Screening of CPT1A-Targeting Lipid Metabolism Modulators Using Mitochondrial Membrane Chromatography.

Carnitine palmitoyltransferase 1A (CPT1A), which resides on the mitochondrial outer membrane, serves as the rate-limiting enzyme of fatty acid ß-oxidation. Identifying the compounds targeting CPT1A warrants a promising candidate for modulating lipid metabolism. In this study, we developed a CPT1A-overexpressed mitochondrial membrane chromatography (MMC) to screen the compounds with affinity for CPT1A. Cells overexpressing CPT1A were cultured, and subsequently, their mitochondrial membrane was isolated and immobilized on amino-silica gel cross-linked by glutaraldehyde. After packing the mitochondrial membrane column, retention components of MMC were performed with LC/MS, whose analytic peaks provided structural information on compounds that might interact with mitochondrial membrane proteins. With the newly developed MMC-LC/MS approach, several Chinese traditional medicine extracts, such as Scutellariae Radix and Polygoni Cuspidati Rhizoma et Radix (PCRR), were analyzed. Five noteworthy compounds, baicalin, baicalein, wogonoside, wogonin, and resveratrol, were identified as enhancers of CPT1A enzyme activity, with resveratrol being a new agonist for CPT1A. The study suggests that MMC serves as a reliable screening system for efficiently identifying modulators targeting CPT1A from complex extracts.

EPRIM: An approach of identifying cancer immune-related epigenetic regulators.

Epigenetic regulation contributes to the dysregulation of gene expression involved in cancer biology. Nevertheless, the roles of epigenetic regulators (ERs) in tumor immunity and immune response remain basically unclear. Here, we developed the epigenetic regulator in immunology (EPRIM) approach to identify immune-related ERs and comprehensively dissected the ER regulation in tumor immune response across 33 cancers. The identified immune-related ERs were related to immune infiltration and could stratify cancer patients into two risk groups in multiple independent datasets. These patient groups were characterized by distinct immune functions, immune infiltrates, driver gene mutations, and prognoses. Furthermore, we constructed an immune ER-based signature and highlighted its potential utility in predicting clinical benefit from immunotherapy and selecting therapeutic agents. Taken together, our identification and evaluation of immune-related ERs highlight the usefulness of EPRIM for the understanding of ERs in immune regulation and the clinical relevance in evaluation of cancer patient prognosis and response to immune checkpoint blockade therapy.

The clinical value of Aspergillus-specific IgG antibody test in the diagnosis of nonneutropenic invasive pulmonary aspergillosis.

OBJECTIVES: Aspergillus-specific IgG antibody (Asp IgG) has been successfully applied in the diagnosis of chronic pulmonary aspergillosis. We explored its value in nonneutropenic invasive pulmonary aspergillosis (IPA) by a multicenter, prospective, and controlled study. METHODS: We enrolled 372 clinically suspected nonneutropenic patients with IPA from February 2015 to August 2022. After excluding 4 cases with Aspergillus colonization, the remaining 368 cases were finally confirmed as patients with IPA (n = 99), or non-IPA patients (n = 269) consisting of community-acquired pneumonia (n = 206), tuberculosis (n = 22), nontuberculous mycobacteria (n = 5), lung abscess (n = 6), or noninfectious diseases (n = 30). Asp IgG in plasma samples was tested by enzyme-linked immunosorbent assay. RESULTS: At cut-off value of ≥80 AU/mL, Asp IgG had much higher sensitivity (59.6% vs. 19.2%, p < 0.0001), but lower specificity (77.0% vs. 96.3%, p < 0.0001) than serum galactomannan (GM) (cut-off value of ≥1.0), and similar sensitivity (59.6% vs. 55.6%, p = 0.611) but lower specificity (77.0% vs. 91.2%, p = 0.001) than bronchoalveolar lavage fluid (BALF) GM (cut-off value of ≥1.0), respectively. Combination diagnosis of either positive for Asp IgG or BALF GM had higher sensitivity (81.0% vs. 55.6%, p = 0.002), but lower specificity (75.2% vs. 91.2%, p = 0.001) than BALF GM alone. The receiver operating characteristic curve showed that Asp IgG had an optimal diagnostic value when the cut-off value was 56.6 AU/ml, and the sensitivity and specificity were 77.8% and 63.9%, respectively. DISCUSSIONS: The diagnostic value of Asp IgG for IPA is superior to serum GM, and a little inferior to BALF GM in nonneutropenic patients with IPA. Considering the convenience of taking blood samples, it is a good screening and diagnostic method for nonneutropenic patients with IPA, especially for those who cannot bear invasive procedures.

Assembly of Guanine Crystals as a Low-Polarizing Broadband Multilayer Reflector in a Spider, Phoroncidia rubroargentea.

The diminishing of the polarization effect is important in the applications of dielectric multilayer reflectors in many optical systems, such as low-loss broadband waveguides, optical fibers, and LEDs. Low-polarizing broadband reflections were identified from birefringent-guanine-crystal-based multilayer reflectors in the skins of some fish. Previous models for these intriguing natural optical phenomena suggested the combined action of two populations of guanine crystals with an orthogonal low-refractive-index optic axis. Here we report a novel realization of polarization-insensitive broadband reflectivity in a spider, Phoroncidia rubroargentea, based solely on the type of guanine crystals with the low-refractive-index optic axis normal to the crystal plates. We examined the three-dimensional structure of the guanine assembly in the spider and performed finite-difference time-domain (FDTD) optical modeling of the guanine-based multilayer reflector. Comparative modeling studies reveal that the biological selection of the guanine crystal type and specific spatial arrangement work synergistically to optimize the polarization-insensitive broadband reflection. This study demonstrates the importance of both crystallographic characteristics and 3D arrangement of guanine crystals in understanding relevant natural optical effects and also provides new insights into similar broadband, low-polarizing reflections in biological optical systems. Learning from relevant biofunctional assembly of guanine crystals could promote the bioinspired design of nonpolarizing dielectric multilayer reflectors.

NLRP3, NLRC4 and NLRC5 Gene Polymorphisms Associate with Susceptibility of Pulmonary Aspergillosis in Non-Neutropenic Patients.

BACKGROUND: Non-neutropenic pulmonary aspergillosis is one of the most common and serious fungal infections. Previous studies have shown that single nucleotide polymorphisms (SNPs) of pattern recognition receptors genes are associated with susceptibility to aspergillosis. NOD-like receptors (NLRs) play an important role in the immunological response against fungal infection. In this study, we investigated the relationship between polymorphisms of three NLRs and susceptibility to pulmonary aspergillosis disease in non-neutropenic patients. METHODS: We included 73 patients with proven pulmonary aspergillosis and 103 healthy controls. A total of sixteen SNPs in the NLRP3, NLRC4, and NLRC5 genes were detected by PCR-direct sequencing. Then, we evaluated the association between these polymorphisms and susceptibility to aspergillosis. RESULTS: Fifteen SNPs were consistent with Hardy-Weinberg equilibrium except for NLRP3 rs7525979. A total of eight SNPs (NLRP3 rs3806265, NLRC4 rs212704 and NLRC5 rs1684579, rs12598522, rs3995817, rs3995818, rs34531240, rs28438857) were observed an association with susceptibility of pulmonary aspergillosis. The CC homozygote of NLRP3 rs3806265, TT homozygote of NLRC5 rs1684579 and T allele of NLRC5 rs12598522 were associated with a higher risk of aspergillosis while TT homozygote of NLRC4 rs212704 was associated with a lower risk of aspergillosis. Especially in the invasive pulmonary aspergillosis subgroup, the TT homozygote of NLRC5 rs1684579 and rs3995817, the CC homozygote of NLRC5 rs34531240 and rs28438857, GG homozygote of NLRC5 rs3995818, the C allele and CC homozygote of NLRP3 rs3806265 were associated with higher susceptibility. CONCLUSIONS: This study showed an association between polymorphisms of NLRP3, NLRC4, and NLRC5 and susceptibility to pulmonary aspergillosis for the first time. Further investigations in larger populations are needed, and functional studies are also required to investigate the function of these NLRs in aspergillosis, as well as other fungal infection diseases.

Mosaic composition of RIP1-RIP3 signalling hub and its role in regulating cell death.

RIP1 and RIP3, cell death mediators, form fibrous amyloids. How RIP1/RIP3 amyloidal oligomers assemble functional necrosomes and control cell death is largely unknown. Here we use super-resolution microscopy to directly visualize cellular necrosomes as mosaics of RIP1 and RIP3 oligomers. The small (initial) mosaic complexes are round, and the large mosaics are in a rod shape. RIP3 oligomers with sizes of tetramer or above are the domains in mosaics that allow MLKL, recruited by phosphorylated RIP3, to oligomerize for necroptosis. Unexpectedly, RIP1 autophosphorylation not only controls the ordered oligomerization of RIP1 but also is required for RIP1-initiated RIP3 homo-oligomerization in correct organization, which is indispensable for the formation of functional rod-shaped mosaics. Similarly, apoptosis initiated by enzymatically defective RIP3 requires the formation of rod-shaped mosaics of RIP3 and RIP1 oligomers. The revealing of nanoscale architecture of necrosomes here innovates our understanding of the structural and organizational basis of this signalling hub in cell death.

CCAAT/enhancer binding protein (C/EBP) delta promotes the expression of PTX3 and macrophage phagocytosis during A. fumigatus infection.

Given the increasing incidence of pulmonary aspergillosis, it is important to understand the natural defense mechanisms by which the body can kill Aspergillus fumigatus conidia. Pentraxin 3 (PTX3) plays a nonredundant role in resistance to A. fumigatus. Here, we found that the key predicted PTX3 transcription factor, CCAAT/enhancer-binding protein δ (CEBPD), was up-regulated during A. fumigatus conidia infection. Functionally, CEBPD significantly promoted the expression of PTX3 and the phagocytic ability of macrophages. Mechanistically, CEBPD activated the PTX3 by directly binding to the promoter region of the PTX3 gene. We also showed that the RNA-binding protein human antigen R promoted CEBPD expression. These findings provide new insights into the crucial role of CEBPD in the phagocytosis of A. fumigatus conidia by macrophages and highlight this protein as a potential therapeutic target for invasive pulmonary aspergillosis.

Identification and Validation of CYBB, CD86, and C3AR1 as the Key Genes Related to Macrophage Infiltration of Gastric Cancer.

Gastric cancer (GC) is rampant around the world. Most of the GC cases are detected in advanced stages with poor prognosis. The identification of marker genes for early diagnosis is of great significance. Studying the tumor environment is helpful to acknowledge the process of tumorigenesis, development, and metastasis. Twenty-two kinds of immune cells were calculated by CIBERSORT from Gene Expression Omnibus (GEO) database. Subsequently, higher infiltration of macrophages M0 was discovered in GC compared with normal tissues. WGCNA was utilized to construct the network and then identify key modules and genes related to macrophages in TCGA. Finally, 18 hub genes were verified. In the PPI bar chart, the top 3 genes were chosen as hub genes involved in most pathways. On the TIMER and THPA websites, it is verified that the expression levels of CYBB, CD86, and C3AR1 genes in tumor tissues were higher than those in normal tissues. These genes may work as biomarkers or targets for accurate diagnosis and treatment of GC in the future. Our findings may be a new strategy for the treatment of GC.

Quantifying the optimal strategy of population control of quorum sensing network in Escherichia coli.

Biological functions of bacteria can be regulated by monitoring their own population density induced by the quorum sensing system. However, quantitative insight into the system's dynamics and regulatory mechanism remain challenging. Here, we construct a comprehensive mathematical model of the synthetic quorum sensing circuit that controls population density in Escherichia coli. Simulations agree well with experimental results obtained under different ribosome-binding site (RBS) efficiencies. We present a quantitative description of the component dynamics and show how the components respond to isopropyl-ß-D-1-thiogalactopyranoside (IPTG) induction. The optimal IPTG-induction range for efficiently controlling population density is quantified. The controllable area of population density by acyl-homoserine lactone (AHL) permeability is quantified as well, indicating that high AHL permeability should be treated with a high dose of IPTG, while low AHL permeability should be induced with low dose for efficiently controlling. Unexpectedly, an oscillatory behavior of the growth curve is observed with proper RBS-binding strengths and the oscillation is greatly restricted by the bacterial death induced by toxic metabolic by-products. Moreover, we identify that the mechanism underlying the emergence of oscillation is determined by the negative feedback loop structure within the signaling. Bifurcation analysis and landscape theory are further employed to study the stochastic dynamic and global stability of the system, revealing two faces of toxic metabolic by-products in controlling oscillatory behavior. Overall, our study presents a quantitative basis for understanding and new insights into the control mechanism of quorum sensing system, providing possible clues to guide the development of more rational control strategy.

Microscopic origins of the crystallographically preferred growth in evaporation-induced colloidal crystals.

Unlike crystalline atomic and ionic solids, texture development due to crystallographically preferred growth in colloidal crystals is less studied. Here we investigate the underlying mechanisms of the texture evolution in an evaporation-induced colloidal assembly process through experiments, modeling, and theoretical analysis. In this widely used approach to obtain large-area colloidal crystals, the colloidal particles are driven to the meniscus via the evaporation of a solvent or matrix precursor solution where they close-pack to form a face-centered cubic colloidal assembly. Via two-dimensional large-area crystallographic mapping, we show that the initial crystal orientation is dominated by the interaction of particles with the meniscus, resulting in the expected coalignment of the close-packed direction with the local meniscus geometry. By combining with crystal structure analysis at a single-particle level, we further reveal that, at the later stage of self-assembly, however, the colloidal crystal undergoes a gradual rotation facilitated by geometrically necessary dislocations (GNDs) and achieves a large-area uniform crystallographic orientation with the close-packed direction perpendicular to the meniscus and parallel to the growth direction. Classical slip analysis, finite element-based mechanical simulation, computational colloidal assembly modeling, and continuum theory unequivocally show that these GNDs result from the tensile stress field along the meniscus direction due to the constrained shrinkage of the colloidal crystal during drying. The generation of GNDs with specific slip systems within individual grains leads to crystallographic rotation to accommodate the mechanical stress. The mechanistic understanding reported here can be utilized to control crystallographic features of colloidal assemblies, and may provide further insights into crystallographically preferred growth in synthetic, biological, and geological crystals.

A risk-predictive model for invasive pulmonary aspergillosis in patients with acute exacerbation of chronic obstructive pulmonary disease.

OBJECTIVES: Invasive pulmonary aspergillosis (IPA) is increasingly reported in chronic obstructive pulmonary disease (COPD) patients. These patients often have poor clinical outcomes. Early recognition of IPA in COPD is always challenging. We aimed to develop and validate a risk model using readily available clinical parameters to predict IPA for acute exacerbation of COPD (AECOPD) patients. METHODS: We performed a retrospective cohort study. AECOPD patients who were admitted to Jinling Hospital between January 2012 and December 2017 were included. 880 AECOPD patients were randomly divided into the training set (70%, n = 616) and validation set (30%, n = 264). A nomogram model was developed using multivariate logistic regression from training set. The discrimination and calibration of model were validated internally. Decision curve analyses assessed the clinical utility of the nomogram. RESULTS: The incidence of IPA in hospitalized AECOPD patients was 9.6% in the training set (59 cases of IPA) and 9.1% in the validation set (24 cases of IPA), respectively. The nomogram model consisted of independent factors associated with IPA included lung function GOLD III-IV, use of broad-spectrum antibiotic over 10 days in the last month, oral or intravenous corticosteroids (prednisone) over 265 mg in the last 3 months and serum albumin < 30 g/L. The model performed good discrimination and calibration in validation set (c-statistic, 0.79 [95%CI 0.68-0.90]). The 95%CI region of calibration belt did not cross the 45-degree diagonal bisector line (P = 0.887). CONCLUSION: The simple risk predictive model for earlier recognition of IPA is useful in hospitalized AECOPD patients.

Clinical features and prognostic analysis of patients with Aspergillus isolation during acute exacerbation of chronic obstructive pulmonary disease.

BACKGROUND: Lower respiratory tract (LRT) specimen culture is widely performed for the identification of Aspergillus. We investigated the clinical features and prognosis of patients with Aspergillus isolation from LRT specimens during acute exacerbation of chronic obstructive pulmonary disease (AECOPD). METHODS: This is a 6-year single-center, real-world study. 75 cases out of 1131 hospitalized AECOPD patients were positive for Aspergillus. These patients were carefully evaluated and finally diagnosed of pulmonary aspergillosis (PA, 60 cases, 80%) or colonization (15 cases, 20%). Comparisons of clinical data were performed between these two groups. A cox regression model was used to confirm prognostic factors of Aspergillus infection. RESULTS: The PA group had worse lung function and higher rates of systemic corticosteroid use and broad-spectrum antibiotic use before admission than the colonization group. The PA group had significantly higher in-hospital mortality and 180-day mortality than the colonization group (45% (27/60) vs. 0% (0/15), p = 0.001, and 52.5% (31/59) vs. 6.7% (1/15), p < 0.001, respectively). By multivariable analysis among Aspergillus infection patients, antifungal therapy (HR 0.383, 95% CI 0.163-0.899, p = 0.027) was associated with improved survival, whereas accumulated dose of systemic steroids > 700 mg (HR 2.452, 95% CI 1.134-5.300, p = 0.023) and respiratory failure at admission (HR 5.983, 95% CI 2.487-14.397, p < 0.001) were independently associated with increased mortality. Significant survival differential was observed among PA patients without antifungals and antifungals initiated before and after Aspergillus positive culture (p = 0.001). CONCLUSIONS: Aspergillus isolation in hospitalized AECOPD patients largely indicated PA. AECOPD patients with PA had worse prognosis than those with Aspergillus colonization. Empirical antifungal therapy is warranted to improve the prognosis for Aspergillus infection.

Epidemiological Trends of Coronavirus Disease 2019 in China.

Background: The Coronavirus Disease 2019 (COVID-19) epidemic broke out in Wuhan, China, and it spread rapidly. Since January 23, 2020, China has launched a series of unusual and strict measures, including the lockdown of Wuhan city to contain this highly contagious disease. We collected the epidemiological data to analyze the trend of this epidemic in China. Methods: We closely tracked the Chinese and global official websites to collect the epidemiological information about COVID-19. The number of total and daily new confirmed cases of COVID-19 in China was presented to illustrate the trend of this epidemic. Results: On January 23, 2020, 835 confirmed COVID-19 cases were reported in China. On February 6, 2020, there were 31,211 cases. By February 20, 2020, the number reached as high as 75,993. Most cases were distributed in and around Wuhan, Hubei province. Since January 23, 2020, the number of daily new cases in China except Hubei province reached a peak of 890 on the eleventh day and then it declined to a low level of 34 within two full-length incubation periods (28 days), and the number of daily new cases in Hubei also started to decrease on the twelfth day, from 3,156 on February 4, 2020 to 955 on February 15, 2020. Conclusion: The COVID-19 epidemic has been primarily contained in China. The battle against this epidemic in China has provided valuable experiences for the rest of the world. Strict measures need to be taken as earlier as possible to prevent its spread.

Anti-cross-correlation between the adjacent open and closed durations of Markovian channels.

We show that a non-Markovian behavior can appear in a type of Markovian multimeric channel. Such a channel consists of N independent subunits, and each subunit has at least one open state and more than one closed state. Suppose the open state of the channel is defined as M out of N subunits in the open state with N>M>0. We show that, although the gating dynamics for each subunit between open and closed states is Markovian, the channel can show a memory behavior of weak anti-cross-correlation between the adjacent open and closed durations. Our study indicates that a non-Markovian binary time series can be obtained from a linear superposition of some independent channel subunits with Markovian gating dynamics.

Homologous genes of epidermal patterning factor regulate stomatal development in rice.

Stomata are microscopic pores on the surface of leaves through which water as vapor passes to the atmosphere and CO2 uptake for the photosynthesis. The signaling peptides of the epidermal patterning factor (EPF) family regulate stomatal development and density in Arabidopsis. Several putative homologs of EPF/EPFL exist in rice genome. To understand their possible involvement in stomatal formation, in this study we generated a series of transgenic lines including reporter promoter fusions, down-regulation and overexpression and demonstrated drastic differences in stomatal densities between different genotypes, as elevated expression of OsEPF1 or OsEPF2 greatly reduced stomatal density in rice, whereas ectopic overexpression of either OsEPF1 or OsEPF2 significantly decreased the high stomatal frequency of both mutant lines of epf2 and epf1epf2 Arabidopsis. Conversely, knocking down OsEPFL9 transcription conferred transgenic plants with fewer stomata than WT in rice, whereas overexpressing rice OsEPFL9 gene could cause excessive production of stomata in Arabidopsis. In conclusion, homologs of EPF/EPFL regulate stomatal development in a generally highly conserved way yet there exist function distinctions between dicot and monocot plants.