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Laser pulses of moderate intensities with durations of either 1.5 ps or 120 fs were employed to excite the Na3 molecule to its electronic B state. Using a pump–probe technique the temporal evolution of the two-photon ionization signal could be resolved in real time. Different vibrational modes of the excited trimer are detected selectively. While the ps laser pulses yield preferential excitation of the slow pseudorotational mode with a period of 3 ps, the use of ∼10 times shorter pulses allows the trimer’s symmetric stretch mode with a 310–320 fs period for the first 5 ps to be observed. These complementary experimental results can be explained to a great extent by quantum dynamical simulations of the pump–probe experiments. The calculations are performed on three-dimensional ab initio potential energy and transition dipole surfaces. Thus all three vibrational degrees of freedom of the Na3 molecule are included in the theoretical treatment. The time-dependent wave-packet dynamics elucidate the effect of ultrafast state preparation on the molecular dynamics. Extensive theoretical calculations manifest the possibility of initiating the molecular dynamics dominantly in selected modes during a certain time span by variation of the pump–pulse duration. © 1996 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Mixed phospholipid and glycolipid monolayers likely coat the surfaces of pressurised gas nanobubbles within the hydraulic systems of plants. The lipid coatings bond to water under negative pressure and are thus stretched out of equilibrium. In this work, we have used molecular dynamics simulations to produce trajectories of a biologically relevant mixed monolayer, pulled at mild negative pressures (-1.5 to -4.5 MPa). Pore formation within the monolayer is observed at both 270 and 310 K, and proceeds as an activated process once the lipid tails fully transition from the two dimensional liquid condensed to liquid expanded phase. Pressure:area isotherms showed reduced surface pressure under slight supercooling ( T = 270 K) at all observed areas per lipid. Finally, Rayleigh-Plesset simulations were used to predict evolving nanobubble size using the calculated pressure:area isotherms as dynamic surface tensions. We confirm the existence of a second critical radius with respect to runaway growth, above the homogeneous cavitation radius., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

The properties of clouds, such as their reflectivity or their likelihood to precipitate, depend on whether the cloud droplets are liquid or frozen. Thus, understanding the ice nucleation mechanisms is essential for the development of reliable climate models. Most ice nucleation in the atmosphere is heterogeneous, i.e. , caused by ice nucleating particles such as mineral dusts or organic aerosols. In this regard, K-feldspar minerals have attracted great interest recently as they have been identified as one of the most important ice nucleating particles under mixed-phase cloud conditions. The mechanism by which feldspar minerals facilitate ice nucleation remains, however, elusive. Here, we present atomic force microscopy (AFM) experiments on microcline (001) performed in an ultrahigh vacuum and at the solid-water interface together with density functional theory (DFT) and molecular dynamics (MD) calculations. Our ultrahigh vacuum data reveal features consistent with a hydroxyl-terminated surface. This finding suggests that water in the residual gas readily reacts with the surface. Indeed, the corresponding DFT calculations confirm a dissociative water adsorption. Three-dimensional AFM measurements performed at the mineral-water interface unravel a layered hydration structure with two features per surface unit cell. A comparison with MD calculations suggests that the structure observed in AFM corresponds to the second hydration layer rather than the first water layer. In agreement with previous computation results, no ice-like structure is seen, questioning an explanation of the ice nucleation ability by lattice match. Our results provide an atomic-scale benchmark for the clean and water-covered microcline (001) plane, which is mandatory for understanding the ice nucleation mechanism on feldspar minerals.

Background: Decreased insulin availability and high blood glucose levels, the hallmark features of poorly controlled diabetes, drive disease progression and are associated with decreased skeletal muscle mass. We have shown that mice with β-cell dysfunction and normal insulin sensitivity have decreased skeletal muscle mass. This project asks how insulin deficiency impacts on the structure and function of the remaining skeletal muscle in these animals., Methods: Skeletal muscle function was determined by measuring exercise capacity and specific muscle strength prior to and after insulin supplementation for 28 days in 12-week-old mice with conditional β-cell deletion of the ATP binding cassette transporters ABCA1 and ABCG1 (β-DKO mice). Abca1 and Abcg1 floxed (fl/fl) mice were used as controls. RNAseq was used to quantify changes in transcripts in soleus and extensor digitorum longus muscles. Skeletal muscle and mitochondrial morphology were assessed by transmission electron microscopy. Myofibrillar Ca 2+ sensitivity and maximum isometric single muscle fibre force were assessed using MyoRobot biomechatronics technology., Results: RNA transcripts were significantly altered in β-DKO mice compared with fl/fl controls (32 in extensor digitorum longus and 412 in soleus). Exercise capacity and muscle strength were significantly decreased in β-DKO mice compared with fl/fl controls (P = 0.012), and a loss of structural integrity was also observed in skeletal muscle from the β-DKO mice. Supplementation of β-DKO mice with insulin restored muscle integrity, strength and expression of 13 and 16 of the dysregulated transcripts in and extensor digitorum longus and soleus muscles, respectively., Conclusions: Insulin insufficiency due to β-cell dysfunction perturbs the structure and function of skeletal muscle. These adverse effects are rectified by insulin supplementation., (© 2023 The Authors. Journal of Cachexia, Sarcopenia and Muscle published by Wiley Periodicals LLC.)

Soil microbial necromass is an important contributor to soil organic matter (>50%) and it is largely composed of microbial residues. In soils, fragmented cell wall residues are mostly found in their polysaccharide forms of fungal chitin and bacterial peptidoglycan. Microbial necromass biomarkers, particularly amino sugars (AS) such as glucosamine (GlcN) and muramic acid (MurA) have been used to trace fungal and bacterial residues in soils, and to distinguish carbon (C) found in microbial residues from non-microbial organic C. Neutral sugars (NS), particularly the hexose/pentose ratio, have also been proposed as tracers of plant polysaccharides in soils. In our study, we extended the range of biomarkers to include AS and NS compounds in the biomass of 120 species belonging to archaea, bacteria, fungi, or plants. GlcN was the most common AS found in all taxa, contributing 42-91% to total AS content, while glucose was the most common NS found, contributing 56-79% to total NS. We identified talosaminuronic acid, found in archaeal pseudopeptidoglycan, as a new potential biomarker specific for Euryarchaeota. We compared the variability of these compounds between the different taxonomic groups using multivariate approaches, such as non-metric multidimensional scaling (NMDS) and partial least squares discriminant analysis (PLS-DA) and statistically evaluated their biomarker potential via indicator species analysis. Both NMDS and PLS-DA showcased the variability in the AS and NS contents between the different taxonomic groups, highlighting their potential as necromass residue biomarkers and allowing their extension from separating bacterial and fungal necromass to separating microbes from plants. Finally, we estimated new conversion factors where fungal GlcN is converted to fungal C by multiplying by 10 and MurA is converted to bacterial C by multiplying by 54. Conversion factors for talosaminuronic acid and galactosamine are also proposed to allow estimation of archaeal or all-microbial necromass residue C, respectively., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)

Molecular dynamics (MD) simulations of gas-phase chemical reactions are typically carried out on a small number of molecules near thermal equilibrium by means of various thermostatting algorithms. Correct equipartitioning of kinetic energy among translations, rotations, and vibrations of the simulated reactants is critical for many processes occurring in the gas phase. As thermalizing collisions are infrequent in gas-phase simulations, the thermostat has to efficiently reach equipartitioning in the system during equilibration and maintain it throughout the actual simulation. Furthermore, in non-equilibrium simulations where heat is released locally, the action of the thermostat should not lead to unphysical changes in the overall dynamics of the system. Here, we explore issues related to both obtaining and maintaining thermal equilibrium in MD simulations of an exemplary ion-molecule dimerization reaction. We first compare the efficiency of global (Nosé-Hoover and Canonical Sampling through Velocity Rescaling) and local (Langevin) thermostats for equilibrating a system of flexible compounds and find that of these three only the Langevin thermostat achieves equipartition in a reasonable simulation time. We then study the effect of the unphysical removal of latent heat released during simulations involving multiple dimerization events. As the Langevin thermostat does not produce the correct dynamics in the free molecular regime, we only consider the commonly used Nosé-Hoover thermostat, which is shown to effectively cool down the reactants, leading to an overestimation of the dimerization rate. Our findings underscore the importance of thermostatting for the proper thermal initialization of gas-phase systems and the consequences of global thermostatting in non-equilibrium simulations., (© 2023 Author(s). Published under an exclusive license by AIP Publishing.)

Methanogenic archaea possess diverse metabolic characteristics and are an ecologically and biotechnologically important group of anaerobic microorganisms. Although the scientific and biotechnological value of methanogens is evident with regard to their methane-producing physiology, little is known about their amino acid excretion, and virtually nothing is known about the lipidome at different substrate concentrations and temperatures on a quantitative comparative basis. Here, we present the lipidome and a comprehensive quantitative analysis of proteinogenic amino acid excretion as well as methane, water, and biomass production of the three autotrophic, hydrogenotrophic methanogens Methanothermobacter marburgensis, Methanothermococcus okinawensis, and Methanocaldococcus villosus under varying temperatures and nutrient supplies. The patterns and rates of production of excreted amino acids and the lipidome are unique for each tested methanogen and can be modulated by varying the incubation temperature and substrate concentration, respectively. Furthermore, the temperature had a significant influence on the lipidomes of the different archaea. The water production rate was much higher, as anticipated from the rate of methane production for all studied methanogens. Our results demonstrate the need for quantitative comparative physiological studies connecting intracellular and extracellular constraints of organisms to holistically investigate microbial responses to environmental conditions. IMPORTANCE Biological methane production by methanogenic archaea has been well studied for biotechnological purposes. This study reveals that methanogenic archaea actively modulate their lipid inventory and proteinogenic amino acid excretion pattern in response to environmental changes and the possible utilization of methanogenic archaea as microbial cell factories for the targeted production of lipids and amino acids.

The development of a sustainable energy economy is one of the great challenges in the current times of climate crisis and growing energy demands. Industrial production of the fifth-generation biofuel methane by microorganisms has the potential to become a crucial biotechnological milestone of the post fossil fuel era. Therefore, reproducible cultivation and scale-up of methanogenic archaea (methanogens) is essential for enabling biomass generation for fundamental studies and for defining peak performance conditions for bioprocess development. This study provides a comprehensive revision of established and optimization of novel methods for the cultivation of the model organism Methanococcus maripaludis S0001. In closed batch mode, 0.05 L serum bottles cultures were gradually replaced by 0.4 L Schott bottle cultures for regular biomass generation, and the time for reaching peak optical density (OD 578 ) values was reduced in half. In 1.5 L reactor cultures, various agitation, harvesting and transfer methods were compared resulting in a specific growth rate of 0.16 h -1 and the highest recorded OD 578 of 3.4. Finally, a 300-fold scale-up from serum bottles was achieved by growing M . maripaludis for the first time in a 22 L stainless steel bioreactor with 15 L working volume. Altogether, the experimental approaches described in this study contribute to establishing methanogens as essential organisms in large-scale biotechnology applications, a crucial stage of an urgently needed industrial evolution toward sustainable biosynthesis of energy and high value products., Competing Interests: AR, BR, and SK-MRR declare to have competing commercial and financial interests due to their employment in the Arkeon GmbH. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Palabikyan, Ruddyard, Pomper, Novak, Reischl and Rittmann.)

Atmospheric nucleation from precursor gases is a significant source of cloud condensation nuclei in the troposphere and thus can affect the Earth's radiative balance. Sulfuric acid, ammonia, and amines have been identified as key nucleation precursors in the atmosphere. Studies have also shown that atmospheric ions can react with sulfuric acid to form stable clusters in a process referred to as ion-induced nucleation (IIN). IIN follows similar reaction pathways as chemical ionization, which is used to detect and measure nucleation precursors via atmospheric pressure chemical ionization mass spectrometers. The rate at which ions form clusters depends on the ion-molecule rate constant. However, the rate constant varies based on the ion composition, which is often not known in the atmosphere. Previous studies have examined ion-molecule rate constants for sulfuric acid and nitrate ions but not for other atmospherically relevant ions like acetate. We report the relative rate constants of ion-molecule reactions between nitrate and acetate ions reacting with sulfuric acid. The ion-molecule rate constant for acetate and sulfuric acid is estimated to be a factor of 1.9-2.4 times higher than that of the known rate constant for nitrate and sulfuric acid. Using quantum chemistry, we find that acetate has a higher dipole moment and polarizability than nitrate. This may contribute to an increase in the collision cross-sectional area between acetate and sulfuric acid and lead to a greater reaction rate constant than nitrate. The ion-molecule rate constant for acetate with sulfuric acid will help quantify the contribution of acetate ions to atmospheric ion-induced new particle formation.

Nucleation of clusters from the gas phase is a widely encountered phenomenon, yet rather little is understood about the underlying out-of-equilibrium dynamics of this process. The classical view of nucleation assumes isothermal conditions where the nucleating clusters are in thermal equilibrium with their surroundings. However, in all first-order phase transitions, latent heat is released, potentially heating the clusters and suppressing the nucleation. The question of how the released energy affects cluster temperatures during nucleation as well as the growth rate remains controversial. To investigate the nonisothermal dynamics and energetics of homogeneous nucleation, we have performed molecular dynamics simulations of a supersaturated vapor in the presence of thermalizing carrier gas. The results obtained from these simulations are compared against kinetic modeling of isothermal nucleation and classical nonisothermal theory. For the studied systems, we find that nucleation rates are suppressed by two orders of magnitude at most, despite substantial release of latent heat. Our analyses further reveal that while the temperatures of the entire cluster size populations are elevated, the temperatures of the specific clusters driving the nucleation flux evolve from cold to hot when growing from subcritical to supercritical sizes and resolve the apparent contradictions regarding cluster temperatures. Our findings provide unprecedented insight into realistic nucleation events and allow us to directly assess earlier theoretical considerations of nonisothermal nucleation.

Objective: Decellularizing solid organs is a promising top-down process to produce acellular bio-scaffolds for 'de novo' regrowth or application as tissue 'patches' that compensate, e.g., large volumetric muscle loss in reconstructive surgery. Therefore, generating standardized acellular muscle scaffolds marks a pressing area of need. Although animal muscle decellularization protocols were established, those are mostly manually performed and lack defined bioreactor environments and metrologies to assess decellularization quality in real-time. To close this gap, we engineered an automated bioreactor system to provide chemical decellularization solutions to immersed whole rat gastrocnemius medialis muscle through perfusion of the main feeding arteries., Results: Perfusion control is adjustable according to decellularization quality feedback. This was assessed both from (i) ex situ assessment of sarcomeres/nuclei through multiphoton fluorescence and label-free Second Harmonic Generation microscopy and DNA quantification, along with (ii) in situ within the bioreactor environment assessment of the sample's passive mechanical elasticity., Conclusion: We find DNA and sarcomere-free constructs after 72 h of 0.1% SDS perfusion-decellularization. Furthermore, passive elasticity can be implemented as additional online decellularization quality measure, noting a threefold elasticity decrease in acellular constructs., Significance: Our MyoBio represents a novel and useful automated bioreactor environment for standardized and controlled generation of acellular whole muscle scaffolds as a valuable source for regenerative medicine.

Background: A common polymorphism (R577X) in the ACTN3 gene results in the complete absence of the Z-disc protein α-actinin-3 from fast-twitch muscle fibres in ~ 16% of the world's population. This single gene polymorphism has been subject to strong positive selection pressure during recent human evolution. Previously, using an Actn3KO mouse model, we have shown in fast-twitch muscles, eccentric contractions at L 0  + 20% stretch did not cause eccentric damage. In contrast, L 0  + 30% stretch produced a significant ~ 40% deficit in maximum force; here, we use isolated single fast-twitch skeletal muscle fibres from the Actn3KO mouse to investigate the mechanism underlying this., Methods: Single fast-twitch fibres are separated from the intact muscle by a collagenase digest procedure. We use label-free second harmonic generation (SHG) imaging, ultra-fast video microscopy and skinned fibre measurements from our MyoRobot automated biomechatronics system to study the morphology, visco-elasticity, force production and mechanical strength of single fibres from the Actn3KO mouse. Data are presented as means ± SD and tested for significance using ANOVA., Results: We show that the absence of α-actinin-3 does not affect the visco-elastic properties or myofibrillar force production. Eccentric contractions demonstrated that chemically skinned Actn3KO fibres are mechanically weaker being prone to breakage when eccentrically stretched. Furthermore, SHG images reveal disruptions in the myofibrillar alignment of Actn3KO fast-twitch fibres with an increase in Y-shaped myofibrillar branching., Conclusions: The absence of α-actinin-3 from the Z-disc in fast-twitch fibres disrupts the organisation of the myofibrillar proteins, leading to structural weakness. This provides a mechanistic explanation for our earlier findings that in vitro intact Actn3KO fast-twitch muscles are significantly damaged by L 0  + 30%, but not L 0  + 20%, eccentric contraction strains. Our study also provides a possible mechanistic explanation as to why α-actinin-3-deficient humans have been reported to have a faster decline in muscle function with increasing age, that is, as sarcopenia reduces muscle mass and force output, the eccentric stress on the remaining functional α-actinin-3 deficient fibres will be increased, resulting in fibre breakages., (© 2022. The Author(s).)

Aims: Desminopathies comprise hereditary myopathies and cardiomyopathies caused by mutations in the intermediate filament protein desmin that lead to severe and often lethal degeneration of striated muscle tissue. Animal and single cell studies hinted that this degeneration process is associated with massive ultrastructural defects correlating with increased susceptibility of the muscle to acute mechanical stress. The underlying mechanism of mechanical susceptibility, and how muscle degeneration develops over time, however, has remained elusive., Methods: Here, we investigated the effect of a desmin mutation on the formation, differentiation, and contractile function of in vitro-engineered three-dimensional micro-tissues grown from muscle stem cells (satellite cells) isolated from heterozygous R349P desmin knock-in mice., Results: Micro-tissues grown from desmin-mutated cells exhibited spontaneous unsynchronised contractions, higher contractile forces in response to electrical stimulation, and faster force recovery compared with tissues grown from wild-type cells. Within 1 week of culture, the majority of R349P desmin-mutated tissues disintegrated, whereas wild-type tissues remained intact over at least three weeks. Moreover, under tetanic stimulation lasting less than 5 s, desmin-mutated tissues partially or completely ruptured, whereas wild-type tissues did not display signs of damage., Conclusions: Our results demonstrate that the progressive degeneration of desmin-mutated micro-tissues is closely linked to extracellular matrix fibre breakage associated with increased contractile forces and unevenly distributed tensile stress. This suggests that the age-related degeneration of skeletal and cardiac muscle in patients suffering from desminopathies may be similarly exacerbated by mechanical damage from high-intensity muscle contractions. We conclude that micro-tissues may provide a valuable tool for studying the organization of myocytes and the pathogenic mechanisms of myopathies., (© 2021 The Authors. Neuropathology and Applied Neurobiology published by John Wiley & Sons Ltd on behalf of British Neuropathological Society.)

Objective: Muscle biomechanics is set by the spacing of repetitive striation patterns of individual sarcomeres within single muscle fibres of stacked myofibrils. Sarcomere lengths (SL) are rather unequally distributed than of equal distance. This non-uniformity may affect both, force production as well as passive-elastic deformation. However, online recording of SL during axially imposed strains is cumbersome due to a lack of compact technologies., Methods: To fuse SL pattern recognition with restoration force assessments during quasi-static axial stretch, we implemented live tracking of SL distributions simultaneous to voice-coil actuated stretch and restoration force recordings in our MyoRobot 2.0 automated biomechatronics platform. Both were obtained online during stretch-relaxation cycles of murine single muscle fibres., Results: Under quasi-static stretch conditions (  ∼ 1 μm/s fibre length changes), almost no apparent hysteresis was detected in single fibres. SL showed a non-uniform distribution. While mean SL varied between 2.6 μm and 3.4 μm upon 140% stretch, two populations of fibres were noticed: one showing a minor change in SL distribution with stretch, and one becoming more equally distributed upon stretch., Conclusion: A roughly 5% SL variability under rest either diminishes or remains almost unaltered upon elastic axial deformation. This may reflect differential impact of mostly extra-sarcomeric components to stretch in this stretch range., Significance: The augmented functionality of the MyoRobot 2.0 towards online sarcomere analyses within single fibres shall provide a valuable tool for the muscle community to study the contribution of serial elastic and force producing elements in health and disease models.

During the cardiac cycle, electrical excitation is coupled with mechanical response of the myocardium. Besides the active contraction, passive mechanics plays an important role, and its behaviour differs in healthy and diseased hearts as well as among different animal species. The aim of this study is the characterisation of passive mechanical properties in healthy and infarcted rat myocardium by means of mechanical testing and subsequent parameter fitting. Elasticity assessments via uniaxial extension tests are performed on healthy and infarcted tissue samples from left ventricular rat myocardium. In order to fully characterise the orthotropic cardiac tissue, our experimental data are combined with other previously published tests in rats - shear tests on healthy myocardium and equibiaxial tests on infarcted tissue. In a first step, we calibrate the Holzapfel-Ogden strain energy function in the healthy case. Sa far, this orthotropic constitutive law for the passive myocardium has been fitted to experimental data in several species, however there is a lack of an appropriate parameter set for the rat. With our determined parameters, a finite element simulation of the end-diastolic filling is performed. In a second step, we propose a model for the infarcted tissue. It is represented as a mixture of intact myocardium and a transversely isotropic scar structure. In our mechanical experiments, the tissue after myocardial infarction shows significantly stiffer behaviour than in the healthy case, and the stiffness correlates with the amount of fibrosis. A similar relationship is observed in the computational simulation of the end-diastolic filling. We conclude that our new proposed material model can capture the behaviour of two kinds of tissues - healthy and infarcted rat myocardium, and its calibration with the fitted parameters represents the experimental data well., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Studies of vapor phase nucleation have largely been restricted to one of two limiting cases-nucleation controlled by a substantial free energy barrier or the collisional limit where the barrier is negligible. For weakly bound systems, exploring the transition between these regimes has been an experimental challenge, and how nucleation evolves in this transition remains an open question. We overcome these limitations by combining complementary Laval expansion experiments, providing new particle formation data for carbon dioxide over a uniquely broad range of conditions. Our experimental data together with a kinetic model using rate constants from high-level quantum chemical calculations provide a comprehensive picture of new particle formation as nucleation transitions from a barrier-dominated process to the collisional limit.

We propose a novel method based on template matching for the recognition of liquid water, cubic ice (ice I c ), hexagonal ice (ice I h ), clathrate hydrates, and different interfacial structures in atomistic and coarse-grained simulations of water and ice. The two template matrices represent staggered and eclipsed conformations, which are the building blocks of hexagonal and cubic ice and clathrate crystals. The algorithm is rotationally invariant and highly robust against imperfections in the ice structure, and its sensitivity for recognizing ice-like structures can be tuned for different applications. Unlike most other algorithms, it can discriminate between cubic, hexagonal, clathrate, mixed, and other interfacial ice types and is therefore well suited to study complex systems and heterogeneous ice nucleation.

Background: Prolonged critically ill patients frequently develop debilitating muscle weakness that can affect both peripheral nerves and skeletal muscle. In-depth knowledge on the temporal contribution of neural and muscular components to muscle weakness is currently incomplete., Methods: We used a fluid-resuscitated, antibiotic-treated, parenterally fed murine model of prolonged (5 days) sepsis-induced muscle weakness (caecal ligation and puncture; n = 148). Electromyography (EMG) measurements were performed in two nerve-muscle complexes, combined with histological analysis of neuromuscular junction denervation, axonal degeneration, and demyelination. In situ muscle force measurements distinguished neural from muscular contribution to reduced muscle force generation. In myofibres, imaging and biomechanics were combined to evaluate myofibrillar contractile calcium sensitivity, sarcomere organization, and fibre structural properties. Myosin and actin protein content and titin gene expression were measured on the whole muscle., Results: Five days of sepsis resulted in increased EMG latency (P = 0.006) and decreased EMG amplitude (P < 0.0001) in the dorsal caudal tail nerve-tail complex, whereas only EMG amplitude was affected in the sciatic nerve-gastrocnemius muscle complex (P < 0.0001). Myelin sheath abnormalities (P = 0.2), axonal degeneration (number of axons; P = 0.4), and neuromuscular junction denervation (P = 0.09) were largely absent in response to sepsis, but signs of axonal swelling [higher axon area (P < 0.0001) and g-ratio (P = 0.03)] were observed. A reduction in maximal muscle force was present after indirect nerve stimulation (P = 0.007) and after direct muscle stimulation (P = 0.03). The degree of force reduction was similar with both stimulations (P = 0.2), identifying skeletal muscle, but not peripheral nerves, as the main contributor to muscle weakness. Myofibrillar calcium sensitivity of the contractile apparatus was unaffected by sepsis (P ≥ 0.6), whereas septic myofibres displayed disorganized sarcomeres (P < 0.0001) and altered myofibre axial elasticity (P < 0.0001). Septic myofibres suffered from increased rupturing in a passive stretching protocol (25% more than control myofibres; P = 0.04), which was associated with impaired myofibre active force generation (P = 0.04), linking altered myofibre integrity to function. Sepsis also caused a reduction in muscle titin gene expression (P = 0.04) and myosin and actin protein content (P = 0.05), but not the myosin-to-actin ratio (P = 0.7)., Conclusions: Prolonged sepsis-induced muscle weakness may predominantly be related to a disruption in myofibrillar cytoarchitectural structure, rather than to neural abnormalities., (© 2021 The Authors. Journal of Cachexia, Sarcopenia and Muscle published by John Wiley & Sons Ltd on behalf of the Society on Sarcopenia, Cachexia and Wasting Disorders.)

Bioprocesses converting carbon dioxide with molecular hydrogen to methane (CH 4 ) are currently being developed to enable a transition to a renewable energy production system. In this study, we present a comprehensive physiological and biotechnological examination of 80 methanogenic archaea (methanogens) quantifying growth and CH 4 production kinetics at hyperbaric pressures up to 50 bar with regard to media, macro-, and micro-nutrient supply, specific genomic features, and cell envelope architecture. Our analysis aimed to systematically prioritize high-pressure and high-performance methanogens. We found that the hyperthermophilic methanococci Methanotorris igneus and Methanocaldococcoccus jannaschii are high-pressure CH 4 cell factories. Furthermore, our analysis revealed that high-performance methanogens are covered with an S-layer, and that they harbour the amino acid motif Tyr α444 Gly α445 Tyr α446 in the alpha subunit of the methyl-coenzyme M reductase. Thus, high-pressure biological CH 4 production in pure culture could provide a purposeful route for the transition to a carbon-neutral bioenergy sector.

Large scale molecular dynamics simulations of the homogeneous nucleation of carbon dioxide in an argon atmosphere were carried out at temperatures between 75 and 105 K. Extensive analyses of the nucleating clusters' structural and energetic properties were performed to quantify these details for the supersonic nozzle experiments described in the first part of this series [Dingilian et al., Phys. Chem. Chem. Phys., 2020, 22, 19282-19298]. We studied ten different combinations of temperature and vapour pressure, leading to nucleation rates of 10 23 -10 25 cm -3 s -1 . Nucleating clusters possess significant excess energy from monomer capture, and the observed cluster temperatures during nucleation - on both sides of the critical cluster size - are higher than that of the carrier gas. Despite strong undercooling with respect to the triple point, most clusters are clearly liquid-like during the nucleation stage. Only at the lowest simulation temperatures and vapour densities, clusters containing over 100 molecules are able to undergo a second phase transition to a crystalline solid. The formation free energies retrieved from the molecular dynamics simulations were used to improve the classical nucleation theory by introducing a Tolman-like term into the classical liquid-drop model expression for the formation free energy. This simulation-based theory predicts the simulated nucleation rates perfectly, and improves the prediction of the experimental rates compared to self-consistent classical nucleation theory.

We studied the homogeneous nucleation of carbon dioxide in the carrier gas argon for concentrations of CO2 ranging from 2 to 39 mole percent using three experimental methods. Position-resolved pressure trace measurements (PTM) determined that the onset of nucleation occurred at temperatures between 75 and 92 K with corresponding CO2 partial pressures of 39 to 793 Pa. Small angle X-ray scattering (SAXS) measurements provided particle size distributions and aerosol number densities. Number densities of approximately 1012 cm-3, and characteristic times ranging from 6 to 13 μs, resulted in measured nucleation rates on the order of 5 × 1017 cm-3 s-1, values that are consistent with other nucleation rate measurements in supersonic nozzles. Finally, we used Fourier transform infrared (FTIR) spectroscopy to identify that the condensed CO2 particles were crystalline cubic solids with either sharp or rounded corners. Molecular dynamics simulations, however, suggest that CO2 forms liquid-like critical clusters before transitioning to the solid phase. Furthermore, the critical clusters are not in thermal equilibrium with the carrier gas. Comparisons with nucleation theories were therefore made assuming liquid-like critical clusters and incorporating non-isothermal correction factors.

Muscle biomechanics relies on active motor protein assembly and passive strain transmission through cytoskeletal structures. The desmin filament network aligns myofibrils at the z-discs, provides nuclear-sarcolemmal anchorage and may also serve as memory for muscle repositioning following large strains. Our previous analyses of R349P desmin knock-in mice, an animal model for the human R350P desminopathy, already depicted pre-clinical changes in myofibrillar arrangement and increased fiber bundle stiffness. As the effect of R349P desmin on axial biomechanics in fully differentiated single muscle fibers is unknown, we used our MyoRobot to compare passive visco-elasticity and active contractile biomechanics in single fibers from fast- and slow-twitch muscles from adult to senile mice, hetero- or homozygous for the R349P desmin mutation with wild type littermates. We demonstrate that R349P desmin presence predominantly increased axial stiffness in both muscle types with a pre-aged phenotype over wild type fibers. Axial viscosity and Ca2+-mediated force were largely unaffected. Mutant single fibers showed tendencies towards faster unloaded shortening over wild type fibers. Effects of aging seen in the wild type appeared earlier in the mutant desmin fibers. Our single-fiber experiments, free of extracellular matrix, suggest that compromised muscle biomechanics is not exclusively attributed to fibrosis but also originates from an impaired intermediate filament network.

In this study, we have investigated the influence of the tip on the three-dimensional scanning force microscopy (3D-SFM) images of calcite-water interfaces by experiments and simulations. We calculated 3D force images by simulations with the solvent tip approximation (STA), Ca, CO3 and OH tip models. For all the 3D images, the z profiles at the surface Ca and CO3 sites alternately show oscillatory peaks corresponding to the hydration layers. However, the peak heights and spacings become larger when the mechanical stability of the tip becomes higher. For analyzing the xy slices of the 3D force images, we developed the extended STA (E-STA) model which allowed us to reveal the strong correlation between the hydration structure just under the tip and the atomic-scale force contrasts. Based on these understandings on the image features showing the strong tip dependence, we developed a method for objectively estimating the similarity between 3D force images. With this method, we compared the simulated images with the three experimentally obtained ones. Among them, two images showed a relatively high similarity with the image obtained by the simulation with the Ca or the CO3 tip model. Based on these agreements, we characterized the hydration structure and mechanical stability of the experimentally used tips. The understanding and methodology presented here should help us to derive accurate information on the tip and the interfacial structure from experimentally obtained 3D-SFM images.

The development of suitable synthetic scaffolds for use as human tendon grafts to repair tendon ruptures remains a significant engineering challenge. Previous synthetic tendon grafts have demonstrated suboptimal tissue ingrowth and synovitis due to wear particles from fiber-to-fiber abrasion. In this study, we present a novel fiber-reinforced hydrogel (FRH) that mimics the hierarchical structure of the native human tendon for synthetic tendon graft material. Ultrahigh molecular weight polyethylene (UHMWPE) fibers were impregnated with either biosynthetic polyvinyl alcohol/gelatin hydrogel (FRH-PG) or with polyvinyl alcohol/gelatin + strontium-hardystonite (Sr-Ca 2 ZnSi 2 O 7 , Sr-HT) composite hydrogel (FRH-PGS). The scaffolds were fabricated and assessed to evaluate their suitability for tendon graft applications. The microstructure of both FRH-PG and FRH-PGS showed successful impregnation of the hydrogel component, and the tendon scaffolds exhibited equilibrium water content of ∼70 wt %, similar to the values reported for native human tendon, compared to ∼50 wt % water content retained in unmodified UHMWPE fibers. The tensile strength of FRH-PG and FRH-PGS (77.0-81.8 MPa) matched the range of human Achilles' tendon tensile strengths reported in the literature. In vitro culture of rat tendon stem cells showed cell and tissue infiltration into both FRH-PG and FRH-PGS after 2 weeks, and the presence of Sr-HT ceramic particles influenced the expression of tenogenic markers. On the other hand, FRH-PG supported the proliferation of murine C2C12 myoblasts, whereas FRH-PGS seemingly did not support it under static culture conditions. In vivo implantation of FRH-PG and FRH-PGS scaffolds into full-thickness rat patellar tendon defects showed good collagenous tissue ingrowth into these scaffolds after 6 weeks. This study demonstrates the potential viability for our FRH-PG and FRH-PGS scaffolds to be used for off-the-shelf biosynthetic tendon graft material.

Formate is one of the key compounds of the microbial carbon and/or energy metabolism. It owes a significant contribution to various anaerobic syntrophic associations, and may become one of the energy storage compounds of modern energy biotechnology. Microbial growth on formate was demonstrated for different bacteria and archaea, but not yet for species of the archaeal phylum Crenarchaeota. Here, we show that Desulfurococcus amylolyticus DSM 16532, an anaerobic and hyperthermophilic Crenarchaeon, metabolises formate without the production of molecular hydrogen. Growth, substrate uptake, and production kinetics on formate, glucose, and glucose/formate mixtures exhibited similar specific growth rates and similar final cell densities. A whole cell conversion experiment on formate revealed that D. amylolyticus converts formate into carbon dioxide, acetate, citrate, and ethanol. Using bioinformatic analysis, we examined whether one of the currently known and postulated formate utilisation pathways could be operative in D. amylolyticus . This analysis indicated the possibility that D. amylolyticus uses formaldehyde producing enzymes for the assimilation of formate. Therefore, we propose that formate might be assimilated into biomass through formaldehyde dehydrogenase and the oxidative pentose phosphate pathway. These findings shed new light on the metabolic versatility of the archaeal phylum Crenarchaeota.

Lipids and amino acids are regarded as important biomarkers for the search for extraterrestrial life in the Solar System. Such biomarkers may be used to trace methanogenic life on other planets or moons in the Solar System, such as Saturn's icy moon Enceladus. However, little is known about the environmental conditions shaping the synthesis of lipids and amino acids. Here, we present the lipid production and amino acid excretion patterns of the methanogenic archaeon Methanothermococcus okinawensis after exposing it to different multivariate concentrations of the inhibitors ammonium, formaldehyde, and methanol present in the Enceladian plume. M. okinawensis shows different patterns of lipid and amino acids excretion, depending on the amount of these inhibitors in the growth medium. While methanol did not show a significant impact on growth, lipid or amino acid production rates, ammonium and formaldehyde strongly affected these parameters. These findings are important for understanding the eco-physiology of methanogens on Earth and have implications for the use of biomarkers as possible signs of extraterrestrial life for future space missions in the Solar System.

Mutations in the Des gene coding for the muscle-specific intermediate filament protein desmin lead to myopathies and cardiomyopathies. We previously generated a R349P desmin knock-in mouse strain as a patient-mimicking model for the corresponding most frequent human desmin mutation R350P. Since nothing is known about the age-dependent changes in the biomechanics of affected muscles, we investigated the passive and active biomechanics of small fiber bundles from young (17-23 wks), adult (25-45 wks) and aged (>60 wks) heterozygous and homozygous R349P desmin knock-in mice in comparison to wild-type littermates. We used a novel automated biomechatronics platform, the MyoRobot, to perform coherent quantitative recordings of passive (resting length-tension curves, visco-elasticity) and active (caffeine-induced force transients, pCa-force, 'slack-tests') parameters to determine age-dependent effects of the R349P desmin mutation in slow-twitch soleus and fast-twitch extensor digitorum longus small fiber bundles. We demonstrate that active force properties are not affected by this mutation while passive steady-state elasticity is vastly altered in R349P desmin fiber bundles compatible with a pre-aged phenotype exhibiting stiffer muscle preparations. Visco-elasticity on the other hand, was not altered. Our study represents the first systematic age-related characterization of small muscle fiber bundle preparation biomechanics in conjunction with inherited desminopathy.

Desulfurococcus amylolyticus DSM 16532 is an anaerobic and hyperthermophilic crenarchaeon known to grow on a variety of different carbon sources, including monosaccharides and polysaccharides. Furthermore, D. amylolyticus is one of the few archaea that are known to be able to grow on cellulose. Here, we present the metabolic reconstruction of D. amylolyticus' central carbon metabolism. Based on the published genome, the metabolic reconstruction was completed by integrating complementary information available from the KEGG, BRENDA, UniProt, NCBI, and PFAM databases, as well as from available literature. The genomic analysis of D. amylolyticus revealed genes for both the classical and the archaeal version of the Embden-Meyerhof pathway. The metabolic reconstruction highlighted gaps in carbon dioxide-fixation pathways. No complete carbon dioxide-fixation pathway such as the reductive citrate cycle or the dicarboxylate-4-hydroxybutyrate cycle could be identified. However, the metabolic reconstruction indicated that D. amylolyticus harbors all genes necessary for glucose metabolization. Closed batch experimental verification of glucose utilization by D. amylolyticus was performed in chemically defined medium. The findings from in silico analyses and from growth experiments are discussed with respect to physiological features of hyperthermophilic organisms.

Skeletal muscle is an archetypal organ whose structure is tuned to match function. The magnitude of order in muscle fibers and myofibrils containing motor protein polymers determines the directed force output of the summed force vectors and, therefore, the muscle's power performance on the structural level. Structure and function can change dramatically during disease states involving chronic remodeling. Cellular remodeling of the cytoarchitecture has been pursued using noninvasive and label-free multiphoton second harmonic generation (SHG) microscopy. Hereby, structure parameters can be extracted as a measure of myofibrillar order and thus are suggestive of the force output that a remodeled structure can still achieve. However, to date, the parameters have only been an indirect measure, and a precise calibration of optical SHG assessment for an exerted force has been elusive as no technology in existence correlates these factors.  We engineered a novel, automated, high-precision biomechatronics system into a multiphoton microscope allows simultaneous isometric Ca 2+ -graded force or passive viscoelasticity measurements and SHG recordings. Using this MechaMorph system, we studied force and SHG in single EDL muscle fibers from wt and mdx mice; the latter serves as a model for compromised force and abnormal myofibrillar structure. We present Ca 2+ -graded isometric force, pCa-force curves, passive viscoelastic parameters and 3D structure in the same fiber for the first time. Furthermore, we provide a direct calibration of isometric force to morphology, which allows noninvasive prediction of the force output of single fibers from only multiphoton images, suggesting a potential application in the diagnosis of myopathies.

Accumulation of carbon dioxide (CO 2 ), associated with global temperature rise, and drastically decreasing fossil fuels necessitate the development of improved renewable and sustainable energy production processes. A possible route for CO 2 recycling is to employ autotrophic and hydrogenotrophic methanogens for CO 2 -based biological methane (CH 4 ) production (CO 2 -BMP). In this study, the physiology and productivity of Methanobacterium thermaggregans was investigated in fed-batch cultivation mode. It is shown that M. thermaggregans can be reproducibly adapted to high agitation speeds for an improved CH 4 productivity. Moreover, inoculum size, sulfide feeding, pH, and temperature were optimized. Optimization of growth and CH 4 productivity revealed that M. thermaggregans is a slightly alkaliphilic and thermophilic methanogen. Hitherto, it was only possible to grow seven autotrophic, hydrogenotrophic methanogenic strains in fed-batch cultivation mode. Here, we show that after a series of optimization and growth improvement attempts another methanogen, M. thermaggregas could be adapted to be grown in fed-batch cultivation mode to cell densities of up to 1.56 g L -1 . Moreover, the CH 4 evolution rate (MER) of M. thermaggregans was compared to Methanothermobacter marburgensis, the CO 2 -BMP model organism. Under optimized cultivation conditions, a maximum MER of 96.1 ± 10.9 mmol L -1  h -1 was obtained with M. thermaggregans-97% of the maximum MER that was obtained utilizing M. marburgensis in a reference experiment. Therefore, M. thermaggregans can be regarded as a CH 4 cell factory highly suited to be applicable for CO 2 -BMP.

It seems natural to assume that defects at mineral surfaces critically influence interfacial processes such as the dissolution and growth of minerals in water. The experimental verification of this claim, however, is challenging and requires real-space methods with utmost spatial resolution, such as atomic force microscopy (AFM). While defects at mineral-water interfaces have been resolved in 2D AFM images before, the perturbation of the surrounding hydration structure has not yet been analyzed experimentally. In this Letter, we demonstrate that point defects on the most stable and naturally abundant calcite (10.4) surface can be resolved using high-resolution 3D AFM-even within the fifth hydration layer. Our analysis of the hydration structure surrounding the point defect shows a perturbation of the hydration with a lateral extent of approximately one unit cell. These experimental results are corroborated by molecular dynamics simulations.

Mechanical properties of nanoscale objects can be measured with an atomic force microscope (AFM) tip. However, the continuum models typically used to relate the force measured at a certain indentation depth to quantities such as the elastic modulus, may not be valid at such small scales, where the details of atomistic processes need to be taken into account. On the other hand, molecular dynamics (MD) simulations of nanoindentation, which can offer understanding at an atomistic level, are often performed on systems much smaller than the ones studied experimentally. Here, we present large scale MD simulations of the nanoindentation of single crystal and penta-twinned gold nanorod samples on a silicon substrate, with a spherical diamond AFM tip apex. Both the sample and tip sizes and geometries match commercially available products, potentially linking simulation and experiment. Different deformation mechanisms, involving the creation, migration and annihilation of dislocations are observed depending on the nanorod crystallographic structure and orientation. Using the Oliver-Pharr method, the Young's moduli of the (100) terminated and (110) terminated single crystal nanorods, and the penta-twinned nanorod, have been determined to be 103 ± 2, 140 ± 4 and 108 ± 2 GPa, respectively, which is in good agreement with bending experiments performed on nanowires.