Molecular simulation of methane hydrate growth confined into a silica pore

Financiaciado para publicación en acceso aberto: Universidade de Vigo/CISUGThe growth of a methane hydrate seed within a silica slit pore of fixed width has been studied using All- Atom Molecular Dynamics (AA-MD). An AA force field has been used to describe the molecules of the solid silica substrate, with a-quartz crystalline structure. The crystallisation of hydrates in confined geometries is not well understood yet, and the objective of this work is to study the hydrate growth inside a silica pore using molecular simulation. Both NVT and NpT ensembles were used in the AA-MD simulations to analyse the hydrate growth from an initial seed. Results showed that the boundary conditions imposed by the nanometric slit pore yielded a hydrate with structural defects, filling the accessible space between the silica walls. The water molecules which were not incorporated to the initial seed hydrate formed a high density water layer trapped between the silica walls and the crystallised hydrate. These results provide an interesting insight into the hydrate crystallisation process in confined geometries, resembling those found in natural hydrate deposits.Ministerio de Ciencia e Innovación | Ref. PID2021-125081NB-I00FEDER | Ref. SOE2/P1/P0823Xunta de Galicia | Ref. FSE-GALICIA 2014–2020Fundação para a Ciência e a Tecnologia | Ref. UIDB/50011/2020Fundação para a Ciência e a Tecnologia | Ref. UIDP/50011/2020Fundação para a Ciência e a Tecnologia | Ref. LA/ P/0006/2020Ministerio de Ciencia e Innovación | Ref. PID2019-105898GA-C22Comunidad de Madrid | Ref. APOYOJOVENES- 01HQ1S-129-B5E4M

Molecular simulations of the synthesis of periodic mesoporous silica phases at high surfactant concentrations

Molecular dynamics simulations of a coarse-grained model are used to study the formation mechanism of periodic mesoporous silica over a wide range of cationic surfactant concentrations. This follows up on an earlier study of systems with low surfactant concentrations. We started by studying the phase diagram of the surfactant-water system and found that our model shows good qualitative agreement with experiments with respect to the surfactant concentrations where various phases appear. We then considered the impact of silicate species upon the morphologies formed. We have found that even in concentrated surfactant systems --in the concentration range where pure surfactant solutions yield a liquid crystal phase -- the liquid-crystal templating mechanism is not viable because the preformed liquid crystal collapses as silica monomers are added into the solution. Upon the addition of silica dimers, a new phase-separated hexagonal array is formed. The preformed liquid crystals were found to be unstable in the presence of monomeric silicates. In addition, the silica dimer is found to be essential for mesoscale ordering at both low and high surfactant concentrations. Our results support the view that a cooperative interaction of anionic silica oligomers and cationic surfactants determines the mesostructure formation in the M41S family of materials.publishe

CARB-ES-19 Multicenter Study of Carbapenemase-Producing Klebsiella pneumoniae and Escherichia coli From All Spanish Provinces Reveals Interregional Spread of High-Risk Clones Such as ST307/OXA-48 and ST512/KPC-3

ObjectivesCARB-ES-19 is a comprehensive, multicenter, nationwide study integrating whole-genome sequencing (WGS) in the surveillance of carbapenemase-producing K. pneumoniae (CP-Kpn) and E. coli (CP-Eco) to determine their incidence, geographical distribution, phylogeny, and resistance mechanisms in Spain.MethodsIn total, 71 hospitals, representing all 50 Spanish provinces, collected the first 10 isolates per hospital (February to May 2019); CPE isolates were first identified according to EUCAST (meropenem MIC > 0.12 mg/L with immunochromatography, colorimetric tests, carbapenem inactivation, or carbapenem hydrolysis with MALDI-TOF). Prevalence and incidence were calculated according to population denominators. Antibiotic susceptibility testing was performed using the microdilution method (EUCAST). All 403 isolates collected were sequenced for high-resolution single-nucleotide polymorphism (SNP) typing, core genome multilocus sequence typing (cgMLST), and resistome analysis.ResultsIn total, 377 (93.5%) CP-Kpn and 26 (6.5%) CP-Eco isolates were collected from 62 (87.3%) hospitals in 46 (92%) provinces. CP-Kpn was more prevalent in the blood (5.8%, 50/853) than in the urine (1.4%, 201/14,464). The cumulative incidence for both CP-Kpn and CP-Eco was 0.05 per 100 admitted patients. The main carbapenemase genes identified in CP-Kpn were blaOXA–48 (263/377), blaKPC–3 (62/377), blaVIM–1 (28/377), and blaNDM–1 (12/377). All isolates were susceptible to at least two antibiotics. Interregional dissemination of eight high-risk CP-Kpn clones was detected, mainly ST307/OXA-48 (16.4%), ST11/OXA-48 (16.4%), and ST512-ST258/KPC (13.8%). ST512/KPC and ST15/OXA-48 were the most frequent bacteremia-causative clones. The average number of acquired resistance genes was higher in CP-Kpn (7.9) than in CP-Eco (5.5).ConclusionThis study serves as a first step toward WGS integration in the surveillance of carbapenemase-producing Enterobacterales in Spain. We detected important epidemiological changes, including increased CP-Kpn and CP-Eco prevalence and incidence compared to previous studies, wide interregional dissemination, and increased dissemination of high-risk clones, such as ST307/OXA-48 and ST512/KPC-3

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Rationalizing the design of pluronics-surfactant mixed micelles through molecular simulations and experiments

Aqueous systems comprising polymers and surfactants are technologically important complex fluids with tuneable features dependant on the chemical nature of each constituent, overall composition in mixed systems and solution conditions. The phase behavior and self-assembly of amphiphilic polymers can be changed drastically in the presence of conventional ionic surfactants and needs to be clearly understood. The phase behavior and self-aggregation dynamics of a triblock copolymer (Pluronics® L81, EO3PO43EO3) in the presence of three cationic surfactants (with 12C long alkyl chain but with different structural features) viz. dodecyltrimethylammonium bromide (DTAB), didodecyldimethylammonium bromide (DDAB), and ethanediyl-1,2-bis(dimethyldodecylammonium bromide) (12-2-12) were investigated in aqueous solution environment. The nanoscale micellar size expressed as hydrodynamic diameter (Dh) of copolymer-surfactant mixed aggregates was evaluated using dynamic light scattering (DLS) while the presence of varied micellar geometry of L81-cationic surfactant mixed micelles were probed using small-angle neutron scattering (SANS) approach. The obtained findings were further validated from molecular dynamics (MD) simulations, employing a simple and transferable coarse-grained (CG) molecular model based on the MARTINI force field. L81 remained molecularly dissolved upto ~20 oC but phase separates forming turbid/ translucent dispersion close to its CP and existed as unstable vesicles. However, it exhibited interesting phase behavior expressed in terms of blue point (BP) and double cloud point (CP) with the progressive addition of different cationic surfactants leading to mixed micellar systems with triggered morphology transition from unstable vesicles to polymer-rich micelles to cationic surfactant-rich micelles. The energetics of the clouding phenomenon assessed for the copolymer in the presence of cationic surfactants showed a stamped expansion in CP which is attributed to the non-cooperative association of L81 and surfactants. Such amendment in the morphology of copolymer nanoaggregates in the presence of cationic surfactants has been well ascribed from scattering data. This is further rationalized employing the molecular dynamics (MD) approach which validated the effective interactions between Pluronics®-cationic surfactant mix micelles. Thus, our experimental results integrated with MD yield a deep insight on the nanoscale interactions controlling the micellar aggregation (Pluronics®-rich micelles and surfactant-rich micelles) in the investigated mixed system

Sex differences in oncogenic mutational processes

Funder: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology); doi: https://doi.org/10.13039/501100002790Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762Funder: Canada Foundation for Innovation (Fondation canadienne pour l'innovation); doi: https://doi.org/10.13039/501100000196Funder: Terry Fox Research Institute (Institut de Recherche Terry Fox); doi: https://doi.org/10.13039/501100004376Abstract: Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research

Sex differences in oncogenic mutational processes

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Peer reviewe

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that -80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAFPeer reviewe

Integrated approaches to unravel the impact of protein lipoxidation on macromolecular interactions

15 p.-5 fig.-3 tab.Protein modification by lipid derived reactive species or lipoxidation is increased during oxidative stress, a common feature observed in many pathological conditions. Biochemical and functional consequences of lipoxidation include changes in the conformation and assembly of the target proteins, altered recognition of ligands and/or cofactors, changes in the interactions with DNA or protein-protein interactions, modifications in membrane partitioning and binding and/or subcellular localization. These changes may impact, directly or indirectly, signaling pathways involved in the activation of cell defense mechanisms, but when these are overwhelmed they may lead to pathological outcomes. Mass spectrometry provides state of the art approaches for the identification and characterization of lipoxidized proteins/residues and the modifying species. Nevertheless, understanding the complexity of the functional effects of protein lipoxidation requires the use of additional methodologies. Herein, biochemical and biophysical methods used to detect and measure functional effects of protein lipoxidation at different levels of complexity, from in vitro and reconstituted cell-like systems to cells, are reviewed, focusing especially on macromolecular interactions. Knowledge generated through innovative and complementary technologies will contribute to comprehend the role of lipoxidation in pathophysiology and, ultimately, its potential as target for therapeutic intervention.This work was supported by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement number 675132 (http://cordis.europa.eu/project/rcn/198275_en.html), and by grants from the Spanish Ministerio de Economía y Competitividad (MINECO/FEDER, http://www.mineco.gob.es/portal/site/mineco/idi) SAF2015-68590-R to DPS and BFU2016-75471-C2-1-P to GR, and RETIC Aradyal from ISCIII/FEDER (RD16/0006/0021) to DPS.Peer reviewe