Modeling of solvent flow effects in enzyme catalysis under physiological conditions

A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with absorbing boundaries are combined with densities obtained from explicit simulation to obtain the overall probability density for the total reaction cycle time of the enzymatic system. The method is used to investigate the catalytic transfer of a phosphoryl group in a phosphoglycerate kinase-ADP-bis phosphoglycerate system, one of the steps of glycolysis. The direct simulation of the enzyme-substrate binding and reaction is carried out using an elastic network model for the protein, and the solvent motions are described by multiparticle collision dynamics, which incorporates hydrodynamic flow effects. Systems where solvent-enzyme coupling occurs through explicit intermolecular interactions, as well as systems where this coupling is taken into account by including the protein and substrate in the multiparticle collision step, are investigated and compared with simulations where hydrodynamic coupling is absent. It is demonstrated that the flow of solvent particles around the enzyme facilitates the large-scale hinge motion of the enzyme with bound substrates, and has a significant impact on the shape of the probability densities and average time scales of substrate binding for substrates near the enzyme, the closure of the enzyme after binding, and the overall time of completion of the cycle.Comment: 15 pages in double column forma

Mental representations of the supernatural: A cluster analysis of religiosity, spirituality and paranormal belief

The aim of the study was to establish a new typology of belief in the supernatural; categorising people, based on their levels of religiosity, spirituality and paranormal belief. Examining how the various beliefs are defined was a further objective. The reasons for people having different levels of these beliefs were discussed, highlighting ‘Metaphysical Chauvinism’ as a possible explanation. Previous research that used variousmethods to measure religiosity, spirituality and paranormal belief were discussed. Participants (n = 307) completed an online survey consisting of the revised Religious Life Inventory (rRLI), the Intrinsic Spirituality Scale (ISS) and the revised Paranormal Belief Scale (rPBS). Two cluster analyses were performed: one on the three main scales and a secondary analysis on the ISS, the subscales of the rRLI and the rPBS. The results revealed a four cluster solution for each analysis. For the main analysis the clusters were ‘believers’, ‘paranormal believers’, ‘sceptics’ and ‘religious believers’. Metaphysical Chauvinism was supported; however, it was acknowledged that there still appears to be a lack of consensus when defining supernatural beliefs. It is proposed that the cluster analysis approach is more effective than a simple scale when trying establish how a person believes

Blip glitches in Advanced LIGO data

Blip glitches are short noise transients present in data from ground-based gravitational-wave observatories. These glitches resemble the gravitational-wave signature of massive binary black hole mergers. Hence, the sensitivity of transient gravitational-wave searches to such high-mass systems and other potential short duration sources is degraded by the presence of blip glitches. The origin and rate of occurrence of this type of glitch have been largely unknown. In this paper we explore the population of blip glitches in Advanced LIGO during its first and second observing runs. On average, we find that Advanced LIGO data contains approximately two blip glitches per hour of data. We identify four subsets of blip glitches correlated with detector auxiliary or environmental sensor channels, however the physical causes of the majority of blips remain unclear

Liver carnitine metabolism after partial hepatectomy in the rat Effects of nutritional status and inhibition of carnitine palmitoyltransferase

AbstractThis study examined the effects of partial hepatectony on hepatic carnitine and acylcarnitine concentrations in fed or 24 h-starved partially hepatectonized (PH) or sham-operated (SO) rats at 1 or 4 days after surgery. The ratio of free to esterified carnitine was low in fed PH rats at day 1 : the low ratio was increased to the SO value when mitochondrial fat oxidation was inhibited by 2-tetradecylglycidate. Starvation (24 h) increased plasma [non-esterified fatty acid] in PH or SO rats, the increases being greater at day 1 than at day 4. Hepatic [long-chain acylcarnitine] were also increased. These latter increases were a consequence of increased mitochondrial fat oxidation since they were not observed in PH or SO rats treated with 2-tetradecylglycidate. Whereas the starvation-induced increase in long-chain acylcarnitine was associated with increased [ketone body] in livers of SO rats at both day 1 and day 4 after surgery, [ketone body] was inappropriately low for the steady-state long-chain [acylcarnitine] in livers of PH rats at the first post-operative day. This was not a consequence of a decrease in [total carnitine] in the liver. The results are discussed with reference to the role of the liver in determining the relative proportions of the fat fuels available for extrahepatic tissues and the effects of liver cell proliferation on hepatic triacylclycerol metabolism

Anatomy ontologies and potential users: bridging the gap.

MOTIVATION: To evaluate how well current anatomical ontologies fit the way real-world users apply anatomy terms in their data annotations. METHODS: Annotations from three diverse multi-species public-domain datasets provided a set of use cases for matching anatomical terms in two major anatomical ontologies (the Foundational Model of Anatomy and Uberon), using two lexical-matching applications (Zooma and Ontology Mapper). RESULTS: Approximately 1500 terms were identified; Uberon/Zooma mappings provided 286 matches, compared to the control and Ontology Mapper returned 319 matches. For the Foundational Model of Anatomy, Zooma returned 312 matches, and Ontology Mapper returned 397. CONCLUSIONS: Our results indicate that for our datasets the anatomical entities or concepts are embedded in user-generated complex terms, and while lexical mapping works, anatomy ontologies do not provide the majority of terms users supply when annotating data. Provision of searchable cross-products for compositional terms is a key requirement for using ontologies.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Nail abnormalities identified in an ageing study of 30 inbred mouse strains.

In a large-scale ageing study, 30 inbred mouse strains were systematically screened for histologic evidence of lesions in all organ systems. Ten strains were diagnosed with similar nail abnormalities. The highest frequency was noted in NON/ShiLtJ mice. Lesions identified fell into two main categories: acute to chronic penetration of the third phalangeal bone through the hyponychium with associated inflammation and bone remodelling or metaplasia of the nail matrix and nail bed associated with severe orthokeratotic hyperkeratosis replacing the nail plate. Penetration of the distal phalanx through the hyponychium appeared to be the initiating feature resulting in nail abnormalities. The accompanying acute to subacute inflammatory response was associated with osteolysis of the distal phalanx. Evaluation of young NON/ShiLtJ mice revealed that these lesions were not often found, or affected only one digit. The only other nail unit abnormality identified was sporadic subungual epidermoid inclusion cysts which closely resembled similar lesions in human patients. These abnormalities, being age-related developments, may have contributed to weight loss due to impacts upon feeding and should be a consideration for future research due to the potential to interact with other experimental factors in ageing studies using the affected strains of mice.American Hair Research Society Mentorship Grants (to SL and AM) Ellison Medical Foundation (to JPS) National Institutes of Health (AG025707, for the Shock Aging Center). The Jackson Laboratory Shared Scientific Services were supported in part by a Basic Cancer Center Core Grant from the National Cancer Institute (CA034196)

Interactions between interfaces dictate stimuli-responsive emulsion behaviour

Stimuli-responsive emulsions offer a dual advantage, combining long-term storage with controlled release triggered by external cues such as pH or temperature changes. This study establishes that thermo-responsive emulsion behaviour is primarily determined by interactions between, rather than within, interfaces. Consequently, the stability of these emulsions is intricately tied to the nature of the stabilizing microgel particles - whether they are more polymeric or colloidal, and the morphology they assume at the liquid interface. The colloidal properties of the microgels provide the foundation for the long-term stability of Pickering emulsions. However, limited deformability can lead to non-responsive emulsions. Conversely, the polymeric properties of the microgels enable them to spread and flatten at the liquid interface, enabling stimuli-responsive behaviour. Furthermore, microgels shared between two emulsion droplets in flocculated emulsions facilitate stimuli-responsiveness, regardless of their internal architecture. This underscores the pivotal role of microgel morphology and the forces they exert on liquid interfaces in the control and design of stimuli-responsive emulsions and interfaces.ISSN:2041-172

Online carbohydrate 3D structure validation with the Privateer web app

Owing to the difficulties associated with working with carbohydrates, validating glycan 3D structures prior to deposition into the Protein Data Bank has become a staple of the structure-solution pipeline. The Privateer software provides integrative methods for the validation, analysis, refinement and graphical representation of 3D atomic structures of glycans, both as ligands and as protein modifiers. While Privateer is free software, it requires users to install any of the structural biology software suites that support it or to build it from source code. Here, the Privateer web app is presented, which is always up to date and available to be used online (https://privateer.york.ac.uk) without installation. This self-updating tool, which runs locally on the user's machine, will allow structural biologists to simply and quickly analyse carbohydrate ligands and protein glycosylation from a web browser whilst retaining all confidential information on their devices

DermO; an ontology for the description of dermatologic disease

Background: There have been repeated initiatives to produce standard nosologies and terminologies for cutaneous disease, some dedicated to the domain and some part of bigger terminologies such as ICD-10. Recently, formally structured terminologies, ontologies, have been widely developed in many areas of biomedical research. Primarily, these address the aim of providing comprehensive working erminologies for domains of knowledge, but because of the knowledge contained in the relationships between terms they can also be used computationally for many purposes. Results: We have developed an ontology of cutaneous disease, constructed manually by domain experts. With more than 3000 terms, DermO represents the most comprehensive formal dermatological disease terminology available. The disease entities are categorized in 20 upper level terms, which use a variety of features such as anatomical location, heritability, affected cell or tissue type, or etiology, as the features for classification, in line with professional practice and nosology in dermatology. Available in OBO flatfile and OWL 2 formats, it is integrated semantically with other ontologies and terminologies describing diseases and phenotypes. We demonstrate the application of DermO to text mining the biomedical literature and in the creation of a network describing the phenotypic relationships between cutaneous diseases. Conclusions: DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders. We envision that in the future it may be applied to the creation and mining of electronic health records, clinical training and basic research, as it supports automated inference and reasoning, and for the broader integration of skin disease information with that from other domain