Basal actomyosin pulses expand epithelium coordinating cell flattening and tissue elongation.

Actomyosin networks constrict cell area and junctions to alter cell and tissue shape. However, during cell expansion under mechanical stress, actomyosin networks are strengthened and polarized to relax stress. Thus, cells face a conflicting situation between the enhanced actomyosin contractile properties and the expansion behaviour of the cell or tissue. To address this paradoxical situation, we study late Drosophila oogenesis and reveal an unusual epithelial expansion wave behaviour. Mechanistically, Rac1 and Rho1 integrate basal pulsatile actomyosin networks with ruffles and focal adhesions to increase and then stabilize basal area of epithelial cells allowing their flattening and elongation. This epithelial expansion behaviour bridges cell changes to oocyte growth and extension, while oocyte growth in turn deforms the epithelium to drive cell spreading. Basal pulsatile actomyosin networks exhibit non-contractile mechanics, non-linear structures and F-actin/Myosin-II spatiotemporal signal separation, implicating unreported expanding properties. Biophysical modelling incorporating these expanding properties well simulates epithelial cell expansion waves. Our work thus highlights actomyosin expanding properties as a key mechanism driving tissue morphogenesis.

Time-integrated BMP signaling determines fate in a stem cell model for early human development.

How paracrine signals are interpreted to yield multiple cell fate decisions in a dynamic context during human development in vivo and in vitro remains poorly understood. Here we report an automated tracking method to follow signaling histories linked to cell fate in large numbers of human pluripotent stem cells (hPSCs). Using an unbiased statistical approach, we discover that measured BMP signaling history correlates strongly with fate in individual cells. We find that BMP response in hPSCs varies more strongly in the duration of signaling than the level. However, both the level and duration of signaling activity control cell fate choices only by changing the time integral. Therefore, signaling duration and level are interchangeable in this context. In a stem cell model for patterning of the human embryo, we show that signaling histories predict the fate pattern and that the integral model correctly predicts changes in cell fate domains when signaling is perturbed. Our data suggest that mechanistically, BMP signaling is integrated by SOX2.

Microbiome metabolite quantification methods enabling insights into human health and disease.

Many of the health-associated impacts of the microbiome are mediated by its chemical activity, producing and modifying small molecules (metabolites). Thus, microbiome metabolite quantification has a central role in efforts to elucidate and measure microbiome function. In this review, we cover general considerations when designing experiments to quantify microbiome metabolites, including sample preparation, data acquisition and data processing, since these are critical to downstream data quality. We then discuss data analysis and experimental steps to demonstrate that a given metabolite feature is of microbial origin. We further discuss techniques used to quantify common microbial metabolites, including short-chain fatty acids (SCFA), secondary bile acids (BAs), tryptophan derivatives, N-acyl amides and trimethylamine N-oxide (TMAO). Lastly, we conclude with challenges and future directions for the field.

Persistent Biofluid Small-Molecule Alterations Induced by Trypanosoma cruzi Infection Are Not Restored by Parasite Elimination.

Chagas disease (CD), caused by Trypanosoma cruzi (T. cruzi) protozoa, is a complicated parasitic illness with inadequate medical measures for diagnosing infection and monitoring treatment success. To address this gap, we analyzed changes in the metabolome of T. cruzi-infected mice via liquid chromatography tandem mass spectrometry of clinically accessible biofluids: saliva, urine, and plasma. Urine was the most indicative of infection status across mouse and parasite genotypes. Metabolites perturbed by infection in urine include kynurenate, acylcarnitines, and threonylcarbamoyladenosine. Based on these results, we sought to implement urine as a tool for the assessment of CD treatment success. Strikingly, it was found that mice with parasite clearance following benznidazole antiparasitic treatment had an overall urine metabolome comparable to that of mice that failed to clear parasites. These results provide a complementary hypothesis to explain clinical trial data in which benznidazole treatment did not improve patient outcomes in late-stage disease, even in patients with successful parasite clearance. Overall, this study provides insights into new small-molecule-based CD diagnostic methods and a new approach to assess functional responses to treatment.

Localized cardiac small molecule trajectories and persistent chemical sequelae in experimental Chagas disease.

Post-infectious conditions present major health burdens but remain poorly understood. In Chagas disease (CD), caused by Trypanosoma cruzi parasites, antiparasitic agents that successfully clear T. cruzi do not always improve clinical outcomes. In this study, we reveal differential small molecule trajectories between cardiac regions during chronic T. cruzi infection, matching with characteristic CD apical aneurysm sites. Incomplete, region-specific, cardiac small molecule restoration is observed in animals treated with the antiparasitic benznidazole. In contrast, superior restoration of the cardiac small molecule profile is observed for a combination treatment of reduced-dose benznidazole plus an immunotherapy, even with less parasite burden reduction. Overall, these results reveal molecular mechanisms of CD treatment based on simultaneous effects on the pathogen and on host small molecule responses, and expand our understanding of clinical treatment failure in CD. This link between infection and subsequent persistent small molecule perturbation broadens our understanding of infectious disease sequelae.

Persistent biofluid small molecule alterations induced by Trypanosoma cruzi infection are not restored by antiparasitic treatment.

Chagas Disease (CD), caused by Trypanosoma cruzi (T. cruzi) protozoa, is a complicated parasitic illness with inadequate medical measures for diagnosing infection and monitoring treatment success. To address this gap, we analyzed changes in the metabolome of T. cruzi-infected mice via liquid chromatography tandem mass spectrometry analysis of clinically-accessible biofluids: saliva, urine, and plasma. Urine was the most indicative of infection status, across mouse and parasite genotypes. Metabolites perturbed by infection in the urine include kynurenate, acylcarnitines, and threonylcarbamoyladenosine. Based on these results, we sought to implement urine as a tool for assessment of CD treatment success. Strikingly, it was found that mice with parasite clearance following benznidazole antiparasitic treatment had comparable overall urine metabolome to mice that failed to clear parasites. These results match with clinical trial data in which benznidazole treatment did not improve patient outcomes in late-stage disease. Overall, this study provides insights into new small molecule-based CD diagnostic methods and a new approach to assess functional treatment response.

Localized cardiac metabolic trajectories and post-infectious metabolic sequelae in experimental Chagas disease.

Post-infectious conditions, where clinical symptoms fail to resolve even after pathogen clearance, present major health burdens. However, the mechanisms involved remain poorly understood. In Chagas disease (CD), caused by the parasite Trypanosoma cruzi, antiparasitic agents can clear T. cruzi but late-stage treatment does not improve clinical cardiac outcomes. In this study, we revealed differential metabolic trajectories of cardiac regions during T. cruzi infection, matching sites of clinical symptoms. Incomplete, region-specific, cardiac metabolic restoration was observed in animals treated with the antiparasitic benznidazole, even though parasites were successfully cleared. In contrast, superior metabolic restoration was observed for a combination treatment of reduced-dose benznidazole plus an immunotherapy (Tc24-C4 T. cruzi flagellar protein and TLR4 agonist adjuvant), even though parasite burden reduction was lower. Overall, these results provide a mechanism to explain prior clinical treatment failures in CD and to test novel candidate treatment regimens. More broadly, our results demonstrate a link between persistent metabolic perturbation and post-infectious conditions, with broad implications for our understanding of post-infectious disease sequelae.

Molecular networking in infectious disease models.

Small molecule metabolites are the product of many enzymatic reactions. Metabolomics thus opens a window into enzyme activity and function, integrating effects at the post-translational, proteome, transcriptome and genome level. In addition, small molecules can themselves regulate enzyme activity, expression and function both via substrate availability mechanisms and through allosteric regulation. Metabolites are therefore at the nexus of infectious diseases, regulating nutrient availability to the pathogen, immune responses, tropism, and host disease tolerance and resilience. Analysis of metabolomics data is however complex, particularly in terms of metabolite annotation. An emerging valuable approach to extend metabolite annotations beyond existing compound libraries and to identify infection-induced chemical changes is molecular networking. In this chapter, we discuss the applications of molecular networking in the context of infectious diseases specifically, with a focus on considerations relevant to these biological systems.

Regulation of cell attachment, spreading, and migration by hydrogel substrates with independently tunable mesh size.

Hydrogels are widely used as substrates to investigate interactions between cells and their microenvironment as they mimic many attributes of the extracellular matrix. The stiffness of hydrogels is an important property that is known to regulate cell behavior. Beside stiffness, cells also respond to structural cues such as mesh size. However, since the mesh size of hydrogel is intrinsically coupled to its stiffness, its role in regulating cell behavior has never been independently investigated. Here, we report a hydrogel system whose mesh size and stiffness can be independently controlled. Cell behavior, including spreading, migration, and formation of focal adhesions is significantly altered on hydrogels with different mesh sizes but with the same stiffness. At the transcriptional level, hydrogel mesh size affects cellular mechanotransduction by regulating nuclear translocation of yes-associated protein. These findings demonstrate that the mesh size of a hydrogel plays an important role in cell-substrate interactions. STATEMENT OF SIGNIFICANCE: Hydrogels are ideal platforms with which to investigate interactions between cells and their microenvironment as they mimic many physical properties of the extracellular matrix. However, the mesh size of hydrogels is intrinsically coupled to their stiffness, making it challenging to investigate the contribution of mesh size to cell behavior. In this work, we use hydrogel-on-glass substrates with defined thicknesses whose stiffness and mesh size can be independently tuned. We use these substrates to isolate the effects of mesh size on cell behavior, including attachment, spreading, migration, focal adhesion formation and YAP localization in the nucleus. Our results show that mesh size has significant, yet often overlooked, effects, on cell behavior, and contribute to a further understanding of cell-substrate interactions.

Enabling Quantitative Analysis of Surface Small Molecules for Exposomics and Behavioral Studies.

Workplace chemical exposures are a major source of occupational injury. Although over half of these are skin exposures, exposomics research often focuses on chemical levels in the air or in worker biofluids such as blood and urine. Until now, one limitation has been the lack of methods to quantitatively measure surface chemical transfer. Outside the realm of harmful chemicals, the small molecules we leave behind on surfaces can also reveal important aspects of human behavior. In this study, we developed a swab-based quantitative approach to determine small molecule concentrations across common surfaces. We demonstrate its utility using one drug, cyclobenzaprine, on metal surfaces, and two human-derived metabolites, carnitine and phenylacetylglutamine, on four common surfaces: linoleum flooring, plastified laboratory workbench, metal, and Plexiglas. We observed peak areas proportional to surface analyte concentrations at 45 min and 1 week after deposition, enabling quantification of molecule abundance on workplace built environment surfaces. In contrast, this method was unsuitable for analysis of oleanolic acid, for which we did not observe a strong linear proportional relationship following swab-based recovery from surfaces. Overall, this method paves the way for future quantitative exposomics studies in analyte-specific and surface-specific frameworks.

Structural Alternation in Heat Shock Proteins of Activated Macrophages.

The inflammatory response of macrophages is an orderly and complex process under strict regulation accompanied by drastic changes in morphology and functions. It is predicted that proteins will undergo structural changes during these finely regulated processes. However, changes in structural proteome in macrophages during the inflammatory response remain poorly characterized. In the present study, we applied limited proteolysis coupled mass spectrometry (LiP-MS) to identify proteome-wide structural changes in lipopolysaccharide (LPS)-activated macrophages. We identified 386 structure-specific proteolytic fingerprints from 230 proteins. Using the Gene Ontology (GO) biological process enrichment, we discovered that proteins with altered structures were enriched into protein folding-related terms, in which HSP60 was ranked as the most changed protein. We verified the structural changes in HSP60 by using cellular thermal shift assay (CETSA) and native CETSA. Our results showed that the thermal stability of HSP60 was enhanced in activated macrophages and formed an HSP10-less complex. In conclusion, we demonstrate that in situ structural systems biology is an effective method to characterize proteomic structural changes and reveal that the structures of chaperone proteins vary significantly during macrophage activation.

Selective Methane Oxidation to Methanol on ZnO/Cu2O/Cu(111) Catalysts: Multiple Site-Dependent Behaviors.

Because of the abundance of natural gas in our planet, a major goal is to achieve a direct methane-to-methanol conversion at medium to low temperatures using mixtures of methane and oxygen. Here, we report an efficient catalyst, ZnO/Cu2O/Cu(111), for this process investigated using a combination of reactor testing, scanning tunneling microscopy, ambient-pressure X-ray photoemission spectroscopy, density functional calculations, and kinetic Monte Carlo simulations. The catalyst is capable of methane activation at room temperature and transforms mixtures of methane and oxygen to methanol at 450 K with a selectivity of ∼30%. This performance is not seen for other heterogeneous catalysts which usually require the addition of water to enable a significant conversion of methane to methanol. The unique coarse structure of the ZnO islands supported on a Cu2O/Cu(111) substrate provides a collection of multiple centers that display different catalytic activity during the reaction. ZnO-Cu2O step sites are active centers for methanol synthesis when exposed to CH4 and O2 due to an effective O-O bond dissociation, which enables a methane-to-methanol conversion with a reasonable selectivity. Upon addition of water, the defected O-rich ZnO sites, introduced by Zn vacancies, show superior behavior toward methane conversion and enhance the overall methanol selectivity to over 80%. Thus, in this case, the surface sites involved in a direct CH4 → CH3OH conversion are different from those engaged in methanol formation without water. The identification of the site-dependent behavior of ZnO/Cu2O/Cu(111) opens a design strategy for guiding efficient methane reformation with high methanol selectivity.

Flavonoid 4,4'-dimethoxychalcone suppresses cell proliferation via dehydrogenase inhibition and oxidative stress aggravation.

Flavonoids are natural polyphenolic compounds with a diverse array of biological activities and health-promoting effects. Recent studies have found that 4,4'-dimethoxychalcone (DMC) promoted longevity via autophagy; however, its targets are currently unknown. Herein, we employed an unbiased thermal proteome profiling (TPP) method and identified multiple targets of DMC, including ALDH1A3, ALDH2, and PTGES2. We further determined the dissociation constant (Kd) of DMC and ALDH1A3 to be 2.8 µM using microscale thermophoresis (MST) analysis, which indicated that DMC inhibited ALDH1A3 activity and aggravated cellular oxidative stress. DMC treatment significantly increased cellular reactive oxygen species (ROS) production and inhibited cancer cell growth. Quantitative proteomic analysis showed that DMC upregulated proteins associated with stress-responses and downregulated proteins associated with cell cycle progression, and this was confirmed using cell cycle analysis. Taken together, we showed that TPP is an effective tool with which to identify flavonoid targets and set a precedent for deciphering flavonoid function in the future. We have demonstrated that DMC inhibited cell proliferation via ROS-induced cell cycle arrest and is an anti-proliferative agent in cancer treatment.

Central role of metabolism in Trypanosoma cruzi tropism and Chagas disease pathogenesis.

Chagas disease is a neglected tropical disease caused by Trypanosoma cruzi parasites. During mammalian infection, T. cruzi alternates between an intracellular stage and extracellular stage. T. cruzi adapts its metabolism to this lifestyle, while also reshaping host metabolic pathways. Such host metabolic adaptations compensate for parasite-induced stress, but may promote parasite survival and proliferation. Recent work has demonstrated that metabolism controls parasite tropism and location of Chagas disease symptoms, and regulates whether infection is mild or severe. Such findings have important translational applications with regards to treatment and diagnostic test development, though further research is needed with regards to in vivo parasite metabolic gene expression, relationship between magnitude of local metabolic perturbation, parasite strain and disease location, and host-parasite-microbiota co-metabolism.

Reaction Pathway for Coke-Free Methane Steam Reforming on a Ni/CeO2 Catalyst: Active Sites and the Role of Metal-Support Interactions.

Methane steam reforming (MSR) plays a key role in the production of syngas and hydrogen from natural gas. The increasing interest in the use of hydrogen for fuel cell applications demands development of catalysts with high activity at reduced operating temperatures. Ni-based catalysts are promising systems because of their high activity and low cost, but coke formation generally poses a severe problem. Studies of ambient-pressure X-ray photoelectron spectroscopy (AP-XPS) indicate that CH4/H2O gas mixtures react with Ni/CeO2(111) surfaces to form OH, CH x , and CH x O at 300 K. All of these species are easy to form and desorb at temperatures below 700 K when the rate of the MSR process is accelerated. Density functional theory (DFT) modeling of the reaction over ceria-supported small Ni nanoparticles predicts relatively low activation barriers between 0.3 and 0.7 eV for complete dehydrogenation of methane to carbon and the barrierless activation of water at interfacial Ni sites. Hydroxyls resulting from water activation allow for CO formation via a COH intermediate with a barrier of about 0.9 eV, which is much lower than that through a pathway involving lattice oxygen from ceria. Neither methane nor water activation is a rate-determining step, and the OH-assisted CO formation through the COH intermediate constitutes a low-barrier pathway that prevents carbon accumulation. The interactions between Ni and the ceria support and the low metal loading are crucial for the reaction to proceed in a coke-free and efficient way. These results pave the way for further advances in the design of stable and highly active Ni-based catalysts for hydrogen production.

Metal-Support Interactions and C1 Chemistry: Transforming Pt-CeO2 into a Highly Active and Stable Catalyst for the Conversion of Carbon Dioxide and Methane.

There is an ongoing search for materials which can accomplish the activation of two dangerous greenhouse gases like carbon dioxide and methane. In the area of C1 chemistry, the reaction between CO2 and CH4 to produce syngas (CO/H2), known as methane dry reforming (MDR), is attracting a lot of interest due to its green nature. On Pt(111), high temperatures must be used to activate the reactants, leading to a substantial deposition of carbon which makes this metal surface useless for the MDR process. In this study, we show that strong metal-support interactions present in Pt/CeO2(111) and Pt/CeO2 powders lead to systems which can bind CO2 and CH4 well at room temperature and are excellent and stable catalysts for the MDR process at moderate temperature (500 °C). The behavior of these systems was studied using a combination of in situ/operando methods (AP-XPS, XRD, and XAFS) which pointed to an active Pt-CeO2-x interface. In this interface, the oxide is far from being a passive spectator. It modifies the chemical properties of Pt, facilitating improved methane dissociation, and is directly involved in the adsorption and dissociation of CO2 making the MDR catalytic cycle possible. A comparison of the benefits gained by the use of an effective metal-oxide interface and those obtained by plain bimetallic bonding indicates that the former is much more important when optimizing the C1 chemistry associated with CO2 and CH4 conversion. The presence of elements with a different chemical nature at the metal-oxide interface opens the possibility for truly cooperative interactions in the activation of C-O and C-H bonds.

Alterations to the Cardiac Metabolome Induced by Chronic T. cruzi Infection Relate to the Degree of Cardiac Pathology.

Chronic Chagasic cardiomyopathy (CCC) is a Neglected Tropical Disease caused by the parasite Trypanosoma cruzi. The pathognomonic findings in symptomatic CCC patients and animal models includes diffuse cardiac fibrosis and inflammation with persistent parasite presence in the heart. This study investigated chemical alterations in different regions of the heart in relation to cardiac pathology indicators to better understand the long-term pathogenesis of this neglected disease. We used data from echocardiography, fibrosis biomarkers, and histopathological analysis to fully evaluate cardiac pathology. Metabolites isolated from the pericardial and endocardial sides of the right ventricular myocardium were analyzed by liquid chromatography tandem mass spectrometry. The endocardial sections contained significantly less cardiac inflammation and fibrosis than the pericardial sections. Cardiac levels of acylcarnitines, phosphocholines, and other metabolites were significantly disrupted in accordance with cardiac fibrosis, inflammation, and serum fibrosis biomarker levels. These findings have potential implications in treatment and monitoring for CCC patients.

Dynamic structure of active sites in ceria-supported Pt catalysts for the water gas shift reaction.

Oxide-supported noble metal catalysts have been extensively studied for decades for the water gas shift (WGS) reaction, a catalytic transformation central to a host of large volume processes that variously utilize or produce hydrogen. There remains considerable uncertainty as to how the specific features of the active metal-support interfacial bonding-perhaps most importantly the temporal dynamic changes occurring therein-serve to enable high activity and selectivity. Here we report the dynamic characteristics of a Pt/CeO2 system at the atomic level for the WGS reaction and specifically reveal the synergistic effects of metal-support bonding at the perimeter region. We find that the perimeter Pt0 - O vacancy-Ce3+ sites are formed in the active structure, transformed at working temperatures and their appearance regulates the adsorbate behaviors. We find that the dynamic nature of this site is a key mechanistic step for the WGS reaction.

Mesoscopic dynamic model of epithelial cell division with cell-cell junction effects.

Cell division is central for embryonic development, tissue morphogenesis, and tumor growth. Experiments have evidenced that mitotic cell division is manipulated by the intercellular cues such as cell-cell junctions. However, it still remains unclear how these cortical-associated cues mechanically affect the mitotic spindle machinery, which determines the position and orientation of the cell division. In this paper, a mesoscopic dynamic cell division model is established to explore the integrated regulations of cortical polarity, microtubule pulling forces, cell deformability, and internal osmotic pressure. We show that the distributed pulling forces of astral microtubules play a key role in encoding the instructive cortical cues to orient and position the spindle of a dividing cell. The present model can not only predict the spindle orientation and position, but also capture the morphological evolution of cell rounding. The theoretical results agree well with relevant experiments both qualitatively and quantitatively. This work sheds light on the mechanical linkage between cell cortex and mitotic spindle, and holds potential in regulating cell division and sculpting tissue morphology.