Rate-independent hysteretic energy dissipation in collagen fibrils.

Nanoindentation cycles measured with an atomic force microscope on hydrated collagen fibrils exhibit a rate-independent hysteresis with return point memory. This previously unknown energy dissipation mechanism describes in unified form elastoplastic indentation, capillary adhesion, and surface leveling at indentation velocities smaller than 1 µm s-1, where viscous friction is negligible. A generic hysteresis model, based on force-distance data measured during one large approach-retract cycle, predicts the force (output) and the dissipated energy for arbitrary indentation trajectories (input). While both quantities are rate independent, they do depend nonlinearly on indentation history and on indentation amplitude.

A Nonlinear Delay Model for Metabolic Oscillations in Yeast Cells.

We introduce two time-delay models of metabolic oscillations in yeast cells. Our model tests a hypothesis that the oscillations occur as multiple pathways share a limited resource which we equate to the number of available ribosomes. We initially explore a single-protein model with a constraint equation governing the total resource available to the cell. The model is then extended to include three proteins that share a resource pool. Three approaches are considered at constant delay to numerically detect oscillations. First, we use a spectral element method to approximate the system as a discrete map and evaluate the stability of the linearized system about its equilibria by examining its eigenvalues. For the second method, we plot amplitudes of the simulation trajectories in 2D projections of the parameter space. We use a history function that is consistent with published experimental results to obtain metabolic oscillations. Finally, the spectral element method is used to convert the system to a boundary value problem whose solutions correspond to approximate periodic solutions of the system. Our results show that certain combinations of total resource available and the time delay, lead to oscillations. We observe that an oscillation region in the parameter space is between regions admitting steady states that correspond to zero and constant production. Similar behavior is found with the three-protein model where all proteins require the same production time. However, a shift in the protein production rates peaks occurs for low available resource suggesting that our model captures the shared resource pool dynamics.

Technical note: Determining equivalent squares of high-energetic photon fields.

PURPOSE: We developed a method based on a physical pencil beam model for accurate equivalent square calculations for rectangular and irregular fields, for different definitions of equivalent squares, for beams with and without flattening filter, different photon energies, and depths in water. METHODS: We considered two equivalent square definitions: equal dose at a point on the beam axis and equal depth dose, measured as tissue phantom ratio at 20 and 10 cm depth ( TPR 20 , 10 $\text{TPR}_{20,10}$ ). As dose engine, we used an analytical pencil beam model. By integrating the pencil beam kernels, we assigned square fields to rectangular fields minimizing the dose, respectively, the TPR 20 , 10 $\text{TPR}_{20,10}$ difference. The results were compared with measurements at 100 mm depth for nominal beam energies of 6 and 18 MV, the Sterling equation, the geometric mean, and data from BJR Suppl 25 (British Institute of Radiology, 1996). RESULTS: Pencil beam results were closest to the measurements. An energy dependence of several millimeters for small field dimensions and depth dependencies for very elongated fields were observed. For the assignment of WFF square to FFF rectangular fields, using the equal- TPR 20 , 10 $\text{TPR}_{20,10}$ definition, our method agrees with previously published results. For circular fields approximated by leaves, we found deviations to the data from BJR Suppl. 25 below 1 mm for diameters smaller than 200 mm. CONCLUSIONS: Our study shows that the validity range for geometric mean and Sterling equation is limited. Ergo, instead of specifying specific validity ranges, we suggest using the pencil beam method, valid for all aspect ratios, including elongated fields in the primary dose dominated regime. We published our method as python library and graphical user interface on GitHub. Users can choose between two definitions of equivalent square and between WFF and FFF fields. The implemented pencil beam method for irregular fields is also usable for quality assurance such as monitor unit checks.

Technological robot-Machine tool collaboration for agile production.

The flexibility and efficiency in parts production can be significantly increased through the technological cooperation of industrial robots and machine tools. The paper presents an approach in which a robot, in addition to the classic handling tasks, enhance machine tools by additional manufacturing technologies and thus beneficially supports workpiece machining. This can take place in various configurations, starting with pre- and final machining by the robot outside the machine, through sequential cooperative machining of the workpiece clamped in the machine, to parallel, synchronized machining of a workpiece in the machine. The approach results in a novel type of collaborative manufacturing equipment for matrix production that will improve the versatility, efficiency and profitability in production.

Insights into the Correlation between Residual Stresses, Phase Transformation, and Wettability of Femtosecond Laser-Irradiated Ductile Iron.

Despite numerous studies on the wettability behavior of ductile iron after ultrafast laser structuring, the correlation between the phase change due to the interaction with an intense pulse and wettability is not yet well understood. In the present work, phase transformations of ductile iron substrates after femtosecond laser irradiation are investigated and correlated with the wettability behavior. Laser parameters such as fluence (F), cumulative fluence (CH), number of pulses (N), and scan speed were varied to produce hierarchical structures with different morphologies and phase concentrations. Our outcomes indicated that substrates with higher concentrations of austenite in the absence of hierarchical structures have a superhydrophilic nature despite being stored in an ambient atmosphere for several days and the application of a vacuum process. In addition, we measured the concomitant residual stresses after laser irradiation using the X-ray diffraction (XRD) method and established a relationship with the doses of CH and induced micro/nanostructures. Transmission electron microscopy (TEM) revealed that laser-structured surfaces are covered with oxides; moreover, phase transformation occurs at the near-subsurface layer.

Dynamics of a driven harmonic oscillator coupled to pairwise interacting Ising spins in random fields.

In general we are interested in dynamical systems coupled to complex hysteresis. Therefore as a first step we investigated recently the dynamics of a periodically driven damped harmonic oscillator coupled to independent Ising spins in a random field. Although such a system does not produce hysteresis, we showed how to characterize the dynamics of such a piecewise-smooth system, especially in the case of a large number of spins [Zech, Otto, and Radons, Phys. Rev. E 101, 042217 (2020)2470-004510.1103/PhysRevE.101.042217]. In this paper we extend our model to spin dimers, thus pairwise interacting spins. We show in which cases two interacting spins can show elementary hysteresis, and we give a connection to the Preisach model, which allows us to consider an infinite number of spin pairs. This thermodynamic limit leads us to a dynamical system with an additional hysteretic force in the form of a generalized play operator. By using methods from general chaos theory, piecewise-smooth system theory, and statistics we investigate the chaotic behavior of the dynamical system for a few spins and also in the case of a larger number of spins by calculating bifurcation diagrams, Lyapunov exponents, fractal dimensions, and self-averaging properties. We find that the fractal dimensions and the magnetization are in general not self-averaging quantities. We show how the dynamical properties of the piecewise-smooth system for a large number of spins differs from the system in its thermodynamic limit.

Surviving Serum: the Escherichia coli iss Gene of Extraintestinal Pathogenic E. coli Is Required for the Synthesis of Group 4 Capsule.

Extraintestinal pathogenic Escherichia coli (ExPEC) strains constitute a serious and emerging clinical problem, as they cause a variety of infections and are usually highly antibiotic resistant. Many ExPEC strains are capable of evading the bactericidal effects of serum and causing sepsis. One critical factor for the development of septicemia is the increased serum survival (iss) gene, which is highly correlated with complement resistance and lethality. Although it is very important, the function of the iss gene has not been elucidated so far. We have been studying the serum survival of a septicemic strain of E. coli serotype O78, which has a group 4 capsule. Here, we show that the iss gene is required for the synthesis of capsules, which protect the bacteria from the bactericidal effect of complement. Moreover, we show that the deletion of the iss gene results in significantly increased binding of the complement proteins that constitute the membrane attack complex to the bacterial surface.

SppI Forms a Membrane Protein Complex with SppA and Inhibits Its Protease Activity in Bacillus subtilis.

The membrane protease SppA of Bacillus subtilis was first described as a signal peptide peptidase and later shown to confer resistance to lantibiotics. Here, we report that SppA forms octameric complexes with YteJ, a membrane protein of thus-far-unknown function. Interestingly, sppA and yteJ deletion mutants exhibited no protein secretion defects. However, these mutant strains differed significantly in their resistance to antimicrobial peptides. In particular, sppA mutant cells displayed increased sensitivity to the lantibiotics nisin and subtilin and the human lysozyme-derived cationic antimicrobial peptide LP9. Importantly, YteJ was shown to antagonize SppA activity both in vivo and in vitro, and this SppA-inhibitory activity involved the C-terminal domain of YteJ, which was therefore renamed SppI. Most likely, SppI-mediated control is needed to protect B. subtilis against the potentially detrimental protease activity of SppA since a mutant overexpressing sppA by itself displayed defects in cell division. Altogether, we conclude that the SppA-SppI complex of B. subtilis has a major role in protection against antimicrobial peptides.IMPORTANCE Our study presents new insights into the molecular mechanism that regulates the activity of SppA, a widely conserved bacterial membrane protease. We show that the membrane proteins SppA and SppI form a complex in the Gram-positive model bacterium B. subtilis and that SppI inhibits SppA protease activity in vitro and in vivo Furthermore, we demonstrate that the C-terminal domain of SppI is involved in SppA inhibition. Since SppA, through its protease activity, contributes directly to resistance to lantibiotic peptides and cationic antibacterial peptides, we propose that the conserved SppA-SppI complex could play a major role in the evasion of bactericidal peptides, including those produced as part of human innate immune defenses.

A Lactococcal Phage Protein Promotes Viral Propagation and Alters the Host Proteomic Response During Infection.

The lactococcal virulent phage p2 is a model for studying the Skunavirus genus, the most prevalent group of phages causing milk fermentation failures in cheese factories worldwide. This siphophage infects Lactococcus lactis MG1363, a model strain used to study Gram-positive lactic acid bacteria. The structural proteins of phage p2 have been thoroughly described, while most of its non-structural proteins remain uncharacterized. Here, we developed an integrative approach, making use of structural biology, genomics, physiology, and proteomics to provide insights into the function of ORF47, the most conserved non-structural protein of unknown function among the Skunavirus genus. This small phage protein, which is composed of three α-helices, was found to have a major impact on the bacterial proteome during phage infection and to significantly reduce the emergence of bacteriophage-insensitive mutants.

Tryptic Shaving of Staphylococcus aureus Unveils Immunodominant Epitopes on the Bacterial Cell Surface.

The opportunistic pathogen Staphylococcus aureus has become a major threat for human health and well-being by developing resistance to antibiotics and by fast evolution into new lineages that rapidly spread within the healthy human population. This calls for development of active or passive immunization strategies to prevent or treat acute phase infections. Since no such anti-staphylococcal immunization approaches are available for clinical implementation, the present studies were aimed at identifying new leads for their development. For this purpose, we profiled the cell-surface-exposed staphylococcal proteome under infection-mimicking conditions by combining two approaches for "bacterial shaving" with immobilized or soluble trypsin and subsequent mass spectrometry analysis of liberated peptides. In parallel, non-covalently cell-wall-bound proteins extracted with potassium thiocyanate and the exoproteome fraction were analyzed by gel-free proteomics. All data are available through ProteomeXchange accession PXD000156. To pinpoint immunodominant bacterial-surface-exposed epitopes, we screened selected cell-wall-attached proteins of S. aureus for binding of immunoglobulin G from patients who have been challenged by different types of S. aureus due to chronic wound colonization. The combined results of these analyses highlight particular cell-surface-exposed S. aureus proteins with highly immunogenic exposed epitopes as potential targets for development of protective anti-staphylococcal immunization strategies.

Dynamics of a driven harmonic oscillator coupled to independent Ising spins in random fields.

We aim at an understanding of the dynamical properties of a periodically driven damped harmonic oscillator coupled to a Random Field Ising Model (RFIM) at zero temperature, which is capable of showing complex hysteresis. The system is a combination of a continuous (harmonic oscillator) and a discrete (RFIM) subsystem, which classifies it as a hybrid system. In this paper we focus on the hybrid nature of the system and consider only independent spins in quenched random local fields, which can already lead to complex dynamics such as chaos and multistability. We study the dynamic behavior of this system by using the theory of piecewise-smooth dynamical systems and discontinuity mappings. Specifically, we present bifurcation diagrams and Lyapunov exponents as well as results for the shape and the dimensions of the attractors and the self-averaging behavior of the attractor dimensions and the magnetization. Furthermore we investigate the dynamical behavior of the system for an increasing number of spins and the transition to the thermodynamic limit, where the system behaves like a driven harmonic oscillator with an additional nonlinear smooth external force.

Functional association of the stress-responsive LiaH protein and the minimal TatAyCy protein translocase in Bacillus subtilis.

The bacterial twin-arginine (Tat) pathway serves in the exclusive secretion of folded proteins with bound cofactors. While Tat pathways in Gram-negative bacteria and chloroplast thylakoids consist of conserved TatA, TatB and TatC subunits, the Tat pathways of Bacillus species and many other Gram-positive bacteria stand out for their minimalist nature with the core translocase being composed of essential TatA and TatC subunits only. Here we addressed the question whether the minimal TatAyCy translocase of Bacillus subtilis recruits additional cellular components that modulate its activity. To this end, TatAyCy was purified by affinity- and size exclusion chromatography, and interacting co-purified proteins were identified by mass spectrometry. This uncovered the cell envelope stress responsive LiaH protein as an accessory subunit of the TatAyCy complex. Importantly, our functional studies show that Tat expression is tightly trailed by LiaH induction, and that LiaH itself determines the capacity and quality of TatAyCy-dependent protein translocation. In contrast, LiaH has no role in high-level protein secretion via the general secretion (Sec) pathway. Altogether, our observations show that protein translocation by the minimal Tat translocase TatAyCy is tightly intertwined with an adequate bacterial response to cell envelope stress. This is consistent with a critical need to maintain cellular homeostasis, especially when the membrane is widely opened to permit passage of large fully-folded proteins via Tat.

Laminar chaos in experiments and nonlinear delayed Langevin equations: A time series analysis toolbox for the detection of laminar chaos.

Recently, it was shown that certain systems with large time-varying delay exhibit different types of chaos, which are related to two types of time-varying delay: conservative and dissipative delays. The known high-dimensional turbulent chaos is characterized by strong fluctuations. In contrast, the recently discovered low-dimensional laminar chaos is characterized by nearly constant laminar phases with periodic durations and a chaotic variation of the intensity from phase to phase. In this paper we extend our results from our preceding publication [Hart, Roy, Müller-Bender, Otto, and Radons, Phys. Rev. Lett. 123, 154101 (2019)PRLTAO0031-900710.1103/PhysRevLett.123.154101], where it is demonstrated that laminar chaos is a robust phenomenon, which can be observed in experimental systems. We provide a time series analysis toolbox for the detection of robust features of laminar chaos. We benchmark our toolbox by experimental time series and time series of a model system which is described by a nonlinear Langevin equation with time-varying delay. The benchmark is done for different noise strengths for both the experimental system and the model system, where laminar chaos can be detected, even if it is hard to distinguish from turbulent chaos by a visual analysis of the trajectory.

Comprehensive Spectral Library from the Pathogenic Bacterium Streptococcus pneumoniae with Focus on Phosphoproteins.

To understand bacterial reactions to environmental stress or infection-related processes, it is necessary to identify the involved proteins. In mass spectrometry-based proteomics, the method of choice for spectra-to-peptide-match is database search, but in recent times, spectral libraries have come into focus. Here, we built a mass spectral library from Streptococcus pneumoniae D39, reflecting 76% of the theoretical proteome of the organism. Besides the proteins themselves, posttranslational protein modifications especially reveal central hubs of regulation in bacterial pathogenesis. Here, for example, phosphorylation events are involved in the signal transduction and regulation of virulence. Although there have been major advances in phosphoproteomics, identification of this modification is still challenging. To enhance the number of phosphorylated peptides, which can be reproducibly detected, a comprehensive mass spectral library of the S. pneumoniae D39 phosphoproteome has been compiled in addition to the comprehensive total proteome mass spectral library. The phosphopeptide library was manually validated, and the data quality was additionally proven by analyses of synthetic phosphorylated peptides. In total, 128 phosphorylated proteins were revealed, of which many are involved in glycolysis, purine metabolism, protein biosynthesis, and virulence. The publicly available, thoroughly validated spectral libraries are an excellent resource to improve and speed up future investigations on the proteome and phosphoproteome of pneumococci.

Bacterioplankton reveal years-long retention of Atlantic deep-ocean water by the Tropic Seamount.

Seamounts, often rising hundreds of metres above surrounding seafloor, obstruct the flow of deep-ocean water. While the retention of deep-water by seamounts is predicted from ocean circulation models, its empirical validation has been hampered by large scale and slow rate of the interaction. To overcome these limitations we use the growth of planktonic bacteria to assess the retention time of deep-ocean water by a seamount. The selected Tropic Seamount in the North-Eastern Atlantic is representative for the majority of isolated seamounts, which do not affect the surface ocean waters. We prove deep-water is retained by the seamount by measuring 2.4× higher bacterial concentrations in the seamount-associated or 'sheath'-water than in deep-ocean water unaffected by seamounts. Genomic analyses of flow-sorted, dominant sheath-water bacteria confirm their planktonic origin, whilst proteomic analyses of the sheath-water bacteria, isotopically labelled in situ, indicate their slow growth. According to our radiotracer experiments, it takes the sheath-water bacterioplankton 1.5 years to double their concentration. Therefore, the seamount should retain the deep-ocean water for 1.8 years for the deep-ocean bacterioplankton to grow to the 2.4× higher concentration in the sheath-water. We propose that turbulent mixing of the seamount sheath-water stimulates bacterioplankton growth by increasing cell encounter rate with ambient dissolved organic molecules.

Time delay effects in the control of synchronous electricity grids.

The expansion of inverter-connected generation facilities (i.e., wind and photovoltaics) and the removal of conventional power plants is necessary to mitigate the impacts of climate change, whereas conventional generation with large rotating generator masses provides stabilizing inertia, inverter-connected generation does not. Since the underlying power system and the control mechanisms that keep it close to a desired reference state were not designed for such a low inertia system, this might make the system vulnerable to disturbances. In this paper, we will investigate whether the currently used control mechanisms are able to keep a low inertia system stable and how this is affected by the time delay between a frequency deviation and the onset of the control action. We integrate the control mechanisms used in Continental Europe into a model of coupled oscillators which resembles the second order Kuramoto model. This model is then used to investigate how the interplay of changing inertia, network topology, and delayed control affects the stability of the interconnected power system. To identify regions in the parameter space that make stable grid operation possible, the linearized system is analyzed to create the system's stability chart. We show that lower and distributed inertia could have a beneficial effect on the stability of the desired synchronous state.

Laminar Chaos in Experiments: Nonlinear Systems with Time-Varying Delays and Noise.

A new type of dynamics called laminar chaos was recently discovered through a theoretical analysis of a scalar delay differential equation with time-varying delay. Laminar chaos is a low-dimensional dynamics characterized by laminar phases of nearly constant intensity with periodic durations and a chaotic variation of the intensity from one laminar phase to the next laminar phase. This is in stark contrast to the typically observed higher-dimensional turbulent chaos, which is characterized by strong fluctuations. In this Letter we provide the first experimental observation of laminar chaos by studying an optoelectronic feedback loop with time-varying delay. The noise inherent in the experiment requires the development of a nonlinear Langevin equation with variable delay. The results show that laminar chaos can be observed in higher-order systems, and that the phenomenon is robust to noise and a digital implementation of the variable time delay.

Ariadne's Thread in the Analytical Labyrinth of Membrane Proteins: Integration of Targeted and Shotgun Proteomics for Global Absolute Quantification of Membrane Proteins.

The field of systems biology has been rapidly developing in the past decade. However, the data produced by "omics" approaches is lagging behind the requirements of this field, especially when it comes to absolute abundances of membrane proteins. In the present study, a novel approach for large-scale absolute quantification of this challenging subset of proteins has been established and evaluated using osmotic stress management in the Gram-positive model bacterium Bacillus subtilis as proof-of-principle precedent. Selected membrane proteins were labeled using a SNAP-tag, which allowed us to visually inspect the enrichment of the membrane fraction by immunoassays. Absolute membrane protein concentrations were determined via shotgun proteomics by spiking crude membrane extracts of chromosomally SNAP-tagged and wild-type B. subtilis strains with protein standards of known concentration. Shotgun data was subsequently calibrated by targeted mass spectrometry using SNAP as an anchor protein, and an enrichment factor was calculated in order to obtain membrane protein copy numbers per square micrometer. The presented approach enabled the accurate determination of physiological changes resulting from imposed hyperosmotic stress, thereby offering a clear visualization of alterations in membrane protein arrangements and shedding light on putative membrane complexes. This straightforward and cost-effective methodology for quantitative proteome studies can be implemented by any research group with mass spectrometry expertise. Importantly, it can be applied to the full spectrum of physiologically relevant conditions, ranging from environmental stresses to the biotechnological production of small molecules and proteins, a field heavily relying on B. subtilis secretion capabilities.

Exoproteome Heterogeneity among Closely Related Staphylococcus aureus t437 Isolates and Possible Implications for Virulence.

Staphylococcus aureus with spa-type t437 has been identified as a predominant community-associated methicillin-resistant S. aureus clone from Asia, which is also encountered in Europe. Molecular typing has previously shown that t437 isolates are highly similar regardless of geographical regions or host environments. The present study was aimed at assessing to what extent this high similarity is actually reflected in the production of secreted virulence factors. We therefore profiled the extracellular proteome, representing the main reservoir of virulence factors, of 20 representative clinical isolates by mass spectrometry. The results show that these isolates can be divided into three groups and nine subgroups based on exoproteome abundance signatures. This implies that S. aureus t437 isolates show substantial exoproteome heterogeneity. Nonetheless, 30 highly conserved extracellular proteins, of which about 50% have a predicted role in pathogenesis, were dominantly identified. To approximate the virulence of the 20 investigated isolates, we employed infection models based on Galleria mellonella and HeLa cells. The results show that the grouping of clinical isolates based on their exoproteome profile can be related to virulence. We consider this outcome important as our approach provides a tool to pinpoint differences in virulence among seemingly highly similar clinical isolates of S. aureus.

A homopolymeric adenosine tract in the promoter region of nspA influences factor H-mediated serum resistance in Neisseria meningitidis.

Although usually asymptomatically colonizing the human nasopharynx, the Gram-negative bacterium Neisseria meningitidis (meningococcus) can spread to the blood stream and cause invasive disease. For survival in blood, N. meningitidis evades the complement system by expression of a polysaccharide capsule and surface proteins sequestering the complement regulator factor H (fH). Meningococcal strains belonging to the sequence type (ST-) 41/44 clonal complex (cc41/44) cause a major proportion of serogroup B meningococcal disease worldwide, but they are also common in asymptomatic carriers. Proteome analysis comparing cc41/44 isolates from invasive disease versus carriage revealed differential expression levels of the outer membrane protein NspA, which binds fH. Deletion of nspA reduced serum resistance and NspA expression correlated with fH sequestration. Expression levels of NspA depended on the length of a homopolymeric tract in the nspA promoter: A 5-adenosine tract dictated low NspA expression, whereas a 6-adenosine motif guided high NspA expression. Screening German cc41/44 strain collections revealed the 6-adenosine motif in 39% of disease isolates, but only in 3.4% of carriage isolates. Thus, high NspA expression is associated with disease, but not strictly required. The 6-adenosine nspA promoter is most common to the cc41/44, but is also found in other hypervirulent clonal complexes.