cerevisiae) strain cdc25H at 36 °C. In the CytoTrap two-hybrid system, detection of protein interaction occurs in the cytoplasm near cell membrane and is not dependent on transcription activation of reporter genes. Hence, the system is particularly useful for identifying interaction partners of transcription factors and proteins that need post-translational modification in the cytoplasm, which could not be used as bait proteins in conventional transactivation-based yeast two-hybrid systems. Here we describe the construction of a cDNA library from the model plant Arabidopsis and a procedure for screening interaction proteins of AtSR1/CAMTA3, a Ca2+/CaM-regulated transcription factor from this library. This procedure could be adapted to identify interacting partners of interested proteins from other organisms.
Vanillin Assay of Arabidopsis Seeds for Proanthocyanidins
香草醛法检测拟南芥种子的原花青素
Proanthocyanidins (PAs) are colorless flavonoid polymers and deposit in Arabidopsis seed coat specifically. Oxidation of PAs gives rise to brown color of mature seeds. PA accumulation can be affected by a number of growth conditions, such as temperature and sun light. PAs, which are converted from anthocyanidins, can protect seeds from outer environment and have a positive effect in seed longevity (Debeaujon, 2003). Vanillin turns red upon binding to leucoanthoanthocyanidins, catechins and monomers and terminal subunits of PAs (Butler et al., 1982; Deshpande et al., 1986). Based on this principle, PA deposition in Arabidopsis seed coat can be visualized.
In situ Digestion of Wheat Cell-wall Polysaccharides
小麦细胞壁多糖的原位消化
Cell walls of the wheat endosperm are mostly composed of arabinoxylans (AX) and mixed (1→3), (1→4)-β-glucans (BG) (Saulnier et al., 2012). Here, we present an optimized protocol to degrade enzymatically these cell-wall polysaccharides into oligosaccharides, directly from wheat grain cross sections. The main difficulty is to provide a sufficient amount of humidity for the enzyme to be active, while the amount of liquid at the surface of the tissue should stay low to prevent any delocalization of the released products. With this protocol, enzymatic degradation was shown to be efficient and delocalization of released oligosaccharides was estimated below 50 µm (Veličković et al., 2014). Although it can be employed for other purposes, this in situ enzymatic digestion was primarily developed to obtain molecular images of the cross-sections of wheat endosperm by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (Veličković et al., 2014). The cell wall polysaccharides are heterogeneous in structure, exhibit high masses and are entangled into complex networks. Thus, they are not amenable to direct analysis by mass spectrometry and they need to be degraded into smaller compounds as a first step. In this protocol, additional steps corresponding to the deposition of the MALDI matrix are also described.
Purification of Starch Granules from Arabidopsis Leaves and Determination of Granule-Bound Starch Synthase Activity
植物叶片淀粉粒的纯化和淀粉粒结合的淀粉合酶的活性分析
Starch constitutes the most important carbon reserve in plants and is composed of branched amylopectin and linear amylose. The latter is synthesized exclusively by the Granule-Bound Starch Synthase (GBSS, EC 2.4.1.21). Here we report a readily reproducible, specific and highly sensitive protocol, which includes the isolation of intact starch granules from Arabidopsis thaliana leaves and the subsequent determination of GBSS activity. We have applied this method to study GBSS activity in diurnal cycles in vegetative growth and during the photoperiodic transition to flowering in Arabidopsis (Tenorio et al., 2003; Ortiz-Marchena et al., 2014).