The organism and its double: An approach to the individual

The individual is certainly the most complex entity that we know until now. Current research converges on a triad-like understanding of the biological individual as an interface of a mechanism and an ecosystem. The present article wants to propose a more generic concept of individual by integrating the functional role of its qualitative characteristics. Modules-problems ensuing from this generic model will serve as a matrix in the elaboration of a future integral biomathics, while category theory will be its syntactic base.     

A novel approach to identifying beta-secretase inhibitors: bis-statine peptide mimetics discovered using structure and spot synthesis

Beta-secretase 1 (BACE1) is an aspartic protease believed to play a critical role in Alzheimer's disease. Inhibitors of this enzyme have been designed by incorporating the non-cleavable hydroxyethylene and statine isosteres into peptides corresponding to BACE1 substrate sequences. We sought to develop new methods to quickly characterize and optimize inhibitors based on the statine core. Minimal sequence requirements for binding were first established using both crystallography and peptide spot synthesis. These shortened peptide inhibitors were then optimized by using spot synthesis to perform iterative cycles of substitution and deletion. The present study resulted in the identification of novel "bis-statine" inhibitors shown by crystallography to have a unique binding mode. Our results demonstrate the application of peptide spot synthesis as an effective method for enhancing peptidomimetic drug discovery.     

Inhibition ofras oncogene: A novel approach to antineoplastic therapy

The most frequently detected oncogene alterations, both in animal and human cancers, are the mutations in the ras oncogene family. These oncogenes are mutated or overexpressed in many human tumors, with a high incidence in tumors of the pancreas, thyroid, colon, lung and certain types of leukemia. Ras is a small guanine nucleotide binding protein that transduces biological information from the cell surface to cytoplasmic components within cells. The signal is transduced to the cell nucleus through second messengers, and it ultimately induces cell division. Oncogenic forms of p21(ras) lead to unregulated, sustained signaling through downstream effectors. The ras family of oncogenes is involved in the development of both primary tumors and metastases making it a good therapeutic target. Several therapeutic approaches to cancer have been developed pointing to reducing the altered gene product or to eliminating its biological function: (1) gene therapy with ribozymes, which are able to break down specific RNA sequences, or with antisense oligonucleotides, (2) immunotherapy through passive or active immunization protocols, and (3) inhibition of p21(ras) farnesylation either by inhibition of farnesyl transferase or synthesis inhibition of farnesyl moieties.     

An attempt to prevent senescence: A mitochondrial approach

Antioxidants specifically addressed to mitochondria have been studied to determine if they can decelerate senescence of organisms. For this purpose, a project has been established with participation of several research groups from Russia and some other countries. This paper summarizes the first results of the project. A new type of compounds (SkQs) comprising plastoquinone (an antioxidant moiety), a penetrating cation, and a decane or pentane linker has been synthesized. Using planar bilayer phospholipid membrane (BLM), we selected SkQ derivatives with the highest permeability, namely plastoquinonyl-decyl-triphenylphosphonium (SkQ1), plastoquinonyl-decyl-rhodamine 19 (SkQR1), and methylplastoquinonyldecyltriphenylphosphonium (SkQ3). Anti- and prooxidant properties of these substances and also of ubiquinonyl-decyl-triphenylphosphonium (MitoQ) were tested in aqueous solution, detergent micelles, liposomes, BLM, isolated mitochondria, and cell cultures. In mitochondria, micromolar cationic quinone derivatives were found to be prooxidants, but at lower (sub-micromolar) concentrations they displayed antioxidant activity that decreases in the series SkQ1 = SkQR1 > SkQ3 > MitoQ. SkQ1 was reduced by mitochondrial respiratory chain, i.e. it is a rechargeable antioxidant. Nanomolar SkQ1 specifically prevented oxidation of mitochondrial cardiolipin. In cell cultures, SkQR1, a fluorescent SkQ derivative, stained only one type of organelles, namely mitochondria. Extremely low concentrations of SkQ1 or SkQR1 arrested H₂O₂-induced apoptosis in human fibroblasts and HeLa cells. Higher concentrations of SkQ are required to block necrosis initiated by reactive oxygen species (ROS). In the fungus Podospora anserina, the crustacean Ceriodaphnia affinis, Drosophila, and mice, SkQ1 prolonged lifespan, being especially effective at early and middle stages of aging. In mammals, the effect of SkQs on aging was accompanied by inhibition of development of such age-related diseases and traits as cataract, retinopathy, glaucoma, balding, canities, osteoporosis, involution of the thymus, hypothermia, torpor, peroxidation of lipids and proteins, etc. SkQ1 manifested a strong therapeutic action on some already pronounced retinopathies, in particular, congenital retinal dysplasia. With drops containing 250 nM SkQ1, vision was restored to 67 of 89 animals (dogs, cats, and horses) that became blind because of a retinopathy. Instillation of SkQ1-containing drops prevented the loss of sight in rabbits with experimental uveitis and restored vision to animals that had already become blind. A favorable effect of the same drops was also achieved in experimental glaucoma in rabbits. Moreover, the SkQ1 pretreatment of rats significantly decreased the H₂O₂ or ischemia-induced arrhythmia of the isolated heart. SkQs strongly reduced the damaged area in myocardial infarction or stroke and prevented the death of animals from kidney ischemia. In p53^−/− mice, 5 nmol/kg × day SkQ1 decreased the ROS level in the spleen and inhibited appearance of lymphomas to the same degree as million-fold higher concentration of conventional antioxidant NAC. Thus, SkQs look promising as potential tools for treatment of senescence and age-related diseases.     

Successional state dynamics: A novel approach to modeling nonequilibrium foodweb dynamics

Communities and ecosystems are often far from equilibrium, but our understanding of nonequilibrium dynamics has been hampered by a paucity of analytical tools. Here I describe a novel approach to modeling seasonally forced food webs, called “successional state dynamics” (SSD). It is applicable to communities where species dynamics are fast relative to the external forcing, such as plankton and other microbes, diseases, and some insect communities. The approach treats succession as a series of state transitions driven by both the internal dynamics of species interactions and external forcing. First, I motivate the approach with numerical solutions of a seasonally forced predator-prey model. Second, I describe how to set up and analyze an SSD model. Finally, I apply the techniques to three additional models of two-species interactions: resource competition (r-K selection), facilitation, and flip-flop competition (where the competitive hierarchy alternates over time). This approach allows easy and thorough exploration of how dynamics depend on the environmental forcing regime, and uncovers unexpected phenomena such as multiple stable annual trajectories and year-to-year irregularity in successional trajectories (chaos).     

Crippling ratio: A novel approach to assess hunting-induced wounding of wild animals

In order to use recreational hunting as a socially acceptable management tool, the practice of this activity should adhere strictly to the ethical standards of animal welfare and the conservation guidelines on sustainable harvest. A key measure in this regard is monitoring the negative side effects of hunting associated with crippling of wild animals. This study introduces “crippling ratio” (the number of individuals crippled for each successfully bagged) as a novel approach to evaluate hunter performance in a way that accounts for differences in population size and harvest pressure, and which therefore can be used to evaluate initiatives launched to reduce wounding of wild game. We demonstrate that crippling ratios of Svalbard-breeding Pink-footed Geese Anser brachyrhynchus has been declining steadily over the last 25 years despite an increasing harvest rate. Hence, for juvenile birds that have not previously experienced a hunting season, and therefore can be used as a direct measure of annual variation in the crippling ratio, the number of geese crippled for each goose bagged dropped from 1.00 in 1992–0.11 in 2016. This corresponds to an 89% reduction in crippling frequency. Among adult birds the ratio dropped from 9.75 in 1992–1.99 in 2016, corresponding to a reduction of 80%. This positive development might be ascribed to effective awareness campaigns, training of hunters and adjustment of hunting techniques in both Denmark and, recently, Norway. It exemplifies that monitoring the outcome of management programmes is an important element in ensuring that measures introduced to manage wildlife are socially defensible.     

Bioluminescent kinase strips: A novel approach to targeted and flexible kinase inhibitor profiling

In addition to target efficacy, drug safety is a major requirement during the drug discovery process and is influenced by target specificity. Therefore, it is imperative that every new drug candidate be profiled against various liability panels that include protein kinases. Here, an effective methodology to streamline kinase inhibitor profiling is described. An accessible standardized profiling system for 112 protein kinases covering all branches of the kinome was developed. This approach consists of creating different sets of kinases and their corresponding substrates in multi-tube strips. The kinase stocks are pre-standardized for optimal kinase activity and used for inhibitor profiling using a bioluminescent ADP detection assay. We show that these strips can routinely generate inhibitor selectivity profiles for small or broad kinase family panels. Lipid kinases were also assembled in strip format and profiled together with protein kinases. We identified two specific PI3K inhibitors that have off-target effects on CK2 that were not reported before and would have been missed if compounds were not profiled against lipid and protein kinases simultaneously. To validate the accuracy of the data generated by this method, we confirmed that the inhibition potencies observed are consistent with published values produced by more complex technologies such as radioactivity assays.     

A novel approach to the van der pol oscillator: Natural frequency and entrainment

Abstract

The physics of the van der Pol oscillator as realized by the Meissner circuit is discussed by analogy to the beat phenomenon and by a consequent analysis of current balance. The current balance method leads to a new, very accurate equation for the dependence of the oscillator frequency on the feedback parameter. Several aspects of entrainment (existence, limited frequency range, dependence on parameters, phase shift) can be explained, too. Numerical results are presented which have been obtained by solving the homogeneous and inhomogeneous van der Pol equation with a Runge‐Kutta method.     

Split GFP complementation assay: a novel approach to quantitatively measure aggregation of tau in situ: effects of GSK3beta activation and caspase 3 cleavage

To quantitatively measure tau aggregation in situ , we established a cell model system using a split green fluorescence protein (GFP) complementation assay. In this assay the more aggregated the protein of interest the lower the GFP fluorescence. Tau microtubule-binding domain constructs, whose aggregation characteristics have been described previously ( Khlistunova et al. 2006 ), were used to validate the assay. The aggregation-prone construct exhibited the lowest GFP intensity whereas the aggregation-resistant construct showed the highest GFP intensity. To examine the role of glycogen synthase kinase 3β (GSK3β) activity and caspase 3 cleavage on tau aggregation, GFP complementation of full length (T4), caspase-cleaved (T4C3), and pseudophosphorylated at S396/S404 (T4-2EC) tau was examined in the presence of an active or a kinase-dead GSK3β. Extensive phosphorylation of T4 by GSK3β resulted in increased GFP intensity. T4C3 showed neither efficient phosphorylation nor a significant GFP intensity change by GSK3β. The GFP intensity of T4-2EC was significantly reduced by GSK3β accompanying its presence in the sarkosyl-insoluble fraction, thus demonstrating that T4-2EC was partitioning into aggregates. This indicates that if the majority of tau is phosphorylated at S396/S404, in combination with increased GSK3β activity, tau aggregation is favored. These data demonstrate that split GFP complementation may be a valuable approach to determine the aggregation process in living cells.     

A novel approach to overcome temozolomide resistance in glioma and melanoma: Inactivation of MGMT by gene therapy

Malignant glioma is the most common primary brain tumor. Malignant melanoma is the most malignant of skin tumor. The two malignancies are poorly responsive to conventional treatment regimens such as chemotherapy. Temozolomide (TMZ) is a DNA-alkylating agent used for the treatment of glioma, astrocytoma, and melanoma. Resistance to alkylating agents such as TMZ correlates with increased expression of DNA repair protein O6-methylguanine-DNA methyltransferase (MGMT). Several studies in animal models have demonstrated that decreasing MGMT level with gene therapy could overcome TMZ resistance and enhance tumor cell death. In the present review, we provide an overview of recent advances in this field.     

A simple approach to improve the sensitivity of enzyme-linked immunosorbent assay: Using the IMAPlate 5RC96 for result readout

In this article, we describe a new enzyme-linked immunosorbent assay (ELISA) setup to improve the sensitivity of commercial or homemade ELISAs. In the new ELISA setup, an IMAPlate 5RC96, a disposable multi-utility lab device developed by NCL New Concept Lab is used as a self-uptaking microcuvette array to read out the result of the ELISA that is performed in the normal 96-well plate with reduced substrate solution and stop solution. A commercial interleukin-6 (IL-6) ELISA reagent kit was used for the evaluation. Compared with the conventional ELISA setup, the new ELISA setup could easily increase the absorbance values by up to more than 10-fold. Therefore, the sensitivity (change in absorbance/change in concentration [ΔAbs/ΔConc]) is increased accordingly. In addition, methods to extend the upper detection limit of plate readers for the IMAPlate 5RC96 are described. This new ELISA setup may be more notable for the approach employed than for the specific analyte. It should generally be applicable to any conventional ELISA and should serve as an example of a simple solution that increases the detection sensitivity and/or detection range of other assays as well. We expect the approach to have a substantial practical impact on analytical methods and to accelerate discovery, research, and application of analytes at low concentration in life sciences and diagnostics.     

The ApoCorrect assay: a novel, rapid method to determine the biological functionality of radiolabeled and fluorescent Annexin A5

N-[4-(3)H]Benzoylglycylglycylglycine ([(3)H]BzG(3)) was tested as a probe for detecting hydroxyl radicals (*OH). Aerated solutions of l-ascorbate generated *OH, which oxidized [(3)H]BzG(3), yielding hydrophilic (probably hydroxylated) derivatives plus tritiated water. The (3)H(2)O was separated from organic products and remaining [(3)H]BzG(3) on Dowex-1. (3)H(2)O production was much greater with *OH than with other reactive oxygen species (ROS) (e.g., H(2)O(2), superoxide). The slight (3)H(2)O production in the presence of H(2)O(2) or superoxide was blocked by *OH scavengers (e.g., glycerol, mannitol, butan-1-ol) that do not scavenge H(2)O(2) or superoxide. This indicates that (3)H(2)O production was caused by *OH and that other ROS only generated any (3)H(2)O by forming traces of *OH. Doses of *OH that caused detectable nonenzymic polysaccharide scission also caused (3)H(2)O production, indicating that [(3)H]BzG(3) is a sensitive *OH probe in studies of polymer scission. The ability of scavengers and chelators to protect against ascorbate-mediated polysaccharide scission paralleled their ability to inhibit concurrent (3)H(2)O production, indicating that both processes were due to *OH. Thus, [(3)H]BzG(3) is a simple, specific, sensitive, and robust probe for detecting *OH production in vitro. It may have applications for in vivo detection of extracellular *OH in arthritic joints and of apoplastic *OH in plant cell walls.     

A novel computer modeling approach to the structures of small bioactive peptides: The structure of gonadotropin releasing hormone

A novel computer modeling approach suitable for the structure analysis of small bioactive peptides has been developed. This approach involves identification of conformational patterns in protein structure data bank based on the sequence homology with the bioactive peptide. The models built on the basis of this homology and having common conformational patterns are analyzed under the structural constraints derived from the activity data of various synthetic analogs of the peptide. Application of this procedure to the gonadotropin releasing hormone (GnRH) resulted in a library of possible structures for GnRH, 9 among which shared a common β-turn. Further analysis of the structures containing the β-turn motif, in the context of the structure–activity data, led to a model for the active conformation of GnRH. The topology of the putative receptor binding site of the hormone is defined by a contiguous surface formed through an appropriate juxtaposition of the N-terminal pGlu¹ the guanidyl group of Arg⁸, aromatic side chain of Trp³, and the Gly¹⁰-NH₂ at the C-terminal end. ©Wiley-Liss, Inc.     

A novel approach to decoy set generation: designing a physical energy function having local minima with native structure characteristics

We suggest a new approach to the generation of candidate structures (decoys) for ab initio prediction of protein structures. Our method is based on random sampling of conformation space and subsequent local energy minimization. At the core of this approach lies the design of a novel type of energy function. This energy function has local minima with native structure characteristics and wide basins of attraction. The current work presents our motivation for deriving such an energy function and also tests the derived energy function.Our approach is novel in that it takes advantage of the inherently rough energy landscape of proteins, which is generally considered a major obstacle for protein structure prediction. When local minima have wide basins of attraction, the protein's conformation space can be greatly reduced by the convergence of large regions of the space into single points, namely the local minima corresponding to these funnels. We have implemented this concept by an iterative process. The potential is first used to generate decoy sets and then we study these sets of decoys to guide further development of the potential. A key feature of our potential is the use of cooperative multi-body interactions that mimic the role of the entropic and solvent contributions to the free energy.The validity and value of our approach is demonstrated by applying it to 14 diverse, small proteins. We show that, for these proteins, the size of conformation space is considerably reduced by the new energy function. In fact, the reduction is so substantial as to allow efficient conformational sampling. As a result we are able to find a significant number of near-native conformations in random searches performed with limited computational resources.     

Thiolactomycin inhibits d-aspartate oxidase: A novel approach to probing the active site environment

d-Aspartate oxidase (DDO) and d-amino acid oxidase (DAO) are flavin adenine dinucleotide (FAD)-containing flavoproteins that catalyze the oxidative deamination of d-amino acids. While several functionally and structurally important amino acid residues have been identified in the DAO protein, little is known about the structure–function relationships of DDO. In the search for a potent DDO inhibitor as a novel tool for investigating its structure–function relationships, a large number of biologically active compounds of microbial origin were screened for their ability to inhibit the enzymatic activity of mouse DDO. We discovered several compounds that inhibited the activity of mouse DDO, and one of the compounds identified, thiolactomycin (TLM), was then characterized and evaluated as a novel DDO inhibitor. TLM reversibly inhibited the activity of mouse DDO with a mixed type of inhibition more efficiently than meso-tartrate and malonate, known competitive inhibitors of mammalian DDOs. The selectivity of TLM was investigated using various DDOs and DAOs, and it was found that TLM inhibits not only DDO, but also DAO. Further experiments with apoenzymes of DDO and DAO revealed that TLM is most likely to inhibit the activities of DDO and DAO by competition with both the substrate and the coenzyme, FAD. Structural models of mouse DDO/TLM complexes supported this finding. The binding mode of TLM to DDO was validated further by site-directed mutagenesis of an active site residue, Arg-237. Collectively, our findings show that TLM is a novel, active site-directed DDO inhibitor that will be useful for elucidating the molecular details of the active site environment of DDO.     

A novel approach to biological control with entomopathogenic nematodes: Prophylactic control of the peachtree borer, Synanthedon exitiosa

Generally, microbial control agents such as entomopathogenic nematodes are applied in a curative manner for achieving pest suppression; prophylactic applications are rare. In this study, we determined the ability of two Steinernema carpocapsae strains (All and Hybrid) to prophylactically protect peach trees from damage caused by the peachtree borer, Synanthedon exitiosa, which is a major pest of stone fruit trees in North America. In prior studies, the entomopathogenic nematodes S. carpocapsae and Heterorhabditis bacteriophora caused field suppression when applied in a curative manner to established S. exitiosa populations. In our current study, nematodes were applied three times (at 150,000–300,000 infective juveniles/tree) during September and October of 2005, 2006, and 2007. A control (water only) and a single application of chlorpyrifos (at the labeled rate) were also made each year. The presence of S. exitiosa damage was assessed each year in the spring following the treatment applications. Following applications in 2006, we did not detect any differences among treatments or the control (possibly due to a low and variable S. exitiosa infestation of that orchard). Following applications in 2005 and 2007, however, the nematode and chemical treatments caused significant damage suppression. The percentage of trees with S. exitiosa damage in treated plots ranged from 0% damage in 2005 to 16% in plots treated with S. carpocapsae (Hybrid) in 2007. In control plots damage ranged from 25% (2005) to 41% (2007). Our results indicate that nematodes applied in a preventative manner during S. exitios’s oviposition period can reduce insect damage to levels similar to what is achieved with recommended chemical insecticide treatments.