Mechanical manifestations of cardiac activity and the functional state of the vessels
Methods for measuring mechanical aspects of cardiac activity and vessel functional state
Source record↗
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DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation
DNA methylation maintenance by DNMT1 is an essential process in mammals but molecular mechanisms connecting DNA methylation patterns and enzyme activity remain elusive. Here, we systematically analyzed the specificity of DNMT1, revealing a pronounced influence of the DNA sequences flanking the target CpG site on DNMT1 activity. We determined DNMT1 structures in complex with preferred DNA substrates revealing that DNMT1 employs flanking sequence-dependent base flipping mechanisms, with large structural rearrangements of the DNA correlating with low catalytic activity. Moreover, flanking sequences influence the conformational dynamics of the active site and cofactor binding pocket. Importantly, we show that the flanking sequence preferences of DNMT1 highly correlate with genomic methylation in human and mouse cells, and 5-azacytidine triggered DNA demethylation is more pronounced at CpG sites with flanks disfavored by DNMT1. Overall, our findings uncover the intricate interplay between CpG-flanking sequence, DNMT1-mediated base flipping and the dynamic landscape of DNA methylation.
59 BASIC BIOLOGICAL SCIENCES↗
Deciphering enhancer sequence using thermodynamics-based models and convolutional neural networks
Abstract Deciphering the sequence-function relationship encoded in enhancers holds the key to interpreting non-coding variants and understanding mechanisms of transcriptomic variation. Several quantitative models exist for predicting enhancer function and underlying mechanisms; however, there has been no systematic comparison of these models characterizing their relative strengths and shortcomings. Here, we interrogated a rich data set of neuroectodermal enhancers in Drosophila, representing cis- and trans- sources of expression variation, with a suite of biophysical and machine learning models. We performed rigorous comparisons of thermodynamics-based models implementing different mechanisms of activation, repression and cooperativity. Moreover, we developed a convolutional neural network (CNN) model, called CoNSEPT, that learns enhancer ‘grammar’ in an unbiased manner. CoNSEPT is the first general-purpose CNN tool for predicting enhancer function in varying conditions, such as different cell types and experimental conditions, and we show that such complex models can suggest interpretable mechanisms. We found model-based evidence for mechanisms previously established for the studied system, including cooperative activation and short-range repression. The data also favored one hypothesized activation mechanism over another and suggested an intriguing role for a direct, distance-independent repression mechanism. Our modeling shows that while fundamentally different models can yield similar fits to data, they vary in their utility for mechanistic inference. CoNSEPT is freely available at: https://github.com/PayamDiba/CoNSEPT.
59 BASIC BIOLOGICAL SCIENCES↗
PayamDiba/CoNSEPT
Deciphering the sequence-function relationship encoded in enhancers holds the key to interpreting non-coding variants and understanding mechanisms of transcriptomic variation. Several quantitative models exist for predicting enhancer function and underlying mechanisms; however, there has been no systematic comparison of these models characterizing their relative strengths and shortcomings. Here, we interrogated a rich data set of neuroectodermal enhancers in Drosophila, representing cis- and trans- sources of expression variation, with a suite of biophysical and machine learning models. We performed rigorous comparisons of thermodynamics-based models implementing different mechanisms of activation, repression and cooperativity. Moreover, we developed a convolutional neural network (CNN) model, called CoNSEPT, that learns enhancer ‘grammar’ in an unbiased manner. CoNSEPT is the first general-purpose CNN tool for predicting enhancer function in varying conditions, such as different cell types and experimental conditions, and we show that such complex models can suggest interpretable mechanisms. We found model-based evidence for mechanisms previously established for the studied system, including cooperative activation and short-range repression. The data also favored one hypothesized activation mechanism over another and suggested an intriguing role for a direct, distance-independent repression mechanism. Our modeling shows that while fundamentally different models can yield similar fits to data, they vary in their utility for mechanistic inference.
Dibaeinia, Payam↗
Actively Controlled Shaft Seals for Aerospace Applications
This study experimentally investigates an actively controlled mechanical seal for aerospace applications. The seal of interest is a gas seal, which is considerably more compact than previous actively controlled mechanical seals that were developed for industrial use. In a mechanical seal, the radial convergence of the seal interface has a primary effect on the film thickness. Active control of the film thickness is established by controlling the radial convergence of the seal interface with a piezoelectric actuator. An actively controlled mechanical seal was initially designed and evaluated using a mathematical model. Based on these results, a seal was fabricated and tested under laboratory conditions. The seal was tested with both helium and air, at rotational speeds up to 3770 rad/sec, and at sealed pressures as high as 1.48 x 10(exp 6) Pa. The seal was operated with both manual control and with a closed-loop control system that used either the leakage rate or face temperature as the feedback. The output of the controller was the voltage applied to the piezoelectric actuator. The seal operated successfully for both short term tests (less than one hour) and for longer term tests (four hours) with a closed-loop control system. The leakage rates were typically 5-15 slm (standard liters per minute), and the face temperatures were generally maintained below 100C. When leakage rate was used as the feedback signal, the setpoint leakage rate was typically maintained within 1 slm. However, larger deviations occurred during sudden changes in sealed pressure. When face temperature was used as the feedback signal, the setpoint face temperature was generally maintained within 3 C, with larger deviations occurring when the sealed pressure changes suddenly. the experimental results were compared to the predictions from the mathematical model. The model was successful in predicting the trends in leakage rate that occurred as the balance ratio and sealed pressure changed, although the leakage rates were not quantitatively predicted with a high degree of accuracy. This model could be useful in providing valuable design information for future actively controlled mechanical seals.
Salant, Richard F.↗
Asymmetric adsorption by quartz - A model for the prebiotic origin of optical activity
One mechanism previously proposed for the abiotic accumulation of molecules of one chirality in nature is asymmetric adsorption on the chiral surfaces of optically active quartz crystals. Earlier literature in this field is reviewed, with the conclusion that previous investigations of this phenomenon, using optical rotation criteria, have afforded ambiguous results. We now have studied the adsorption of radioactive D- and L-alanine on powdered d- and l-quartz, using change in radioactivity level as a criterion for both gross and differential adsorption, d-Quartz preferentially adsorbed D-alanine from anhydrous dimethyl-formamide solution, and l-quartz L-alanine. The differential adsorption varied between 1.0 and 1.8%. The implications of these observations are discussed from the viewpoint of early chemical evolution and the origin of optically active organic compounds in nature.
Bonner, W. M.↗
Mechanisms of O 2 Activation by Mononuclear Non-Heme Iron Enzymes
We report two major subclasses of mononuclear non-heme ferrous enzymes use two electron-donating organic cofactors (α-ketoglutarate or pterin) to activate O2 to form Fe IV =O intermediates that further react with their substrates through hydrogen atom abstraction or electrophilic aromatic substitution. New spectroscopic methodologies have been developed, enabling the study of the active sites in these enzymes and their oxygen intermediates. Coupled to electronic structure calculations, the results of these spectroscopies provide fundamental insight into mechanism. This Perspective summarizes the results of these studies in elucidating the mechanism of dioxygen activation to form the Fe IV =O intermediate and the geometric and electronic structure of this intermediate that enables its high reactivity and selectivity in product formation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Sample Preparation and Experimental Design for In Situ Multi-Beam Transmission Electron Microscopy Irradiation Experiments
We discuss the need to understand materials exposed to overlapping extreme environments such as high temperature, radiation, or mechanical stress. When these stressors are combined there may be synergistic effects that enable unique microstructural evolution mechanisms to activate. Understanding of these mechanisms is necessary for the input and refinement of predictive models and critical for engineering of next generation materials. The basic physics and underlying mechanisms require advanced tools to be investigated. The in situ ion irradiation transmission electron microscope (I 3 TEM) is designed to explore these principles. To quantitatively probe the complex dynamic interactions in materials, careful preparation of samples and consideration of experimental design is required. Particular handling or preparation of samples can easily introduce damage or features that obfuscate the measurements. There is no one correct way to prepare a sample; however, many mistakes can be made. The most common errors and things to consider are highlighted within. The I 3 TEM has many adjustable variables and a large potential experimental space, therefore it is best to design experiments with a specific scientific question or questions in mind. Experiments have been performed on large number of sample geometries, material classes, and with many irradiation conditions. The following are a subset of examples that demonstrate unique in situ capabilities utilizing the I 3 TEM. Au nanoparticles prepared by drop casting have been used to investigate the effects of single ion strikes. Au thin films have been used in studies on the effects of multibeam irradiation on microstructure evolution. Zr films have been exposed to irradiation and mechanical tension to examine creep. Ag nanopillars were subjected to simultaneous high temperature, mechanical compression, and ion irradiation to study irradiation induced creep as well. These results impact fields including: structural materials, nuclear energy, energy storage, catalysis, and microelectronics in space environments.
47 OTHER INSTRUMENTATION↗
A Discussion of Zero Spring Rate Mechanisms Used for the Active Isolation Mount Experiment
In the summer of 1995 the Structural Dynamics Branch at NASA Langley Research Center set out to conceive a small, lightweight, low frequency isolation mount that could be used for spaceflight experiments. The Engineering Design Branch undertook the task of developing the isolation mount. This report describes the engineering process that led to three phases of a study entitled "Active Isolation Mounts" (AIM). A zero spring rate mechanism was used to achieve low fundamental frequencies for a payloads in the 1 to 10 pound range. It worked by balancing both a positive and a negative stiffness so that the net result was a small positive stiffness. The study demonstrated devices that could reduce the initial corner frequency by a factor of six for brief periods and a factor of two for extended periods. The designs were relatively simple and minimized weight, volume, and power. They could be scaled down and they were made of spaceflight compatible materials. All designs offered the ability to continuously vary the fundamental frequency. Yet, the goal of reducing the frequency by an order of magnitude was not achieved because the systems were too unstable at low frequencies. There was a trade between performance and stability.
Teter, John E., Jr.↗
Actively controlled shaft seals for aerospace applications
This study experimentally investigates an actively controlled mechanical seal for aerospace applications. The seal of interest is a gas seal, which is considerably more compact than previous actively controlled mechanical seals that were developed for industrial use. In a mechanical seal, the radial convergence of the seal interface has a primary effect on the film thickness. Active control of the film thickness is established by controlling the radial convergence of the seal interface with piezoelectric actuator. An actively controlled mechanical seal was initially designed and evaluated using a mathematical model. Based on these results, a seal was fabricated and tested under laboratory conditions. The seal was tested with both helium and air, at rotational speeds up to 3770 rad/sec, and at sealed pressures as high as 1.48 x 10(exp 6) Pa. The seal was operated with both manual control and with a closed-loop control system that used either the leakage rate or face temperature as the feedback. The output of the controller was the voltage applied to the piezoelectric actuator. The seal operated successfully for both short term tests (less than one hour) and for longer term tests (four hours) with a closed-loop control system. The leakage rates were typically 5-15 slm (standard liters per minute), and the face temperatures were generally maintained below 100 C. When leakage rate was used as the feedback signal, the setpoint leakage rate was typically maintained within 1 slm. However, larger deviations occurred during sudden changes in sealed pressure. When face temperature was used as the feedback signal, the setpoint face temperature was generally maintained within 3 C, with larger deviations occurring when the sealed pressure changed suddenly.
Salant, Richard F.↗
Elucidating the Morphological Instability Mechanisms During Electrodeposition of Active Metals
The primary aim of this investigation is to elucidate the mechanisms by which a group of metals pertinent to battery technology exhibit unstable growth morphology during electrodeposition, which are crucial for the operational efficacy of batteries. The metals under consideration include alkali metals alongside zinc, all of which are characterized by high atomic mobility and reactivity with the electrolytes employed in battery systems. These materials represent promising electrode candidates for next-generation rechargeable batteries that are anticipated to deliver significantly enhanced energy density at a reduced cost. Nevertheless, the widespread occurrence of distinctly non-uniform morphologies, exemplified by the emergence of filamentous and moss-like structures, constitutes a significant impediment to their effective utilization, as it leads to accelerated capacity degradation and potential internal short circuits. This study addresses a critical question that has thus far garnered limited attention: Does the residual stress induced by the plating process play an instrumental role in inducing the morphological instability? Utilizing zinc as the primary model system, this project will be executed through three interconnected tasks: (1) the quantification of the relationship between plating stress and electroplating morphologies, (2) the three-dimensional imaging of the microstructure of the mossy structure at the nanoscale, and (3) the development of a mesoscale electroplating model to interpret empirical findings and generate additional predictive insights.
25 ENERGY STORAGE↗
The relationship between dislocation density and flow stress in materials deforming by a Peierls-Nabarro mechanism.
Thermally activated deformation relating flow stress to square root of dislocation density
TEMPERATURE EFFECT↗
Growth factor involvement in tension-induced skeletal muscle growth
Long-term manned space travel will require a better understanding of skeletal muscle atrophy which results from microgravity. Astronaut strength and dexterity must be maintained for normal mission operations and for emergency situations. Although exercise in space slows the rate of muscle loss, it does not prevent it. A biochemical understanding of how gravity/tension/exercise help to maintain muscle size by altering protein synthesis and/or degradation rate should ultimately allow pharmacological intervention to prevent muscle atrophy in microgravity. The overall objective is to examine some of the basic biochemical processes involved in tension-induced muscle growth. With an experimental in vitro system, the role of exogenous and endogenous muscle growth factors in mechanically stimulated muscle growth are examined. Differentiated avian skeletal myofibers can be 'exercised' in tissue culture using a newly developed dynamic mechanical cell stimulator device which simulates different muscle activity patterns. Patterns of mechanical activity which significantly affect muscle growth and metabolic characteristics were found. Both exogenous and endogenous growth factors are essential for tension-induced muscle growth. Exogenous growth factors found in serum, such as insulin, insulin-like growth factors, and steroids, are important regulators of muscle protein turnover rates and mechanically-induced muscle growth. Endogenous growth factors are synthesized and released into the culture medium when muscle cells are mechanically stimulated. At least one family of mechanically induced endogenous factors, the prostaglandins, help to regulate the rates of protein turnover in muscle cells. Endogenously synthesized IGF-1 is another. The interaction of muscle mechanical activity and these growth factors in the regulation of muscle protein turnover rates with our in vitro model system is studied.
Vandenburgh, Herman H.↗
Editorial: Structure and mechanism of microbial membrane active transporters
Membrane active transporters play essential roles in microbial physiology. They couple energy transduction to conformational changes that drive translocation of nutrients, substrates and ions, as well as molecular communication. The structure and function of microbial membrane active transporters are highly diverse. Typical examples include the primary active transporters in the ATP-binding cassette (ABC) superfamily (Thomas and Tampé, 2020; Davidson et al., 2008; Locher et al., 2002), the secondary active transporters in the Major Facilitator Superfamily (MFS) (Drew et al., 2021; Kaback and Guan, 2019), and the ligand-gated porins in the TonB-dependent transporter (TBDT) family (Klebba et al., 2021). As structural, proteogenomic, and computational methods advance, active transporters are increasingly recognized as dynamic molecular machines whose mechanisms can now be visualized and modeled with remarkable precision, building on decades of biochemical and biophysical discovery that established the foundations of this field. The transporter studies recruited in this Research Topic provide us with new insights into the field including structure-function of sugar transporters in yeast, structural prediction and classification of ABC complexes in Bacillus subtilis, Type VI Secretion System (T6SS) in Bacteroides fragilis, amino acids uptake in Escherichia coli and bacterial spore germination.
mechanism↗
Experiments on the amplification of optical activity
Chemical mechanisms for the amplification of small, abiotically produced enantiomeric excesses leading to the complete stereo specificity of all biochemical reactions observed in the present-day biosphere are investigated quantitatively. Partial copolymerization of a mixture of R- and S-leucine or R- and S-valine N-carboxy anhydrides containing a known excess of one enantiomer was induced and the enantiomeric composition of the resulting oligomer was analyzed by gas chromatography. It is found that the 50% polymerization of leucine mixtures having excesses of 8 to 70% of either enantiomer leads to a significant enhancement of the enantiomeric excess of the polymer, accompanied by a corresponding decrease in the enantiomeric excess of the unpolymerized residue. On the other hand, 25-50% polymerization of valine mixtures is observed to result in polymers showing a decreased enantiomeric excess relative to the starting mixture and corresponding increases in those of the residue. Results of the leucine polymerization are interpreted as supporting the theory of steric interactions between the monomer and the helical structure of the polymer leading to the enrichment of one enantiomer, and possible mechanisms for the reverse stereospecificity observed in valine are discussed.
Blair, N. E.↗
Understanding the effect of mechanical strains on the catalytic activity of transition metals
The effect of mechanical strains on the volcano plot for the HER and for the ORR was determined from first principles calculations for thirteen transition metals. The lines stand for the variation in the catalytic activity of each metal as a function of the applied elastic strain.
Chemistry↗
A study of the mechanism of the pairwise activity of the vestibular apparatus <k izucheniyu mekhanizma parnoy raboty vestibulyarnogo apparata<
Electrophysiological study of vestibular apparatus mechanisms and interconnections between canals and nuclei in medulla oblongata of cats
CAT↗
Influence of Ti‐incorporated Zeolite Topology and Pore Condensation on Vapor Phase Propylene Epoxidation Kinetics with Gaseous H 2 O 2
Abstract Vapor‐phase propylene (C 3 H 6 ) epoxidation kinetics with hydrogen peroxide (H 2 O 2 ) strongly reflects the physical properties of Ti‐incorporated zeolite catalysts and the presence of spectating molecules (“solvent”) near active sites even without a bulk liquid phase. Steady‐state turnover rates of C 3 H 6 epoxidation and product selectivities vary by orders of magnitudes, depending on the zeolite silanol ((SiOH) x ) density, pore topology (MFI, *BEA, FAU), and the quantity of condensed acetonitrile (CH 3 CN) molecules nearby active sites, under identical reaction mechanisms sharing activated H 2 O 2 intermediates on Ti surfaces. Individual kinetic analyses for propylene oxide (PO) ring‐opening, homogeneous diol oxidative cleavage, and homogeneous aldehyde oxidation reveal that secondary reaction kinetics following C 3 H 6 epoxidation responds more sensitively to the changes in zeolite physical properties and pore condensation with CH 3 CN. Thus, higher PO selectivities achieved in hydrophilic Ti‐MFI at steady‐state reflect the preferential stabilization of transition states for C 3 H 6 epoxidation (a primary reaction) relative to PO ring‐opening and oxidative cleavage (secondary reactions) that solvation effects that reflect interactions among condensed CH 3 CN within pores and the extended pore structure.
Kwon, Ohsung↗