Enhancing insights: exploring the information content of calorespirometric ratio in dynamic soil microbial growth processes through calorimetry.

Catalytic activity of microbial communities maintains the services and functions of soils. Microbial communities require energy and carbon for microbial growth, which they obtain by transforming organic matter (OM), oxidizing a fraction of it and transferring the electrons to various terminal acceptors. Quantifying the relations between matter and energy fluxes is possible when key parameters such as reaction enthalpy (∆rH), energy use efficiency (related to enthalpy) (EUE), carbon use efficiency (CUE), calorespirometric ratio (CR), carbon dioxide evolution rate (CER), and the apparent specific growth rate (µapp) are known. However, the determination of these parameters suffers from unsatisfying accuracy at the technical (sample size, instrument sensitivity), experimental (sample aeration) and data processing levels thus affecting the precise quantification of relationships between carbon and energy fluxes. To address these questions under controlled conditions, we analyzed microbial turnover processes in a model soil amended using a readily metabolizable substrate (glucose) and three commercial isothermal microcalorimeters (MC-Cal/100P, TAM Air and TAM III) with different sample sizes meaning varying volume-related thermal detection limits (LODv) (0.05-1mW L-1). We conducted aeration experiments (aerated and un-aerated calorimetric ampoules) to investigate the influence of oxygen limitation and thermal perturbation on the measurement signal. We monitored the CER by measuring the additional heat caused by CO2 absorption using a NaOH solution acting as a CO2 trap. The range of errors associated with the calorimetrically derived µapp, EUE, and CR was determined and compared with the requirements for quantifying CUE and the degree of anaerobicity (ηA). Calorimetrically derived µapp and EUE were independent of the instrument used. However, instruments with a low LODv yielded the most accurate results. Opening and closing the ampoules for oxygen and CO2 exchange did not significantly affect metabolic heats. However, regular opening during calorimetrically derived CER measurements caused significant measuring errors due to strong thermal perturbation of the measurement signal. Comparisons between experimentally determined CR, CUE,ηA, and modeling indicate that the evaluation of CR should be performed with caution.

Using NMR to Monitor TET-Dependent Methylcytosine Dioxygenase Activity and Regulation.

The active removal of DNA methylation marks is governed by the ten-eleven translocation (TET) family of enzymes (TET1-3), which iteratively oxidize 5-methycytosine (5mC) into 5-hydroxymethycytosine (5hmC), and then 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). TET proteins are frequently mutated in myeloid malignancies or inactivated in solid tumors. These methylcytosine dioxygenases are α-ketoglutarate (αKG)-dependent and are, therefore, sensitive to metabolic homeostasis. For example, TET2 is activated by vitamin C (VC) and inhibited by specific oncometabolites. However, understanding the regulation of the TET2 enzyme by different metabolites and its activity remains challenging because of limitations in the methods used to simultaneously monitor TET2 substrates, products, and cofactors during catalysis. Here, we measure TET2-dependent activity in real time using NMR. Additionally, we demonstrate that in vitro activity of TET2 is highly dependent on the presence of VC in our system and is potently inhibited by an intermediate metabolite of the TCA cycle, oxaloacetate (OAA). Despite these opposing effects on TET2 activity, the binding sites of VC and OAA on TET2 are shared with αKG. Overall, our work suggests that NMR can be effectively used to monitor TET2 catalysis and illustrates how TET activity is regulated by metabolic and cellular conditions at each oxidation step.

Function and mechanism of TREM2 in bacterial infection.

Triggering receptor expressed on myeloid cells 2 (TREM2), which is a lipid sensing and phagocytosis receptor, plays a key role in immunity and inflammation in response to pathogens. Here, we review the function and signaling of TREM2 in microbial binding, engulfment and removal, and describe TREM2-mediated inhibition of inflammation by negatively regulating the Toll-like receptor (TLR) response. We further illustrate the role of TREM2 in restoring organ homeostasis in sepsis and soluble TREM2 (sTREM2) as a diagnostic marker for sepsis-associated encephalopathy (SAE). Finally, we discuss the prospect of TREM2 as an interesting therapeutic target for sepsis.

Visual Detection and Image Processing of Parking Space Based on Deep Learning.

The automatic parking system based on vision is greatly affected by uneven lighting, which is difficult to make an accurate judgment on parking spaces in the case of complex image information. To solve this problem, this paper proposes a parking space visual detection and image processing method based on deep learning. Firstly, a 360-degree panoramic system was designed to photograph the vehicle environment. The image has been processed to obtain a panoramic aerial view, which was input as the original image of the parking space detection system. Secondly, the Faster R-CNN (Region-Convolutional Neural Network) parking detection model was established based on deep learning. It was aimed to detect and extract the parking space from the input image. Thirdly, the problems of uneven illumination and complex background were solved effectively by removing the background light from the image. Finally, a parking space extraction method based on the connected region has been designed, which further simplified the parking space extraction and image processing. The experiment results show that the mAP (mean Average Precision) value of the Faster R-CNN model using 101-Floor ResNet as the feature extraction network is 89.30%, which is 2.28% higher than that of the Faster R-CNN model using 50-Floor ResNet as the feature extraction network. The model built in this paper can detect most parking spaces well. The position of the output target box is accurate. In some test scenarios, the confidence of parking space recognition can even reach 100%. In summary, the proposed method can realize the effective identification and accurate positioning of parking spaces.

Global analysis of the energy landscapes of molecular crystal structures by applying the threshold algorithm.

Polymorphism in molecular crystals has important consequences for the control of materials properties and our understanding of crystallization. Computational methods, including crystal structure prediction, have provided important insight into polymorphism, but have usually been limited to assessing the relative energies of structures. We describe the implementation of the Monte Carlo threshold algorithm as a method to provide an estimate of the energy barriers separating crystal structures. By sampling the local energy minima accessible from multiple starting structures, the simulations yield a global picture of the crystal energy landscapes and provide valuable information on the depth of the energy minima associated with crystal structures. We present results from applying the threshold algorithm to four polymorphic organic molecular crystals, examine the influence of applying space group symmetry constraints during the simulations, and discuss the relationship between the structure of the energy landscape and the intermolecular interactions present in the crystals.

TREM2 Dictates Antibacterial Defense and Viability of Bone Marrow-derived Macrophages during Bacterial Infection.

Macrophages undergo profound metabolic reprogramming to join key immunoregulatory functions, which can be initiated by pattern recognition receptors. TREM2 (triggering receptor expressed on myeloid cells 2), a macrophage phagocytic receptor, plays pivotal roles in sepsis by enhancing bacterial clearance, which is associated with regulation of reactive oxygen species (ROS) production. However, how intracellular ROS participate in TREM2-mediated bactericidal activity remains unclear. This study was designed to investigate the organelle source and biological activity of ROS in the context of TREM2-mediated immune defense during Escherichiacoli infection. Bone marrow-derived macrophages (BMDMs) were transfected with TREM2-overexpressing adenoviruses or control viruses and challenged with E. coli. The BMDMs were administered to mouse models with local E. coli infection. In addition, monocytic TREM2 expression, NOX2 concentrations, and pyroptosis were detected in patients with bacterial sepsis. General ROS production was found to be comparable between TREM2-overexpressing and control BMDMs upon E. coli challenge. The deficiency of Nox2 led to impaired phagosome degradation and lack of bactericidal ability and abolished TREM2-mediated protective activity against pulmonary E. coli infection. Overexpression of TREM2 suppressed mitochondrial ROS generation, inhibited NLRP3/caspase-1 inflammasome activation, and finally protected BMDMs from gasdermin D-mediated pyroptosis during pulmonary E. coli infection. The protective role of TREM2 was further confirmed in mice with abdominal E. coli infection. Moreover, monocytic TREM2 expression was positively correlated with NOX2 concentrations and negatively correlated with pyroptosis and disease severity in patients with bacterial sepsis. Collectively, TREM2 controls macrophage immune functions by fine-tuning ROS generation and enhances the host defense against bacterial infection. Our data suggest that TREM2 is a promising candidate target for sepsis therapy.

Exploration and Optimization in Crystal Structure Prediction: Combining Basin Hopping with Quasi-Random Sampling.

We describe the implementation of a Monte Carlo basin hopping (BH) global optimization procedure for the prediction of molecular crystal structures. The BH method is combined with quasi-random (QR) structure generation in a hybrid method for crystal structure prediction, QR-BH, which combines the low-discrepancy sampling provided by QR sequences with BH efficiency at locating low energy structures. Through tests on a set of single-component molecular crystals and co-crystals, we demonstrate that QR-BH provides faster location of low energy structures than pure QR sampling, while maintaining the efficient location of higher energy structures that are important for identifying important polymorphs.

Triggering receptor expressed on myeloid Cells-2 (TREM2) inhibits steroidogenesis in adrenocortical cell by macrophage-derived exosomes in lipopolysaccharide-induced septic shock.

PURPOSE: Endogenously produced glucocorticoids exhibit immunomodulating properties and are of pivotal importance for sepsis outcome. Uncontrolled activation of the immune-adrenal crosstalk increases the risk of sepsis-related death. Triggering receptor expressed on myeloid cells-2 (TREM2) is richly expressed on macrophages and has been demonstrated to improve outcome of sepsis by enhancing elimination of pathogens. However, the role and mode of action of macrophage TREM2 on adrenocortical steroidogenesis remains unclear in septic shock. METHODS: The acute septic shock model was established by intraperitoneally challenging wild-type (WT) and TREM2 knock-out (Trem2-/-) mice with lipopolysaccharide (LPS, 30 mg/kg). The mice were assessed for TREM2 expression and local inflammation in adrenal gland and for synthesis of corticotropin releasing hormone (CRH) and adrenocorticotropic hormone (ACTH) in vivo. Bone marrow-derived macrophages or macrophage-derived exosomes were isolated from WT and Trem2-/- mice and were co-cultured with adrenocortical cells. The expression of steroidogenic enzymes and corticosterone production was assessed. RESULTS: Genetic deficiency of TREM2 caused significantly higher corticosterone levels at the early stage of LPS-induced septic shock; whereas TREM2 deficiency neither increased CRH and ACTH nor exacerbated the inflammation in adrenocortical tissue during septic shock. Ex vivo study revealed that Trem2-/- macrophages significantly promoted the expression of steroidogenic enzymes and increased production of corticosterone. Furthermore, Trem2-/- macrophage-derived exosomes were able to mimic Trem2-/- macrophages in enhancing adrenocortical steroidogenesis. CONCLUSIONS: At the early stage of LPS-induced septic shock, corticosterone biosynthesis can be inhibited by macrophage TREM2 in adrenocortical cells, which might partially associate with macrophage-derived exosomes.

Triggering Receptor Expressed on Myeloid Cells-2 Protects Aged Mice Against Sepsis by Mitigating the IL-23/IL-17A Response.

BACKGROUND: Advancing age is an independent predictor of mortality in septic patients. Recent animal studies were unable to reflect this clinical pathophysiological process, largely hampering the development of new efficacious therapies. Triggering receptor expressed on myeloid cells-2 (TREM-2) is a novel immune regulator with multiple activities. However, very little is known about the regulatory role of TREM-2 in sepsis upon aging. METHODS: Blood samples were collected from septic patients within 24 h after intensive care unit admission. The patients were preselected into two groups based on the age (age with ≥60 years old and age with <60 years old). Sepsis in aged mice was induced by cecal ligation and puncture. The expression of TREM-2 was evaluated in septic patients and aged septic mice. Aged macrophages overexpressing TREM-2 and green fluorescent protein (GFP) were administered to aged septic mice after cecal ligation and puncture. Survival rate was monitored, and bacterial load and inflammatory mediators levels were evaluated. In vivo IL-23 function was blocked using appropriate monoclonal antibodies. RESULTS: The expression levels of TREM-2 were downregulated in both aged septic patients and aged septic mice. The administration of TREM-2-overexpressing macrophages significantly prolonged survival and alleviated organ injury in the aged septic mice. The protective effect did not affect host bacterial burden, but markedly inhibited the host IL-17A response, as determined by a multiplex cytokine assay. Screening the expression of IL-17A-related activating factors revealed that the IL-23 level in TREM-2-overexpressing macrophages was significantly lower than that in GFP-expressing macrophages. Blocking IL-23 after the administration of GFP-expressing macrophages protected aged mice against sepsis. CONCLUSIONS: TREM-2 prolonged survival of aged mice from sepsis by finely modulating the IL-23/IL-17A immune pathway. These results provide previously unidentified mechanistic insight into immune regulation by TREM-2 and new therapeutic targets in sepsis upon aging.

Airway Epithelial Hepcidin Coordinates Lung Macrophages and Immunity Against Bacterial Pneumonia.

BACKGROUND: Hepcidin is a liver-derived master regulator of iron metabolism through its molecular target ferroportin, the only known mammalian iron exporter. Accumulated evidence has shown the important roles of hepatic hepcidin in host defense and infections. Hepcidin is also expressed by airway epithelial cells. However, the function of epithelial hepcidin during bacterial pneumonia remains unknown. METHODS: Pneumonia was induced in hepcidin-1-deficient and wild-type mice using the most common bacterial agents, and the effects of hepcidin on survival, bacterial burden, iron status, and macrophage phagocytosis after bacterial pneumonia were assessed. RESULTS: Hepcidin levels decreased in airway epithelium during common pneumonia, while lung macrophage-derived ferroportin levels and pulmonary iron concentrations increased. Lack of hepcidin in the airway epithelium worsened the outcomes of pneumonia. Manipulation of hepcidin level in the airway epithelium in mice with macrophage-specific ferroportin deletion did not affect the progress of pneumonia. Increased pulmonary iron concentration not only facilitated bacterial growth but also led to the defective phagocytic function of lung macrophages via activation of RhoA GTPase through oxidation of RhoGDI. Furthermore, enhancing the hepcidin level in the airway epithelium rescued mice from lethal bacterial pneumonia. CONCLUSIONS: These findings identify an uncharacterized important role of airway epithelial hepcidin in protection against bacterial pneumonia and provide the basis for novel alternative therapeutic strategies for combatting bacterial pneumonia in future translational research.