DeepEnzyme: a robust deep learning model for improved enzyme turnover number prediction by utilizing features of protein 3D-structures.

Turnover numbers (kcat), which indicate an enzyme's catalytic efficiency, have a wide range of applications in fields including protein engineering and synthetic biology. Experimentally measuring the enzymes' kcat is always time-consuming. Recently, the prediction of kcat using deep learning models has mitigated this problem. However, the accuracy and robustness in kcat prediction still needs to be improved significantly, particularly when dealing with enzymes with low sequence similarity compared to those within the training dataset. Herein, we present DeepEnzyme, a cutting-edge deep learning model that combines the most recent Transformer and Graph Convolutional Network (GCN) to capture the information of both the sequence and 3D-structure of a protein. To improve the prediction accuracy, DeepEnzyme was trained by leveraging the integrated features from both sequences and 3D-structures. Consequently, DeepEnzyme exhibits remarkable robustness when processing enzymes with low sequence similarity compared to those in the training dataset by utilizing additional features from high-quality protein 3D-structures. DeepEnzyme also makes it possible to evaluate how point mutations affect the catalytic activity of the enzyme, which helps identify residue sites that are crucial for the catalytic function. In summary, DeepEnzyme represents a pioneering effort in predicting enzymes' kcat values with improved accuracy and robustness compared to previous algorithms. This advancement will significantly contribute to our comprehension of enzyme function and its evolutionary patterns across species.

Efficient deep-blue electroluminescence from Ce-based metal halide.

Rare earth ions with d-f transitions (Ce3+, Eu2+) have emerged as promising candidates for electroluminescence applications due to their abundant emission spectra, high light conversion efficiency, and excellent stability. However, directly injecting charge into 4f orbitals remains a significant challenge, resulting in unsatisfied external quantum efficiency and high operating voltage in rare earth light-emitting diodes. Herein, we propose a scheme to solve the difficulty by utilizing the energy transfer process. X-ray photoelectron spectroscopy and transient absorption spectra suggest that the Cs3CeI6 luminescence process is primarily driven by the energy transfer from the I2-based self-trapped exciton to the Ce-based Frenkel exciton. Furthermore, energy transfer efficiency is largely improved by enhancing the spectra overlap between the self-trapped exciton emission and the Ce-based Frenkel exciton excitation. When implemented as an active layer in light-emitting diodes, they show the maximum brightness and external quantum efficiency of 1073 cd m-2 and 7.9%, respectively.

Development and evaluation of 4WSS electric-driven chassis for high-clearance sprayer.

Introduction: The high clearance sprayer with conventional steering mechanisms, as an intelligent spraying machine, is frequently stuck or broken in muddy fields due to the excessive torque load. Methods: A Four-Wheel Self-Steering (4WSS) electric-driven chassis with a smaller turning radius and better passability is developed to handle complex agricultural terrains. The 4WSS chassis is mainly composed of two custom-designed steering bridges and four in-wheel drive motors. It can achieve steering and driving forward simultaneously through coordinate differential speed control of drive motors, saving a set of dedicated servo steering systems and requiring less torque during steering compared to conventional structures. A kinematic model depicting the speed relationships between four wheels is established via geometric analysis, and a Speed Distribution Controller (SDC) is designed to accomplish locomotion objectives. Results: Experimental results demonstrate the effectiveness of the new prototype 4WSS chassis system in tracking speed and steering angle. Compared to conventional agricultural chassis, the 4WSS chassis has a smaller turning radius of 2,877 mm. Discussion: The 4WSS chassis exhibits superior performance in typical field conditions, including muddy terrain, deep gullies, and ridges.

Impact of Corticosteroids on the Proportions of Circulating Tfh Cell Subsets in Patients With Systemic Lupus Erythematous.

Objectives: This study aimed to analyze the distribution of T follicular helper (Tfh) cells in lupus patients, and the effects of steroids on circulating Tfh cells. Methods: Circulating Tfh cell subsets were defined by multicolor flow cytometry as Tfh17, Tfh2 or Tfh1 subpopulations of CXCR5+CD45RA-CD4+ T cells in the peripheral blood of SLE patients and healthy controls. To test the effects of corticosteroid on Tfh cells, PBMC harvested from both SLE and healthy controls were cocultured with dexamethasone, and then analyzed by Flow cytometry. Results: The proportion of Tfh17 cells in SLE patients was increased significantly compared with healthy controls. Additionally, patients with an active disease had reduced Tfh1 subsets than those with an inactive disease and healthy controls. The frequency of Tfh2 cells was associated with the proportion of circulating plasmablasts and the amount of anti-dsDNA. Dexamethasone reduced the percentage of Tfh2 cells while increased the proportion of Tfh17 subset in gated CXCR5+CD45RA-CD4+ T cells. Conclusion: Our study investigated the distribution of circulating Tfh subsets in lupus patients. Corticosteroids treatment not only down-regulated the proportion of circulating Tfh cells, but also altered the distribution of Tfh subsets in vivo and in vitro.

Overexpression of TRAF4 promotes lung cancer growth and EGFR-dependent phosphorylation of ERK5.

Tumor necrosis factor receptor-associated factor 4 (TRAF4) is overexpressed in a variety of carcinomas of different origins, but its role in tumorigenesis remains incompletely understood. Previous studies suggest that TRAF4 promotes epidermal growth factor receptor (EGFR) activation in non-small cell lung cancer (NSCLC). However, the downstream signaling pathway of TRAF4-mediated EGFR activation, as well as its effects on tumor cells, have not been fully elucidated. Here we report that TRAF4 overexpression is associated with increased activity of extracellular signal-regulated kinase 5 (ERK5) in NSCLC tissues. Activation of ERK5 was dependent on TRAF4-mediated EGFR activation, since inhibition of either TRAF4 or EGFR dramatically abolished phosphorylation of ERK5. Mechanistically, EGFR recruited mitogen-activated protein kinase kinase kinase 3 (MEKK3), an upstream kinase of ERK5, in a TRAF4-dependent manner. Thus, our data suggest that an EGFR-TRAF4-MEKK3-ERK5 axis promotes the proliferation of tumor cells, and this may be a potential target for therapeutic intervention of NSCLC.

IL-6 alters migration capacity of CD4+Foxp3+ regulatory T cells in systemic lupus erythematosus.

Regulatory T cells (Tregs) are impaired in human systemic lupus erythematosus (SLE) and involved in disease pathogenesis. However, the mechanisms responsible for the Treg dysfunction in SLE remain unclear. In this study, we aimed to investigate the chemotaxis of Treg response to inflammatory stimulation. Sixty two patients were enrolled, and chemokine receptors, including CCR4, CCR5, CCR6, CCR8 and CXCR3 on CD4+Foxp3+Tregs and non-Treg CD4 T cells, were analysed using FACS. The expression of CCR4 and CCR6 on Tregs of SLE patients decreased, while the expression of CCR4 on non-Treg CD4 T cells increased, as compared with those of age- and sex-matched healthy donors. In parallel, in SLE, the chemotactic capacity of non-Treg CD4 T cells response to CCR4 and CCR6 ligands dramatically increased, while that of Tregs significantly decreased. Moreover, we found that cytokines IL-6 and IL-10 positively and negatively modulate the expression of those receptors respectively. IL-6, the significantly increased cytokine in active SLE, dramatically elevated CCR4 and CCR6 expression on non-Treg CD4 T cells. However, as for Tregs, these cells produced more IL-10 than non-Treg CD4 T cells upon IL-6 stimulation, and these IL-10 led to the inhibition of CCR4 and CCR6. In sum, our data provided new evidence suggesting a functional deficiency of Tregs in SLE. It may suggest that those dysfunctional Tregs have less access to the inflammation locus to exert inhibitory capacity.

Surfactant protein-A inhibits thymic stromal lymphopoietin-mediated T follicular helper cell differentiation and IgE production in asthma.

Lung surfactant protein A (SP-A) is critical for immunomodulation. Thymic stromal lymphopoietin (TSLP)-activated dendritic cells (DCs) drive T follicular helper (Tfh) cells differentiation in allergic asthma. We employed wild-type (WT) and SP-A-/- mice injected with TSLP and ovalbumin (OVA)-activated DCs and challenged with OVA. Compared with WT mice, we showed that allergic inflammation was dramatically increased in SP-A-/- mice. In parallel, both IL-4-producing CD45RA-CXCR5+PD-1+CD4+ cells (Tfh2) and IgE were markedly increased in SP-A-/- mice. Further study showed that SP-A prohibited TSLP activated-DCs from expressing OX40L. When we blocked OX40L-OX40 and IL-4R signaling, the differentiation of Tfh2 and IgE responses in SP-A-/- mice was significantly inhibited. In severe asthma patients, SP-A is dysfunctional in modulating the TSLP-DCs-mediated differentiation of Tfh cells. This study suggests that SP-A acts as a modulator of Tfh differentiation and IgE generation in asthma.

Dipotassium glycyrrhizinate relieves leptospira-induced nephritis in vitro and in vivo.

Chronic leptospirosis usually occurs during sublethal doses infection of susceptible animal and reservoir host, which typical symptom is interstitial nephritis, and leptospira urine, contaminating the environment and threatening other susceptible animals and humans. Dipotassium glycyrrhizinate (DG) is a replacement for glycyrrhizic acid, which exhibits anti-inflammation, immunomodulation effects. This study is to investigate whether DG relieves leptospira-induced nephritis. In vitro, DG inhibited the leptospira-induced transcription levels of IL-1ß, IL-6, TNF-α, RANTES, MCP-1 and iNOS, and protein levels of IL-1ß and TNF-α, and downregulated NF-κB and MAPK pathway in TCMK-1 cells. In vivo, DG attenuated the kidney histopathological change and downregulated the expression of IL-1ß and TNF-α, as well as reduced kidney leptospiral burden. In summary, DG alleviated leptospira-induced inflammation through inhibitory NF-κB and MAPK pathway, and DG decreased the renal colonization of leptospires in mice.

C. elegans neurons have functional dendritic spines.

Dendritic spines are specialized postsynaptic structures that transduce presynaptic signals, are regulated by neural activity and correlated with learning and memory. Most studies of spine function have focused on the mammalian nervous system. However, spine-like protrusions have been reported in C. elegans (Philbrook et al., 2018), suggesting that the experimental advantages of smaller model organisms could be exploited to study the biology of dendritic spines. Here, we used super-resolution microscopy, electron microscopy, live-cell imaging and genetics to show that C. elegans motor neurons have functional dendritic spines that: (1) are structurally defined by a dynamic actin cytoskeleton; (2) appose presynaptic dense projections; (3) localize ER and ribosomes; (4) display calcium transients triggered by presynaptic activity and propagated by internal Ca++ stores; (5) respond to activity-dependent signals that regulate spine density. These studies provide a solid foundation for a new experimental paradigm that exploits the power of C. elegans genetics and live-cell imaging for fundamental studies of dendritic spine morphogenesis and function.

Ginkgo Biloba Extract Inhibits Metastasis and ERK/Nuclear Factor kappa B (NF-κB) Signaling Pathway in Gastric Cancer.

BACKGROUND Ginkgo biloba extract (EGb761), a standard extract of the Chinese traditional medicine Ginkgo biloba, plays an anti-tumor role in various cancers. However, whether EGb761 is involved in the invasion and metastasis of gastric cancer remains unclear. MATERIAL AND METHODS In the current study, cell viability assay, Western blotting, wound-healing assay, Transwell invasion assay, and orthotopic transplantation model were performed to explore the effects of EGb761 on gastric cancer. RESULTS In vitro, the results showed that EGb761 suppressed the proliferation of gastric cancer cells in a dose-dependent manner. Furthermore, the migration and invasiveness were weakened and the protein levels of p-ERK1/2, NF-kappaB P65, NF-kappaB p-P65, and MMP2 were decreased by EGb761 or U0126 (an inhibitor of ERK signaling pathway) exposure in gastric cancer cells. Moreover, the combined treatment with EGb761 and U0126 significantly inhibited ERK, NF-kappaB signaling pathway, and the expression of MMP2 than those of single drug. In vivo, EGb761 inhibited the tumor growth and hepatic metastasis of gastric cancer in the mouse model. Results of immunohistochemistry indicated that the expression of ERK1/2, NF-kappaB P65 and MMP2 were decreased by EGb761 in the tumor tissues. CONCLUSIONS EGb761 plays a vital role in the suppression of metastasis and ERK/NF-kappaB signaling pathway in gastric cancer.

NATF (Native and Tissue-Specific Fluorescence): A Strategy for Bright, Tissue-Specific GFP Labeling of Native Proteins in Caenorhabditis elegans.

GFP labeling by genome editing can reveal the authentic location of a native protein, but is frequently hampered by weak GFP signals and broad expression across a range of tissues that may obscure cell-specific localization. To overcome these problems, we engineered a Native And Tissue-specific Fluorescence (NATF) strategy that combines genome editing and split-GFP to yield bright, cell-specific protein labeling. We use clustered regularly interspaced short palindromic repeats CRISPR/Cas9 to insert a tandem array of seven copies of the GFP11 ß-strand (gfp11x7 ) at the genomic locus of each target protein. The resultant gfp11x7 knock-in strain is then crossed with separate reporter lines that express the complementing split-GFP fragment (gfp1-10) in specific cell types, thus affording tissue-specific labeling of the target protein at its native level. We show that NATF reveals the otherwise undetectable intracellular location of the immunoglobulin protein OIG-1 and demarcates the receptor auxiliary protein LEV-10 at cell-specific synaptic domains in the Caenorhabditis elegans nervous system.

Sphingosine kinase 1 promotes the metastasis of colorectal cancer by inducing the epithelial­mesenchymal transition mediated by the FAK/AKT/MMPs axis.

It was demonstrated that Sphingosine kinase 1 (SphK1) promotes tumor progression and confers the malignancy phenotype of colorectal cancer by activating the focal adhesion kinase (FAK) pathway. However, further clarification is required to determine if SphK1 promotes the metastasis of colorectal cancer by inducing epithelial­mesenchymal transition (EMT), and its mechanisms have not been fully elucidated. Immunohistochemistry staining was used to detect protein expression in normal colonic mucosa tissues and colorectal cancer tissues. Cells were transfected to overexpress SphK1, downregulate SphK1 or downregulate FAK. An MTT assay was used to detect the drug toxicity to cells. Transwell and wound healing assays were used to detect cell migration ability. Reverse transcription­polymerase chain reaction and western blot analysis were used to detect the expression of mRNA and protein, respectively. Scanning electron microscopy was used to observe the microvilli and pseudopodia of the cells. The analysis of protein expression in 114 human colorectal cancer tissues demonstrated that the expressions of SphK1, FAK, phosphorylated (p)­FAK, E­cadherin and vimentin were associated with the metastasis of colorectal cancer. Furthermore, the patients with colorectal cancer with SphK1­positive cancer demonstrated poorer prognosis compared with SphK1­negative cancer. FAK knockdown and SphK1 knockdown of human colon cancer RKO cells inhibited the EMT and migrational potency, along with the expression of p­FAK, p­protein kinase B (AKT) and matrix metalloproteinase (MMP)2/9. In contrast, SphK1 overexpression promoted EMT, migrational potency, and the expression of p­FAK, p­AKT and MMP2/9 in HT29 cells. Additionally, the EMT and migrational potency of SphK1­overexpressing HT29 cells was suppressed by a FAK inhibitor, and the expression of p­FAK, p­AKT and MMP2/9 was suppressed by blocking the FAK pathway. In conclusion, SphK1 promoted the migration and metastasis of colon cancer by inducing EMT mediated by the FAK/AKT/MMPs axis.

Double-balloon enteroscopy in diagnosis of small intestinal disease / 中国内镜杂志

Objective To explore the clinical value of double-balloon enterocopy (DBE) in diagnosis of small intestinal diseases. Methods The clinical and endoscope image data of 231 patients with suspected small bowel disease who underwent DBE from January 2008 to May 2016 were analyzed. Result 231 patients received 257 times of DBE examination, 112 of them were performed by oral and 93 by anal route, 26 patients were underwent by both approaches. The detection rate of intestine diseases was 64.9% (150/231), include 33 cases (14.3%) of nonspecific enteritis, 27 cases (11.7%) of crohn's disease, 19 cases (8.2%) of ulcer, 13 cases (5.6%) of intestinal vascular malformation, 12 cases (5.2%) of small intestinal stromal tumor. The lesion detection rate in obscure abdominal pain and obscure gastrointestinal bleeding were 59.6% (62/104) and 67.0% (63/94). In all patients, there were 1 case of small bowel perforation, the remaining patients had no serious complications such as bleeding and perforation. Conclusion The positive detection rate of double-balloon enteroscopy examination is high, and the double-balloon enteroscopy examination is relatively safe. So, double-balloon enterscopy examination has high diagnostic value for detecting small intestine diseases.

Double-balloon enteroscopy in diagnosis of small intestinal disease / 中国内镜杂志

Objective To explore the clinical value of double-balloon enterocopy (DBE) in diagnosis of small intestinal diseases. Methods The clinical and endoscope image data of 231 patients with suspected small bowel disease who underwent DBE from January 2008 to May 2016 were analyzed. Result 231 patients received 257 times of DBE examination, 112 of them were performed by oral and 93 by anal route, 26 patients were underwent by both approaches. The detection rate of intestine diseases was 64.9% (150/231), include 33 cases (14.3%) of nonspecific enteritis, 27 cases (11.7%) of crohn's disease, 19 cases (8.2%) of ulcer, 13 cases (5.6%) of intestinal vascular malformation, 12 cases (5.2%) of small intestinal stromal tumor. The lesion detection rate in obscure abdominal pain and obscure gastrointestinal bleeding were 59.6% (62/104) and 67.0% (63/94). In all patients, there were 1 case of small bowel perforation, the remaining patients had no serious complications such as bleeding and perforation. Conclusion The positive detection rate of double-balloon enteroscopy examination is high, and the double-balloon enteroscopy examination is relatively safe. So, double-balloon enterscopy examination has high diagnostic value for detecting small intestine diseases.

Transcriptional Control of Synaptic Remodeling through Regulated Expression of an Immunoglobulin Superfamily Protein.

Neural circuits are actively remodeled during brain development, but the molecular mechanisms that trigger circuit refinement are poorly understood. Here, we describe a transcriptional program in C. elegans that regulates expression of an Ig domain protein, OIG-1, to control the timing of synaptic remodeling. DD GABAergic neurons reverse polarity during larval development by exchanging the locations of pre- and postsynaptic components. In newly born larvae, DDs receive cholinergic inputs in the dorsal nerve cord. These inputs are switched to the ventral side by the end of the first larval (L1) stage. VD class GABAergic neurons are generated in the late L1 and are postsynaptic to cholinergic neurons in the dorsal nerve cord but do not remodel. We investigated remodeling of the postsynaptic apparatus in DD and VD neurons using targeted expression of the acetylcholine receptor (AChR) subunit, ACR-12::GFP. We determined that OIG-1 antagonizes the relocation of ACR-12 from the dorsal side in L1 DD neurons. During the L1/L2 transition, OIG-1 is downregulated in DD neurons by the transcription factor IRX-1/Iroquois, allowing the repositioning of synaptic inputs to the ventral side. In VD class neurons, which normally do not remodel, the transcription factor UNC-55/COUP-TF turns off IRX-1, thus maintaining high levels of OIG-1 to block the removal of dorsally located ACR-12 receptors. OIG-1 is secreted from GABA neurons, but its anti-plasticity function is cell autonomous and may not require secretion. Our study provides a novel mechanism by which synaptic remodeling is set in motion through regulated expression of an Ig domain protein.

Newspaper coverage of tobacco issues: an analysis of print news in Chinese cities, 2008-2011.

OBJECTIVE: The purpose of this study was to determine to what extent Chinese media coverage of tobacco issues in 17 Chinese cities comprises messaging known to motivate healthy behaviour. METHODS: This study involved a content analysis of 4821 articles that contained at least one full paragraph focused on tobacco issues from newspapers published in cities that participated in the Tobacco-Free City-Gates Tobacco Control Project in China between 1 January 2008 and 30 June 2011. RESULTS: The number of tobacco-focused articles increased over the study period. The number of articles varied considerably among different newspapers and cities. Education, prevention and cessation programs (35%) were the most frequent theme. There was also considerable variation in the volume of coverage each month. News articles were the most frequent article type (70%). The majority of the articles (72%) were positive for tobacco control. There were significant differences between party newspapers and local newspapers in prominence, article type, slant and fear appeal. One quarter (n=729) of the articles mentioned the severity of tobacco use, while only 10% of the articles referred to susceptibility to the threat. CONCLUSIONS: The coverage of events was predominantly positive toward tobacco control. However, media reports could better support tobacco control efforts if they did a better job at provoking an emotional response to the harms of tobacco use and promoting a sense among smokers that they can succeed in quitting smoking.