Gibberellin promotes cambium reestablishment during secondary vascular tissue regeneration after girdling in an auxin-dependent manner in Populus.

Secondary vascular tissue (SVT) development and regeneration are regulated by phytohormones. In this study, we used an in vitro SVT regeneration system to demonstrate that gibberellin (GA) treatment significantly promotes auxin-induced cambium reestablishment. Altering GA content by overexpressing or knocking down ent-kaurene synthase (KS) affected secondary growth and SVT regeneration in poplar. The poplar DELLA gene GIBBERELLIC ACID INSENSITIVE (PtoGAI) is expressed in a specific pattern during secondary growth and cambium regeneration after girdling. Overexpression of PtoGAI disrupted poplar growth and inhibited cambium regeneration, and the inhibition of cambium regeneration could be partially restored by GA application. Further analysis of the PtaDR5:GUS transgenic plants, the localization of PIN-FORMED 1 (PIN1) and the expression of auxin-related genes found that an additional GA treatment could enhance the auxin response as well as the expression of PIN1, which mediates auxin transport during SVT regeneration. Taken together, these findings suggest that GA promotes cambium regeneration by stimulating auxin signal transduction.

Complexity of type IV collagens: from network assembly to function.

Collagens form complex networks in the extracellular space that provide structural support and signaling cues to cells. Network-forming type IV collagens are the key structural components of basement membranes. In this review, we discuss how the complexity of type IV collagen networks is established, focusing on collagen α chain selection in type IV collagen protomer and network formation; covalent crosslinking in type IV collagen network stabilization; and the differences between solid-state type IV collagen in the extracellular matrix and soluble type IV collagen fragments. We further discuss how complex type IV collagen networks exert their physiological and pathological functions through cell surface integrin and nonintegrin receptors.

A deep boosting based approach for capturing the sequence binding preferences of RNA-binding proteins from high-throughput CLIP-seq data.

Characterizing the binding behaviors of RNA-binding proteins (RBPs) is important for understanding their functional roles in gene expression regulation. However, current high-throughput experimental methods for identifying RBP targets, such as CLIP-seq and RNAcompete, usually suffer from the false negative issue. Here, we develop a deep boosting based machine learning approach, called DeBooster, to accurately model the binding sequence preferences and identify the corresponding binding targets of RBPs from CLIP-seq data. Comprehensive validation tests have shown that DeBooster can outperform other state-of-the-art approaches in RBP target prediction. In addition, we have demonstrated that DeBooster may provide new insights into understanding the regulatory functions of RBPs, including the binding effects of the RNA helicase MOV10 on mRNA degradation, the potentially different ADAR1 binding behaviors related to its editing activity, as well as the antagonizing effect of RBP binding on miRNA repression. Moreover, DeBooster may provide an effective index to investigate the effect of pathogenic mutations in RBP binding sites, especially those related to splicing events. We expect that DeBooster will be widely applied to analyze large-scale CLIP-seq experimental data and can provide a practically useful tool for novel biological discoveries in understanding the regulatory mechanisms of RBPs. The source code of DeBooster can be downloaded from http://github.com/dongfanghong/deepboost.

Topological localization of monomeric C-reactive protein determines proinflammatory endothelial cell responses.

The activation of endothelial cells (ECs) by monomeric C-reactive protein (mCRP) has been implicated in contributing to atherogenesis. However, the potent proinflammatory actions of mCRP on ECs in vitro appear to be incompatible with the atheroprotective effects of mCRP in a mouse model. Because mCRP is primarily generated within inflamed tissues and is rapidly cleared from the circulation, we tested whether these discrepancies can be explained by topological differences in response to mCRP within blood vessels. In a Transwell culture model, the addition of mCRP to apical (luminal), but not basolateral (abluminal), surfaces of intact human coronary artery EC monolayers evoked a significant up-regulation of MCP-1, IL-8, and IL-6. Such polarized stimulation of mCRP was observed consistently regardless of EC type or experimental conditions (e.g. culture of ECs on filters or extracellular matrix-coated surfaces). Accordingly, we detected enriched lipid raft microdomains, the major surface sensors for mCRP on ECs, in apical membranes, leading to the preferential apical binding of mCRP and activation of ECs through the polarized induction of the phospholipase C, p38 MAPK, and NF-κB signaling pathways. Furthermore, LPS and IL-1ß induction of EC activation also exhibited topological dependence, whereas TNF-α did not. Together, these results indicate that tissue-associated mCRP likely contributes little to EC activation. Hence, topological localization is an important, but often overlooked, factor that determines the contribution of mCRP and other proinflammatory mediators to chronic vascular inflammation.

Inhibition of macrophage polarization prohibits growth of human osteosarcoma.

Osteosarcoma is the most malignant bone tumor characterized by high local aggressiveness and poor therapeutic outcome. Tumor-associated macrophages (TAM) have been shown to participate in the development and progress of many types of cancer cells. However, whether TAM may play a role in the pathogenesis of osteosarcoma is largely unknown. In a mouse model of human osteosarcoma implantation, we showed that the recruited macrophages at the site of the implanted tumor were polarized to an M2 subtype (same as TAM) during the development and growth of the osteosarcoma. In a loss-of-function experiment, we deleted these TAM with a specific macrophage-eliminating liposome, which resulted in decreased tumor growth. Moreover, when the epidermal growth factor receptor (EGFR) in the implanted cancer cells was inhibited by shRNA, the tumor failed to grow in response to the recruited macrophages. Taken together, for the first time, we show that the growth of an osteosarcoma is EGFR signaling-dependent and TAM-mediated. Our data suggest that TAM and EGFR may be good targets for treating human osteosarcoma.

Joint Imbalance Adaptation for Radiology Report Generation.

Purpose: Radiology report generation, translating radiological images into precise and clinically relevant description, may face the data imbalance challenge - medical tokens appear less frequently than regular tokens; and normal entries are significantly more than abnormal ones. However, very few studies consider the imbalance issues, not even with conjugate imbalance factors. Methods: In this study, we propose a Joint Imbalance Adaptation (JIMA) model to promote task robustness by leveraging token and label imbalance. JIMA predicts entity distributions from images and generates reports based on these distributions and image features. We employ a hard-to-easy learning strategy that mitigates overfitting to frequent labels and tokens, thereby encouraging the model to focus more on rare labels and clinical tokens. Results: JIMA shows notable improvements (16.75% - 50.50% on average) across evaluation metrics on IU X-ray and MIMIC-CXR datasets. Our ablation analysis proves that JIMA's enhanced handling of infrequent tokens and abnormal labels counts the major contribution. Human evaluation and case study experiments further validate that JIMA can generate more clinically accurate reports. Conclusion: Data imbalance (e.g., infrequent tokens and abnormal labels) leads to the underperformance of radiology report generation. Our curriculum learning strategy successfully reduce data imbalance impacts by reducing overfitting on frequent patterns and underfitting on infrequent patterns. While data imbalance remains challenging, our approach opens new directions for the generation task.

Type IV collagen α5 chain promotes luminal breast cancer progression through c-Myc-driven glycolysis.

Cancer cell metabolism reprogramming is one of the hallmarks of cancer. Cancer cells preferentially utilize aerobic glycolysis, which is regulated by activated oncogenes and the tumor microenvironment. Extracellular matrix (ECM) in the tumor microenvironment, including the basement membranes (BMs), is dynamically remodeled. However, whether and how ECM regulates tumor glycolysis is largely unknown. We show that type IV collagens, components of BMs essential for the tissue integrity and proper function, are differentially expressed in breast cancer subtypes that α5 chain (α5(IV)) is preferentially expressed in the luminal-type breast cancer and is regulated by estrogen receptor-α. α5(IV) is indispensable for luminal breast cancer development. Ablation of α5(IV) significantly reduces the growth of luminal-type breast cancer cells and impedes the development of luminal-type breast cancer. Impaired cell growth and tumor development capability of α5(IV)-ablated luminal breast cancer cells is attributed to the reduced expression of glucose transporter and glycolytic enzymes and impaired glycolysis in luminal breast cancer cells. Non-integrin collagen receptor discoidin domain receptor-1 (DDR1) expression and p38 mitogen-activated protein kinase activation are attenuated in α5(IV)-ablated luminal breast cancer cells, resulting in reduced c-Myc oncogene expression and phosphorylation. Ectopic expression of constitutively active DDR1 or c-Myc restores the expression of glucose transporter and glycolytic enzymes, and thereafter restores aerobic glycolysis, cell proliferation, and tumor growth of luminal breast cancer. Thus, type IV collagen α5 chain is a luminal-type breast cancer-specific microenvironmental regulator modulating cancer cell metabolism.

Developments in FRET- and BRET-Based Biosensors.

Resonance energy transfer technologies have achieved great success in the field of analysis. Particularly, fluorescence resonance energy transfer (FRET) and bioluminescence resonance energy transfer (BRET) provide strategies to design tools for sensing molecules and monitoring biological processes, which promote the development of biosensors. Here, we provide an overview of recent progress on FRET- and BRET-based biosensors and their roles in biomedicine, environmental applications, and synthetic biology. This review highlights FRET- and BRET-based biosensors and gives examples of their applications with their design strategies. The limitations of their applications and the future directions of their development are also discussed.

IRF4 suppresses osteogenic differentiation of BM-MSCs by transcriptionally activating miR-636/DOCK9 axis.

OBJECTIVES: Osteoblasts are derived from Bone Marrow-derived Mesenchymal Stem Cells (BM-MSCs), which play an indispensable role in bone formation. In this study, the authors aim to investigate the role of IRF4 in the osteogenic differentiation of BM-MSCs and its potential molecular mechanism. METHODS: The authors used lentivirus infection to overexpress IRF4 in BM-MSCs. The expression of IRF4 and osteogenesis-related genes were detected by qRT-PCR and western blot analysis. The osteogenic differentiation of BM-MSCs was evaluated by Alkaline Phosphatase (ALP) activity, Alizarin red staining, and Alkaline Phosphatase (ALP) staining. Chromatin Immunoprecipitation (ChIP), Dual-Luciferase reporter assay and RNA Immunoprecipitation Assay were applied to confirm the regulatory mechanism between IRF4, miR-636 and DOCK9. RESULTS: The authors found IRF4 was down-regulated during the osteogenic differentiation of BM-MSCs, and IRF4 overexpression could decrease the osteogenic differentiation of BM-MSCs by specifically promoting the reduction of Alkaline Phosphatase (ALP) activity and down-regulating osteogenic indicators, including OCN, OPN, Runx2 and CollA1. Mechanistically, IRF4 activated microRNA-636 (miR-636) expression via binding to its promoter region, and Dedicator of Cytokinesis 9 (DOCK9) was identified as the target of miR-636 in BM-MSCs. Moreover, the damage in the capacity of osteogenic differentiation of BM-MSCs induced by IRF4 overexpression could be rescued by miR-636 inhibition. CONCLUSIONS: In summary, this paper proposed that IRF4/miR-636/DOCK9 may be considered as targets for the treatment of osteoporosis (OP).

Heterologous expression of bacterial cytochrome P450 from Microbacterium keratanolyticum ZY and its application in dichloromethane dechlorination.

Dichloromethane (DCM) is a volatile halogenated hydrocarbon with teratogenic, mutagenic and carcinogenic effects. Biodegradation is generally regarded as an effective and economical approach of pollutant disposal. In this study, a novel strain was isolated and its cytochrome P450 was heterologously expressed for DCM degradation. The isolate, Microbacterium keratanolyticum ZY, was characterized as a Gram-positive, rod-shaped and flagella-existed bacterium without spores (GenBank No. SUB8814364; CCTCC M 2019953). After successive whole-genome sequencing, assembly and annotation, eight identified functional genes (encoding cytochrome P450, monooxygenase, dehalogenase and hydrolase) were successfully cloned and expressed in Escherichia coli BL21 (DE3). The recombinant strain expressing cytochrome P450 presented the highest degradation efficiency (90.6%). Moreover, the specific activity of the recombinant cytochrome P450 was more than 1.2 times that of the recombinant dehalogenase (from Methylobacterium rhodesianum H13) under their optimum conditions. The kinetics of DCM degradation by recombinant cytochrome P450 was well fitted with the Haldane model and the value of maximum specific degradation rate was determined to be 0.7 s-1. The DCM degradation might occur through successive hydroxylation, dehydrohalogenation, dechlorination and oxidation to generate gem-halohydrin, formyl chloride, formaldehyde and formic acid. The study helps to comprehensively understand the DCM dechlorination process under the actions of bacterial functional enzymes (cytochrome P450 and dehalogenase).

Enhanced dechlorination of an enzyme-catalyzed electrolysis system by ionic liquids: Electron transfer, enzyme activity and dichloromethane diffusion.

Enzyme-catalyzed electrolysis system (EES) is a promising technique for the efficient dechlorination of pollutants. In this study, ionic liquids (ILs) was first introduced to enhance the dichloromethane dechlorination performance of an EES. An imidazole-based IL, 1-ethyl-3-methylimidazole tetrafluoroborate ([EMIM][BF4]), was chosen due to its excellent performance on dechlorination enhancement than other three ILs. The cyclic voltammograms with different scan rates shows that the presence of IL increased the apparent electron transfer rate constant (ks) from 0.008 to 0.013 s-1. The calculated surface electroactive species concentration (τc) also increased from 7.8 × 10-9 to 9.5 × 10-9 mol cm-2. Electrochemical impedance spectroscopy analysis illustrates that the IL mainly weakened the interfacial resistance between electrolyte and cathode to accelerate the electron communication in the EES. The introduction of IL facilitated the regeneration of reduced glutathione from oxidized glutathione, whereas inhibited the catalytic activity of dehalogenase via the disruption of secondary structure shown in circular dichroism spectra. The presence of IL was also facilitated the dichloromethane diffusion from electrolyte to cathode. The mass transfer rate constants of dichloromethane (km,d) increased by 6.9 times after the addition of IL. The optimum volume concentration, pH value, reaction temperature and applied voltage were 20%, 7, 35 °C and -0.8 V vs Ag/AgCl, respectively. The study is helpful to understand the promotion mechanism of IL on the dechlorination performance of EES when it is adopted as a treatment technique.

Dynamically remodeled hepatic extracellular matrix predicts prognosis of early-stage cirrhosis.

Liver cirrhosis remains major health problem. Despite the progress in diagnosis of asymptomatic early-stage cirrhosis, prognostic biomarkers are needed to identify cirrhotic patients at high risk developing advanced stage disease. Liver cirrhosis is the result of deregulated wound healing and is featured by aberrant extracellular matrix (ECM) remodeling. However, it is not comprehensively understood how ECM is dynamically remodeled in the progressive development of liver cirrhosis. It is yet unknown whether ECM signature is of predictive value in determining prognosis of early-stage liver cirrhosis. In this study, we systematically analyzed proteomics of decellularized hepatic matrix and identified four unique clusters of ECM proteins at tissue damage/inflammation, transitional ECM remodeling or fibrogenesis stage in carbon tetrachloride-induced liver fibrosis. In particular, basement membrane (BM) was heavily deposited at the fibrogenesis stage. BM component minor type IV collagen α5 chain expression was increased in activated hepatic stellate cells. Knockout of minor type IV collagen α5 chain ameliorated liver fibrosis by hampering hepatic stellate cell activation and promoting hepatocyte proliferation. ECM signatures were differentially enriched in the biopsies of good and poor prognosis early-stage liver cirrhosis patients. Clusters of ECM proteins responsible for homeostatic remodeling and tissue fibrogenesis, as well as basement membrane signature were significantly associated with disease progression and patient survival. In particular, a 14-gene signature consisting of basement membrane proteins is potent in predicting disease progression and patient survival. Thus, the ECM signatures are potential prognostic biomarkers to identify cirrhotic patients at high risk developing advanced stage disease.

Celluar Folding Determinants and Conformational Plasticity of Native C-Reactive Protein.

C-reactive protein (CRP) is an acute phase reactant secreted by hepatocytes as a pentamer. The structure formation of pentameric CRP has been demonstrated to proceed in a stepwise manner in live cells. Here, we further dissect the sequence determinants that underlie the key steps in cellular folding and assembly of CRP. The initial folding of CRP subunits depends on a leading sequence with a conserved dipeptide that licenses the formation of the hydrophobic core. This drives the bonding of the intra-subunit disulfide requiring a favorable niche largely conferred by a single residue within the C-terminal helix. A conserved salt bridge then mediates the assembly of folded subunits into pentamer. The pentameric assembly harbors a pronounced plasticity in inter-subunit interactions, which may form the basis for a reversible activation of CRP in inflammation. These results provide insights into how sequence constraints are evolved to dictate structure and function of CRP.

Conformational folding and disulfide bonding drive distinct stages of protein structure formation.

The causal relationship between conformational folding and disulfide bonding in protein oxidative folding remains incompletely defined. Here we show a stage-dependent interplay between the two events in oxidative folding of C-reactive protein (CRP) in live cells. CRP is composed of five identical subunits, which first fold spontaneously to a near-native core with a correctly positioned C-terminal helix. This process drives the formation of the intra-subunit disulfide bond between Cys36 and Cys97. The second stage of subunit folding, however, is a non-spontaneous process with extensive restructuring driven instead by the intra-subunit disulfide bond and guided by calcium binding-mediated anchoring. With the folded subunits, pentamer assembly ensues. Our results argue that folding spontaneity is the major determinant that dictates which event acts as the driver. The stepwise folding pathway of CRP further suggests that one major route might be selected out of the many in theory for efficient folding in the cellular environment.

IRF4 suppresses osteogenic differentiation of BM-MSCs by transcriptionally activating miR-636/DOCK9 axis

Abstract Objectives Osteoblasts are derived from Bone Marrow-derived Mesenchymal Stem Cells (BM-MSCs), which play an indispensable role in bone formation. In this study, the authors aim to investigate the role of IRF4 in the osteogenic differentiation of BM-MSCs and its potential molecular mechanism. Methods The authors used lentivirus infection to overexpress IRF4 in BM-MSCs. The expression of IRF4 and osteogenesis-related genes were detected by qRT-PCR and western blot analysis. The osteogenic differentiation of BM-MSCs was evaluated by Alkaline Phosphatase (ALP) activity, Alizarin red staining, and Alkaline Phosphatase (ALP) staining. Chromatin Immunoprecipitation (ChIP), Dual-Luciferase reporter assay and RNA Immunoprecipitation Assay were applied to confirm the regulatory mechanism between IRF4, miR-636 and DOCK9. Results The authors found IRF4 was down-regulated during the osteogenic differentiation of BM-MSCs, and IRF4 overexpression could decrease the osteogenic differentiation of BM-MSCs by specifically promoting the reduction of Alkaline Phosphatase (ALP) activity and down-regulating osteogenic indicators, including OCN, OPN, Runx2 and CollA1. Mechanistically, IRF4 activated microRNA-636 (miR-636) expression via binding to its promoter region, and Dedicator of Cytokinesis 9 (DOCK9) was identified as the target of miR-636 in BM-MSCs. Moreover, the damage in the capacity of osteogenic differentiation of BM-MSCs induced by IRF4 overexpression could be rescued by miR-636 inhibition. Conclusions In summary, this paper proposed that IRF4/miR-636/DOCK9 may be considered as targets for the treatment of osteoporosis (OP).

Computational Protein Design Using AND/OR Branch-and-Bound Search.

The computation of the global minimum energy conformation (GMEC) is an important and challenging topic in structure-based computational protein design. In this article, we propose a new protein design algorithm based on the AND/OR branch-and-bound (AOBB) search, a variant of the traditional branch-and-bound search algorithm, to solve this combinatorial optimization problem. By integrating with a powerful heuristic function, AOBB is able to fully exploit the graph structure of the underlying residue interaction network of a backbone template to significantly accelerate the design process. Tests on real protein data show that our new protein design algorithm is able to solve many problems that were previously unsolvable by the traditional exact search algorithms, and for the problems that can be solved with traditional provable algorithms, our new method can provide a large speedup by several orders of magnitude while still guaranteeing to find the global minimum energy conformation (GMEC) solution.

Experimental Research on Differentiation-Inducing Growth of Nerve Lateral Bud by HUC-MSCs Chitosan Composite Conduit.

This study is intended to explore the role of human umbilical-cord-derived mesenchymal stem cells (HUC-MSCs) in nerve end-to-side anastomosis, as well as in the induction and promotion of growth of nerve lateral bud. The chitosan nerve conduit was prepared based on the biological characteristics of chitosan, and the nerve conduit was filled with HUC-MSCs, and was used to bridge the nerve end-to-side anastomotic stoma. The experimental animals were randomly assigned into three groups (10 in each group), and the nerve end-to-side anastomosis was conducted: (1) group A (control group): traditional tibial nerve-common peroneal nerve end-to-side anastomosis; (2) group B (experimental group 1): tibial nerve-common peroneal nerve end-to-side anastomotic stoma bridged with chitosan nerve conduit; (3) group C (experimental group 2): tibial nerve-common peroneal nerve end-to-side anastomotic stoma bridged by chitosan nerve conduit filled with HUC-MSCs. General morphological observation, nerve electrophysiology, and anti-S-100 immunohistochemistry were performed. All experimental animals survived, and no infections were found at operative incisions. The nerve continuity was in good condition through visual observation when sampling, which is mild adhesion to the surrounding tissue and easy to be separated. 12 W HUC-MSCs chitosan composite nerve conduits were degraded completely after operation. Electrophysiological test showed that the nerve conduction velocity (NCV) in group C was significantly higher than that in group A or group B (p < 0.01). There were no significant differences between NCVs of group A and group B. Toluidine blue staining and transmission electron microscope showed that the number of the medullated fibers and the myelin sheath thickness in group C were larger than those in group A or B. There were no significant differences between the numbers of the medullated fibers and between the myelin sheath thicknesses of groups A and B. By means of anti-S-100 immunohistochemistry, the arrangement of a large number of brown-red proliferating schwann cells around the regenerated nerve fibers in group C could be found, while fewer and sparse brown-red matters and very poor growth of schwann cells could be observed in groups A and B. Slightly more favorable situation could be observed in group B compared with group A. HUC-MSCs play obviously an important role in promoting nerve regeneration during the nerve end-to-side anastomosis, which induces the growth of axis bud, accelerates the growth velocity of regenerated fiber, and promotes the growth and maturity of schwann cells.

Selective inhibition of STAT1 reduces spinal cord injury in mice.

The signal transducer and activator of transcription 1 (STAT1) is associated with neuronal cell death after cerebral ischemia. However, the role of STAT1 in the spinal cord injury (SCI) remains unclear. Here, we examined whether STAT1 blockade reduces neural tissue damage and locomotor impairment after SCI in mice. The small interfering RNA against STAT1 (STAT1 siRNA) or control non-targeting siRNA was injected intraperitoneally into SCI mice. Histological damage and locomotor function were evaluated. Inflammatory markers and apoptosis were determined. STAT1 siRNA treatment significantly decreased the histological damage following SCI. STAT1 siRNA-treated mice showed significantly improved locomotor function compared with the controls. Furthermore, TNF-α, IL-1ß, and IL-6 levels at the injured site from the STAT1 siRNA-treated group were significantly reduced and IL-10 increased, in comparison with controls. The NF-κB activation and apoptosis in SCI were also inhibited. These results reveal that selective STAT1 inhibition reduced neural tissue damage and locomotor impairment by regulating inflammatory response and possibly apoptosis. STAT1 represents a novel therapeutic target after SCI.

[Characteristics of biofilm phase during the long-term degradation of a toluene-contaminated gas stream using BTF].

This study analyzes the accumulation and distribution of biomass and changes in properties of biofilm in a long-term biotrickling filter (BTF) system in order to investigate the correlation between the biofilm phase properties and the performance. After a long-term operation of 130 days, the BTF showed a deterioration in degradation performance and an increase in pressure drop with a gradual increase of biofilm thickness and uneven distribution of biomass. Meanwhile, the porosity of the upper and lower layers decreased from 85% and 82% in the start-up period to 65% and 40%, respectively, as a result of the excessive accumulation of biomass and its non-uniform distribution. The AWCD values showed a decreasing trend indicating that the biological activity decreased with the aging of biofilm in the long-term BTF. The contents of total extracellular polymeric substances (EPS) and protein in the later period were twice as much as those in the start-up period. The value of protein to polysaccharide (PN/PS) ratio increased from 0.3 to 0.95, and showed positive correlation with the surface hydrophobicity of the biofilm, which increased from 33% to 73% accordingly. The mean molecular weight of EPS decreased during the operation of BTF. The result of FTIR further showed that the main chemical composition of EPS changed in the long-term BTF accordingly, possibly resulting in the deterioration of performance in the long-term BTF. The above experimental results could be very helpful for reducing the clogging and performance deterioration in long-term BTF.