Theoretical Investigation of the Reaction of O(1D) with Formamide.

Carbamic acid (H2NCOOH) is a small organic molecule that is terrestrially unstable in condensed phases under ambient conditions but could survive in the low densities and temperatures of the interstellar medium. In this work, the reaction of formamide (H2NCOH) and electronically excited oxygen atoms in the 1D state, namely, O(1D), has been investigated computationally to determine the feasibility of carbamic acid production. Geometries for carbamic acid and other potential reaction products have been calculated, as well as all pertinent transition states. In addition, harmonic and anharmonic frequency calculations were performed to determine quartic and sextic centrifugal distortion constants for all products. This work enables spectroscopic predictions that can guide the experimental search for carbamic acid. Presented here are the calculations, geometries, molecular constants, and spectral predictions for possible products of the reaction between formamide and O(1D), as well as a discussion of which products are favored.

Unraveling the metastasis-preventing effect of miR-200c in vitro and in vivo.

Advanced breast cancer, as well as ineffective treatments leading to surviving cancer cells, can result in the dissemination of these malignant cells from the primary tumor to distant organs. Recent research has shown that microRNA 200c (miR-200c) can hamper certain steps of the invasion-metastasis cascade. However, it is still unclear whether miR-200c expression alone is sufficient to prevent breast cancer cells from metastasis formation. Hence, we performed a xenograft mouse experiment with inducible miR-200c expression in MDA-MB 231 cells. The ex vivo analysis of metastatic sites in a multitude of organs, including lung, liver, brain, and spleen, revealed a dramatically reduced metastatic burden in mice with miR-200c-expressing tumors. A fundamental prerequisite for metastasis formation is the motility of cancer cells and, therefore, their migration. Consequently, we analyzed the effect of miR-200c on collective- and single-cell migration in vitro, utilizing MDA-MB 231 and MCF7 cell systems with genetically modified miR-200c expression. Analysis of collective-cell migration revealed confluence-dependent motility of cells with altered miR-200c expression. Additionally, scratch assays showed an enhanced predisposition of miR-200c-negative cells to leave cell clusters. The in-between stage of collective- and single-cell migration was validated using transwell assays, which showed reduced migration of miR-200c-positive cells. Finally, to measure migration at the single-cell level, a novel assay on dumbbell-shaped micropatterns was performed, which revealed that miR-200c critically determines confined cell motility. All of these results demonstrate that sole expression of miR-200c impedes metastasis formation in vivo and migration in vitro and highlights miR-200c as a metastasis suppressor in breast cancer.

Ion-mediated condensation controls the mechanics of mitotic chromosomes.

During mitosis in eukaryotic cells, mechanical forces generated by the mitotic spindle pull the sister chromatids into the nascent daughter cells. How do mitotic chromosomes achieve the necessary mechanical stiffness and stability to maintain their integrity under these forces? Here we use optical tweezers to show that ions involved in physiological chromosome condensation are crucial for chromosomal stability, stiffness and viscous dissipation. We combine these experiments with high-salt histone depletion and theory to show that chromosomal elasticity originates from the chromatin fibre behaving as a flexible polymer, whereas energy dissipation can be explained by modelling chromatin loops as an entangled polymer solution. Taken together, we show how collective properties of mitotic chromosomes, a biomaterial of incredible complexity, emerge from molecular properties, and how they are controlled by the physico-chemical environment.

Nuclear deformation and dynamics of migrating cells in 3D confinement reveal adaptation of pulling and pushing forces.

Eukaryotic cells show an astounding ability to remodel their shape and cytoskeleton and to migrate through pores and constrictions smaller than their nuclear diameter. However, the relation of nuclear deformation and migration dynamics in confinement remains unclear. Here, we study the mechanics and dynamics of mesenchymal cancer cell nuclei transitioning through three-dimensional compliant hydrogel channels. We find a biphasic dependence of migration speed and transition frequency on channel width, peaking at widths comparable to the nuclear diameter. Using confocal imaging and hydrogel bead displacement, we determine nuclear deformations and corresponding forces during confined migration. The nucleus deforms reversibly with a reduction in volume during confinement. With decreasing channel width, the nuclear shape during transmigration changes biphasically, concomitant with the transitioning dynamics. Our proposed physical model explains the observed nuclear shapes and transitioning dynamics in terms of the cytoskeletal force generation adapting from purely pulling-based to a combined pulling- and pushing-based mechanism with increasing nuclear confinement.

Short-term aerobic exercise prevents development of glucocorticoid myopathic features in aged skeletal muscle in a sex-dependent manner.

Older adults are vulnerable to glucocorticoid-induced muscle atrophy and weakness, with sex potentially influencing their susceptibility to those effects. Aerobic exercise can reduce glucocorticoid-induced muscle atrophy in young rodents. However, it is unknown whether aerobic exercise can prevent glucocorticoid myopathy in aged muscle. The objectives of this study were to define the extent to which sex influences the development of glucocorticoid myopathy in aged muscle, and to determine the extent to which aerobic exercise training protects against myopathy development. Twenty-four-month-old female (n = 30) and male (n = 33) mice were randomized to either sedentary or aerobic exercise groups. Within their respective groups, mice were randomized to either daily treatment with dexamethasone (DEX) or saline. Upon completing treatments, the contractile properties of the triceps surae complex were assessed in situ. DEX marginally lowered muscle mass and soluble protein content in both sexes, which was attenuated by aerobic exercise only in females. DEX increased sub-tetanic force and rate of force development only in females, which was not influenced by aerobic exercise. Muscle fatigue was higher in both sexes following DEX, but aerobic exercise prevented fatigue induction only in females. The sex-specific differences to muscle function in response to DEX treatment coincided with sex-specific changes to the content of proteins related to calcium handling, mitochondrial quality control, reactive oxygen species production, and glucocorticoid receptor in muscle. These findings define several important sexually dimorphic changes to aged skeletal muscle physiology in response to glucocorticoid treatment and define the capacity of short-term aerobic exercise to protect against those changes. KEY POINTS: There are sexually dimorphic effects of glucocorticoids on aged skeletal muscle physiology. Glucocorticoid-induced changes to aged muscle contractile properties coincide with sex-specific differences in the content of calcium handling proteins. Aerobic exercise prevents glucocorticoid-induced fatigue only in aged females and coincides with differences in the content of mitochondrial quality control proteins and glucocorticoid receptors.

Loop-extruders alter bacterial chromosome topology to direct entropic forces for segregation.

Entropic forces have been argued to drive bacterial chromosome segregation during replication. In many bacterial species, however, specifically evolved mechanisms, such as loop-extruding SMC complexes and the ParABS origin segregation system, contribute to or are even required for chromosome segregation, suggesting that entropic forces alone may be insufficient. The interplay between and the relative contributions of these segregation mechanisms remain unclear. Here, we develop a biophysical model showing that purely entropic forces actually inhibit bacterial chromosome segregation until late replication stages. By contrast, our model reveals that loop-extruders loaded at the origins of replication, as observed in many bacterial species, alter the effective topology of the chromosome, thereby redirecting and enhancing entropic forces to enable accurate chromosome segregation during replication. We confirm our model predictions with polymer simulations: purely entropic forces do not allow for concurrent replication and segregation, whereas entropic forces steered by specifically loaded loop-extruders lead to robust, global chromosome segregation during replication. Finally, we show how loop-extruders can complement locally acting origin separation mechanisms, such as the ParABS system. Together, our results illustrate how changes in the geometry and topology of the polymer, induced by DNA-replication and loop-extrusion, impact the organization and segregation of bacterial chromosomes.

Physical models of bacterial chromosomes.

The interplay between bacterial chromosome organization and functions such as transcription and replication can be studied in increasing detail using novel experimental techniques. Interpreting the resulting quantitative data, however, can be theoretically challenging. In this minireview, we discuss how connecting experimental observations to biophysical theory and modeling can give rise to new insights on bacterial chromosome organization. We consider three flavors of models of increasing complexity: simple polymer models that explore how physical constraints, such as confinement or plectoneme branching, can affect bacterial chromosome organization; bottom-up mechanistic models that connect these constraints to their underlying causes, for instance, chromosome compaction to macromolecular crowding, or supercoiling to transcription; and finally, data-driven methods for inferring interpretable and quantitative models directly from complex experimental data. Using recent examples, we discuss how biophysical models can both deepen our understanding of how bacterial chromosomes are structured and give rise to novel predictions about bacterial chromosome organization.

Post-translational modifications of vertebrate striated muscle myosin heavy chains.

Post-translational modifications (PTMs) play a crucial role in regulating the function of many sarcomeric proteins, including myosin. Myosins comprise a family of motor proteins that play fundamental roles in cell motility in general and muscle contraction in particular. A myosin molecule consists of two myosin heavy chains (MyHCs) and two pairs of myosin light chains (MLCs); two MLCs are associated with the neck region of each MyHC's N-terminal head domain, while the two MyHC C-terminal tails form a coiled-coil that polymerizes with other MyHCs to form the thick filament backbone. Myosin undergoes extensive PTMs, and dysregulation of these PTMs may lead to abnormal muscle function and contribute to the development of myopathies and cardiovascular disorders. Recent studies have uncovered the significance of PTMs in regulating MyHC function and showed how these PTMs may provide additional modulation of contractile processes. Here, we discuss MyHC PTMs that have been biochemically and/or functionally studied in mammals' and rodents' striated muscle. We have identified hotspots or specific regions in three isoforms of myosin (MYH2, MYH6, and MYH7) where the prevalence of PTMs is more frequent and could potentially play a significant role in fine-tuning the activity of these proteins.

Multiplexed Immunofluorescence and Single-Molecule RNA Fluorescence In Situ Hybridization in Mouse Skeletal Myofibers.

RNA fluorescence in situ hybridization (FISH) is a powerful method to determine the abundance and localization of mRNA molecules in cells. While modern RNA FISH techniques allow quantification at single molecule resolution, most methods are optimized for mammalian cell culture and are not easily applied to in vivo tissue settings. Single-molecule RNA detection in skeletal muscle cells has been particularly challenging due to the thickness and high autofluorescence of adult muscle tissue and a lack of in vitro models for mature muscle cells (myofibers). Here, we present a method for isolation of adult myofibers from mouse skeletal muscle and detection of single mRNA molecules and proteins using multiplexed RNA FISH and immunofluorescence.

Geometry-Sensitive Protrusion Growth Directs Confined Cell Migration.

The migratory dynamics of cells can be influenced by the complex microenvironment through which they move. It remains unclear how the motility machinery of confined cells responds and adapts to their microenvironment. Here, we propose a biophysical mechanism for a geometry-dependent coupling between cellular protrusions and the nucleus that leads to directed migration. We apply our model to geometry-guided cell migration to obtain insights into the origin of directed migration on asymmetric adhesive micropatterns and the polarization enhancement of cells observed under strong confinement. Remarkably, for cells that can choose between channels of different size, our model predicts an intricate dependence for cellular decision making as a function of the two channel widths, which we confirm experimentally.

Learning dynamical models of single and collective cell migration: a review.

Single and collective cell migration are fundamental processes critical for physiological phenomena ranging from embryonic development and immune response to wound healing and cancer metastasis. To understand cell migration from a physical perspective, a broad variety of models for the underlying physical mechanisms that govern cell motility have been developed. A key challenge in the development of such models is how to connect them to experimental observations, which often exhibit complex stochastic behaviours. In this review, we discuss recent advances in data-driven theoretical approaches that directly connect with experimental data to infer dynamical models of stochastic cell migration. Leveraging advances in nanofabrication, image analysis, and tracking technology, experimental studies now provide unprecedented large datasets on cellular dynamics. In parallel, theoretical efforts have been directed towards integrating such datasets into physical models from the single cell to the tissue scale with the aim of conceptualising the emergent behaviour of cells. We first review how this inference problem has been addressed in both freely migrating and confined cells. Next, we discuss why these dynamics typically take the form of underdamped stochastic equations of motion, and how such equations can be inferred from data. We then review applications of data-driven inference and machine learning approaches to heterogeneity in cell behaviour, subcellular degrees of freedom, and to the collective dynamics of multicellular systems. Across these applications, we emphasise how data-driven methods can be integrated with physical active matter models of migrating cells, and help reveal how underlying molecular mechanisms control cell behaviour. Together, these data-driven approaches are a promising avenue for building physical models of cell migration directly from experimental data, and for providing conceptual links between different length-scales of description.

A threshold of 100 or more colony-forming units on the anesthesia machine predicts bacterial pathogen detection: a retrospective laboratory-based analysis.

PURPOSE: Preventing the spread of pathogens in the anesthesia work area reduces surgical site infections. Improved cleaning reduces the percentage of anesthesia machine samples with ≥ 100 colony-forming units (CFU) per surface area sampled. Targeting a threshold of < 100 CFU when cleaning anesthesia machines may be associated with a lower prevalence of bacterial pathogens. We hypothesized that anesthesia work area reservoir samples returning < 100 CFU would have a low (< 5%) prevalence of pathogens. METHODS: In this retrospective cohort study of bacterial count data from nine hospitals, obtained between 2017 and 2022, anesthesia attending and assistants' hands, patient skin sites (nares, axilla, and groin), and anesthesia machine (adjustable pressure-limiting valve and agent dials) reservoirs were sampled at case start and at case end. The patient intravenous stopcock set was sampled at case end. The isolation of ≥ 1 CFU of Staphylococcus aureus, methicillin-resistant Staphylococcus aureus, Enterococcus, vancomycin-resistant Enterococcus, gram-negative (i.e., Klebsiella, Acinetobacter, Pseudomonas, and Enterobacter spp.) or coagulase-negative Staphylococcus was compared for reservoir samples returning ≥ 100 CFU vs those returning < 100 CFU. RESULTS: Bacterial pathogens were isolated from 24% (7,601/31,783) of reservoir samples, 93% (98/105) of operating rooms, and 83% (2,170/2,616) of cases. The ratio of total pathogen isolates to total CFU was < 0.0003%. Anesthesia machine reservoirs returned ≥ 100 CFU for 44% (2,262/5,150) of cases. Twenty-three percent of samples returning ≥ 100 CFU were positive for ≥ 1 bacterial pathogen (521/2,262; 99% lower confidence limit, 22%) vs 3% of samples returning < 100 CFU (96/2,888; 99% upper limit, 4%). CONCLUSIONS: Anesthesia machine reservoir samples returning < 100 CFU were associated with negligible pathogen detection. This threshold can be used for assessment of terminal, routine, and between-case cleaning of the anesthesia machine and equipment. Such feedback may be useful because the 44% prevalence of ≥ 100 CFU was comparable to the 46% (25/54) reported earlier from an unrelated hospital.

RéSUMé: OBJECTIF: La prévention de la propagation des agents pathogènes dans la zone de travail de l'anesthésie réduit les infections du site opératoire. L'amélioration du nettoyage réduit le pourcentage d'échantillons de l'appareil d'anesthésie présentant ≥ 100 unités de formation de colonie (UFC) par surface échantillonnée. Le fait de cibler un seuil < 100 UFC lors du nettoyage des appareils d'anesthésie pourrait être associé à une prévalence plus faible d'agents pathogènes bactériens. Nous avons émis l'hypothèse que les échantillons des réservoirs de la zone de travail d'anesthésie < 100 UFC résulteraient en une faible prévalence (< 5 %) d'agents pathogènes. MéTHODE: Dans cette étude de cohorte rétrospective des données de décompte bactérien de neuf hôpitaux, obtenues entre 2017 et 2022, les mains des anesthésiologistes et des assistant·es en anesthésie, les sites cutanés des patient·es (narines, aisselles et aines) et les réservoirs de l'appareil d'anesthésie (soupape de réglage de limitation de pression et cadrans d'agent) ont été échantillonnés au début et à la fin de chaque cas. Les échantillons sur l'ensemble de robinets d'arrêt intraveineux des patient·es ont été prélevés à la fin de chaque cas. L'isolement de ≥ 1 UFC de staphylocoque doré, de staphylocoque doré résistant à la méthicilline, d'entérocoque, d'entérocoque résistant à la vancomycine, de staphylocoque à Gram négatif (c.-à-d. Klebsiella, Acinetobacter, Pseudomonas et Enterobacter spp.) ou à coagulase négative a été comparé pour les échantillons de réservoir retournant ≥ 100 UFC vs ceux qui comportaient < 100 UFC. RéSULTATS: Des bactéries pathogènes ont été isolées dans 24 % (7601/31 783) des échantillons de réservoir, 93 % (98/105) des salles d'opération et 83 % (2170/2616) des cas. Le rapport entre le nombre total d'isolats d'agents pathogènes et le nombre total d'UFC était de < 0,0003 %. Les échantillons pris sur les réservoirs d'appareils d'anesthésie ont retourné ≥ 100 UFC dans 44 % (2262/5150) des cas. Vingt-trois pour cent des échantillons retournés ≥ 100 UFC étaient positifs pour ≥ 1 agent pathogène bactérien (521/2262; limite de confiance inférieure à 99 %, 22 %) vs 3 % des échantillons retournant < 100 UFC (96/2888 ; 99 % de la limite supérieure, 4 %). CONCLUSION: Les échantillons pris sur les réservoirs de l'appareil d'anesthésie comportant < 100 UFC étaient associés à une détection négligeable d'agents pathogènes. Ce seuil peut être utilisé pour l'évaluation du nettoyage final, de routine et entre les cas de l'appareil et de l'équipement d'anesthésie. Une telle rétroaction peut être utile parce que la prévalence de 44 % de ≥ 100 UFC était comparable aux 46 % (25/54) rapportés précédemment dans un autre hôpital.

Troponin Structural Dynamics in the Native Cardiac Thin Filament Revealed by Cryo Electron Microscopy.

Cardiac muscle contraction occurs due to repetitive interactions between myosin thick and actin thin filaments (TF) regulated by Ca2+ levels, active cross-bridges, and cardiac myosin-binding protein C (cMyBP-C). The cardiac TF (cTF) has two nonequivalent strands, each comprised of actin, tropomyosin (Tm), and troponin (Tn). Tn shifts Tm away from myosin-binding sites on actin at elevated Ca2+ levels to allow formation of force-producing actomyosin cross-bridges. The Tn complex is comprised of three distinct polypeptides - Ca2+-binding TnC, inhibitory TnI, and Tm-binding TnT. The molecular mechanism of their collective action is unresolved due to lack of comprehensive structural information on Tn region of cTF. C1 domain of cMyBP-C activates cTF in the absence of Ca2+ to the same extent as rigor myosin. Here we used cryo-EM of native cTFs to show that cTF Tn core adopts multiple structural conformations at high and low Ca2+ levels and that the two strands are structurally distinct. At high Ca2+ levels, cTF is not entirely activated by Ca2+ but exists in either partially or fully activated state. Complete dissociation of TnI C-terminus is required for full activation. In presence of cMyBP-C C1 domain, Tn core adopts a fully activated conformation, even in absence of Ca2+. Our data provide a structural description for the requirement of myosin to fully activate cTFs and explain increased affinity of TnC to Ca2+ in presence of active cross-bridges. We suggest that allosteric coupling between Tn subunits and Tm is required to control actomyosin interactions.

Malate production, sugar metabolism, and redox homeostasis in the leaf growth zone of Rye (Secale cereale) increase stress tolerance to aluminum stress: A biochemical and genome-wide transcriptional study.

Global soil acidification is increasing, enlarging aluminum (Al) availability in soils, leading to reductions in plant growth. This study investigates the effect of Al stress on the leaf growth zones of Rye (Secale cereale, cv Beira). Kinematic analysis showed that the effect of Al on leaf growth rates was mainly due to a reduced cell production rate in the meristem. Transcriptomic analysis identified 2272 significantly (log2fold > |0.5| FDR < 0.05) differentially expressed genes (DEGs) for Al stress. There was a downregulation in several DEGs associated with photosynthetic processes and an upregulation in genes for heat/light response, and H2O2 production in all leaf zones. DEGs associated with heavy metals and malate transport were increased, particularly, in the meristem. To determine the putative function of these processes in Al tolerance, we performed biochemical analyses comparing the tolerant Beira with an Al sensitive variant RioDeva. Beira showed improved sugar metabolism and redox homeostasis, specifically in the meristem compared to RioDeva. Similarly, a significant increase in malate and citrate production, which are known to aid in Al detoxification in plants, was found in Beira. This suggests that Al tolerance in Rye is linked to its ability for Al exclusion from the leaf meristem.

HTS driven by fluorescence lifetime detection of FRET identifies activators and inhibitors of cardiac myosin.

Small molecules that bind to allosteric sites on target proteins to alter protein function are highly sought in drug discovery. High-throughput screening (HTS) assays are needed to facilitate the direct discovery of allosterically active compounds. We have developed technology for high-throughput time-resolved fluorescence lifetime detection of fluorescence resonance energy transfer (FRET), which enables the detection of allosteric modulators by monitoring changes in protein structure. We tested this approach at the industrial scale by adapting an allosteric FRET sensor of cardiac myosin to high-throughput screening (HTS), based on technology provided by Photonic Pharma and the University of Minnesota, and then used the sensor to screen 1.6 million compounds in the HTS facility at Bristol Myers Squibb. The results identified allosteric activators and inhibitors of cardiac myosin that do not compete with ATP binding, demonstrating high potential for FLT-based drug discovery.

The duration of glucocorticoid treatment alters the anabolic response to high-force muscle contractions.

Glucocorticoids induce a myopathy that includes loss of muscle mass and strength. Resistance exercise may reverse the muscle loss because it induces an anabolic response characterized by increases in muscle protein synthesis and potentially suppressing protein breakdown. Whether resistance exercise induces an anabolic response in glucocorticoid myopathic muscle is unknown, which is a problem because long-term glucocorticoid exposure alters the expression of genes that may prevent an anabolic response by limiting activation of pathways such as the mechanistic target of rapamycin in complex 1 (mTORC1). The purpose of this study was to assess whether high-force contractions initiate an anabolic response in glucocorticoid myopathic muscle. The anabolic response was analyzed by treating female mice with dexamethasone (DEX) for 7 days or 15 days. After treatment, the left tibialis anterior muscle of all mice was contracted via electrical stimulation of the sciatic nerve. Muscles were harvested 4 h after contractions. Rates of muscle protein synthesis were estimated using the SUnSET method. After 7 days of treatment, high-force contractions increased protein synthesis and mTORC1 signaling in both groups. After 15 days of treatment, high-force contractions activated mTORC1 signaling equally in both groups, but protein synthesis was only increased in control mice. The failure to increase protein synthesis may be because baseline synthetic rates were elevated in DEX-treated mice. The LC3 II/I ratio marker of autophagy was decreased by contractions regardless of treatment duration. These data show duration of glucocorticoid treatment alters the anabolic response to high-force contractions.NEW & NOTEWORTHY Glucocorticoid myopathy is the most common, toxic, noninflammatory myopathy. Our work shows that high-force contractions increase protein synthesis in skeletal muscle following short-term glucocorticoid treatment. However, longer duration glucocorticoid treatment results in anabolic resistance to high-force contractions despite activation of the mechanistic target of rapamycin in complex 1 (mTORC1) signaling pathway. This work defines potential limits for high-force contractions to activate the processes that would restore lost muscle mass in glucocorticoid myopathic patients.