Oxidative stress-resistance assay for screening yeast strains overproducing heterologous proteins

Many natural proteins have been developed into drugs and produced for direct application. Identifying improved hosts to achieve high-level heterologous protein production is a challenge in the study of heterologous protein expression in recombinant yeast. In this study, a novel high-throughput assay to screen such overproducing Saccharomyces cerevisiae strains was systematically developed. The protocol designed was based on screening host strain derivatives with increased superoxide dismutase dependent resistance to oxidative stress. Yeast cells transformed with recombinant plasmid carrying SOD1 gene as a reporter responded exquisitely to oxidative stress induced by elevated concentrations of paraquat. Improved yeast strains resulting from screening clones subjected to genome shuffling through selective pressure argue for a more effective screening system compared with traditonal selection. Moreover, this approach can be employed in general biochemical analysis without utilization of flow cytometry or well plate reader. Therefore, it is expected that the high-throughput assay would make superior strains producing heterologous proteins.     

Principlism and the ethical appraisal of clinical trials

For nearly two decades, the process of reviewing the ethical merit of research involving human subjects has been based on the application of principles initially described in the U.S. National Commission's Belmont Report, and later articulated more fully by Beauchamp and Childress in their Principles of Biomedical Ethics. Recently, the use of ethical principles for deliberating about moral problems in medicine and research, referred to in the pejorative sense as "principlism", has come under scrutiny. In this paper we argue that these principles can provide a foundation for the source of ethical appraisal of human research, but are not themselves wholly adequate for this purpose. Therefore, we further propose that (1) principles should be understood as heuristics that can be "specified" as described by De Grazia (1992), and (2) that the principle-based approach should be supplemented by formally incorporating "sensitivity to context" into the evaluation of clinical trials.     

Mitochondrial oxidative stress and respiratory chain dysfunction account for liver toxicity during amiodarone but not dronedarone administration

The role played by oxidative stress in amiodarone-induced mitochondrial toxicity is debated. Dronedarone shows pharmacological properties similar to those of amiodarone but several differences in terms of toxicity. In this study, we analyzed the effects of the two drugs on liver mitochondrial function by administering an equivalent human dose to a rat model. Amiodarone increased mitochondrial H(2)O(2) synthesis, which in turn induced cardiolipin peroxidation. Moreover, amiodarone inhibited Complex I activity and uncoupled oxidative phosphorylation, leading to a reduction in the hepatic ATP content. We also observed a modification of membrane phospholipid composition after amiodarone administration. N-acetylcysteine completely prevented such effects. Although dronedarone shares with amiodarone the capacity to induce uncoupling of oxidative phosphorylation, it did not show any of the oxidative effects and did not impair mitochondrial bioenergetics. Our data provide important insights into the mechanism of mitochondrial toxicity induced by amiodarone. These results may greatly influence the clinical application and toxicity management of these two antiarrhythmic drugs.     

Mutagenesis and cardiovascular diseases Molecular mechanisms, risk factors, and protective factors

Although no generalization can be made, it is of interest that cancer, cardiovascular diseases, and other chronic conditions often share common risk factors and common protective factors as well as common pathogenetic determinants, such as DNA damage, oxidative stress, and chronic inflammation. Atherosclerosis is the most important cause of vascular forms representing the major cause of death in the population of many geographical areas. A great deal of studies support the "response-to-injury" theory. A variety of experimental and epidemiological findings are also in favor of the somatic mutation theory, which maintains that the earliest event in the atherogenic process is represented by mutations in arterial smooth muscle cells, akin to formation of a benign tumor. These two theories can be harmonized, also taking into account the highly diversified nature of atherosclerotic lesions. Molecular epidemiology studies performed in our laboratory and other laboratories have shown that DNA adducts are systematically present in arterial smooth muscle cells, and their levels are correlated with atherogenic risk factors known from traditional epidemiology. Oxidative DNA damage was also consistently detected in these cells. The role of glutathione S-transferase polymorphisms on the frequency of the above molecular alterations and of arterial diseases is rather controversial. Prevention of both cancer and atherosclerosis is based on avoidance of exposure to risk factors and on fortification of the host defense mechanisms by means of dietary principles and chemopreventive drugs.     

OTO: Ontology Term Organizer

Background

The need to create controlled vocabularies such as ontologies for knowledge organization and access has been widely recognized in various domains. Despite the indispensable need of thorough domain knowledge in ontology construction, most software tools for ontology construction are designed for knowledge engineers and not for domain experts to use. The differences in the opinions of different domain experts and in the terminology usages in source literature are rarely addressed by existing software.

Methods

OTO software was developed based on the Agile principles. Through iterations of software release and user feedback, new features are added and existing features modified to make the tool more intuitive and efficient to use for small and large data sets. The software is open source and built in Java.

Results

Ontology Term Organizer (OTO; http://biosemantics.arizona.edu/OTO/) is a user-friendly, web-based, consensus-promoting, open source application for organizing domain terms by dragging and dropping terms to appropriate locations. The application is designed for users with specific domain knowledge such as biology but not in-depth ontology construction skills. Specifically OTO can be used to establish is_a, part_of, synonym, and order relationships among terms in any domain that reflects the terminology usage in source literature and based on multiple experts’ opinions. The organized terms may be fed into formal ontologies to boost their coverage. All datasets organized on OTO are publicly available.

Conclusion

OTO has been used to organize the terms extracted from thirty volumes of Flora of North America and Flora of China combined, in addition to some smaller datasets of different taxon groups. User feedback indicates that the tool is efficient and user friendly. Being open source software, the application can be modified to fit varied term organization needs for different domains.     

Targeted screening for biogenic amine transporters: potential applications for natural products

The biogenic amine transporters (BATs) are integral membrane proteins that terminate the actions of dopamine (DA), serotonin (5-HT) and norepinephrine (NE) by pumping these substrates from the extracellular space back into the nerve terminal. Numerous drugs and medications target BATs, acting as inhibitors or substrates. This paper will review some of the methods used to measure the activity of test drugs at the BATs. These methods include traditional uptake inhibition assays and transporter binding assays, as well as methods developed in our lab to determine if a test agent is a BAT substrate or inhibitor. Newer methods, developed in our lab, are used to determine the potency of test drugs as BAT substrates in a relatively high throughput manner. The potential application of these methods to characterizing natural products will be discussed in reference to results obtained with "purified" natural products, such as ephedrine stereoisomers.     

Application of the “-Omic-” technologies in phytomedicine

The proof of efficacy of phytopreparations and the determination of their mode of action are permanent challenges for an evidence-based phytotherapy. The technology platform of genomics, proteomics and metabolomics ("-omic-" technologies) are high-throughput technologies. They increase substantially the number of proteins/genes that can be detected simultaneously and have the potential to relate complex mixtures to complex effects in the form of gene/protein expression profiles. Provided that phytopreparation-specific signatures in the form of gene/protein expression profiles can be developed, these technologies will be useful for the chemical and pharmacological standardization and the proof of the toxicological potential of a plant extract. Over a long-term perspective they may economize the proof of efficacy, the determination of the mode of action of phytomedicines and allow to investigate herbal extracts without prominent active principle(s). The application of this genomics revealed already that gene expression profiles induced by single drugs and the ones induced by the combination of the same drugs can be entirely different. These results make the information of the mode of action of isolated "active principles/lead substances" of phytopreparations questionable. The application of the "-omic-" technologies may lead to a change of paradigms towards the application of complex mixtures in medicine and open the new field of phytogenomics, -proteomics and -metabolomics.     

中枢神经系统疾病治疗性抗体药物应用进展

单克隆抗体药物是一种新兴的治疗药物,具有高选择性,被用于多种疾病的治疗,如肿瘤、免疫疾病等,也可以用于中枢神经系统疾病,如阿尔茨海默病、帕金森病、中风和脑肿瘤等。然而,因为血脑屏障低通透性,限制了抗体药物在中枢神经系统疾病治疗中的应用,在很多神经系统疾病临床试验中,抗体药物并没有取得预期效果。如今,人们利用血脑屏障上内源性转运蛋白介导,设计了可以通过血脑屏障的抗体药物。对通过血脑屏障治疗性抗体药物研发进展及其应用前景进行了综述。     

Oxidative erythrocyte membrane damage in hereditary spherocytosis.

The occurrence, in Hereditary Spherocytosis, of an oxidative damage to red blood cell membranes was studied by "in vitro" treatment of the erythrocytes with tert-butylhydroperoxide, methylene blue, or phenylhydrazine. Spherocytes were found to be more sensitive than normal erythrocytes to the action of these drugs. Tert-butylhydroperoxide caused a more intense lipid peroxidation as well as more extensive membrane protein alterations, namely spectrin degradation, formation of high molecular weight aggregates, and globin binding to the membrane. Marked spectrin degradation was also induced by methylene blue and by phenylhydrazine, which differed from each other for their effects on the generation of membrane-bound globin and of intermediate proteolysis products. Spectrin appeared therefore to be, in Hereditary Spherocytosis, a highly sensitive target to oxidative stress, a phenomenon which may, also "in vivo", increase the rate of spectrin loss thus enhancing erythrocyte fragility.     

Targeted delivery of therapeutics to endothelium

The endothelium is a target for therapeutic and diagnostic interventions in a plethora of human disease conditions including ischemia, inflammation, edema, oxidative stress, thrombosis and hemorrhage, and metabolic and oncological diseases. Unfortunately, drugs have no affinity to the endothelium, thereby limiting the localization, timing, specificity, safety, and effectiveness of therapeutic interventions. Molecular determinants on the surface of resting and pathologically altered endothelial cells, including cell adhesion molecules, peptidases, and receptors involved in endocytosis, can be used for drug delivery to the endothelial surface and into intracellular compartments. Drug delivery platforms such as protein conjugates, recombinant fusion constructs, targeted liposomes, and stealth polymer carriers have been designed to target drugs and imaging agents to these determinants. We review endothelial target determinants and drug delivery systems, describe parameters that control the binding of drug carriers to the endothelium, and provide examples of the endothelial targeting of therapeutic enzymes designed for the treatment of acute vascular disorders including ischemia, oxidative stress, inflammation, and thrombosis. This work was supported by NIH grants HL71175, HL078785, HL087036, and HL73940 and by a pilot grant from TAPITMAT/PENN to V.M. and also by NIH HL007954 to E.S. and by AHA fellowships to E.S. and B.D.     

Bisection of biotinylated soft spherical structures

Biotin, a water soluble vitamin, upon conjugation with ditryptophan methyl ester affords soft spherical structures in the nanometer to micrometer range. The evolution of such morphology is ascribed to favorable interaction between biotin and tryptophan residues as suggested for high affinity biotin–avidin interaction. We report unprecedented observation that biotinylated soft spherical structures undergo bisection to reveal hemispherical capsule-like structures, in the presence of avidin. This study suggests singular approach of tuning bioinspired morphologies via natural principles of interaction and affinity. We envisage that such hemispherical capsules provide an expeditious entry into interesting soft structures which may be harnessed for potential applications.     

Novel soft steroids: effects on cell growth in vitro and on wound healing in the mouse.

Evaluation of three "soft" steroids is described. The test compounds were compared with the standard anti-inflammatory steroids betamethasone and prednicarbate in two studies. Soft steroids are designed based on the "inactive metabolite approach" to be rapidly inactivated by predictable metabolism after performing their therapeutic function. Consequently, lower circulating (peripheral) levels of potentially harmful steroids result, and undesirable systemic and local side effects are minimized. The soft and standard steroids behaved similarly in an in vitro cell culture model, whereas in a whole animal study the advantages of the soft steroids were evident.     

DNA intercalative potential of marketed drugs testing positive in in vitro cytogenetics assays

We have previously noted that the Physicians' Desk Reference (PDR) contains over 80 instances in which a drug elicited a positive genotoxic response in one or more in vitro assays, despite having no obvious structural features predictive of covalent drug/DNA interactive potential or known mechanistic basis. Furthermore, in most cases, these drugs were "missed" by computational genotoxicity-predicting models such as DEREK, MCASE and TOPKAT. We have previously reported the application of a V79 cell-based model and a 3D DNA docking model for predicting non-covalent chemical/DNA interactions. Those studies suggested that molecules that are very widely structurally diverse may be capable of intercalating into DNA. To determine whether such non-covalent drug/DNA interactions might be involved in unexpected drug genotoxicity, we evaluated, using both models where possible, 56 marketed pharmaceuticals, 40 of which were reported as being clastogenic in in vitro cytogenetics assays (chromosome aberrations/mouse lymphoma assay). As seen before, the two approaches showed good concordance (62%) and 26 of the 40 (65%) drugs exhibiting in vitro clastogenicity were predicted as intercalators by one or both methods. This finding provides support for the hypothesis that non-covalent DNA interaction may be a common mechanism of clastogenicity for many drugs having no obvious structural alerts for covalent DNA interaction.     

Lipid peroxidation cannot be used as a universal criterion of oxidative stress

Oxidative stress is a term used to denote the imbalance between the concentrations of reactive oxygen and nitrogen species and the defense mechanisms of the body. Although it is generally accepted that such an imbalance plays a pivotal role in many pathologies, the term "oxidative stress" remains ill defined. In an attempt to evaluate the relationship between various assays of oxidative stress, we have analyzed the correlations between the results reported in those publications in which "oxidative stress" has been assayed by at least two methods. We found good correlations between the concentrations of several peroxidation products, including malondialdehyde, F2-Isoprostanes, lipid hydroperoxides, conjugated dienes, glutathione and protein carbonyls, but not with other criteria of "individual oxidative status" such as the concentration of antioxidants and products of DNA fragmentation (the "comet" assay). In light of these findings, we divide the assays used for evaluation of "oxidative stress" into the following three categories: (i) assays based on measuring the concentrations of oxidation products of lipids, proteins and DNA, as well as the concentrations of antioxidants, (ii) assays used to evaluate the oxidative and reductive capacity of biological fluids and (iii) assays used to evaluate the ex vivo susceptibility of lipids to oxidation upon their exposure to a source of free radicals. Our analyses demonstrate that oxidative stress cannot be defined in universal terms. Two results are of special interest:1.the commonly used criteria based on lipid peroxidation can not be regarded as a general estimate of the individual "oxidative status".2.the levels of antioxidants exhibit a non-monotonic relation with other criteria for oxidative stress. Further research is required to evaluate the significance of the latter finding.     

Natural and engineered precision antibiotics in the context of resistance

Antibiotics are essential weapons in our fight against infectious disease, yet the consequences of broad-spectrum antibiotic use on microbiome stability and pathogen resistance are prompting investigations into more selective alternatives. Echoing the advent of precision medicine in oncology, precision antibiotics with focused activities are emerging as a means of addressing infections without damaging microbiomes or incentivizing resistance. Historically, antibiotic design principles have been gleaned from Nature, and reinvestigation of overlooked antibacterials is now providing scaffolds and targets for the design of pathogen-specific drugs. In this perspective, we summarize the biosynthetic and antibacterial mechanisms used to access these activities, and discuss how such strategies may be co-opted through engineering approaches to afford precision antibiotics.     

Water-based nanoparticulate polymeric system for protein delivery

This article features a new production technology for nanoparticles comprised of multicomponent polymeric complexes that are candidates for delivery vehicles of biological molecules such as proteins and drugs. Biocompatible and mostly natural polymers are fabricated into thermodynamically stable nanoparticles insoluble in water and buffered media, in the absence of organic solvents, using two types of processing: batch and continuous. Careful choice of construction materials and the superposition of several interacting principles during their production allow for the customization of the physicochemical properties of the structures. Detailed experiments in batch and continuous systems allowed time-dependent stoichiometric characterization of the production process and an understanding of fundamental assembly principles of such supramolecular structures. Continuous-flow production is shown to provide more consistent data in terms of product quality and consistency, with further possibility of process development and commercialization. The development of nanoparticles using the described methodology is expected to lead to a flexible nanoparticle drug delivery system for medical applications, which has particular bearing to the slow release of drugs, antigens (for vaccine design), and genes (for gene therapy). Several chemistries of particles are presented. Copyright John Wiley & Sons, Inc.     

Encapsulation of the flavonoid quercetin with an arsenic chelator into nanocapsules enables the simultaneous delivery of hydrophobic and hydrophilic drugs with a synergistic effect against chronic arsenic accumulation and oxidative stress

Chronic arsenic exposure causes oxidative stress and mitochondrial dysfunction in the liver and brain. The ideal treatment would be to chelate arsenic and prevent oxidative stress. meso-2,3-Dimercaptosuccinic acid (DMSA) is used to chelate arsenic but its hydrophilicity makes it membrane-impermeative. Conversely, quercetin (QC) is a good antioxidant with limited clinical application because of its hydrophobic nature and limited bioavailability, and it is not possible to solubilize these two compounds in a single nontoxic solvent. Nanocapsules have emerged as a potent drug delivery system and make it feasible to incorporate both hydrophilic and lipophilic compounds. Nanoencapsulated formulations with QC and DMSA either alone or coencapsulated in polylactide-co-glycolide [N(QC+DMSA)] were synthesized to explore their therapeutic application in a rat model of chronic arsenic toxicity. These treatments were compared to administration of quercetin or DMSA alone using conventional delivery methods. Both nanoencapsulated quercetin and nanoencapsulated DMSA were more effective at decreasing oxidative injury in liver or brain compared to conventional delivery methods, but coencapsulation of quercetin and DMSA into nanoparticles had a marked synergistic effect, decreasing liver and brain arsenic levels from 9.5 and 4.8μg/g to 2.2 and 1.5μg/g, respectively. Likewise, administration of coencapsulated quercetin and DMSA virtually normalized changes in mitochondrial function, formation of reactive oxygen species, and liver injury. We conclude that coencapsulation of quercetin and DMSA may provide a more effective therapeutic strategy in the management of arsenic toxicity and also presents a novel way of combining hydrophilic and hydrophobic drugs into a single delivery system.