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Reshared post from Matthew Todd: - https://plus.google.com/1041867...
Original Post from Matthew Todd: The OSM Christmas Top 10 list. In the grand tradition of making lists towards year's end, here's the Top 10 List of molecules most needed right now. Any better ideas? Please suggest below. If you'd like to make any of these in the lab, and have the molecules tested, you're free to do so and be included on the paper that will come out of that work. Which molecules to make next in Open Source Malaria Series 4? The full reasoning is below. The executive summary is that OSM needs these ten molecules: OSM Christmas Top Ten. And if you'd like to synthesise them yourself (open source only please), or suggest better ones, you're free to do so. - Egon Willighagen
CC-BY-SA WikiMedia Commons. I learned yesterday that all employees with a longer contract will be equipped with an Android tablet. That is great news for this blog, because Android uses the Linux kernel. It means two things: ... - Egon Willighagen
3. Op welke tijdschriften heeft de deal met Springer betrekking? […] Tijdschriften / publicaties in Springer Open en Biomed Central (ongeveer 400 tijdschriften). Dit zijn collecties die al volledig open access zijn. Publicaties zijn voor Nederlandse onderzoekers dus volledig vrij toegankelijk (lezen) maar voor publicatie in deze titels moeten... - http://egonw.tumblr.com/post...
Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve - http://www.citeulike.org/user...
Proceedings of the National Academy of Sciences, Vol. 108, No. 38. (20 September 2011), pp. 16050-16055, doi:10.1073/pnas.1102999108 There is increasing, but largely indirect, evidence pointing to an effect of commensal gut microbiota on the central nervous system (CNS). However, it is unknown whether lactic acid bacteria such as Lactobacillus rhamnosus could have a direct effect on neurotransmitter receptors in the CNS in normal, healthy animals. GABA is the main CNS inhibitory neurotransmitter and is significantly involved in regulating many physiological and psychological processes. Alterations in central GABA receptor expression are implicated in the pathogenesis of anxiety and depression, which are highly comorbid with functional bowel disorders. In this work, we show that chronic treatment with L. rhamnosus (JB-1) induced region-dependent alterations in GABAB1b mRNA in the brain with increases in cortical regions (cingulate and prelimbic) and concomitant reductions in expression... - Egon Willighagen
Toll-Like Receptor mRNA Expression Is Selectively Increased in the Colonic Mucosa of Two Animal Models Relevant to Irritable Bowel Syndrome - http://www.citeulike.org/user...
PLoS ONE, Vol. 4, No. 12. (9 December 2009), e8226, doi:10.1371/journal.pone.0008226 Irritable bowel syndrome (IBS) is largely viewed as a stress-related disorder caused by aberrant brain-gut–immune communication and altered gastrointestinal (GI) homeostasis. Accumulating evidence demonstrates that stress modulates innate immune responses; however, very little is known on the immunological effects of stress on the GI tract. Toll-like receptors (TLRs) are critical pattern recognition molecules of the innate immune system. Activation of TLRs by bacterial and viral molecules leads to activation of NF-kB and an increase in inflammatory cytokine expression. It was our hypothesis that innate immune receptor expression may be changed in the gastrointestinal tract of animals with stress-induced IBS-like symptoms. In this study, our objective was to evaluate the TLR expression profile in the colonic mucosa of two rat strains that display colonic visceral hypersensivity; the stress-sensitive... - Egon Willighagen
Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour - http://www.citeulike.org/user...
Nature Reviews Neuroscience, Vol. 13, No. 10. (12 September 2012), pp. 701-712, doi:10.1038/nrn3346 John Cryan, Timothy Dinan - Egon Willighagen
Microbial endocrinology in the microbiome-gut-brain axis: how bacterial production and utilization of neurochemicals influence behavior. - http://www.citeulike.org/user...
PLoS pathogens, Vol. 9, No. 11. (2013) Mark Lyte - Egon Willighagen
Leptin Increases Adult Hippocampal Neurogenesis in Vivo and in Vitro - http://www.citeulike.org/user...
Journal of Biological Chemistry, Vol. 283, No. 26. (27 June 2008), pp. 18238-18247, doi:10.1074/jbc.m800053200 Leptin, an adipose-derived hormone, has been implicated in several physiological processes involving the hippocampus. However, the role of leptin in adult hippocampal neurogenesis remains unknown. Here we show that leptin regulates neurogenesis in the dentate gyrus of adult mice as well as in cultured adult hippocampal progenitor cells. Chronic administration of leptin to adult mice increased cell proliferation without significant effects on the differentiation and the survival of newly proliferated cells in the dentate gyrus. The expression of the long form leptin receptor, LepRb, was detected in hippocampal progenitor cells by reverse transcription-PCR and immunohistochemistry. Leptin treatment also increased proliferation of cultured adult hippocampal progenitor cells. Analysis of signal transduction pathways revealed that leptin stimulated phosphorylation of Akt and STAT3... - Egon Willighagen
Predicting new molecular targets for known drugs. - http://www.citeulike.org/user...
Nature In Nature, Vol. 462, No. 7270. (12 November 2009), pp. 175-181, doi:10.1038/nature08506 Although drugs are intended to be selective, at least some bind to several physiological targets, explaining side effects and efficacy. Because many drug-target combinations exist, it would be useful to explore possible interactions computationally. Here we compared 3,665 US Food and Drug Administration (FDA)-approved and investigational drugs against hundreds of targets, defining each target by its ligands. Chemical similarities between drugs and ligand sets predicted thousands of unanticipated associations. Thirty were tested experimentally, including the antagonism of the beta(1) receptor by the transporter inhibitor Prozac, the inhibition of the 5-hydroxytryptamine (5-HT) transporter by the ion channel drug Vadilex, and antagonism of the histamine H(4) receptor by the enzyme inhibitor Rescriptor. Overall, 23 new drug-target associations were confirmed, five of which were potent (<100... - Egon Willighagen
"The service offers interactive 3D visualisation of structures with chemical interpretations generated... - https://plus.google.com/1041867...
"The service offers interactive 3D visualisation of structures with chemical interpretations generated by our expert editors, displayed using the splendid JSmol visualiser." - Egon Willighagen
Immune-responsive gene 1 protein links metabolism to immunity by catalyzing itaconic acid production - http://www.citeulike.org/user...
Proceedings of the National Academy of Sciences, Vol. 110, No. 19. (7 May 2013), pp. 7820-7825, doi:10.1073/pnas.1218599110 Immunoresponsive gene 1 (Irg1) is highly expressed in mammalian macrophages during inflammation, but its biological function has not yet been elucidated. Here, we identify Irg1 as the gene coding for an enzyme producing itaconic acid (also known as methylenesuccinic acid) through the decarboxylation of cis-aconitate, a tricarboxylic acid cycle intermediate. Using a gain-and-loss-of-function approach in both mouse and human immune cells, we found Irg1 expression levels correlating with the amounts of itaconic acid, a metabolite previously proposed to have an antimicrobial effect. We purified IRG1 protein and identified its cis-aconitate decarboxylating activity in an enzymatic assay. Itaconic acid is an organic compound that inhibits isocitrate lyase, the key enzyme of the glyoxylate shunt, a pathway essential for bacterial growth under specific conditions. Here... - Egon Willighagen
Integrating Pathways of Parkinson's Disease in a Molecular Interaction Map - http://www.citeulike.org/user...
In Molecular Neurobiology, Vol. 49, No. 1. (2014), pp. 88-102, doi:10.1007/s12035-013-8489-4 Parkinson's disease (PD) is a major neurodegenerative chronic disease, most likely caused by a complex interplay of genetic and environmental factors. Information on various aspects of PD pathogenesis is rapidly increasing and needs to be efficiently organized, so that the resulting data is available for exploration and analysis. Here we introduce a computationally tractable, comprehensive molecular interaction map of PD. This map integrates pathways implicated in PD pathogenesis such as synaptic and mitochondrial dysfunction, impaired protein degradation, alpha-synuclein pathobiology and neuroinflammation. We also present bioinformatics tools for the analysis, enrichment and annotation of the map, allowing the research community to open new avenues in PD research. The PD map is accessible at http://minerva.uni.lu/pd_map. KazuhiroA Fujita, Marek Ostaszewski, Yukiko Matsuoka, Samik Ghosh,... - Egon Willighagen
German summary: Vor einigen Wochen wurde an dieser Stelle von einer Initiative berichtet, im Rahmen derer Wikidata-Einträge für alle knapp 40.000 menschlichen Gene angelegt wurden. Hier nun baut Danie... - Egon Willighagen
Elements matter: The context and perception of classical and cosmological elements versus earthly and physical matter in the Rosette Map - http://www.citeulike.org/user...
(14 December 2014), doi:10.6084/m9.figshare.1270516 This is an extension to the preceeding paper (link underneath) and response to TH Ing's (link underneath) review of this paper and discussion of the continents and elements displayed in Voynich manuscript folio f86v. It follows up on the position of classical elements in the medieval cosmos and depiction of physical matter. Juergen Wastl - Egon Willighagen
Efficient Synthesis and Anti-Tubercular Activity of a Series of Spirocycles: An Exercise in Open Science - http://www.citeulike.org/user...
PLoS ONE, Vol. 9, No. 12. (10 December 2014), e111782, doi:10.1371/journal.pone.0111782 Tuberculosis afflicts an estimated 2 billion people worldwide and causes 1.3 million deaths annually. Chemotherapeutic solutions rely on drugs developed many years ago, with only one new therapeutic having been approved in the last 40 years. Given the rise of drug-resistant strains, there is an urgent need for the development of a more robust drug development pipeline. GlaxoSmithKline recently placed the structures and activities of 177 novel anti-tubercular leads in the public domain, as well as the results of ongoing optimisation of some of the series. Since many of the compounds arose from screening campaigns, their provenance was unclear and synthetic routes were in many cases not reported. Here we present the efficient synthesis of several novel analogues of one family of the GSK compounds—termed “Spiros”—using an oxa-Pictet–Spengler reaction. The new compounds are attractive from a medicinal... - Egon Willighagen
Scaling predictive modeling in drug development with cloud computing - http://www.citeulike.org/user...
J. Chem. Inf. Model. (10 December 2014), doi:10.1021/ci500580y Growing data sets with increased time for analysis is hampering predictive modeling in drug discovery. Model building can be carried out on high-performance computer clusters, but these can be expensive to purchase and maintain. We have evaluated ligand-based modeling on cloud computing resources where computations are parallelized and run on Amazon Elastic Cloud. We train models on open datasets of varying sizes for the endpoints logP and Ames mutagenicity and compare with model building parallelized on a traditional high-performance computing cluster. We show that while high-performance computing results in faster model building, the use of cloud computing resources is feasible for large datasets and scales well within cloud instances. An additional advantage of cloud computing is that the costs of predictive models can be easily quantified, and a choice can be made between speed and economy. The easy access to... - Egon Willighagen
diXa: a Data Infrastructure for Chemical Safety Assessment - http://www.citeulike.org/user...
Bioinformatics (12 December 2014), btu827, doi:10.1093/bioinformatics/btu827 Motivation: The field of toxicogenomics (the application of ‘-omics’ technologies to risk assessment of compound toxicities) has expanded in the last decade, partly driven by new legislation, aimed at reducing animal testing in chemical risk assessment but mainly as a result of a paradigm change in toxicology towards the use and integration of genome wide data. Many research groups worldwide have generated large amounts of such toxicogenomics data. However, there is no centralized repository for archiving and making these data and associated tools for their analysis easily available.Results: The Data Infrastructure for Chemical Safety Assessment (diXa) is a robust and sustainable infrastructure storing toxicogenomics data. A central data warehouse is connected to a portal with links to chemical information and molecular and phenotype data. diXa is publicly available through a user-friendly web interface. New... - Egon Willighagen
Egonw: Columns in the ref section. {{Infobox scientist | name = Cameron Neylon | birth_name = David Cameron Neylon | native_name_lang = | image = Cameron Neylon in 2013 at the CERN Workshop on Innovations in Scholarly Communication (OAI8).jpg | image_size = | alt = | caption = Cameron Neylon in 2013 | birth_date = <!-- {{Birth date|YYYY|MM|DD}} --> | birth_place = | death_date = <!-- {{Death date and age|YYYY|MM|DD|YYYY|MM|DD}} (death date then birth date) --> | death_place = | resting_place = | resting_place_coordinates = <!-- {{Coord|LAT|LONG|type:landmark|display=inline,title}} --> | other_names = | residence = | citizenship = | nationality = | fields = {{Plainlist| * [[Biophysics]] * [[Data management]] * [[Open research]]<ref name="googlescholar">{{GoogleScholar|-RuNXZwAAAAJ}}</ref>}} | workplaces = {{Plainlist| * [[PLOS|Public Library of Science (PLOS)]] * [[Flooved]] * [[ISIS neutron source]] * [[Science and Technology Facilities Council|STFC]]}} | patrons = | alma_mater =... - Egon Willighagen
Egonw: Columns in the ref section. {{Infobox scientist | name = | image = Henry Rzepa.jpg | image_size = | alt = | caption = | birth_date = {{Birth year and age|1950}}{{citation needed|date=December 2012}} | birth_place = | death_date = <!-- {{Death date and age|YYYY|MM|DD|YYYY|MM|DD}} (death date then birth date) --> | death_place = | resting_place = | resting_place_coordinates = <!-- {{Coord|LAT|LONG|type:landmark|display=inline,title}} --> | residence = | citizenship = | nationality = | fields = | workplaces = [[Imperial College London]]<br>[[University of Texas at Austin]] | alma_mater = | thesis_title = Hydrogen Transfer Reactions of Indoles | thesis_url = http://ethos.bl.uk/OrderDe... | thesis_year =1974 | doctoral_advisor = Brian Challis | academic_advisors = | doctoral_students = | notable_students = | known_for = | author_abbrev_bot = | author_abbrev_zoo = | influences = [[Michael J. S. Dewar]] | influenced = | awards = | signature = <!--(filename... - Egon Willighagen
Egonw: Added a Authority control section. {{Infobox scientist | name = | image = Henry Rzepa.jpg | image_size = | alt = | caption = | birth_date = {{Birth year and age|1950}}{{citation needed|date=December 2012}} | birth_place = | death_date = <!-- {{Death date and age|YYYY|MM|DD|YYYY|MM|DD}} (death date then birth date) --> | death_place = | resting_place = | resting_place_coordinates = <!-- {{Coord|LAT|LONG|type:landmark|display=inline,title}} --> | residence = | citizenship = | nationality = | fields = | workplaces = [[Imperial College London]]<br>[[University of Texas at Austin]] | alma_mater = | thesis_title = Hydrogen Transfer Reactions of Indoles | thesis_url = http://ethos.bl.uk/OrderDe... | thesis_year =1974 | doctoral_advisor = Brian Challis | academic_advisors = | doctoral_students = | notable_students = | known_for = | author_abbrev_bot = | author_abbrev_zoo = | influences = [[Michael J. S. Dewar]] | influenced = | awards = | signature =... - Egon Willighagen
+Henry Rzepa, are you also putting material from this great series into Wikipedia? - https://plus.google.com/1041867...
+Henry Rzepa, are you also putting material from this great series into Wikipedia? These posts contain the computed potential energy surfaces for a fair few "text-book" reactions. Here I chart the course of the cyclopropanation of alkenes using the Simmons-Smith reagent, as prepa... - Egon Willighagen
Oh, the animate GIF works nice on G+ too! - https://plus.google.com/1041867...
Oh, the animate GIF works nice on G+ too! These posts contain the computed potential energy surfaces for a fair few "text-book" reactions. Here I chart the course of the cyclopropanation of alkenes using the Simmons-Smith reagent, as prepa... - Egon Willighagen
Egonw: Added a visual overview of the Blue Obelisk movement. {{Infobox organization |name = Blue Obelisk |image = BOicon.png |image_border = |size = 50px |alt = |caption = |map = |msize = |malt = |mcaption = |abbreviation = |motto = |formation = 2005 |extinction = |type = |status = |purpose = |headquarters = |location = |region_served = |membership = 23+ |language = English |leader_title = |leader_name = |main_organ = |parent_organization = |affiliations = |num_staff = |num_volunteers = |budget = zero |website = http://www.blueobelisk.org/ |remarks = }} '''Blue Obelisk''' is an informal group of chemists who promote [[open data]], [[open source]], and [[open standards]]; it was initiated by [[Peter Murray-Rust]] and others in 2005.<ref>P. Murray-Rust, The Blue Obelisk, [[Chemistry Development Kit#CDK News|CDK News]], 2005, 2, 43&ndash;46</ref><ref>{{cite journal | last1 = Guha | first1 = R | last2 = Howard | first2 = MT | last3 = Hutchison | first3 = GR | last4 = Murray-Rust | first4... - Egon Willighagen
Shape and Orientation Matter for the Cellular Uptake of Nonspherical Particles - http://www.citeulike.org/user...
Nano Lett., Vol. 14, No. 2. (2 January 2014), pp. 687-693, doi:10.1021/nl403949h Recent advances in nanotechnology have made a whole zoo of particles of different shapes available for applications, but their interaction with biological cells and their toxicity is often not well understood. Experiments have shown that particle uptake by cells is determined by an intricate interplay between physicochemical particle properties like shape, size, and surface functionalization, but also by membrane properties and particle orientation. Our work provides systematic understanding, based on a mechanical description, for membrane wrapping of nanoparticles, viruses, and bacterial forms. For rod-like particles, we find stable endocytotic states with small and high wrapping fraction; an increased aspect ratio is unfavorable for complete wrapping. For high aspect ratios and round tips, the particles enter via a submarine mode, side-first with their long edge parallel to the membrane. For small... - Egon Willighagen
Receptor-Mediated Endocytosis of Nanoparticles of Various Shapes - http://www.citeulike.org/user...
Nano Lett., Vol. 11, No. 12. (2 November 2011), pp. 5391-5395, doi:10.1021/nl2030213 Cellular uptake through endocytosis is crucial for drug delivery and nanomedicine. However, the conditions under which passive endocytosis (i.e., not ATP driven) takes place are not well understood. We report MD simulations of the passive uptake of ligand-coated nanoparticles with varying size, shape, coverage, and membrane-binding strength. We find that the efficiency of passive endocytosis is higher for spherocylindrical particles than for spheres and that endocytosis is suppressed for particles with sharp edges. Robert Vácha, Francisco Martinez-Veracoechea, Daan Frenkel - Egon Willighagen
Aggregation and vesiculation of membrane proteins by curvature-mediated interactions - http://www.citeulike.org/user...
Nature, Vol. 447, No. 7143. (24 May 2007), pp. 461-464, doi:10.1038/nature05840 Membrane remodelling1, 2, 3, 4, 5 plays an important role in cellular tasks such as endocytosis, vesiculation and protein sorting, and in the biogenesis of organelles such as the endoplasmic reticulum or the Golgi apparatus. It is well established that the remodelling process is aided by specialized proteins that can sense4 as well as create6 membrane curvature, and trigger tubulation7, 8, 9 when added to synthetic liposomes. Because the energy needed for such large-scale changes in membrane geometry significantly exceeds the binding energy between individual proteins and between protein and membrane, cooperative action is essential. It has recently been suggested10, 11 that curvature-mediated attractive interactions could aid cooperation and complement the effects of specific binding events on membrane remodelling. But it is difficult to experimentally isolate curvature-mediated interactions from direct... - Egon Willighagen
Powering membrane traffic in endocytosis and recycling - http://www.citeulike.org/user...
Nature Reviews Molecular Cell Biology, Vol. 7, No. 12. (8 November 2006), pp. 897-908, doi:10.1038/nrm2060 Early in evolution, the diversification of membrane-bound compartments that characterize eukaryotic cells was accompanied by the elaboration of molecular machineries that mediate intercompartmental communication and deliver materials to specific destinations. Molecular motors that move on tracks of actin filaments or microtubules mediate the movement of organelles and transport between compartments. The subjects of this review are the motors that power the transport steps along the endocytic and recycling pathways, their modes of attachment to cargo and their regulation. Thierry Soldati, Manfred Schliwa - Egon Willighagen
Tubulin Bond Energies and Microtubule Biomechanics Determined from Nanoindentation in Silico - http://www.citeulike.org/user...
J. Am. Chem. Soc., Vol. 136, No. 49. (12 November 2014), pp. 17036-17045, doi:10.1021/ja506385p Microtubules, the primary components of the chromosome segregation machinery, are stabilized by longitudinal and lateral noncovalent bonds between the tubulin subunits. However, the thermodynamics of these bonds and the microtubule physicochemical properties are poorly understood. Here, we explore the biomechanics of microtubule polymers using multiscale computational modeling and nanoindentations in silico of a contiguous microtubule fragment. A close match between the simulated and experimental force?deformation spectra enabled us to correlate the microtubule biomechanics with dynamic structural transitions at the nanoscale. Our mechanical testing revealed that the compressed MT behaves as a system of rigid elements interconnected through a network of lateral and longitudinal elastic bonds. The initial regime of continuous elastic deformation of the microtubule is followed by the... - Egon Willighagen
linkedISA: semantic representation of ISA-Tab experimental metadata. - http://www.citeulike.org/user...
BMC bioinformatics, Vol. 15 Suppl 14 (27 November 2014), doi:10.1186/1471-2105-15-s14-s4 Reporting and sharing experimental metadata- such as the experimental design, characteristics of the samples, and procedures applied, along with the analysis results, in a standardised manner ensures that datasets are comprehensible and, in principle, reproducible, comparable and reusable. Furthermore, sharing datasets in formats designed for consumption by humans and machines will also maximize their use. The Investigation/Study/Assay (ISA) open source metadata tracking framework facilitates standards-compliant collection, curation, visualization, storage and sharing of datasets, leveraging on other platforms to enable analysis and publication. The ISA software suite includes several components used in increasingly diverse set of life science and biomedical domains; it is underpinned by a general-purpose format, ISA-Tab, and conversions exist into formats required by public repositories. While... - Egon Willighagen
PubChemRDF: Towards a semantic (web) description of PubChem - Egon Willighagen
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