Identifying emerging phenomenon in long temporal phenotyping experiments.

MOTIVATION: The rapid improvement of phenotyping capability, accuracy and throughput have greatly increased the volume and diversity of phenomics data. A remaining challenge is an efficient way to identify phenotypic patterns to improve our understanding of the quantitative variation of complex phenotypes, and to attribute gene functions. To address this challenge, we developed a new algorithm to identify emerging phenomena from large-scale temporal plant phenotyping experiments. An emerging phenomenon is defined as a group of genotypes who exhibit a coherent phenotype pattern during a relatively short time. Emerging phenomena are highly transient and diverse, and are dependent in complex ways on both environmental conditions and development. Identifying emerging phenomena may help biologists to examine potential relationships among phenotypes and genotypes in a genetically diverse population and to associate such relationships with the change of environments or development. RESULTS: We present an emerging phenomenon identification tool called Temporal Emerging Phenomenon Finder (TEP-Finder). Using large-scale longitudinal phenomics data as input, TEP-Finder first encodes the complicated phenotypic patterns into a dynamic phenotype network. Then, emerging phenomena in different temporal scales are identified from dynamic phenotype network using a maximal clique based approach. Meanwhile, a directed acyclic network of emerging phenomena is composed to model the relationships among the emerging phenomena. The experiment that compares TEP-Finder with two state-of-art algorithms shows that the emerging phenomena identified by TEP-Finder are more functionally specific, robust and biologically significant. AVAILABILITY AND IMPLEMENTATION: The source code, manual and sample data of TEP-Finder are all available at: http://phenomics.uky.edu/TEP-Finder/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

An online tool for measuring and visualizing phenotype similarities using HPO.

BACKGROUND: The Human Phenotype Ontology (HPO) is one of the most popular bioinformatics resources. Recently, HPO-based phenotype semantic similarity has been effectively applied to model patient phenotype data. However, the existing tools are revised based on the Gene Ontology (GO)-based term similarity. The design of the models are not optimized for the unique features of HPO. In addition, existing tools only allow HPO terms as input and only provide pure text-based outputs. RESULTS: We present PhenoSimWeb, a web application that allows researchers to measure HPO-based phenotype semantic similarities using four approaches borrowed from GO-based similarity measurements. Besides, we provide a approach considering the unique properties of HPO. And, PhenoSimWeb allows text that describes phenotypes as input, since clinical phenotype data is always in text. PhenoSimWeb also provides a graphic visualization interface to visualize the resulting phenotype network. CONCLUSIONS: PhenoSimWeb is an easy-to-use and functional online application. Researchers can use it to calculate phenotype similarity conveniently, predict phenotype associated genes or diseases, and visualize the network of phenotype interactions. PhenoSimWeb is available at http://120.77.47.2:8080.

Identifying consistent disease subnetworks using DNet.

It is critical to identify disease-specific subnetworks from the vastly available genome-wide gene expression data for elucidating how genes perform high-level biological functions together. Various algorithms have been developed for disease gene identification. However, the topological structure of the disease networks (or even the fraction of the networks) has been left largely unexplored. In this article, we present DNet, a method for the identification of significant disease subnetworks by integrating both the network structure and gene expression information. Our work will lead to the identification of missing key disease genes, which are be highly expressed in a disease-specific gene expression dataset. The experimental evaluation of our method on both the Leukemia and the Duchenne Muscular Dystrophy gene expression datasets show that DNet performs better than the existing state-of-the-art methods. In addition, literature supports were found for the discovered disease subnetworks in a case study.

Identifying term relations cross different gene ontology categories.

BACKGROUND: The Gene Ontology (GO) is a community-based bioinformatics resource that employs ontologies to represent biological knowledge and describes information about gene and gene product function. GO includes three independent categories: molecular function, biological process and cellular component. For better biological reasoning, identifying the biological relationships between terms in different categories are important. However, the existing measurements to calculate similarity between terms in different categories are either developed by using the GO data only or only take part of combined gene co-function network information. RESULTS: We propose an iterative ranking-based method called C r o G O2 to measure the cross-categories GO term similarities by incorporating level information of GO terms with both direct and indirect interactions in the gene co-function network. CONCLUSIONS: The evaluation test shows that C r o G O2 performs better than the existing methods. A genome-specific term association network for yeast is also generated by connecting terms with the high confidence score. The linkages in the term association network could be supported by the literature. Given a gene set, the related terms identified by using the association network have overlap with the related terms identified by GO enrichment analysis.

Tumor microenvironment sensitization via dual-catalysis of carbon-based nanoenzyme for enhanced photodynamic therapy.

Photodynamic therapy (PDT) is limited in tumor therapy due to the mature antioxidant barrier of tumor microenvironment (TME) and phototoxicity/easy-degradation characteristics of photosensitizers. Therefore, we prepared Cu2+-doped hollow carbon nanoparticles (CHC) to protect the loaded photosensitizers and sensitize TME by glutathione-depletion and peroxidase (POD)-like activity for enhanced PDT. CHC significantly increased the maximum speed of POD-like reaction (Vm) of 8.4 times. By coating with hyaluronic acid (HA), the active sites on CHC were temporarily masked with low catalytic property, and restored in response to the overexpressed hyaluronidase in TME. Meanwhile, due to the excellent photothermal conversion efficiency (32.5 %) and hollow structure of CHC, the loaded photosensitizers were well protected from sunlight activation-induced unwanted phototoxicity and rapid degradation under the near-infrared light irradiation. In-vivo anti-tumor experiments demonstrated that the combination of photothermal-photodynamic effect achieved the best anti-tumor effect (tumor inhibition rate at 87.8 %) compared with any monotherapy. In addition, the combination of photothermal and photodynamic effect could efficiently suppress the cell migration, manifesting the reduced number of lung metastasized nodules by 74 %. This work provides an integrated platform for photosensitizers protection and TME sensitization for enhanced PDT.

An ingenious cellulose membrane sensor design strategy for colorimetric detection of Ag+/Hg2+ based on redox reaction.

This paper describes an ingenious cellulose membrane sensor design strategy for colorimetric detection of Ag+/Hg2+ based on redox reaction. The colorless 3,3',5,5'-tetramethylbenzidine (TMB) can be oxidized to blue oxidized TMB (oxTMB) when exposed to Ag+/Hg2+ that with strong oxidizing properties. Based on this phenomenon, TMB can be design as a colorimetric probe for Ag+/Hg2+, and the reaction mechanism and sensing performance of TMB as Ag+/Hg2+ were explored. In addition, the TMB probe-immobilized cellulose membranes (TMB@CMs) were developed by combining TMB with high-purity cellulose membranes (CMs) carrier with porous and polyhydroxy structures. As a platform for probe immobilization, TMB@CMs can effectively improve colorimetric sensing response and stability of TMB. The colorimetric mechanism of TMB@CMs was investigated including in situ oxidation of TMB and immediate immobilization of oxTMB. The experimental results showed that the visual detection limit (VLOD) of Ag+/Hg2+ was 10 µM when TMB was used as colorimetric probe, while the VLOD of the TMB@CMs was 1 µM. In addition, TMB@CMs had good reusability and stability. Through the analysis of SEM, EDS and XPS results, the mechanism of TMB colorimetric detection of Ag+/Hg2+ was that blue oxTMB and Ag/Hg elementals were generated by redox reaction between them. This study not only verified the feasibility of TMB as an Ag+/Hg2+ colorimetric probe, but also designed a probe-immobilized cellulose membrane model with convenient operation, uniform color development and stable color, which effectively improved the colorimetric sensing response and stability.

Mesoporous carbon nanoenzyme as nano-booster for photothermal-enhanced photodynamic therapy compared with graphene oxide.

The over-expressed GSH in tumor microenvironment significantly weakens the lethal reactive oxygen species (ROS) generated by photodynamic therapy (PDT) and catalysis of nanoenzyme. Hence, it is necessary to excavate a versatile and effective vehicle with oxidative stress-enhancement and GSH-depletion capacity to break the redox homeostasis in tumor microenvironment. GO has been reported to possess GSH-depletion and peroxidase (POD)-like capacity. Based on this, PEGylated mesoporous carbon (MC-PEG) was prepared as ICG vehicle to compare with PEGylated graphene oxide (GO-PEG). Excitingly, MC-PEG was found to exhibit three times higher oxidative capacity by POD-like process than GO-PEG, and owned more effective and continuous GSH-depletion capacity to further amplify the oxidative stress. Meanwhile, MC-PEG exhibited better protective effect on the loaded ICG against unwanted light excitation than GO-PEG. Together with the higher photothermal conversion effect, under the NIR light irradiation, MC-PEG could markedly improve the temperature of tumor cells and produce more hydroxyl radical, continuously consume GSH and provide more better protection for ICG compared with GO-PEG, thus further boosting the combination of photothermal and photodynamic effects. The anti-tumor experiment in cell and in-vivo level both validated that ICG/MC-PEG showed better synergistic effect with lower IC50 value and higher tumor suppression rate than ICG/GO-PEG.

Photothermal antibacterial materials to promote wound healing.

Wound healing is a crucial process that restores the integrity and function of the skin and other tissues after injury. However, external factors, such as infection and inflammation, can impair wound healing and cause severe tissue damage. Therefore, developing new drugs or methods to promote wound healing is of great significance. Photothermal therapy (PTT) is a promising technique that uses photothermal agents (PTAs) to convert near-infrared radiation into heat, which can eliminate bacteria and stimulate tissue regeneration. PTT has the advantages of high efficiency, controllability, and low drug resistance. Hence, nanomaterial-based PTT and its related strategies have been widely explored for wound healing applications. However, a comprehensive review of PTT-related strategies for wound healing is still lacking. In this review, we introduce the physiological mechanisms and influencing factors of wound healing, and summarize the types of PTAs commonly used for wound healing. Then, we discuss the strategies for designing nanocomposites for multimodal combination treatment of wounds. Moreover, we review methods to improve the therapeutic efficacy of PTT for wound healing, such as selecting the appropriate wound dressing form, controlling drug release, and changing the infrared irradiation window. Finally, we address the challenges of PTT in wound healing and suggest future directions.

Degradable iron-rich mesoporous dopamine as a dual-glutathione depletion nanoplatform for photothermal-enhanced ferroptosis and chemodynamic therapy.

Glutathione (GSH) is a crucial factor in limiting the effects of chemodynamic therapy (CDT) and ferroptosis, an iron-based cell death pathway. Based on this, we constructed iron-rich mesoporous dopamine (MPDA@Fe) nanovehicles with a dual-GSH depletion function by combining MPDA and Fe. Poly (ethylene glycol) (PEG) was further modified to provide desirable stability (PM@Fe) and glucose oxidase (GOx) was grafted onto PM@Fe (GPM@Fe) to address the limitation of hydrogen peroxide (H2O2). After the nanoparticles reached the tumor site, the weakly acidic microenvironment promoted the release of Fe. Then FeII reacted with H2O2 to generate hydroxyl radical (OH) and FeIII. The generated FeIII was reduced to FeII by GSH, which circularly participated in the Fenton reaction and continuously produced tumor inhibitory free radicals. Meanwhile, GOx consumed glucose to provide H2O2 for the reaction. MPDA had also been reported to deplete GSH. Therefore, dual consumption of GSH led to the destruction of intracellular redox balance and inhibition of glutathione-dependent peroxidase 4 (GPX4) expression, resulting in an increase in lipid peroxides (LPO) and further induction of ferroptosis. Additionally, MPDA-mediated photothermal therapy (PTT) raised the temperature of tumor area and produced photothermal-enhanced cascade effects. Hence, the synergistic strategy that combined dual-GSH depletion-induced ferroptosis, enhanced CDT and photothermal cascade enhancement based on MPDA@Fe could provide more directions for designing nanomedicines for cancer treatment.

Biomimetic smart mesoporous carbon nanozyme as a dual-GSH depletion agent and O2 generator for enhanced photodynamic therapy.

Photodynamic therapy (PDT) has been thriving in the theranostics of cancer in recent years. However, due to a series of problems such as high concentration of GSH and insufficient O2 partial pressure in the tumor micro-environment, it is difficult to achieve the desired therapeutic effects with single PDT. Mesoporous carbon (MC-COOH) has been widely used in photothermal therapy (PTT) due to its high photothermal conversion efficiency and drug loading. In addition, we have discovered that MC-COOH owned high-efficiency glutathione oxidase-like activity for intracellular lasting GSH consumption. Hence, a smart mesoporous carbon nanozyme (CCM) was designed as a dual-GSH depletion agent and O2 generator combined with PTT to overcome the dilemma of PDT. MnO2-doped carbon nanozyme (MC-Mn) was developed as the photothermal vehicles for the efficient loading of photosensitizer (Ce6). Subsequently, 4T1 membrane-coated nanozyme (Ce6/CCM) was constructed to achieve homologous targeting capability. The carbon nanozyme owned the sustained dual-GSH depletion function through MC-COOH and MnO2, which greatly destroyed the antioxidant system of the tumor. Meanwhile, MnO2 could produce affluent O2 in the presence of H2O2, thereby alleviating the hypoxic state of tumor tissues and further promoting the generation of ROS. In addition, the novel carbon nanozyme was designed as photoacoustic imaging (PAI) agent and magnetic resonance imaging (MRI) contrast for real-time imaging during tumor therapy. In summary, this work showed that the biomimetic carbon nanozyme could be used as dual-GSH depletion agent and O2 generator for dual-mode imaging-guided PTT-PDT. STATEMENT OF SIGNIFICANCE: - MC-COOH with highly efficient GSH-OXD activity was first discovered and applied in PDT. - MnO2 acted as an O2 generator and GSH depletion agent to enhance PDT. - The tumor-targeting ability of the nanozyme was improved by cell membrane camouflage. - CCM nanozyme possesses both PAI and MRI dual-mode imaging modalities to guide PDT/PTT.

A mutually beneficial macrophages-mediated delivery system realizing photo/immune therapy.

The accumulation of nanomedicines in tumor tissues determines their therapeutic efficacy. We herein exploit the tropism of macrophages to improve the accumulation and retention time of nanomedicine at tumors. Interestingly, macrophages are not merely as transporters, but killers activated by nanomedicine. The system(M@C-HA/ICG) was established by decorating macrophages with hyaluronic acid-modified hollow mesoporous carbon (C) nanoparticles loading indocyanine green (ICG). Notably, C nanoparticles with superior photothermal conversion capability not merely guarantee the efficient delivery of ICG through high drug loading efficiency and inhibiting the premature leaky, but effectually activate the polarization of macrophages. The results exhibited that those activated macrophages could release pro-inflammatory cytokines (NO, TNF-α, IL-12), while M@C-HA/ICG afforded about 2-fold higher tumor accumulation compared with pure nanoparticle C-HA/ICG and produced heat and singlet oxygen (1O2) under irradiation of an 808 nm laser, realizing the combination of photodynamic therapy (PDT), photothermal therapy (PTT) and cytokines-mediated immunotherapy. Specially, we also investigated the relationship of singlet oxygen (1O2) or temperature and tumor-killing activity for understanding the specific effectual procedure of PDT/PTT synergistic therapy. Overall, we firstly established an "all active" delivery system integrating the features of nanomedicine with biological functions of macrophages, providing a novel insight for cell-mediated delivery platform and tumor targeted multimodality anti-cancer therapy.

Current trends in smart mesoporous silica-based nanovehicles for photoactivated cancer therapy.

Photoactivated therapeutic strategies (photothermal therapy and photodynamic therapy), due to the adjusted therapeutic area, time and light dosage, have prevailed for the fight against tumors. Currently, the monotherapy with limited treatment effect and undesired side effects is gradually replaced by multimodal and multifunctional nanosystems. Mesoporous silica nanoparticles (MSNs) with unique physicochemical advantages, such as huge specific surface area, controllable pore size and morphology, functionalized modification, satisfying biocompatibility and biodegradability, are considered as promising candidates for multimodal photoactivated cancer therapy. Excitingly, the innovative nanoplatforms based on the mesoporous silica nanoparticles provide more and more effective treatment strategies and display excellent antitumor potential. Given the rapid development of antitumor strategies based on MSNs, this review summarizes the current progress in MSNs-based photoactivated cancer therapy, mainly consists of (1) photothermal therapy-related theranostics; (2) photodynamic therapy-related theranostics; (3) multimodal synergistic therapy, such as chemo-photothermal-photodynamic therapy, phototherapy-immunotherapy and phototherapy-radio therapy. Based on the limited penetration of irradiation light in photoactivated therapy, the challenges faced by deep-seated tumor therapy are fully discussed, and future clinical translation of MSNs-based photoactivated cancer therapy are highlighted.

Enhanced Inflammatory Reaction and Thrombosis in High-Fat Diet-Fed ApoE-/- Mice are Attenuated by Celastrol.

OBJECTIVE: High-fat diet (HFD) increases the risk of inflammatory reaction and acute arterial thrombosis. Celastrol has been confirmed to regulate inflammatory cytokine levels in atherosclerotic animal models. However, the anti-thrombotic effects of celastrol have remained to be fully demonstrated. The present study was performed to investigate the beneficial effect of celastrol in HFD-induced inflammatory reaction and thrombosis in apolipoprotein (apo)E-/- mice. MATERIALS AND METHODS: Thrombogenic mice model was established using HFD-fed apoE-/- mice. The levels of mRNA and protein were assayed by RT-qPCR and western blotting, respectively. Immunohistochemistry (IHC) staining was performed to measure the protein expression of matrix metalloproteinase-2 and matrix metalloproteinase-9 in the aortic endothelium of HFD-fed apoE-/- mice. RESULTS: The results demonstrated that the effect of HFD on inflammatory cytokines in mice with apoE-/- background was reversed by celastrol administration, and celastrol treatment inhibited the NOD-like receptor family, pyrin domain containing 3 (NLRP3)/caspase-1/interleukin-1ß signaling cascades in peripheral blood mononuclear cells from HFD-fed apoE-/- mice. In addition, HFD enhanced adenosine diphosphate-induced platelet aggregation in normal C57BL/6 and apoE-/- mice, while celastrol administration reversed this. Furthermore, celastrol inhibited the pro-thrombotic effects of HFD in apoE-/- mice, and the underlying mechanism was mediated, at least partially, through the suppression of matrix metalloproteinase-2 and -9 expression. CONCLUSIONS: Celastrol administration significantly attenuated HFD-induced inflammatory reaction, platelet aggregation and thrombosis in apoE-/- mice, and celastrol may be used as a drug for the prevention of HFD-induced inflammatory reaction and thrombus.

Polydopamine-carbon dots functionalized hollow carbon nanoplatform for fluorescence-imaging and photothermal-enhanced thermochemotherapy.

The low power photothermal therapy can reduce the tissue damage caused by laser irradiation, thus the near-infrared (NIR) absorbing vehicles with high photothermal conversion efficiency are demanded in the low power treatment. Herein, the NIR-absorbing agent polydopamine (PDA) and carbon dots (CDs) were gated on the openings of hollow mesoporous carbon (HMC) to construct a photothermal enhanced multi-functional system (HMC-SS-PDA@CDs). Interestingly, the fluorescence emission wavelength of HMC-SS-PDA@CDs was red-shifted by FRET effect between PDA and CDs, which solved the dilemma of fluorescence quenching of carbon-based materials and was more conducive to cell imaging. The modification of PDA@CDs not only acts as the gatekeepers to realize multi-responsive release of pH, GSH and NIR, but also endows the HMC vehicle with excellent photothermal generation capacity, the possibility for bio-imaging as well as the enhanced stability. Naturally, both the cytological level and the multicellular tumor sphere level demonstrate that the delivery system has good low-power synergistic therapeutic with combination index (CI) of 0.348 and imaging effects. Meanwhile, the combined treatment group showed the highest tumor inhibition rate of 92.6% at 0.75 W/cm2. Therefore, DOX/HMC-SS-PDA@CDs nano-platform had broad application prospects in low power therapy and convenient imaging of carbon-based materials.

Knockdown of long non-coding RNA PVT1 protects human AC16 cardiomyocytes from hypoxia/reoxygenation-induced apoptosis and autophagy by regulating miR-186/Beclin-1 axis.

Myocardial ischemia/reperfusion (I/R) injury is a common consequence of restored blood supply after acute myocardial infarction (AMI), but its underlying mechanisms remain largely elusive. In this study, we aimed to investigate the functional role of long non-coding RNA PVT1 in hypoxia/reoxygenation (H/R)-treated AC16 cardiomyocytes. Our experimental results demonstrated that H/R treatment impaired the viability and increased the apoptosis of AC16 cells, and knockdown of PVT1 blocked the H/R injury. Besides, PVT1 knockdown also reduced excessive autophagy in H/R-treated AC16 cells. Furthermore, we confirmed that PVT1 might serve as a ceRNA for miR-186 in AC16 cells, and rescue experiments showed that miR-186 inhibition blocked the effects of PVT1 knockdown in H/R-treated AC16 cells. In summary, this study implied that PVT1 might be a promising therapeutic target for treating myocardial I/R injury.

Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach.

BACKGROUND: Gene Ontology (GO) is one of the most popular bioinformatics resources. In the past decade, Gene Ontology-based gene semantic similarity has been effectively used to model gene-to-gene interactions in multiple research areas. However, most existing semantic similarity approaches rely only on GO annotations and structure, or incorporate only local interactions in the co-functional network. This may lead to inaccurate GO-based similarity resulting from the incomplete GO topology structure and gene annotations. RESULTS: We present NETSIM2, a new network-based method that allows researchers to measure GO-based gene functional similarities by considering the global structure of the co-functional network with a random walk with restart (RWR)-based method, and by selecting the significant term pairs to decrease the noise information. Based on the EC number (Enzyme Commission)-based groups of yeast and Arabidopsis, evaluation test shows that NETSIM2 can enhance the accuracy of Gene Ontology-based gene functional similarity. CONCLUSIONS: Using NETSIM2 as an example, we found that the accuracy of semantic similarities can be significantly improved after effectively incorporating the global gene-to-gene interactions in the co-functional network, especially on the species that gene annotations in GO are far from complete.

[Meridian three-combined therapy for treatment of ordinary psoriasis: a multi-center randomized controlled study].

OBJECTIVE: To evaluate the effectiveness and safety of the meridian three-combined therapy for treatment of ordinary psoriasis. METHODS: A multi-central, randomized and positive drug controlled trial was adopted, and 233 cases were divided into an observation group of 116 cases and a control group of 117 cases. The observation group was treated with thread embedding at points, blood-letting puncture on the back of ear and auricular point pressing (i.e. meridian three-combined therapy). For thread embedding, 3-4 local points such ear points as Fei (CO14), Gan (CO12), Pizhixia (AT4), Shenmen (TF4) , cephalic and symmetric points of severe parts of the limb skin were selected according to the skin lesion position, and the treatment was given once each two weeks. For ear point tapping and pressing, 3-5 points were selected in each session. And the control group was treated with oral administration of Di yin Tablets, 5 tablets each time, twice each day. After treatment of 6 weeks, the clinical therapeutic effects, the score of skin lesion area, the scores for skin lesion severity and safety were compared in the two groups. RESULTS: The markedly effective rate was 57.8 % in the observation group and 51.3% in the control group with no significant difference between the two groups (P>0.05); after treatment the scores for both the skin lesion area and the skin lesion severity were significantly decreased in the two groups compared with those before treatment (P<0.01), and with a significant difference between the two groups (P>0.05). And the incidence rate of the adverse reaction in the observation group was significantly lower than that in the control group. CONCLUSION: The meridian three-combined therapy is effective and safe for treatment of ordinary psoriasis.