Mass Transfer through Vapor-Liquid Interfaces Studied by Non-Stationary Molecular Dynamics Simulations.

Molecular dynamics (MD) simulations are highly attractive for studying the influence of interfacial effects, such as the enrichment of components, on the mass transfer through the interface. In a recent work, we have presented a steady-state MD simulation method for investigating this phenomenon and tested it using model mixtures with and without interfacial enrichment. The present study extends this work by introducing a non-stationary MD simulation method.

Murine tissue factor disulfide mutation causes a bleeding phenotype with sex specific organ pathology and lethality.

Tissue factor is highly expressed in sub-endothelial tissue. The extracellular allosteric disulfide bond Cys186-Cys209 of human tissue factor shows high evolutionary conservation and in vitro evidence suggests that it significantly contributes to tissue factor procoagulant activity. To investigate the role of this allosteric disulfide bond in vivo, we generated a C213G mutant tissue factor mouse by replacing Cys213 of the corresponding disulfide Cys190-Cys213 in murine tissue factor.

A comprehensive and comparative phenotypic analysis of the collaborative founder strains identifies new and known phenotypes.

The collaborative cross (CC) is a large panel of mouse-inbred lines derived from eight founder strains (NOD/ShiLtJ, NZO/HILtJ, A/J, C57BL/6J, 129S1/SvImJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ). Here, we performed a comprehensive and comparative phenotyping screening to identify phenotypic differences and similarities between the eight founder strains. In total, more than 300 parameters including allergy, behavior, cardiovascular, clinical blood chemistry, dysmorphology, bone and cartilage, energy metabolism, eye and vision, immunology, lung function, neurology, nociception, and pathology were analyzed; in most traits from sixteen females and sixteen males.

Antimicrobial resistance genetic factor identification from whole-genome sequence data using deep feature selection.

Background: Antimicrobial resistance (AMR) is a major threat to global public health because it makes standard treatments ineffective and contributes to the spread of infections. It is important to understand AMR's biological mechanisms for the development of new drugs and more rapid and accurate clinical diagnostics. The increasing availability of whole-genome SNP (single nucleotide polymorphism) information, obtained from whole-genome sequence data, along with AMR profiles provides an opportunity to use feature selection in machine learning to find AMR-associated mutations.

Mutation in the mouse histone gene Hist2h3c1 leads to degeneration of the lens vesicle and severe microphthalmia.

During an ENU (N-ethyl-N-nitrosourea) mutagenesis screen, we observed a dominant small-eye mutant mouse with viable homozygotes. A corresponding mutant line was established and referred to as Aey69 (abnormality of the eye #69). Comprehensive phenotyping of the homozygous Aey69 mutants in the German Mouse Clinic revealed only a subset of statistically significant alterations between wild types and homozygous mutants.

Venous bypass grafts versus arteriovenous loops as recipient vessels for microvascular anastomosis in lower extremity reconstructions: A matched-pair analysis.

Background: Limb salvage in patients with peripheral vascular disease (PVD) and soft tissue defects often requires both a restoration of blood flow to the lower extremity and soft tissue coverage. Outcomes of free tissue transfer may be affected by vein grafts, which can be used for the placement of an autologous venous bypass or an arteriovenous (AV) loop leading to different hemodynamic situations. The purpose of this study was to investigate whether free flap anastomosis to a bypass or an AV loop can be performed with comparable results.

One-Stage versus Two-Stage Arteriovenous Loop Reconstructions: An Experience on 103 Cases from a Single Center.

Background: The optimal time for flap anastomosis to an arteriovenous loop remains controversial. Whether perforator flaps and axially vascularized muscle or fasciocutaneous flaps lead to comparable outcomes in conjunction with arteriovenous loops has not been investigated.

Methods: Medical records from 103 patients undergoing arteriovenous loop reconstruction (76 one-stage and 27 two-stage) between 2007 and 2017 were reviewed.

Three-dimensional phase field modeling of inhomogeneous gas-liquid systems using the PeTS equation of state.

Recently, an equation of state (EoS) for the Lennard-Jones truncated and shifted (LJTS) fluid has become available. As it describes metastable and unstable states well, it is suited for predicting density profiles in vapor-liquid interfaces in combination with density gradient theory (DGT). DGT is usually applied to describe interfaces in Cartesian one-dimensional scenarios.

Study of homogeneous bubble nucleation in liquid carbon dioxide by a hybrid approach combining molecular dynamics simulation and density gradient theory.

A new method for predicting homogeneous bubble nucleation rates of pure compounds from vapor-liquid equilibrium (VLE) data is presented. It combines molecular dynamics simulation on the one side with density gradient theory using an equation of state (EOS) on the other. The new method is applied here to predict bubble nucleation rates in metastable liquid carbon dioxide (CO).

Activity coefficients from molecular simulations using the OPAS method.

A method for determining activity coefficients by molecular dynamics simulations is presented. It is an extension of the OPAS (osmotic pressure for the activity of the solvent) method in previous work for studying the solvent activity in electrolyte solutions. That method is extended here to study activities of all components in mixtures of molecular species.

Standardized, systemic phenotypic analysis reveals kidney dysfunction as main alteration of Kctd1 mutant mice.

Background: Increased levels of blood plasma urea were used as phenotypic parameter for establishing novel mouse models for kidney diseases on the genetic background of C3H inbred mice in the phenotype-driven Munich ENU mouse mutagenesis project. The phenotypically dominant mutant line HST014 was established and further analyzed.

Methods: Analysis of the causative mutation as well as the standardized, systemic phenotypic analysis of the mutant line was carried out.

Influence of bidisperse self-assembled monolayer structure on the slip boundary condition of thin polymer films.

Alkylsilane self-assembled monolayers (SAMs) are often used as model substrates for their ease of preparation and hydrophobic properties. We have observed that these atomically smooth monolayers also provide a slip boundary condition for dewetting films composed of unentangled polymers. This slip length, an indirect measure of the friction between a given liquid and different solids, is switchable and can be increased [R.

Extensive phenotypic characterization of a new transgenic mouse reveals pleiotropic perturbations in physiology due to mesenchymal hGH minigene expression.

The human growth hormone (hGH) minigene used for transgene stabilization in mice has been recently identified to be locally expressed in the tissues where transgenes are active and associated with phenotypic alterations. Here we extend these findings by analyzing the effect of the hGH minigene in TgC6hp55 transgenic mice which express the human TNFR1 under the control of the mesenchymal cell-specific CollagenVI promoter. These mice displayed a fully penetrant phenotype characterized by growth enhancement accompanied by perturbations in metabolic, skeletal, histological and other physiological parameters.

Cardioprotection and lifespan extension by the natural polyamine spermidine.

Aging is associated with an increased risk of cardiovascular disease and death. Here we show that oral supplementation of the natural polyamine spermidine extends the lifespan of mice and exerts cardioprotective effects, reducing cardiac hypertrophy and preserving diastolic function in old mice. Spermidine feeding enhanced cardiac autophagy, mitophagy and mitochondrial respiration, and it also improved the mechano-elastical properties of cardiomyocytes in vivo, coinciding with increased titin phosphorylation and suppressed subclinical inflammation.

The First Scube3 Mutant Mouse Line with Pleiotropic Phenotypic Alterations.

The vertebrate Scube (Signal peptide, CUB, and EGF-like domain-containing protein) family consists of three independent members, Scube1-3, which encode secreted cell surface-associated membrane glycoproteins. Limited information about the general function of this gene family is available, and their roles during adulthood. Here, we present the first Scube3 mutant mouse line (Scube3), which clearly shows phenotypic alterations by carrying a missense mutation in exon 8, and thus contributes to our understanding of SCUBE3 functions.

Sphingomyelin Synthase 1 Is Essential for Male Fertility in Mice.

Sphingolipids and the derived gangliosides have critical functions in spermatogenesis, thus mutations in genes involved in sphingolipid biogenesis are often associated with male infertility. We have generated a transgenic mouse line carrying an insertion in the sphingomyelin synthase gene Sms1, the enzyme which generates sphingomyelin species in the Golgi apparatus. We describe the spermatogenesis defect of Sms1-/- mice, which is characterized by sloughing of spermatocytes and spermatids, causing progressive infertility of male homozygotes.

CIP2A Promotes T-Cell Activation and Immune Response to Listeria monocytogenes Infection.

The oncoprotein Cancerous Inhibitor of Protein Phosphatase 2A (CIP2A) is overexpressed in most malignancies and is an obvious candidate target protein for future cancer therapies. However, the physiological importance of CIP2A-mediated PP2A inhibition is largely unknown. As PP2A regulates immune responses, we investigated the role of CIP2A in normal immune system development and during immune response in vivo.

Generation and Standardized, Systemic Phenotypic Analysis of Pou3f3L423P Mutant Mice.

Increased levels of blood plasma urea were used as phenotypic parameter for establishing novel mouse models for kidney diseases on the genetic background of C3H inbred mice in the phenotype-driven Munich ENU mouse mutagenesis project. The phenotypically recessive mutant line HST011 was established and further analyzed. The causative mutation was detected in the POU domain, class 3 transcription factor 3 (Pou3f3) gene, which leads to the amino acid exchange Pou3f3L423P thereby affecting the conserved homeobox domain of the protein.

Solvent activity in electrolyte solutions from molecular simulation of the osmotic pressure.

A method for determining the activity of the solvent in electrolyte solutions by molecular dynamics simulations is presented. The electrolyte solution is simulated in contact with the pure solvent. Between the two phases, there is a virtual membrane, which is permeable only for the solvent.

Surface tension of the two center Lennard-Jones plus point dipole fluid.

Molecular dynamics simulations are used for systematically studying the surface tension of the two center Lennard-Jones plus point dipole (2CLJD) model fluid. In a dimensionless representation, this model fluid has two parameters describing the elongation and the dipole moment. These parameters were varied in the entire range relevant for describing real fluids resulting in a grid of 38 individual models.

Mildly compromised tetrahydrobiopterin cofactor biosynthesis due to Pts variants leads to unusual body fat distribution and abdominal obesity in mice.

Tetrahydrobiopterin (BH4) is an essential cofactor for the aromatic amino acid hydroxylases, alkylglycerol monooxygenase, and nitric oxide synthases (NOS). Inborn errors of BH4 metabolism lead to severe insufficiency of brain monoamine neurotransmitters while augmentation of BH4 by supplementation or stimulation of its biosynthesis is thought to ameliorate endothelial NOS (eNOS) dysfunction, to protect from (cardio-) vascular disease and/or prevent obesity and development of the metabolic syndrome. We have previously reported that homozygous knock-out mice for the 6-pyruvolytetrahydropterin synthase (PTPS; Pts-ko/ko) mice with no BH4 biosynthesis die after birth.

Exome sequencing identifies a nonsense mutation in Fam46a associated with bone abnormalities in a new mouse model for skeletal dysplasia.

We performed exome sequencing for mutation discovery of an ENU (N-ethyl-N-nitrosourea)-derived mouse model characterized by significant elevated plasma alkaline phosphatase (ALP) activities in female and male mutant mice, originally named BAP014 (bone screen alkaline phosphatase #14). We identified a novel loss-of-function mutation within the Fam46a (family with sequence similarity 46, member A) gene (NM_001160378.1:c.

ls1 mardyn: The Massively Parallel Molecular Dynamics Code for Large Systems.

The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures and currently holds the world record for the largest molecular simulation with over four trillion particles. It enables the application of pair potentials to length and time scales that were previously out of scope for molecular dynamics simulation.

Metabolic switch during adipogenesis: From branched chain amino acid catabolism to lipid synthesis.

Fat cell metabolism has an impact on body homeostasis and its proper function. Nevertheless, the knowledge about simultaneous metabolic processes, which occur during adipogenesis and in mature adipocytes, is limited. Identification of key metabolic events associated with fat cell metabolism could be beneficial in the field of novel drug development, drug repurposing, as well as for the discovery of patterns predicting obesity risk.