Modular Biological Function Is Most Effectively Captured by Combining Molecular Interaction Data Types

PublishedLarge-scale molecular interaction data sets have the potential to provide a comprehensive, system-wide understanding of biological function. Although individual molecules can be promiscuous in terms of their contribution to function, molecular functions emerge from the specific interactions of molecules giving rise to modular organisation. As functions often derive from a range of mechanisms, we demonstrate that they are best studied using networks derived from different sources. Implementing a graph partitioning algorithm we identify subnetworks in yeast protein-protein interaction (PPI), genetic interaction and gene co-regulation networks. Among these subnetworks we identify cohesive subgraphs that we expect to represent functional modules in the different data types. We demonstrate significant overlap between the subgraphs generated from the different data types and show these overlaps can represent related functions as represented by the Gene Ontology (GO). Next, we investigate the correspondence between our subgraphs and the Gene Ontology. This revealed varying degrees of coverage of the biological process, molecular function and cellular component ontologies, dependent on the data type. For example, subgraphs from the PPI show enrichment for 84%, 58% and 93% of annotated GO terms, respectively. Integrating the interaction data into a combined network increases the coverage of GO. Furthermore, the different annotation types of GO are not predominantly associated with one of the interaction data types. Collectively our results demonstrate that successful capture of functional relationships by network data depends on both the specific biological function being characterised and the type of network data being used. We identify functions that require integrated information to be accurately represented, demonstrating the limitations of individual data types. Combining interaction subnetworks across data types is therefore essential for fully understanding the complex and emergent nature of biological function.JIM was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) CASE studentship with industry partner Pfizer and RMA by a BBSRC studentship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Gene Duplication and Environmental Adaptation within Yeast Populations

PublishedPopulation-level differences in the number of copies of genes resulting from gene duplication and loss have recently been recognized as an important source of variation in eukaryotes. However, except for a small number of cases, the phenotypic effects of this variation are unknown. Data from the Saccharomyces Genome Resequencing Project permit the study of duplication in genome sequences from a set of individuals within the same population. These sequences can be correlated with available information on the environments from which these yeast strains were isolated. We find that yeast show an abundance of duplicate genes that are lineage specific, leading to a large degree of variation in gene content between individual strains. There is a detectable bias for specific functions, indicating that selection is acting to preferentially retain certain duplicates. Most strikingly, we find that sets of over- and underrepresented duplicates correlate with the environment from which they were isolated. Together, these observations indicate that gene duplication can give rise to substantial phenotypic differences within populations that in turn can offer a shortcut to evolutionary adaptation.This work was funded by BBSRC grant BB/F007620/1

Dao, harmony and personhood: towards a Confucian ethics of technology

A closer look at the theories and questions in philosophy of technology and ethics of technology shows the absence and marginality of non-Western philosophical traditions in the discussions. Although, increasingly, some philosophers have sought to introduce non-Western philosophical traditions into the debates, there are few systematic attempts to construct and articulate general accounts of ethics and technology based on other philosophical traditions. This situation is understandable, for the questions of modern sciences and technologies appear to be originated from the West; at the same time, the situation is undesirable. The overall aim of this paper, therefore, is to introduce an alternative account of ethics of technology based on the Confucian tradition. In doing so, it is hoped that the current paper can initiate a relatively uncharted field in philosophy of technology and ethics of technology

Preliminary study of the antioxidant properties of flowers and roots of Pyrostegia venusta (Ker Gawl) Miers

<p>Abstract</p> <p>Background</p> <p>Free radical stress leads to tissue injury and can eventually to arthritis, atherosclerosis, diabetes mellitus, neurodegenerative diseases and carcinogenesis. Several studies are ongoing worldwide to find natural antioxidants of plant origin. We assessed the <it>in-vitro </it>antioxidant activities and screened the phytochemical constituents of methanolic extracts of <it>Pyrostegia venusta </it>(Ker Gawl) <it>Miers</it>.</p> <p>Methods</p> <p>We evaluated the antioxidant potential and phytochemical constituents of <it>P. venusta </it>using 1,1-Diphenyl-2-picrylhydrazyl (DPPH), 2, 2'-azinobis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) and ferric reducing antioxidant power (FRAP) assays. Gas chromatography-mass spectroscopy (GC-MS) studies were also undertaken to assess the phytochemical composition of the flower extracts.</p> <p>Results</p> <p>Phytochemical analyses revealed the presence of terpenoids, alkaloids, tannins, steroids, and saponins. The reducing ability of both extracts was in the range (in μm Fe(II)/g) of 112.49-3046.98 compared with butylated hydroxytoluene (BHT; 63.56 ± 2.62), catechin (972.02 ± 0.72 μm) and quercetin 3208.27 ± 31.29. A significant inhibitory effect of extracts of flowers (IC₅₀= 0.018 ± 0.69 mg/ml) and roots (IC₅₀= 0.026 ± 0.94 mg/ml) on ABTS free radicals was detected. The antioxidant activity of the extracts of flowers (95%) and roots (94%) on DPPH radicals was comparable with that of ascorbic acid (98.9%) and BHT (97.6%). GC-MS study revealed the presence of myoinositol, hexadecanoic acid, linoleic acid, palmitic acid and oleic acid in the flower extracts.</p> <p>Conclusion</p> <p>These data suggest that <it>P. venusta </it>is a natural source of antioxidants. The extracts of flowers and roots of <it>P. venusta </it>contain significant amounts of phytochemicals with antioxidative properties and could serve as inhibitors or scavengers of free radicals. <it>P. venusta </it>could be exploited as a potential source for plant-based pharmaceutical products. These results could form a sound basis for further investigation in the potential discovery of new natural bioactive compounds.</p

Creatine Protects against Excitoxicity in an In Vitro Model of Neurodegeneration

Creatine has been shown to be neuroprotective in aging, neurodegenerative conditions and brain injury. As a common molecular background, oxidative stress and disturbed cellular energy homeostasis are key aspects in these conditions. Moreover, in a recent report we could demonstrate a life-enhancing and health-promoting potential of creatine in rodents, mainly due to its neuroprotective action. In order to investigate the underlying pharmacology mediating these mainly neuroprotective properties of creatine, cultured primary embryonal hippocampal and cortical cells were challenged with glutamate or H2O2. In good agreement with our in vivo data, creatine mediated a direct effect on the bioenergetic balance, leading to an enhanced cellular energy charge, thereby acting as a neuroprotectant. Moreover, creatine effectively antagonized the H2O2-induced ATP depletion and the excitotoxic response towards glutamate, while not directly acting as an antioxidant. Additionally, creatine mediated a direct inhibitory action on the NMDA receptor-mediated calcium response, which initiates the excitotoxic cascade. Even excessive concentrations of creatine had no neurotoxic effects, so that high-dose creatine supplementation as a health-promoting agent in specific pathological situations or as a primary prophylactic compound in risk populations seems feasible. In conclusion, we were able to demonstrate that the protective potential of creatine was primarily mediated by its impact on cellular energy metabolism and NMDA receptor function, along with reduced glutamate spillover, oxidative stress and subsequent excitotoxicity

Antioxidant potential of bitter cumin (Centratherum anthelminticum (L.) Kuntze) seeds in in vitro models

<p>Abstract</p> <p>Background</p> <p>Bitter cumin (<it>Centratherum anthelminticum </it>(L.) Kuntze), is a medicinally important plant. Earlier, we have reported phenolic compounds, antioxidant, and anti-hyperglycemic, antimicrobial activity of bitter cumin. In this study we have further characterized the antioxidative activity of bitter cumin extracts in various in vitro models.</p> <p>Methods</p> <p>Bitter cumin seeds were extracted with a combination of acetone, methanol and water. The antioxidant activity of bitter cumin extracts were characterized in various <it>in vitro </it>model systems such as DPPH radical, ABTS radical scavenging, reducing power, oxidation of liposomes and oxidative damage to DNA.</p> <p>Results</p> <p>The phenolic extracts of bitter cumin at microgram concentration showed significant scavenging of DPPH and ABTS radicals, reduced phosphomolybdenum (Mo(VI) to Mo(V)), ferricyanide Fe(III) to Fe(II), inhibited liposomes oxidation and hydroxyl radical induced damage to prokaryotic genomic DNA. The results showed a direct correlation between phenolic acid content and antioxidant activity.</p> <p>Conclusion</p> <p>Bitter cumin is a good source of natural antioxidants.</p

Mechanism of copper(II)-induced misfolding of Parkinson's disease protein

α-synuclein (aS) is a natively unfolded pre-synaptic protein found in all Parkinson's disease patients as the major component of fibrillar plaques. Metal ions, and especially Cu(II), have been demonstrated to accelerate aggregation of aS into fibrillar plaques, the precursors to Lewy bodies. In this work, copper binding to aS is investigated by a combination of quantum and molecular mechanics simulations. Starting from the experimentally observed attachment site, several optimized structures of Cu-binding geometries are examined. The most energetically favorable attachment results in significant allosteric changes, making aS more susceptible to misfolding. Indeed, an inverse kinematics investigation of the configuration space uncovers a dynamically stable β-sheet conformation of Cu-aS that serves as a nucleation point for a second β-strand. Based on these findings, we propose an atomistic mechanism of copper-induced misfolding of aS as an initial event in the formation of Lewy bodies and thus in PD pathogenesis

Personality factors in exercise addiction: a pilot study exploring the role of narcissism, extraversion, and agreeableness

Despite the increased evidence and acceptance of exercise being classed as a behavioral addiction, there is limited research examining personality characteristics within exercise addicts. The purpose of this study was to examine three personality traits (narcissism, extraversion, and agreeableness) and to examine their role in exercise addiction. The sample comprised 114 voluntary participants (74 females and 40 males) who completed the (i) Exercise Addiction Inventory, (ii) Narcissistic Personality Inventory, and (iii) Ten-Item Personality Inventory, as well as demographic questions and questions concerning their engagement and intensity levels of exercise. Results indicated a low incidence of individuals who were classed as at risk of exercise addiction (7%), but a high incidence of symptomatic individuals (75%). Results suggested that extraversion and narcissism may be underlying factors in exercise addiction with no effect for agreeableness. Exercise engagement and intensity were also related to exercise addiction. Further research examining the relationship between personality types and exercise addiction may be useful in identifying individuals at risk for developing exercise addiction

A Synthetic Uric Acid Analog Accelerates Cutaneous Wound Healing in Mice

Wound healing is a complex process involving intrinsic dermal and epidermal cells, and infiltrating macrophages and leukocytes. Excessive oxidative stress and associated inflammatory processes can impair wound healing, and antioxidants have been reported to improve wound healing in animal models and human subjects. Uric acid (UA) is an efficient free radical scavenger, but has a very low solubility and poor tissue penetrability. We recently developed novel UA analogs with increased solubility and excellent free radical-scavenging properties and demonstrated their ability to protect neural cells against oxidative damage. Here we show that the uric acid analog (6, 8 dithio-UA, but not equimolar concentrations of UA or 1, 7 dimethyl-UA) modified the behaviors of cultured vascular endothelial cells, keratinocytes and fibroblasts in ways consistent with enhancement of the wound healing functions of all three cell types. We further show that 6, 8 dithio-UA significantly accelerates the wound healing process when applied topically (once daily) to full-thickness wounds in mice. Levels of Cu/Zn superoxide dismutase were increased in wound tissue from mice treated with 6, 8 dithio-UA compared to vehicle-treated mice, suggesting that the UA analog enhances endogenous cellular antioxidant defenses. These results support an adverse role for oxidative stress in wound healing and tissue repair, and provide a rationale for the development of UA analogs in the treatment of wounds and for modulation of angiogenesis in other pathological conditions