Brain site-specific proteome changes in aging-related dementia

This study is aimed at gaining insights into the brain site-specific proteomic senescence signature while comparing physiologically aged brains with aging-related dementia brains (for example, Alzheimer''s disease (AD)). Our study of proteomic differences within the hippocampus (Hp), parietal cortex (pCx) and cerebellum (Cb) could provide conceptual insights into the molecular mechanisms involved in aging-related neurodegeneration. Using an isobaric tag for relative and absolute quantitation (iTRAQ)-based two-dimensional liquid chromatography coupled with tandem mass spectrometry (2D-LC-MS/MS) brain site-specific proteomic strategy, we identified 950 proteins in the Hp, pCx and Cb of AD brains. Of these proteins, 31 were significantly altered. Most of the differentially regulated proteins are involved in molecular transport, nervous system development, synaptic plasticity and apoptosis. Particularly, proteins such as Gelsolin (GSN), Tenascin-R (TNR) and AHNAK could potentially act as novel biomarkers of aging-related neurodegeneration. Importantly, our Ingenuity Pathway Analysis (IPA)-based network analysis further revealed ubiquitin C (UBC) as a pivotal protein to interact with diverse AD-associated pathophysiological molecular factors and suggests the reduced ubiquitin proteasome degradation system (UPS) as one of the causative factors of AD.     

High throughput screening technology and the small molecules modulating aging related signals

Aging and its related diseases are severe issues in modern society. Many efforts have been made to understand the mechanisms of aging and to find the ways to prevent age-related diseases. Identifying the compounds targeting aging-related signals is a challenging work because there are so many proteins and signals involved. Recently, alone with the progresses in high throughput screening (HTS) technology, increasing numbers of small molecules targeting aging-related pathologic processes have been identified. In this review, we introduce the basic workflow, classification and assay strategies of HTS technology, and sort out known small molecules identified via HTS technology by their roles in aging related diseases, such as neural degenerative diseases, diabetes and tumors. Given the fact that application of HTS on aging research is still at an early stage, we also summarize the cellular mechanisms about aging process, paralleled with the compounds which can modulate the functions of proteins important for aging signals. Finally, we briefly discuss some advanced HTS technologies for their potent applications on the discovery of anti-aging compounds. The main purpose of this review is to provide updated and useful information to those who are interested in pharmacology and HTS technology, but not familiar with aging biology, or vice versa.     

FTIR Spectroscopy as a Tool to Study Age-Related Changes in Cardiac and Skeletal Muscle of Female C57BL/6J Mice

Studying aging is important to further understand the molecular mechanisms underlying this physiological process and, ideally, to identify a panel of aging biomarkers. Animals, in particular mice, are often used in aging studies, since they mimic important features of human aging, age quickly, and are easy to manipulate. The present work describes the use of Fourier Transform Infrared (FTIR) spectroscopy to identify an age-related spectroscopic profile of the cardiac and skeletal muscle tissues of C57BL/6J female mice. We acquired ATR-FTIR spectra of cardiac and skeletal muscle at four different ages: 6; 12; 17 and 24 months (10 samples at each age) and analyzed the data using multivariate statistical tools (PCA and PLS) and peak intensity analyses. The results suggest deep changes in protein secondary structure in 24-month-old mice compared to both tissues in 6-month-old mice. Oligomeric structures decreased with age in both tissues, while intermolecular β-sheet structures increased with aging in cardiac muscle but not in skeletal muscle. Despite FTIR spectroscopy being unable to identify the proteins responsible for these conformational changes, this study gives insights into the potential of FTIR to monitor the aging process and identify an age-specific spectroscopic signature.     

Network-Based Identification of Novel Connections Among Apoptotic Signaling Pathways in Cancer

MicroRNAs (miRNAs), highly conserved, non-coding endogenous RNA and nearly ~22 nucleotides (nt) in length, are well-known to regulate several apoptotic pathways in cancer. In this study, we computationally constructed the initial human apoptotic PPI network by several online databases, and further integrated these high-throughput datasets into a Na?ve Bayesian model to predict protein functional connections. Based on the modified apoptotic network, we identified several apoptotic hub proteins such as TP53, SRC, M3K3/5/8, cyclin-dependent kinase2/6, TNFR16/19, and TGF-?? receptor 1/2. Subsequently, we identified some microRNAs that could target the aforementioned apoptotic hub proteins by using TargetScan, PicTar, and Diana-MicroH. In conclusion, these results demonstrate the PPI network-based identification of new connections amongst apoptotic pathways in cancer, which may shed new light on the intricate relationships between core apoptotic pathways and some targeted miRNAs in human cancers.     

Age-related decline in expression of calnexin

Aging is accompanied by the changes in the cells that decrease their capacity to respond to various forms of stress. Cells are known to respond to stresses through expression of stress-response proteins, heat-shock proteins composed of molecular chaperones. Recent studies suggest that chaperone level and stress-induced chaperone expression could decrease with aging. The aim of the present study is to identify chaperones that show a significant change in protein expression with aging. We used an in vitro aging model system of human diploid fibroblasts (HDF). Proteome analysis of HDF showed that endoplasmic reticulum (ER) chaperone, calnexin, significantly decreased with aging. Oxidative stress-induced expression of calnexin also attenuated in old HDF compared to young cells. These findings suggest calnexin decreases with aging and might contribute to a cytoprotection in a variety of human age-related diseases.     

Isolation and Characterization of Heparan Sulfate from Human Lung Tissues

Glycosaminoglycans are a class of linear, highly negatively charged, O-linked polysaccharides that are involved in many (patho)physiological processes. In vitro experimental investigations of such processes typically involve porcine-derived heparan sulfate (HS). Structural information about human, particularly organ-specific heparan sulfate, and how it compares with HS from other organisms, is very limited. In this study, heparan sulfate was isolated from human lung tissues derived from five donors and was characterized for their overall size distribution and disaccharide composition. The expression profiles of proteoglycans and HS-modifying enzymes was quantified in order to identify the major core proteins for HS. In addition, the binding affinities of human HS to two chemokines—CXCL8 and CCL2—were investigated, which represent important inflammatory mediators in lung pathologies. Our data revealed that syndecans are the predominant proteoglycan class in human lungs and that the disaccharide composition varies among individuals according to sex, age, and health stage (one of the donor lungs was accidentally discovered to contain a solid tumor). The compositional difference of the five human lung HS preparations affected chemokine binding affinities to various degrees, indicating selective immune cell responses depending on the relative chemokine–glycan affinities. This represents important new insights that could be translated into novel therapeutic concepts for individually treating lung immunological disorders via HS targets.     

Aging impairs insulin-stimulated glucose uptake in rat skeletal muscle via suppressing AMPKalpha

Insufficient intracellular fat oxidation is an important contributor to aging-related insulin resistance, while the precise mechanism underlying is unclear. AMP-activated protein kinase (AMPK) is an important regulator of intracellular fat oxidation and was evidenced to play a key role in high-glucose and high-fat induced glucose intolerance. In the present study, we investigated whether altered AMPK expression or activity was also involved in aging-related insulin resistance. Insulin sensitivity of rats' skeletal muscles was evaluated using in-vitro glucose uptake assay. Activity of alpha subunit of AMPK (AMPKalpha) was evaluated by measuring the phosphorylation of both AMPKalpha (P-AMPKalpha) and acetyl-CoA carboxylase (P-ACC), while expression of AMPKalpha was assessed by determining the mRNA levels of AMPKalpha1 and AMPKalpha2, and protein contents of AMPKalpha. Compared with 4-month old rats, 24-month old rats exhibited obviously impaired insulin sensitivity. At the same time, AMPKalpha activity significantly decreased, while AMPKalpha expression did not alter during aging. Glucose transporter 4 expression also decreased in old rats. Compared with 24-month old rats, administration of the specific activator of AMPK, 5-aminoimidazole-4-carboxamide riboside (AICAR), significantly elevated AMPKalpha activity and GluT4 expression. Also, aging-related insulin resistance was significantly ameliorated by AICAR treatment. In conclusion, aging-related insulin resistance is associated with impaired AMPKalpha activity and could be ameliorated by AICAR, thus indicating a possible role of AMPK in aging-induced insulin resistance.     

Prediction of human-Streptococcus pneumoniae protein-protein interactions using logistic regression

Streptococcus pneumoniae is a major cause of mortality in children under five years old. In recent years, the emergence of antibiotic-resistant strains of S. pneumoniae increases the threat level of this pathogen. For that reason, the exploration of S. pneumoniae protein virulence factors should be considered in developing new drugs or vaccines, for instance by the analysis of host-pathogen protein-protein interactions (HP-PPIs). In this research, prediction of protein-protein interactions was performed with a logistic regression model with the number of protein domain occurrences as features. By utilizing HP-PPIs of three different pathogens as training data, the model achieved 57–77 % precision, 64–75 % recall, and 96–98 % specificity. Prediction of human-S. pneumoniae protein-protein interactions using the model yielded 5823 interactions involving thirty S. pneumoniae proteins and 324 human proteins. Pathway enrichment analysis showed that most of the pathways involved in the predicted interactions are immune system pathways. Network topology analysis revealed β-galactosidase (BgaA) as the most central among the S. pneumoniae proteins in the predicted HP-PPI networks, with a degree centrality of 1.0 and a betweenness centrality of 0.451853. Further experimental studies are required to validate the predicted interactions and examine their roles in S. pneumoniae infection.     

Durability of a polymer with triple-shape properties

A series of cyclic thermo-mechanical measurements was conducted on segregated poly(ester urethane) to study substantial changes in triple-shape properties as a result of hydrolytic aging (80 °C). Prior to the analysis of aging effects, a concept of triple-shape testing was elaborated, starting with the implementation of two distinct programming units. The first one included a deformation at 60 °C to ?_m1 = 100% (temporary shape B) and its fixing through soft segment crystallization by cooling to −20 °C under constant strain. The second one consisted of a deformation at −20 °C to ?_m2 = 200% (temporary shape A) and its stabilization through soft segment vitrification as achieved by cooling to −60 °C under fixed strain constraint. Then, gradual heating of the polymer from below to above its thermal transition temperatures gave two independent shape recovery responses in the reverse order of shape fixing: A → B through passing the glass transition by heating from −60 to 23 °C and B → C (back to the permanent shape), when heating the material from 23 to 60 °C and thus above its soft segment melting temperature. In a progressive approach, the storage of loading history through the sequential fixing of two temporary shapes was proven by the development of shape recovery stresses under constrained environment. With the implementation of the two testing methods several aging-related effects could be detected. Good shape fixing abilities ≥90% for both shapes were found and contrasted by significant changes in shape recoverabilities and stress storage capacities. Further insights derived from differential scanning calorimetry (DSC) measurements, indicating an aging-related growth in soft segment crystallinity, and dynamic mechanical analysis (DMA), suggesting a plasticizer effect of water onto the polymer matrix and that aging favoured an increase in cross-linking density.     

Application of capillary immunoelectrophoresis revealed an age‐ and gender‐dependent regulated expression of PrPC in liver

The cellular prion protein (PrPC) is a glycoprotein, anchored to the plasma membrane and abundantly expressed in the central nervous system. The expression of PrPC in the peripheral tissues is low and only little information is available on its functions in the nonneuronal tissues. The antioxidant function of PrPC during the activation of hepatic stellate cells has already been reported. Therefore, the aim of the study was to expand our knowledge on the functions of PrPC by detailed characterization of its expressional profile in the liver. In a combined strategy by using capillary immunoelectrophoresis and standard techniques, we have shown a sexually dimorphic expression of PrPC in mice and human liver tissues. Further, we showed a significant age‐dependent upregulation of PrPC expression in the liver of 14‐ and 9‐month‐old mice as compared to 3 months of age. Therefore, this study may provide new insights into the gender‐specific role of PrPC in the liver, which may further be linked to its protective role against oxidative stress during aging. In addition, the current study also shows an application of immunoelectrophoresis with a low coefficient of variation to analyze the miniscule amount of PrPC in the mouse liver tissue.     

Insights into the early stages of metal nanoparticle formation via first-principle calculations: the roles of citrate and water

The early stages of silver nanoparticle formation in the presence of citrate and water have been investigated via first-principle theoretical calculations. Our study revealed that the charge density of the clusters is a key factor determining the selectivity among various growth pathways. An optimal charge density appears to control the selection between neutral and charged species in cluster growth; partially positively charged clusters are thermodynamically preferred and can serve as seeds for further growth. They interact favorably with both the solvent, leading to their solubility, and the citrate. The solvent (water) plays an important role in cluster growth both on the energetics of reactions including highly charged clusters and on the geometry of the resulting silver structures by preventing the formation of asymmetric ones (a structure directing action). Contrary to the common belief we found, from an energetic viewpoint, that growth of small clusters is not blocked by the citrate. Citrate, by acting as a reducing agent, opens up new channels for cluster growth involving highly charged species. By regulating the cluster charge, cluster-cluster associations may be promoted by the citrate, providing a new mechanistic interpretation for the effect of citrate concentration on nanoparticle size substantially different from the classic nucleation theory. From the citrate-silver and water-silver cluster interactions, linear free energy relationships have been retrieved that provide insights into metal nanoparticle growth mechanisms.     

Cyanogenic Glycoside Analysis in American Elderberry

Cyanogenic glycosides (CNGs) are naturally occurring plant molecules (nitrogenous plant secondary metabolites) which consist of an aglycone and a sugar moiety. Hydrogen cyanide (HCN) is released from these compounds following enzymatic hydrolysis causing potential toxicity issues. The presence of CNGs in American elderberry (AE) fruit, Sambucus nigra (subsp. canadensis), is uncertain. A sensitive, reproducible and robust LC-MS/MS method was developed and optimized for accurate identification and quantification of the intact glycoside. A complimentary picrate paper test method was modified to determine the total cyanogenic potential (TCP). TCP analysis was performed using a camera-phone and UV-Vis spectrophotometry. A method validation was conducted and the developed methods were successfully applied to the assessment of TCP and quantification of intact CNGs in different tissues of AE samples. Results showed no quantifiable trace of CNGs in commercial AE juice. Levels of CNGs found in various fruit tissues of AE cultivars studied ranged from between 0.12 and 6.38 µg/g. In pressed juice samples, the concentration range measured was 0.29–2.36 µg/mL and in seeds the levels were 0.12–2.38 µg/g. TCP was highest in the stems and green berries. Concentration levels in all tissues were generally low and at a level that poses no threat to consumers of fresh and processed AE products.     

Direct identification of proteins from T47D cells and murine brain tissue by matrix-assisted laser desorption/ionization post-source decay/collision-induced dissociation

The purpose of this study is to determine the feasibility of the direct matrix-assisted laser desorption/ionization (MALDI) identification of proteins in fixed T47D breast cancer cells and murine brain tissues. The ability to identify proteins from cells and tissue may lead to biomarkers that effectively predict the onset of defined disease states, and their dynamic behavior could be an important hint for drug target discoveries. Direct tissue application of trypsin allows protein identification in cells and tissues, while maintaining spatial integrity and intracellular organization. Using a chemical printer, matrix was co-registered on trypsinized human T47D breast cancer cells and cryo-preserved sections of murine brain tissue, followed by MALDI post-source decay (PSD) or MALDI collision-induced dissociation (CID), respectively. Mass-to-charge (m/z) data from the cells and brain tissues were processed using Mascot software interrogation of the National Center for Biotechnology Information (NCBI) database. Histone H2B was identified from cultured T47D human breast cancer cells. Tubulin beta2 was identified from mouse brain cortex following an induced stroke. These results suggest that MALDI PSD/CID, combined with bioinformatics, can be used for the direct identification of proteins from cells and tissues. Refinements in preparation techniques may improve this approach to provide a tool for quantitative proteomics and clinical analysis.     

快速老化模型小鼠海马蛋白质组学初步研究

应用双向凝胶电泳结合质谱鉴定, 分析比较6月龄和12月龄快速老化模型小鼠(Senescence-accele-rated mouse, SAM)的快速老化亚系SAM-prone/8(SAMP8)及抗快速老化亚系SAM-resistance/1(SAMR1)海马蛋白表达的差异, 从蛋白质水平初步探讨与老化相关的学习记忆功能障碍的发生机制. 结果表明, 与同龄SAMR1比较, 6月龄SAMP8海马中有15个蛋白点表达显著上调, 5个蛋白点表达显著下调; 12月龄SAMP8海马中有12个蛋白点表达显著上调, 2个蛋白点表达显著下调, 2个蛋白点只在SAMP8中有表达. 应用质谱分析结合数据库检索, 共鉴定了22种蛋白质. 6月龄和12月龄SAMP8与SAMR1海马中表达有明显变化的蛋白按功能可分为如下4类: (1) 能量代谢相关蛋白; (2) 线粒体功能相关蛋白; (3) 信号转导相关蛋白; (4) 其它蛋白. 研究结果表明, SAMP8和SAMR1海马蛋白表达存在明显差异, 其中一些蛋白与SAMP8随龄出现的学习记忆功能减退相关, 并可能为研究或发现促智药物作用的新蛋白靶标提供线索.