Toward an integrative approach to translational exercise biomedicine

“Life requires movement(Aristotle quotes)”.For this longaccompanying human practice,exercise,which has also been well accepted as an active approach to promoting overall health and preventing diseases throughout life,it appears quite surprising that the underlying molecular and cellular mechanisms for its benefits remain poorly understood until very recently,despite the presence of an extensive body of research for the description of multidimensional benefits of exercise.From a historical view of scientific progress,this apparent discrepancy underscores the importance of transferring growing molecular and cellular knowledge to human practice,particularly in highlighting the translational aspect(Figure 1).

The protocadherin alpha cluster is required for axon extension and myelination in the developing central nervous system

In adult mammals, axon regeneration after central nervous system injury is very poor, resulting in persistent functional loss. Enhancing the ability of axonal outgrowth may be a potential treatment strategy because mature neurons of the adult central nervous system may retain the intrinsic ability to regrow axons after injury. The protocadherin （Pcdh） clusters are thought to function in neuronal morphogenesis and in the assembly of neural circuitry in the brain. We cultured primary hippocampal neurons from E17.5 Pcdhα deletion （del-α） mouse embryos. After culture for 1 day, axon length was obviously shorter in del-α neurons compared with wild-type neurons. RNA sequencing of hippocampal E17.5 RNA showed that expression levels of BDNF, Fmod, Nrp2, OGN, and Sema3d, which are associated with axon extension, were significantly down-regulated in the absence of the Pcdhα gene cluster. Using transmission electron microscopy, the ratio of myelinated nerve fibers in the axons of del-α hippocampal neurons was significantly decreased; myelin sheaths of P21 Pcdhα-del mice showed lamellar disorder, discrete appearance, and vacuoles. These results indicate that the Pcdhα cluster can promote the growth and myelination of axons in the neurodevelopmental stage.

Equivalent formulations of “the equation of life”

Motivated by progress in theoretical biology a recent proposal on a general and quantitative dynamical framework for nonequilibrium processes and dynamics of complex systems is briefly reviewed. It is nothing but the evolutionary process discovered by Charles Darwin and Alfred Wallace. Such general and structured dynamics may be tentatively named ＂the equation of life＂. Three equivalent formulations are discussed, and it is also pointed out that such a quantitative dynamical framework leads naturally to the powerfu! Boltzmann-Gibbs distribution and the second law in physics. In this way, the equation of life provides a logically consistent foundation for thermodynamics. This view clarifies a particular outstanding problem and further suggests a unifying principle for physics and biology.

Statistical method for predicting protein absorption peaks in terahertz region

Terahertz vibrational spectroscopy has recently been demonstrated as a novel noninvasive technique for the characterization of biological molecules. But the interpretation of the experimentally measured terahertz absorption bands requires robust computational method. In this paper, we present a statistical method for predicting the absorption peak positions of a macromolecule in the terahertz region. The essence of this method is to calculate the absorption spectra of a biological molecule based on multiple short scale molecular dynamics trajectories instead of using a long time scale trajectory. The method was employed to calculate the absorption peak positions of the protein, thioredoxin from Escherichia coli (E.coli), in the range of 10-25 cm -1 to verify the reliability of this statistical method. The predicted absorption peak positions of thioredoxin show good correlation with measured results demonstrating that the proposed method is effective in terahertz absorption spectra modeling. Such approach can be applied to predict characteristic spectral features of biomolecules in the terahertz region.

Construction of Lyapunov Function for Dissipative Gyroscopic System

We introduce a force decomposition to construct a potential function in deterministic dynamics described by ordinary differential equations in the context of dissipative gyroscopic systems.Such a potential function serves as the corresponding Lyapunov function for the dynamics,hence it gives both quantitative and qualitative descriptions for stability of motion.As an example we apply our force decomposition to a four-dimensional dissipative gyroscopic system.We explicitly obtain the potential function for all parameter regimes in the linear limit,including those regimes where the Lyapunov function was previously believed not to exist.

Detection and surveillance of circulating tumor cells in osteosarcoma for predicting therapy response and prognosis

Objective:Osteosarcoma(OS)is an aggressive,highly metastatic,relatively drug-resistant bone tumor with poor long-term survival rates.The presence and persistence of circulating tumor cells(CTCs)in the peripheral blood are believed to be associated with treatment inefficiency and distant metastases.A blood-based CTC test is thus greatly needed for monitoring disease progression and predicting clinical outcomes.However,traditional methods cannot detect CTCs from tumors of mesenchymal origin such as OS,and research on CTC detection in mesenchymal tumors has been hindered for years.Methods:In this study,we developed a CTC test based on hexokinase 2,a metabolic function-associated marker,for the detection and surveillance of OS CTCs,and subsequently explored its clinical value.Twelve patients with OS were enrolled as the training cohort for serial CTC tests.Dynamic CTC counting,in combination with therapy evaluation and post-treatment follow-up,was used to establish a model for predicting post-chemotherapy evaluation and disease-free survival,and the model was further validated with a cohort of 8 patients with OS.Results:Two dynamic CTC number patterns were identified,and the resulting predictive model exhibited 92%consistency with the clinical outcomes.This model suggested that a single CTC test has similar predictive power to serial CTC analysis.In the validation cohort,the single CTC test exhibited 100%and 87.5%consistency with therapy response and disease-free survival,respectively.Conclusions:Our non-invasive test for detection and surveillance of CTCs enables accurate prediction of therapy efficiency and prognosis,and may be clinically valuable for avoiding inefficient therapy and prolonging survival.

Characterization of N6-methyladenosine long non-coding RNAs in sporadic congenital cataract and age-related cataract

AIM:To characterize the N6-methyladenosine(m6A)modification patterns in long non-coding RNAs(lncRNAs)in sporadic congenital cataract(CC)and age-related cataract(ARC).METHODS:Anterior capsule of the lens were collected from patients with CC and ARC.Methylated RNA immunoprecipitation with next-generation sequencing and RNA sequencing were performed to identify m6A-tagged lncRNAs and lncRNAs expression.Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses and Gene Ontology annotation were used to predict potential functions of the m6A-lncRNAs.RESULTS:Large amount of m6A peaks within lncRNA were identified for both CC and ARC,while the level was much higher in ARC(49870 peaks)than that in CC(18688 peaks),yet those difference between ARC in younger age group(ARC-1)and ARC in elder age group(ARC-2)was quite slight.A total of 1305 hypermethylated and 1178 hypomethylated lncRNAs,as well as 182 differential expressed lncRNAs were exhibited in ARC compared with CC.On the other hand,5893 hypermethylated and 5213 hypomethylated lncRNAs,as well as 155 significantly altered lncRNA were identified in ARC-2 compared with ARC-1.Altered lncRNAs in ARC were mainly associated with the organization and biogenesis of intracellular organelles,as well as nucleotide excision repair.CONCLUSION:Our results for the first time present an overview of the m6A methylomes of lncRNA in CC and ARC,providing a solid basis and uncovering a new insight to reveal the potential pathogenic mechanism of CC and ARC.

Herb-partitioned moxibustion alleviates colon injuries in ulcerative colitis rats

AIM To observe the effect of herb-partitioned moxibustion(HPM) on expression of colonic cytokines in ulcerative colitis(UC) rats.METHODS A UC rat model was established by protein immunization in combination with topical chemical stimulation.Rats in the HPM group(n = 8) received HPM at bilateral Tianshu(ST25) points.The gross injury and pathological scores of the colon were recorded.The expression profile of colonic cytokines was assayed using the protein microarray technique.Specific differential cytokines were selected and verified by ELISA.The corresponding Uni Prot Accessions of the differentially expressed cytokines were retrieved in the Uni Prot database.The pathways involved were analyzed with the help of the KEGG PATHWAY database.The DAVID database was used for functional cluster and pathway analysis.RESULTS HPM improved colon injuries in UC rats,manifested by accelerated repair of ulcers and alleviation of inflammation,and the gross injury and pathological scores both significantly decreased(P < 0.01).Fold change > 1.3 or < 0.77 was taken as the screening standard.There were 77 down-regulated and 9 up-regulated differentially expressed colonic cytokines in the HPM group compared with the model group,and expression of 20 differed significantly(P < 0.05).Twelve of the 20 significantly differentially expressed cytokines [β-catenin,interleukin-1 receptor 6(IL-1 R6),IL-1β,B7-1,nerve growth factor receptor,AMP-activated protein kinase-α1,neuropilin-2,orexin A,adipocyte differentiation-related protein,IL-2,Fas and Fas L] were up-regulated in the model group(n = 3,compared with the normal group) but downregulated in the HPM group(n = 3,compared with the model group).Functional cluster analysis showed that the differentially expressed colonic cytokines in the HPM group regulated apoptosis and protein phosphorylation.KEGG pathway analysis showed that 52 down-regulated and 7 up-regulated differentially expressed colonic cytokines in the HPM group had pathways.The pathways that interacted between the cytokines and their receptors accounted for the largest proportion(28 of the downregulated and 5 of the up-regulated cytokines).CONCLUSION HPM promotes the repair of colon injuries in UC rats,which is related to the regulation of several abnormally expressed cytokines.

Recent progress in targeting the sialylated glycan-SIGLEC axis in cancer immunotherapy

Malignant tumors are complex structures composed of cancer cells and tumor microenvironmental cells.In this complex structure,cells cross-talk and interact,thus jointly promoting cancer development and metastasis.Recently,immunoregulatory molecule-based cancer immunotherapy has greatly improved treatment efficacy for solid cancers,thus enabling some patients to achieve persistent responses or cure.However,owing to the development of drug-resistance and the low response rate,immunotherapy against the available targets PD-1/PD-L1 or CTLA-4 has limited benefits.Although combination therapies have been proposed to enhance the response rate,severe adverse effects are observed.Thus,alternative immune checkpoints must be identified.The SIGLECs are a family of immunoregulatory receptors(known as glyco-immune checkpoints)discovered in recent years.This review systematically describes the molecular characteristics of the SIGLECs,and discusses recent progress in areas including synthetic ligands,monoclonal antibody inhibitors,and Chimeric antigen receptor T(CAR-T)cells,with a focus on available strategies for blocking the sialylated glycan-SIGLEC axis.Targeting glyco-immune checkpoints can expand the scope of immune checkpoints and provide multiple options for new drug development.

Epitope Analysis of Anti-SARS-CoV-2 Neutralizing Antibodies

Coronavirus disease 2019 is threatening thousands of millions of people around the world.In the absence of specific and highly effective medicines,the treatment of infected persons is still very challenging.As therapeutics,neutralizing antibodies(NAbs)have great potential.Many NAbs have been reported,and most target various regions on the receptor-binding domain of the spike(S)protein,or the N-terminal domain.Several NAbs and NAb cocktails have been authorized for emergency use,and more arc in clinical trials or are under development.In this review,considering the angle of binding epitopes on the S protein,we summarize the functions and the underlying mechanisms of a set of well-recognized NAbs and provide guidance for vaccine design and the combinatorial use of these antibodies.In addition,we review the NAbs and NAb cocktails that have been approved for emergency use and discuss the effectiveness of these NAbs for combating severe acute respiratory syndrome coronavirus 2 mutants.

Assessment of XAF1 as A Biomarker to Differentiate Hepatocellular Carcinoma from Nonneoplastic Liver Tissues

Objective： XIAP-associated factor 1 （XAF1） expression has been shown to be related with apoptosis in hepatocellular carcinoma （HCC）. However, the correlation of XAF1 expression with HCC tumor grade has not been intensively assessed. XIAP-associated factor-1 （XAF1） is an important apoptosis inducer in human HCC. The aim of this study is to determine the correlation between XAF1 expression and HCC histopathological grades. Methods： The mRNA levels of XAF1 in 24 paired HCC-nonneoplastic specimens were quantified by real-time reverse transcription PCR （RT-PCR）. Protein levels of XAF1 in 110 paired HCC-noncancer tissues were investigated by immunostaining specimens on a tissue microarray （TMA）. Correlations between XAF1 mRNA levels or protein expression and clinicopathological features were assessed by statistical analysis. Results： Both XAF1 mRNA and protein were significantly under-expressed in HCC tissues compared to their non-neoplastic counterparts. No significant relationship was found between XAF1 mRNA or protein expression and histological tumor grade. Conclusion： All these data suggest that XAF1 is a potential biomarker for differentiating HCC with noncancerous tissues.

Lyapunov function as potential function: A dynamical equivalence

For a physical system, regardless of time reversal symmetry, a potential function serves also as a Lyapunov function, providing convergence and stability information. In this paper, the converse is constructively proved that any dynamics with a Lyapunov function has a corresponding physical realization： a friction force, a Lorentz force, and a potential function. Such construction establishes a set of equations with physical meaning for Lyapunov function and suggests new approaches on the significant unsolved problem namely to construct Lyapunov functions for general nonlinear systems. In addition, a connection is found that the Lyapunov equation is a reduced form of a generalized Einstein relation for linear systems, revealing further insights of the construction.

Dynamical Decomposition of Markov Processes without Detailed Balance

We introduce a dynamical decomposition view in dealing with Markov processes without detailed balance.This work generalizes a previous decomposition framework on continuous-state Markov processes and explicitly gives its correspondence in discrete-state case.We investigate the dynamical roles of decomposed parts by studying the evolution of relative-entropy-like functions.We find a special definition of relative entropy to unify the dynamical roles played by the detailed balance part and the breaking detailed balance part.The evolution of the relative entropy naturally bounds the convergence of the process.

Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission

Dear Editor,The occurrence of concentrated pneumonia cases in Wuhan city,Hubei province of China was first reported on December 30,2019 by the Wuhan Municipal Health Commission(WHO,2020).The pneumonia cases were found to be linked to a large seafood and animal market in Wuhan,and measures for sanitation and disinfection were taken swiftly by the local government agency.The Centers for Disease Control and Prevention(CDC)and Chinese health authorities later determined and announced that a novel coronavirus(CoV),denoted as 2019-nCoV,had caused the pneumonia outbreak in Wuhan city(CDC,2020).Scientists from multiple groups had obtained the virus samples from hospitalized patients(Normile,2020).The isolated viruses were morphologically identical when observed under electron microscopy.

Computational Cellular Dynamics Based on the Chemical Master Equation: A Challenge for Understanding Complexity

Modern molecular biology has always been a great source of inspiration for computational science. Half a century ago, the challenge from understanding macromolecular dynamics has led the way for computations to be part of the tool set to study molecular biology. Twenty-five years ago, the demand from genome science has inspired an entire generation of computer scientists with an interest in discrete mathematics to join the field that is now called bioinformatics. In this paper, we shall lay out a new mathematical theory for dynamics of biochemical reaction systems in a small volume （i.e., mesoscopic） in terms of a stochastic, discrete-state continuous-time formulation, called the chemical master equation （CME）. Similar to the wavefnnction in quantum mechanics, the dynamically changing probability landscape associated with the state space provides a fundamental characterization of the biochemical reaction system. The stochastic trajectories of the dynamics are best known through the simulations using the Gillespie algorithm. In contrast to the Metropolis algorithm, this Monte Carlo sampling technique does not follow a process with detailed balance. We shall show several examples how CMEs are used to model cellular biochemical systems. We shall also illustrate the computational challenges involved： multiscale phenomena, the interplay between stochasticity and nonlinearity, and how macroscopic determinism arises from mesoscopic dynamics. We point out recent advances in computing solutions to the CME, including exact solution of the steady state landscape and stochastic differential equations that offer alternatives to the Gilespie algorithm. We argue that the CME is an ideal system from which one can learn to understand “complex behavior” and complexity theory, and from which important biological insight can be gained.

Targeted Metabolomics Revealed the Regulatory Role of Manganese on Small-Molecule Metabolism of Biofilm Formation in Escherichia coli

Biofilms are special microbial communities produced by many microorganisms,such as bacteria,viruses,and fungi.Biofilms enable the microorganisms to possess the capacity against a diversity of stressful environments.Yet,biofilm formation often causes tough challenges in clinical infections,food quality,and environmental issues,however,the formation mechanism of biofilms are still incompletely understood which seriously impedes the development of new strategies to eradicate biofilms in different niches.In this study,we sought to explore the regulatory role of manganese(Mn^(2+))on small-molecule metabo-lism of biofilm formation in Escherichia coli(E.coli).Using structural imaging assay combined with precision-targeted metabolomics method,to investigate how biofilm formation responded to various concentrations of Mn^(2+),we found that Mn^(2+)could inhibit biofilm formation through the regulation of phenotypic morphology and metabolic reprogramming.Collectively,our work discovered 16 differential functional metabolites and associated three metabolic pathways involving glycolysis,TCA cycle,and tryptophan metabolism that were changed mostly by Mn^(2+)during biofilm formation,which can differentiate biofilms from the relevant planktonic cells.Altogether,this study demonstrated that Mn^(2+)can inhibit biofilm formation to regulate metabolic reprogramming and micro-structure,such effort provides novel insight into the regulation of metabolic features of biofilm formation,which enables the development of new strategies to eradicate biofilm formation for addressing the challenging problems in different areas by targeting the regulation of Mn^(2+)to the biosynthesis and expres-sions of functional metabolites produced by different microorganisms.

Effect of ethanol extract of HPRS, a Traditional Chinese Medicine formula, on HCT116 cell Line

OBJECTIVE: In this study, we investigated the effects of ethanol extract of Hupiruisu Fang(HPRS), a formula of Traditional Chinese Medicine, on HCT116 cell line.METHODS: MKN45, A549, Hela and HCT116 cells were treated with ethanol extract of HPRS alone or the extract plus 5-Fluorouracil(5-FU) for 48 h, and then the cell viabilities were measured using CCK-8Kit. The early apoptosis rate and total apoptosis rate in both HCT116 cells were evaluated by flow cytometry. The m RNA levels of apoptosis-related genes including caspase-3, caspase-8, Bcl2 and Baxwere detected by real-time quantitative polymerase chain reaction. Lastly, the protein activities and expressions of those apoptosis related genes were observed for further verifying the pro-apoptosis of the extract of HPRS.RESULTS: Ethanol extract of HPRS could significantly induce apoptosis in HCT116 cell line. Synergistic analysis revealed that the extract exhibited a significant effect upon 5-FU-associated cytotoxicity in the cell line.CONCLUSION: The ethanol extract of HPRS plus5-FU might have the potential to improve the treatment of colorectal cancer.

Functional protein microarray： an ideal platform for investigating protein binding property

Functional protein microarray is an important tool for high-throughput and large-scale systems biology studies. Besides the progresses that have been made for protein microarray fabrication, significant advancements have also been achieved for applying protein microarrays on determining a variety of protein biochemical activities. Among these applications, detection of protein binding properties, such as protein-protein interactions （PPIs）, protein-DNA interactions （PDIs）, protein-RNA interactions, and antigen-antibody interactions, are straightforward and have substantial impacts on many research fields. In this review, we will focus on the recent progresses in protein-protein, protein-DNA, protein-RNA, protein-small molecule, protein-lipid, protein-glycan, and antigen-antibody interactions. We will also discuss the challenges and future directions of protein microarray technologies. We strongly believe that protein microarrays will soon become an indispensible tool for both basic research and clinical applications.

Systematic evaluation of IgG responses to SARS-CoV-2 spike protein-derived peptides for monitoring COVID-19 patients

Serological tests play an essential role in monitoring and combating the COVID-19 pandemic.Recombinant spike protein(S protein),especially the S1 protein,is one of the major reagents used for serological tests.However,the high cost of S protein production and possible cross-reactivity with other human coronaviruses pose unavoidable challenges.By taking advantage of a peptide microarray with full spike protein coverage,we analyzed 2,434 sera from 858 COVID-19 patients,63 asymptomatic patients and 610 controls collected from multiple clinical centers.Based on the results,we identified several S protein-derived 12-mer peptides that have high diagnostic performance.In particular,for monitoring the IgG response,one peptide(aa 1148-1159 or S2-78)exhibited a sensitivity(95.5%,95%CI 93.7-96.9%)and specificity(96.7%,95%CI 94.8-98.0%)comparable to those of the S1 protein for the detection of both symptomatic and asymptomatic COVID-19 cases.Furthermore,the diagnostic performance of the S2-78(aa 1148-1159)IgG was successfully validated by ELISA in an independent sample cohort.A panel of four peptides,S1-93(aa 553-564),S1-97(aa 577-588),S1-101(aa 601-612)and S1-105(aa 625-636),that likely will avoid potential cross-reactivity with sera from patients infected by other coronaviruses was constructed.The peptides identified in this study may be applied independently or in combination with the S1 protein for accurate,affordable,and accessible COVID-19 diagnosis.

Mass Spectrometry-Based Targeted Metabolomics Revealed the Regulatory Roles of Magnesium on Biofilm Formation in Escherichia coli by Targeting Functional Metabolites

Biofi lms often impose harmful infl uences in many niches involving food contamination,antibiotics resistance,and environmental issues.However,eradicating biofi lms remains diffi cultly because the formation mechanism of biofi lms is still incompletely clarifi ed.Here,we attempted to explore the regulatory role of magnesium(Mg^(2+))on biofi lm formation in Escherichia coli(E.coli)using phenotype visualization with targeted metabolomics method.We found that Mg^(2+)could exert signifi cant infl uence on biofi lm formation with a concentration dependency by regulating phenotypic morphology and triggering metabolic modifi cations of biofi lm.Phenotypic imaging revealed that increasing concentration of Mg^(2+)gradually inhibited biofi lm formation,Mg^(2+)was observed to restore the microstructure of E.coli strain in biofi lms to that in the relevant planktonic cells.In addition,our metabolomics analysis characterized 20 diff erential metabolites and associated two metabolic pathways including nucleotide metabolism and amino acid metabolism that were notably modifi ed during biofi lm formation under the treatments of varied Mg^(2+).Altogether,our work provides a novel insight into the infl uence of Mg^(2+)on biofi lm formation at a metabolic level,which is implicated in the novel solution to disturb biofi lm formation through the regulation of Mg^(2+)and functional metabolite interaction.