In Vitro Analysis of PDZ-dependent CFTR Macromolecular Signaling Complexes

Cystic fibrosis transmembrane conductance regulator (CFTR), a chloride channel located primarily at the apical membranes of epithelial cells, plays a crucial role in transepithelial fluid homeostasis^1-3. CFTR has been implicated in two major diseases: cystic fibrosis (CF)⁴ and secretory diarrhea⁵. In CF, the synthesis or functional activity of the CFTR Cl- channel is reduced. This disorder affects approximately 1 in 2,500 Caucasians in the United States⁶. Excessive CFTR activity has also been implicated in cases of toxin-induced secretory diarrhea (e.g., by cholera toxin and heat stable E. coli enterotoxin) that stimulates cAMP or cGMP production in the gut⁷.Accumulating evidence suggest the existence of physical and functional interactions between CFTR and a growing number of other proteins, including transporters, ion channels, receptors, kinases, phosphatases, signaling molecules, and cytoskeletal elements, and these interactions between CFTR and its binding proteins have been shown to be critically involved in regulating CFTR-mediated transepithelial ion transport in vitro and also in vivo^8-19. In this protocol, we focus only on the methods that aid in the study of the interactions between CFTR carboxyl terminal tail, which possesses a protein-binding motif [referred to as PSD95/Dlg1/ZO-1 (PDZ) motif], and a group of scaffold proteins, which contain a specific binding module referred to as PDZ domains. So far, several different PDZ scaffold proteins have been reported to bind to the carboxyl terminal tail of CFTR with various affinities, such as NHERF1, NHERF2, PDZK1, PDZK2, CAL (CFTR-associated ligand), Shank2, and GRASP^20-27. The PDZ motif within CFTR that is recognized by PDZ scaffold proteins is the last four amino acids at the C terminus (i.e., 1477-DTRL-1480 in human CFTR)²⁰. Interestingly, CFTR can bind more than one PDZ domain of both NHERFs and PDZK1, albeit with varying affinities²². This multivalency with respect to CFTR binding has been shown to be of functional significance, suggesting that PDZ scaffold proteins may facilitate formation of CFTR macromolecular signaling complexes for specific/selective and efficient signaling in cells^16-18.Multiple biochemical assays have been developed to study CFTR-involving protein interactions, such as co-immunoprecipitation, pull-down assay, pair-wise binding assay, colorimetric pair-wise binding assay, and macromolecular complex assembly assay^16-19,28,29. Here we focus on the detailed procedures of assembling a PDZ motif-dependent CFTR-containing macromolecular complex in vitro, which is used extensively by our laboratory to study protein-protein or domain-domain interactions involving CFTR^16-19,28,29.     

Identifying potential areas for biofuel production and evaluating the environmental effects: a case study of the James River Basin in the Midwestern United States

Biofuels are now an important resource in the United States because of the Energy Independence and Security Act of 2007. Both increased corn growth for ethanol production and perennial dedicated energy crop growth for cellulosic feedstocks are potential sources to meet the rising demand for biofuels. However, these measures may cause adverse environmental consequences that are not yet fully understood. This study 1) evaluates the long‐term impacts of increased frequency of corn in the crop rotation system on water quantity and quality as well as soil fertility in the James River Basin and 2) identifies potential grasslands for cultivating bioenergy crops (e.g. switchgrass), estimating the water quality impacts. We selected the soil and water assessment tool, a physically based multidisciplinary model, as the modeling approach to simulate a series of biofuel production scenarios involving crop rotation and land cover changes. The model simulations with different crop rotation scenarios indicate that decreases in water yield and soil nitrate nitrogen (NO₃‐N) concentration along with an increase in NO₃‐N load to stream water could justify serious concerns regarding increased corn rotations in this basin. Simulations with land cover change scenarios helped us spatially classify the grasslands in terms of biomass productivity and nitrogen loads, and we further derived the relationship of biomass production targets and the resulting nitrogen loads against switchgrass planting acreages. The suggested economically efficient (planting acreage) and environmentally friendly (water quality) planting locations and acreages can be a valuable guide for cultivating switchgrass in this basin. This information, along with the projected environmental costs (i.e. reduced water yield and increased nitrogen load), can contribute to decision support tools for land managers to seek the sustainability of biofuel development in this region.     

Different Roles for Contracture and Calpain in Calcium Paradox-Induced Heart Injury

The Ca²⁺ paradox represents a good model to study Ca²⁺ overload injury in ischemic heart diseases. We and others have demonstrated that contracture and calpain are involved in the Ca²⁺ paradox-induced injury. This study aimed to elucidate their roles in this model. The Ca²⁺ paradox was elicited by perfusing isolated rat hearts with Ca²⁺-free KH media for 3 min or 5 min followed by 30 min of Ca²⁺ repletion. The LVDP was measured to reflect contractile function, and the LVEDP was measured to indicate contracture. TTC staining and the quantification of LDH release were used to define cell death. Calpain activity and troponin I release were measured after Ca²⁺ repletion. Ca²⁺ repletion of the once 3-min Ca²⁺ depleted hearts resulted in almost no viable tissues and the disappearance of contractile function. Compared to the effects of the calpain inhibitor MDL28170, KB-R7943, an inhibitor of the Na⁺/Ca²⁺ exchanger, reduced the LVEDP level to a greater extent, which was well correlated with improved contractile function recovery and tissue survival. The depletion of Ca²⁺ for 5 min had the same effects on injury as the 3-min Ca²⁺ depletion, except that the LVEDP in the 5-min Ca²⁺ depletion group was lower than the level in the 3-min Ca²⁺ depletion group. KB-R7943 failed to reduce the level of LVEDP, with no improvement in the LVDP recovery in the hearts subjected to the 5-min Ca²⁺ depletion treatment; however, KB-R7943 preserved its protective effects in surviving tissue. Both KB-R7943 and MDL28170 attenuated the Ca²⁺ repletion-induced increase in calpain activity in 3 min or 5 min Ca²⁺ depleted hearts. However, only KB-R7943 reduced the release of troponin I from the Ca²⁺ paradoxic heart. These results provide evidence suggesting that contracture is the main cause for contractile dysfunction, while activation of calpain mediates cell death in the Ca²⁺ paradox.     

LATS1过表达对肺癌A549细胞增殖及周期的影响

通过过表达手段上调大肿瘤抑制因子1（1arge tumor suppressor gene 1,LATS1）基因在A549细胞中的表达,研究LATS1对A549细胞生长和细胞周期调控的作用。构建过表达LATS1基因的慢病毒载体,转染A549N胞株,采用RT-PCR和蛋白质印迹法检测转染后A549细胞中LATS1、YAPmRNA和蛋白的表达效率;流式细胞术检测细胞凋亡、周期情况：CCK-8检测细胞的增殖水平变化。结果发现,过表达LATS1慢病毒载体转染A549细胞株后,LATS1mRNA及蛋白表达水平高于未处理组及转染空载体组,YAPmRNA及蛋白表达水平低于未处理组及转染空载体组;过表达LATS1慢病毒转染后,A549细胞增殖率从第五天开始低于对照组（P〈0．05）,过表达组细胞G1期比例明显增高（P〈0．05）,凋亡率明显增加（P〈0．05）,差异均有统计学意义。以上结果提示,LATS1可通过下调YAP的表达水平促进A549细胞的凋亡,诱导G1期阻滞,降低细胞的增殖能力。     

Frequency Analysis and Anti-Shock Mechanism of Woodpecker＇s Head Structure

The mechanical properties of the skull and the anti-shock characteristics of woodpecker＇s head were investigated by ex- periment and numerical simulation. We measured the micro-Young＇s modulus of the skull by nano-indentation method and calculated the macro-equivalent Young＇s modulus of the skull at different positions using homogenization theory. Based on the Computerized Tomography （CT） images of woodpecker head, we then built complete and symmetric finite element models of woodpecker＇s skull and its internal structure and performed modal analysis and stress spectrum analysis. The numerical results show that the application of pre-tension force to the hyoid bone can increase the natural frequency of woodpecker＇s head. The first natural frequency under the pre-tension force of 25 N reaches 57 Hz, which is increased by 21.3% from the non-pre-tension state and is more than twice the working frequency of woodpecker （20 Hz 25 Hz）. On the application of impact force to the tip of beak for 0.6 ms, high magnitudes of stress component occur at around 100 Hz and 8,000 Hz, far away from both the working frequencies and the natural frequencies of woodpecker head. The large gaps among the natural, working and stress response frequencies enable the woodpecker to effectively protect its brain from the resonance injury.     

Spectroscopic characterization and molecular weight distribution of dissolved organic matter in sediment porewaters from Lake Erhai, Southwest China

Dissolved organic matter (DOM) in sediment porewaters from Lake Erhai, Southwest China was investigated using dissolved organic carbon (DOC) concentration, UV absorbance, fluorescence and molecular weight distribution. DOC exhibited a high concentration at the sediment–water interface with a rapid decrease to the oxic–anoxic interface at approximately 7 cm, and then increased with depth. Similar trends were also found for the UV absorption coefficients at 254 and 280 nm in the porewaters. DNA in the sediment was also measured, which confirmed the high abundance of aerobic bacteria in the upper layer of the sediment. Both humic-like (peaks A and C) and protein-like (peaks B and D) fluorescence were observed in the porewater DOM, and their fluorescence intensities exhibited a similar porewater profile as DOC concentration. A strong correlation was found between the peak fluorescence intensity ratio r(A, C) and r(D, B). Both the fluorescence index and UV absorption coefficient at 254 nm suggested a dramatic increase in aromaticity of porewater DOM across the oxic–anoxic interface. Porewater DOM exhibited a multimodal distribution of molecular weight with a relatively low polydispersity. The results of this study offer significant insight into the nature and properties of DOM in freshwater ecosystems.     

Magnesium Deficiency Enhances Hydrogen Peroxide Production and Oxidative Damage in Chick Embryo Hepatocyte In Vitro

Magnesium deficiency and oxidative stress have been identified as correlative factors in many diseases. The origin of free radicals correlated with oxidative damage resulting from Mg-deficiency is unclear at the cellular level. To investigate whether hydrogen peroxide (H₂O₂) is associated in the oxidative stress induced by Mg-deficiency, the effect of Mg²⁺ deficiency (0, 0.4, 0.7 mM) on the metabolism of H₂O₂ was investigated in cultured chick embryo hepatocytes. After being cultured in the media with various concentrations of Mg²⁺ for 1, 2, 4, 6 and 10 days, parameters of H₂O₂ production, catalase activity, lipid peroxidation, intracellular total Mg and cell viability were analyzed. Results demonstrated that long-term incubation of chick embryo hepatocyte in extracellular Mg²⁺-deprivative and Mg²⁺-deficient (0.4 mM) states significantly enhanced the production of H₂O₂ (approximately twofold, respectively) and lipid peroxidation in the cell cultures, while decreasing the cell viability. Additionally, the reversing action of Mg²⁺ re-added to 1.0 mM and the partial reversing action of dimethylthiourea suggested that (i) [Mg²⁺]_e deficiency induced the increase of H₂O₂ production, (ii) [Mg²⁺]_e deficiency decreased catalase activity in chick embryo hepatocyte in vitro, subsequently causing oxidative stress and cell peroxidative damage.     

Cryopyrin and pyrin activate caspase-1, but not NF-kappaB, via ASC oligomerization

Mutations in cryopyrin and pyrin proteins are responsible for several autoinflammatory disorders in humans, suggesting that these proteins play important roles in regulating inflammation. Using a HEK293 cell-based reconstitution system that stably expresses ASC and procaspase-1 we demonstrated that neither cryopyrin nor pyrin or their corresponding disease-associated mutants could significantly activate NF-kappaB in this system. However, both cryopyrin and two disease-associated cryopyrin mutants induced ASC oligomerization and ASC-dependent caspase-1 activation, with the disease-associated mutants being more potent than the wild-type (WT) cryopyrin, because of increased self-oligomerization. Contrary to the proposed anti-inflammatory activity of WT pyrin, our results demonstrated that pyrin, like cryopyrin, can also assemble an inflammasome complex with ASC and procaspase-1 leading to ASC oligomerization, caspase-1 activation and interleukin-1beta processing. Thus, we propose that pyrin could function as a proinflammatory molecule.     

TRAF6 regulates cell fate decisions by inducing caspase 8-dependent apoptosis and the activation of NF-kappaB

Tumor necrosis factor receptor-associated factor 6 (TRAF6) functions as an adaptor, positively regulating the NF-kappaB pathway. Here we report a new function of human TRAF6, the direct stimulation of apoptosis. The mechanism of apoptosis induction results from the capacity of human TRAF6 to interact and activate caspase 8. Both the C-terminal TRAF domain of human TRAF6, which directly interacts with the death effector domain of pro-caspase 8, and the N-terminal RING domain, which is required for activation of caspase 8, are necessary for the induction of apoptosis. The role of endogenous TRAF6 in regulating apoptosis was confirmed by extinguishing TRAF6 expression with specific small-hairpin RNA that resulted in diminished spontaneous apoptosis and resistance to induced apoptosis. In contrast to the human molecule, murine TRAF6 displayed less ability to induce apoptosis and a greater capacity to stimulate NF-kappaB activity. Human and murine TRAF6 are similar except in the region between zinc finger 5 and the TRAF domains. Reciprocal transfer of this connecting region completely exchanged the ability of human and murine TRAF6 to induce apoptosis and activate NF-kappaB. Unique regions of TRAF6 therefore play an important role in determining cell fate.     

Prediction and functional analysis of the replication origin of the linear plasmid pSCL2 in Streptomyces clavuligerus

pSCL2 (120 kb), one of the linear plasmids found in Streptomyces clavuligerus NRRL3585, was isolated and partially sequenced. Computational analysis of the central region of pSCL2 revealed the presence of two open reading frames that appear to encode proteins highly homologous to RepL1 and RepL2, replication proteins from pSLA2-L, the large linear plasmid in Streptomyces rochei. The S. clavuligerus open reading frames were designated repC1 and repC2, encoding the proteins RepC1 (150 amino acids) and RepC2 (102 amino acids), respectively. The RepC and RepL proteins have identical translation features and very similar predicted secondary and tertiary structures. Functional analysis confirmed that RepC1 is essential for replication initiation of pSCL2, whereas RepC2 is dispensable but may play a role in copy number control. The RepC and RepL proteins do not show similarity to any other bacterial plasmid replication proteins. Three regions of DNA sequence, Box 1 (1050-850 bp), Box 2 (723-606 bp), and Box 3 (224-168 bp), located upstream of repC1, were also shown to be essential or very important for replication of pSCL2.