Distribution analysis of nonsynonymous polymorphisms within the human kinase gene family

The human kinase gene family is composed of 518 genes that are involved in a diverse spectrum of physiological functions. They are also implicated in a number of diseases and encompass 10% of current drug targets. Contemporary, high-throughput sequencing efforts have identified a rich source of naturally occurring single nucleotide polymorphisms (SNPs) in kinases, a subset of which occur in the coding region of genes (cSNPs) and result in a change in the encoded amino acid sequence (nonsynonymous coding SNP; nscSNPs). What fraction of this naturally occurring variation underlies human disease is largely unknown (uDC), and much of it is assumed not to be disease causing (DC). We pursued a comprehensive computational analysis of the distribution of 1463 nscSNPs and 999 DC nscSNPs within the kinase gene family and have found that DCs are overrepresentated in the kinase catalytic domain and in receptor structures. In addition, the frequencies with which specific amino acid changes occur differ between the DCs and the uDCs, implying different biological characteristics for the two sets of human polymorphisms. Our results provide insights into the sequence and structural phenomena associated with naturally occurring kinase nscSNPs that contribute to human diseases.     

Trehalose and 6-aminohexanoic acid stabilize and renature glucose-6-phosphate dehydrogenase inactivated by glycation and by guanidinium hydrochloride

A number of naturally occurring small organic molecules, primarily involved in maintaining osmotic pressure in the cell, display chaperone-like activity, stabilizing the native conformation of proteins and protecting them from various kinds of stress. Most of them are sugars, polyols, amino acids or methylamines. In addition to their intrinsic protein-stabilizing activity, these small organic stress molecules regulate the activity of some molecular chaperones, and may stabilize the folded state of proteins involved in unfolding or in misfolding diseases, such as Alzheimer's and Parkinson's diseases, or alpha1-antitrypsin deficiency and cystic fibrosis, respectively. Similar to molecular chaperones, most of these compounds have no substrate specificity, but some specifically stabilize certain proteins, e.g., 6-aminohexanoic acid (AHA) stabilizes apolipoprotein A. In the present work, the capacity of 6-aminohexanoic acid to stabilize non-specifically other proteins is demonstrated. Both trehalose and AHA significantly protect glucose-6-phosphate dehydrogenase (G6PD) against glycation-induced inactivation, and renatured enzyme already inactivated by glycation and by guanidinium hydrochloride (GuHCl). To the best of our knowledge, there are no data on the effect of these compounds on protein glycation. The correlation between the recovery of enzyme activity and structural changes indicated by fluorescence spectroscopy and Western blotting contribute to better understanding of the protein stabilization mechanism.     

The roles of polyphenols in cancer chemoprevention

Oxidative stress imposed by reactive oxygen species (ROS) plays a crucial role in the pathophysiology associated with neoplasia, atherosclerosis, and neurodegenerative diseases. The ROS-induced development of cancer involves malignant transformation due to altered gene expression through epigenetic mechanisms as well as DNA mutations. Considerable attention has been focused on identifying naturally occurring antioxidative phenolic phytochemicals that are able to decrease ROS levels, but the efficacies of antioxidant therapies have been equivocal at best. Several studies have shown that some antioxidants exhibit prooxidant activity under certain conditions and potential carcinogenicity under others, and that dietary supplementation with large amounts of a single antioxidant may be deleterious to human health. This article reviews the intracellular signaling pathways that respond to oxidative stress and how they are modulated by naturally occurring polyphenols. The possible toxicity and carcinogenicity of polyphenols is also discussed.     

Natural variation in stress response is related to post-stress parental effort in male house sparrows

The central life-history trade-off between current and future reproductive effort seems to be mediated by corticosterone in birds. However, still little is known about how naturally occurring corticosterone levels during an acute stress may influence subsequent parental behavior. In this study we observed the parental behavior of free-living male house sparrows (Passer domesticus) both before and after they were subjected to a standard capture–handling stress. We investigated the relationships between corticosterone levels, pre- and post-stress parental behavior, while we statistically controlled for a number of other variables using a multivariate regression method, the path analysis. We found that males' baseline feeding rate predicted the body mass of the nestlings, indicating that male parental care is directly linked to fitness. Corticosterone levels were not explained by baseline feeding rate, but both baseline and stress-induced corticosterone levels had a negative influence on the males' post-stress feeding behavior. Moreover, males with large bib size had a stronger stress response and lower post-stress feeding rate than small bibbed males. These results indicate that naturally occurring variation in baseline and stress-induced corticosterone levels may influence subsequent parental decisions: individuals mounting a robust stress response are likely to reduce their parental commitment. Parental effort may be regulated in a complex manner, with corticosterone mediating the life-history trade-off between current reproduction and survival. However, different resolutions of this trade-off were apparent only following the stress, therefore the ability to modulate the stress response and maintain parental care in stressful situations may be important in life-history evolution.     

Evaluation of antiviral activity of different origin compounds by flow cytometry

Against many viral diseases caused for example by HSV, EBV, CMV, HIV, RSV, HCV for which vaccines are not available, chemiotherapeutics seem to have the principal significance. High progress in development of new antiviral compounds is observed. In addition to synthetic compounds a large number of naturally occurring substances have been shown to posses antiviral activity. One of such substance is tannic acid. In this study comparison of antiviral activity of tannic acid, acyclovir (ACV) and ganciclovir (GCV) against cytomegalovirus (CMV) is presented. The MRC5 cells infected with CMV and treated with different compounds were analyzed by flow cytometry and cythopatic effect inhibition test for inhibition of virus replication and by MTT assay for cytotoxity. It has been shown that tannic acid has antiviral activity against cytomegalovirus and that expression of virus antigens measured as median fluorescence intensity (MFI) by flow cytometry can be used for evaluation of virus replication.     

Structure-activity relationship analysis of antioxidant ability and neuroprotective effect of gallic acid derivatives

Gallic acid and its derivatives are a group of naturally occurring polyphenol antioxidants which have recently been shown to have potential healthy effects. In order to understand the relationship between the structures of gallic acid derivatives, their antioxidant activities, and neuroprotective effects, we examined their free radical scavenging effects in liposome and anti-apoptotic activities in human SH-SY5Y cell induced by 6-hydrodopamine autooxidation. It was found that these polyphenol antioxidants exhibited different hydrophobicity and could cross through the liposome membrane to react with 1,1-diphenyl-2-picryl-hydrazyl (DPPH) free radical in a time and dose-dependent manner. At the same time, the structure-antioxidant activity relationship of gallic acid derivatives on scavenging DPPH free radical in the liposome was also analyzed based on theoretical investigations. Analysis of cell apoptosis, intracellular GSH levels, production of ROS and the influx of Ca(2+) indicated that the protective effects of gallic acid derivatives in cell systems under oxidative stress depend on both their antioxidant capacities and hydrophobicity. However, the neuroprotective effects of gallic acid derivatives seem to depend more on their molecular polarities rather than antioxidant activities in the human SH-SY5Y cell line. In conclusion, these results reveal that compounds with high antioxidant activity and appropriate hydrophobicity are generally more effective in preventing the injury of oxidative stress in neurodegenerative diseases.     

α-Lipoic Acid Antioxidant Treatment Limits Glaucoma-Related Retinal Ganglion Cell Death and Dysfunction

Oxidative stress has been implicated in neurodegenerative diseases, including glaucoma. However, due to the lack of clinically relevant models and expense of long-term testing, few studies have modeled antioxidant therapy for prevention of neurodegeneration. We investigated the contribution of oxidative stress to the pathogenesis of glaucoma in the DBA/2J mouse model of glaucoma. Similar to other neurodegenerative diseases, we observed lipid peroxidation and upregulation of oxidative stress-related mRNA and protein in DBA/2J retina. To test the role of oxidative stress in disease progression, we chose to deliver the naturally occurring, antioxidant α-lipoic acid (ALA) to DBA/2J mice in their diet. We used two paradigms for ALA delivery: an intervention paradigm in which DBA/2J mice at 6 months of age received ALA in order to intervene in glaucoma development, and a prevention paradigm in which DBA/2J mice were raised on a diet supplemented with ALA, with the goal of preventing glaucoma development. At 10 and 12 months of age (after 4 and 11 months of dietary ALA respectively), we measured changes in genes and proteins related to oxidative stress, retinal ganglion cell (RGC) number, axon transport, and axon number and integrity. Both ALA treatment paradigms showed increased antioxidant gene and protein expression, increased protection of RGCs and improved retrograde transport compared to control. Measures of lipid peroxidation, protein nitrosylation, and DNA oxidation in retina verified decreased oxidative stress in the prevention and intervention paradigms. These data demonstrate the utility of dietary therapy for reducing oxidative stress and improving RGC survival in glaucoma.     

A liquid chromatography-quadrupole time-of-flight (LC-QTOF)-based metabolomic approach reveals new metabolic effects of catechin in rats fed high-fat diets

Unbalanced diets generate oxidative stress commonly associated with the development of diabetes, atherosclerosis, obesity and cancer. Dietary flavonoids have antioxidant properties and may limit this stress and reduce the risk of these diseases. We used a metabolomic approach to study the influence of catechin, a common flavonoid naturally occurring in various fruits, wine or chocolate, on the metabolic changes induced by hyperlipidemic diets. Male Wistar rats ( n = 8/group) were fed during 6 weeks normolipidemic (5% w/w) or hyperlipidemic (15 and 25%) diets with or without catechin supplementation (0.2% w/w). Urines were collected at days 17 and 38 and analyzed by reverse-phase liquid chromatography-mass spectrometry (LC-QTOF). Hyperlipidic diets led to a significant increase of oxidative stress in liver and aorta, upon which catechin had no effect. Multivariate analyses (PCA and PLS-DA) of the urine fingerprints allowed discrimination of the different diets. Variables were then classified according to their dependence on lipid and catechin intake (ANOVA). Nine variables were identified as catechin metabolites of tissular or microbial origin. Around 1000 variables were significantly affected by the lipid content of the diet, and 76 were fully reversed by catechin supplementation. Four variables showing an increase in urinary excretion in rats fed the high-fat diets were identified as deoxycytidine, nicotinic acid, dihydroxyquinoline and pipecolinic acid. After catechin supplementation, the excretion of nicotinic acid was fully restored to the level found in the rats fed the low-fat diet. The physiological significance of these metabolic changes is discussed.     

Abnormal pulmonary slowly adapting receptors in canine acrylamide neuropathy

Slowly adapting lung stretch receptors (SARs) and their vagal afferents are considered to play an important role in the mediation of numerous respiratory reflexes. The understanding of such reflexes has been facilitated by altering the discharge properties of SARs or by preventing the conduction of SAR-generated impulses to the brain stem. In a number of naturally occurring diseases of the peripheral nervous system, the vagus nerve and vagal reflexes are damaged. We have studied the function of SARs in anesthetized dogs with acrylamide neuropathy, a distal axonopathy that has been used as a model of naturally occurring neuropathies. There was a marked increase in threshold and decrease in firing rate of SARs in dogs with moderate neuropathy. Abnormal SAR discharge patterns were observed, and there was a depletion of those units innervated by the fastest conducting vagal afferent fibers in treated animals. Acrylamide induced degeneration of myelinated fibers in bronchial branches of the vagus nerve. These abnormalities were partially reversed upon withdrawal of the neurotoxin. Acrylamide may be a useful agent in the study of vagally mediated respiratory reflexes. SAR function is likely to be abnormal in diseases of the peripheral nervous system.     

Basement membrane reactivity of antisera to type IV collagen and sera from patients with bullous pemphigoid and epidermolysis bullosa acquisita

The basement membrane antigenic specificities of antibodies to Type IV collagen were compared to naturally occurring antibodies in sera from patients with bullous pemphigoid and epidermolysis bullosa acquisita (EBA) by indirect immunofluorescence, mixed immunofluorescence and immunoabsorption. Results suggested that the three sera reacted with three different basement membrane antigens. In addition, absorption with Types I, II, III, or IV collagen failed to reduce the basement membrane reactivities of bullous pemphigoid or EBA sera. The antibodies to the basement membrane components should be useful in studying skin and mucous membrane diseases including periodontal diseases.     

Cellular responses in sea fan corals: granular amoebocytes react to pathogen and climate stressors

Background

Climate warming is causing environmental change making both marine and terrestrial organisms, and even humans, more susceptible to emerging diseases. Coral reefs are among the most impacted ecosystems by climate stress, and immunity of corals, the most ancient of metazoans, is poorly known. Although coral mortality due to infectious diseases and temperature-related stress is on the rise, the immune effector mechanisms that contribute to the resistance of corals to such events remain elusive. In the Caribbean sea fan corals (Anthozoa, Alcyonacea: Gorgoniidae), the cell-based immune defenses are granular acidophilic amoebocytes, which are known to be involved in wound repair and histocompatibility.

Methodology/Principal Findings

We demonstrate for the first time in corals that these cells are involved in the organismal response to pathogenic and temperature stress. In sea fans with both naturally occurring infections and experimental inoculations with the fungal pathogen Aspergillus sydowii, an inflammatory response, characterized by a massive increase of amoebocytes, was evident near infections. Melanosomes were detected in amoebocytes adjacent to protective melanin bands in infected sea fans; neither was present in uninfected fans. In naturally infected sea fans a concurrent increase in prophenoloxidase activity was detected in infected tissues with dense amoebocytes. Sea fans sampled in the field during the 2005 Caribbean Bleaching Event (a once-in-hundred-year climate event) responded to heat stress with a systemic increase in amoebocytes and amoebocyte densities were also increased by elevated temperature stress in lab experiments.

Conclusions/Significance

The observed amoebocyte responses indicate that sea fan corals use cellular defenses to combat fungal infection and temperature stress. The ability to mount an inflammatory response may be a contributing factor that allowed the survival of even infected sea fan corals during a stressful climate event.     

Muscular dystrophies involving the dystrophin-glycoprotein complex: an overview of current mouse models

The dystrophin-glycoprotein complex (DGC) is a multisubunit complex that connects the cytoskeleton of a muscle fiber to its surrounding extracellular matrix. Mutations in the DGC disrupt the complex and lead to muscular dystrophy. There are a few naturally occurring animal models of DGC-associated muscular dystrophy (e.g. the dystrophin-deficient mdx mouse, dystrophic golden retriever dog, HFMD cat and the delta-sarcoglycan-deficient BIO 14.6 cardiomyopathic hamster) that share common genetic protein abnormalities similar to those of the human disease. However, the naturally occurring animal models only partially resemble human disease. In addition, no naturally occurring mouse models associated with loss of other DGC components are available. This has encouraged the generation of genetically engineered mouse models for DGC-linked muscular dystrophy. Not only have analyses of these mice led to a significant improvement in our understanding of the pathogenetic mechanisms for the development of muscular dystrophy, but they will also be immensely valuable tools for the development of novel therapeutic approaches for these incapacitating diseases.     

Pentacyclic triterpenes. Part 1: the first examples of naturally occurring pentacyclic triterpenes as a new class of inhibitors of glycogen phosphorylases

The semi-synthesis, in vitro and in vivo biological evaluation of corosolic acid (1) and maslinic acid (2) are described. Compounds 1 and 2 represent a new class of inhibitors of glycogen phosphorylases. Both 1 and 2 inhibit the increase of fasted plasma glucose of diabetic mice induced by adrenaline. It is therefore proposed that naturally occurring pentacyclic triterpenes 1 and 2 might reduce blood glucose, at least in part, through inhibiting hepatic glycogen degradation.     

The role of oxidative stress in an equine model of human asthma

Equine recurrent airway obstruction (RAO) is a naturally occurring respiratory disease in horses with many similarities to human asthma and, as a result, has been used as an animal model of this disease. Oxidative stress has been demonstrated to occur in a range of respiratory diseases in human beings including asthma. Quantitatively, horses have a greater non-enzymatic antioxidant capacity in the pulmonary epithelial lining fluid compared to human beings due to high ascorbic acid concentrations, which reflects their ability to synthesise ascorbic acid. Consequently, a greater oxidative load is likely to be required to induce oxidative stress in horses compared to human beings. Induction of acute neutrophilic airway inflammation in RAO horses by exposure to organic dust does not result in marked pulmonary oxidative stress. However, with a more prolonged inflammatory response, the antioxidant capacity is depleted and oxidative stress occurs. Despite the clear evidence of oxidative stress in RAO, there is currently limited data linking oxidative stress with a causal role in the development of the pathophysiological features of RAO, namely airway obstruction, airway hyper-responsiveness, airway inflammation and mucus accumulation. However, pathways do exist whereby oxidants could potentially augment the production of important mediators in RAO. Further work is required to ascertain the benefits of antioxidant supplementation in RAO and to determine the role of oxidative stress in the pathogenesis of the disease. Given the similarities with human asthma, results from RAO horses could enhance the understanding of the role of oxidative stress in human asthma.     

Caffeic acid decreases salinity-induced root nodule superoxide radical accumulation and limits salinity-induced biomass reduction in soybean

Caffeic acid (3,4-dihydroxycinnamic acid; CA) is a cinnamic acid occurring naturally in a variety of plant species. In this study, the effects of caffeic acid (100 μM caffeic acid) on soybean root nodule superoxide content, cell viability and superoxide dismutase (SOD; EC 1.15.1.1) activity were evaluated in the presence and absence of salinity stress (imposed by application of 70 mM NaCl), along with the effects of CA on growth of soybean in the presence or absence of salinity. Treatment with CA caused a decrease in superoxide content, enhanced cell viability and SOD activity, with changes in SOD activity accounted for by increased activity of two manganese SOD isoforms and one copper/zinc SOD isoform. Furthermore, CA improved soybean growth under salinity but reduced soybean biomass in the absence of salinity. We suggest that CA improves soybean salinity stress tolerance, possibly via signals that regulate accumulation of reactive oxygen species (ROS) during salinity stress.     

Th17 Pathway As a Target for Multipotent Stromal Cell Therapy in Dogs: Implications for Translational Research

Detrimental Th17 driven inflammatory and autoimmune disease such as Crohn’s disease, graft versus host disease and multiple sclerosis remain a significant cause of morbidity and mortality worldwide. Multipotent stromal/stem cell (MSC) inhibit Th17 polarization and activation in vitro and in rodent models. As such, MSC based therapeutic approaches are being investigated as novel therapeutic approaches to treat Th17 driven diseases in humans. The significance of naturally occurring diseases in dogs is increasingly recognized as a realistic platform to conduct pre-clinical testing of novel therapeutics. Full characterization of Th17 cells in dogs has not been completed. We have developed and validated a flow-cytometric method to detect Th17 cells in canine blood. We further demonstrate that Th17 and other IL17 producing cells are present in tissues of dogs with naturally occurring chronic inflammatory diseases. Finally, we have determined the kinetics of a canine specific Th17 polarization in vitro and demonstrate that canine MSC inhibit Th17 polarization in vitro, in a PGE₂ independent mechanism. Our findings provide fundamental research tools and suggest that naturally occurring diseases in dogs, such as inflammatory bowel disease, may be harnessed to translate novel MSC based therapeutic strategies that target the Th17 pathway.     

Effect of naturally occurring triterpenoids glycyrrhizic acid, ursolic acid, oleanolic acid and nomilin on the immune system.

The effect of naturally occurring triterpenoid compounds such as glycyrrhizic acid, ursolic acid, oleanolic acid, and nomilin on the immune system was studied using Balb/c mice. Intraperitoneal treatments with 5 doses of these terpenoid compounds were found to enhance the total white blood cells (WBC) count. In ursolic acid, oleanolic acid and nomilin treated animals the maximum total WBC count was observed on the 6th day, while in glycyrrhizic acid treated animals it was observed only on the 9th day after the drug treatment. In ursolic acid, oleanolic acid and nomilin treated animals the percentage of increase in the total WBC count was to 91.48 +/- 4.6%, 135.75 +/- 6.4% and 117.33 +/- 17.9% respectively. In the glycyrrhizic acid treated animals the total WBC count was increased to 114.9 +/- 18%. Bone marrow cellularity and alpha-esterase positive cells were also enhanced by the treatment with these terpenoids. Treatment with various triterpenoids along with antigen produced an enhancement in the specific antibody titre and the number of plaque forming cells (PFC) in the spleen. Triterpenoids remarkably inhibited delayed type hypersensitivity reaction (DTH). These results indicate the immunomodulatory activity of naturally occurring triterpenoids such as glycyrrhizic acid, ursolic acid, oleanolic acid and nomilin.     

Geldanamycin induces Hsp70 and prevents alpha-synuclein aggregation and toxicity in vitro

Geldanamycin (GA) is a naturally occurring benzoquinone ansamycin that induces heat shock protein 70 (Hsp70). GA has been shown to reduce alpha-synuclein induced neurotoxicity in a fly model of Parkinson's disease. We have previously shown that heat shock proteins can prevent alpha-synuclein aggregation and protect against alpha-synuclein induced toxicity in human H4 neuroglioma cells. Here, we hypothesize that GA treatment will reduce alpha-synuclein aggregation and prevent alpha-synuclein induced toxicity and we show that GA can induce Hsp70 in a time- and concentration-dependent manner in H4 cells. Pretreatment with 200nM GA 24h prior to transfection prevented alpha-synuclein aggregation and protected against toxicity. Treatment of cells with pre-existing inclusions with GA did not result in a reduction in the number of cells containing inclusions, suggesting that upregulation of Hsp70 is not sufficient to remove established inclusions. Similarly, Western blot analysis demonstrated that GA treatment could dramatically reduce both total alpha-synuclein and high molecular weight alpha-synuclein aggregates. Taken together, these data suggest that GA is effective in preventing alpha-synuclein aggregation and may represent a pharmacological intervention to therapeutically increase expression of molecular chaperone proteins to treat neurodegenerative diseases where aggregation is central to the pathogenesis.     

吡哆胺-一种天然的AGEs/ALEs抑制剂

衰老及老年相关疾病,如：糖尿病、动脉粥状硬化、各种神经退行性疾病等,与组织蛋白氧化修饰密切相关．在造成蛋白质氧化修饰的反应中,非酶糖基化和脂质过氧化是最重要的两类,它们最终形成非酶糖基化终产物(AGEs)和脂过氧化终产物(ALEs)．基于羰基毒害衰老理论,具有强烈反应活性的羰基类化合物是非酶糖基化和脂质过氧化的共同中间产物,它们是造成蛋白修饰的直接原因之一．吡哆胺是维生素B6的一种天然成分;由于它能直接清除羰基类化合物,从而抑制AGEs／ALEs的生成;又因为吡哆胺对人体副作用很小．因此吡哆胺有望成为一种新型的防治多种老年相关疾病的药物．     

Naturally occurring organic osmolytes: from cell physiology to disease prevention

Osmolytes are naturally occurring organic compounds, which represent different chemical classes including amino acids, methylamines, and polyols. By accumulating high concentrations of osmolytes, organisms adapt to perturbations that can cause structural changes in their cellular proteins. Osmolytes shift equilibrium toward natively-folded conformations by raising the free energy of the unfolded state. As osmolytes predominantly affect the protein backbone, the balance between osmolyte-backbone interactions and amino acid side chain-solvent interactions determines protein folding. Abnormal cell volume regulation significantly contributes to the pathophysiology of several disorders, and cells respond to these changes by importing, exporting, or synthesizing osmolytes to maintain volume homeostasis. In recent years, it has become quite evident that cells regulate many biological processes such as protein folding, protein disaggregation, and protein-protein interactions via accumulation of specific osmolytes. Many genetic diseases are attributed to the problems associated with protein misfolding/aggregation, and it has been shown that certain osmolytes can protect these proteins from misfolding. Thus, osmolytes can be utilized as therapeutic targets for such diseases. In this review article, we discuss the role of naturally occurring osmolytes in protein stability, underlying mechanisms, and their potential use as therapeutic molecules.