Epigenome-Metabolome-Epigenome signaling cascade in cell biological processes

Cell fate determination as a fundamental question in cell biology has been extensively studied at different regulatory levels for many years.However,the mechanisms of multilevel regulation of cell fate determination remain unclear.Recently,we have proposed an Epigenome-Metabolome-Epigenome(E-M-E)signaling cascade model to describe the cross-over cooperation during mouse somatic cell reprogramming.In this review,we summarize the broad roles of E-M-E signaling cascade in different cell biological processes,including cell differentiation and dedifferentiation,cell specialization,cell proliferation,and cell pathologic processes.Precise E-M-E signaling cascades are critical in these cell biological processes,and it is of worth to explore each step of E-M-E signaling cascade.E-M-E signaling cascade model sheds light on and may open a window to explore the mechanisms of multilevel regulation of cell biological processes.

Gene and protein expression profiles of olfactory ensheathing cells from olfactory bulb versus olfactory mucosa

Olfactory ensheathing cells(OECs) from the olfactory bulb(OB) and the olfactory mucosa(OM) have the capacity to repair nerve injury. However, the difference in the therapeutic effect between OB-derived OECs and OM-derived OECs remains unclear. In this study, we extracted OECs from OB and OM and compared the gene and protein expression profiles of the cells using transcriptomics and non-quantitative proteomics techniques. The results revealed that both OB-derived OECs and OM-derived OECs highly expressed genes and proteins that regulate cell growth, proliferation, apoptosis and vascular endothelial cell regeneration. The differentially expressed genes and proteins of OB-derived OECs play a key role in regulation of nerve regeneration and axon regeneration and extension, transmission of nerve impulses and response to axon injury. The differentially expressed genes and proteins of OM-derived OECs mainly participate in the positive regulation of inflammatory response, defense response, cytokine binding, cell migration and wound healing. These findings suggest that differentially expressed genes and proteins may explain why OB-derived OECs and OM-derived OECs exhibit different therapeutic roles. This study was approved by the Animal Ethics Committee of the General Hospital of Ningxia Medical University(approval No. 2017-073) on February 13, 2017.

Expression and regulatory network of long noncoding RNA in rats after spinal cord hemisection injury

Long noncoding RNAs(lncRNAs)participate in a variety of biological processes and diseases.However,the expression and function of lncRNAs after spinal cord injury has not been extensively analyzed.In this study of right side hemisection of the spinal cord at T10,we detected the expression of lncRNAs in the proximal tissue of T10 lamina at different time points and found 445 lncRNAs and 6522 mRNA were differentially expressed.We divided the differentially expressed lncRNAs into 26 expression trends and analyzed Profile 25 and Profile 2,the two expression trends with the most significant difference.Our results showed that the expression of 68 lncRNAs in Profile 25 rose first and remained high 3 days post-injury.There were 387 mRNAs co-expressed with the 68 lncRNAs in Profile 25.The co-expression network showed that the co-expressed genes were mainly enriched in cell division,inflammatory response,FcγR-mediated cell phagocytosis signaling pathway,cell cycle and apoptosis.The expression of 56 lncRNAs in Profile2 first declined and remained low after 3 days post-injury.There were 387 mRNAs co-expressed with the 56 lncRNAs in Profile 2.The co-expression network showed that the co-expressed genes were mainly enriched in the chemical synaptic transmission process and in the signaling pathway of neuroactive ligand-receptor interaction.The results provided the expression and regulatory network of the main lncRNAs after spinal cord injury and clarified their co-expressed gene enriched biological processes and signaling pathways.These findings provide a new direction for the clinical treatment of spinal cord injury.

Proteomic dissection of biological pathways/processes through profiling protein-protein interaction networks

Cellular functions, either under the normal or pathological conditions or under different stresses, are the results of the coordinated action of multiple proteins interacting in macromolecular complexes or assemblies. The precise determination of the specific composition of protein complexes, especially using scalable and high-throughput methods, represents a systematic approach toward revealing particular cellular biological functions. In this regard, the direct profiling protein-protein interactions (PPIs) represent an efficient way to dissect functional pathways for revealing novel protein functions. In this review, we illustrate the technological evolution for the large-scale and precise identification of PPIs toward higher physiologically relevant accuracy. These techniques aim at improving the efficiency of complex pull-down, the signal specificity and accuracy in distinguishing specific PPIs, and the accuracy of identifying physiological relevant PPIs. A newly developed streamline proteomic approach for mapping the binary relationship of PPIs in a protein complex is introduced.

A comparative analysis of differentially expressed genes in rostral and caudal regions after spinal cord injury in rats

The initial mechanical damage of a spinal cord injury(SCI)triggers a progressive secondary injury cascade,which is a complicated process integrating multiple systems and cells.It is crucial to explore the molecular and biological process alterations that occur after SCI for therapy development.The differences between the rostral and caudal regions around an SCI lesion have received little attention.Here,we analyzed the differentially expressed genes between rostral and caudal sites after injury to determine the biological processes in these two segments after SCI.We identified a set of differentially expressed genes,including Col3a1,Col1a1,Dcn,Fn1,Kcnk3,and Nrg1,between rostral and caudal regions at different time points following SCI.Functional enrichment analysis indicated that these genes were involved in response to mechanical stimulus,blood vessel development,and brain development.We then chose Col3a1,Col1a1,Dcn,Fn1,Kcnk3,and Nrg1 for quantitative real-time PCR and Fn1 for immunostaining validation.Our results indicate alterations in different biological events enriched in the rostral and caudal lesion areas,providing new insights into the pathology of SCI.

Field experiment on biological contact oxidation process to treat polluted river water in the Dianchi Lake watershed

In this study two types of biological contact oxidation processes(BCOP),a step-feed(SBCOP)unit and an inter-recycle(IBCOP)unit,were designed to investigate the treatment of heavily polluted river water.The Daqing River,which is the largest pollutant contributor to the Dianchi Lake,one of the most eutrophic freshwater lakes in China,was taken for the case study.It was found that the SBCOP had higher adaptability and better performance in the reduction of COD,TN,and TP,which made it applicable for the treatment of polluted river water entering the Dianchi Lake.Nitrification rate was observed to be greatly affected by the influent temperature.During each season,the nitrification in the SBCOP was higher than that in the IBCOP.TN removal efficiency in the SBCOP was higher than that in the IBCOP during the winter and spring but poorer during the summer,possibly due to the inhibition of denitrification by higher dissolved oxygen level in the summer.Moreover,symbiotic algaebacteria growth may be conducive to the removal of pollutants.

The influence of desiccation on the recovery process of nitrogenase activity in restored biological soil crusts

Dear Editor,Biological soil crusts(BSCs),a layered structure formed by associations of soil organisms and topsoil,dominate arid and semiarid areas and serve important ecological functions in these areas(Eldridge and Greene,1994).Nitrogen fixation by BSCs is the main source of N in arid and semi-arid ecosystems.Desiccation is the most notable factor that influences BSCs,which recover physiological activity only after moistening.By influencing the amount of carbohydrates,

N6-methyladenosine(m6A)modification of ribosomal RNAs(rRNAs):Critical roles in mRNA translation and diseases

key components of the ribosome and the most abundant RNA species,the rRNAs are modified during ribosome formation.N^(6)-methyladenosine(m^(6)A)is a conserved RNA modification occurring on different RNA species including rRNAs.Recently,it has been reported that ZCCHC4 and METTL5 are methyltransferases that mediate m^(6)A modification of human 28S and 18S rRNA,respectively.The newly discovered biological functions of the two methyltransferases include regulation of mRNA translation,cell proliferation,cell differentiation,stress response,and other biological processes.Both of them,especially METTL5,have been proved to be associated with a variety of diseases such as intellectual disability,cancer,congenital dysplasia and have potential clinical application as biomarkers and therapeutic targets.

The Role of Endoplasmic Reticulum Stress in Melanoma

Evidence has shown that endoplasmic reticulum(ER)stress plays a role in the regulation of skin physiological functions such as melanocyte transformation and keratinocyte-related epidermal homeostasis.Other pathological processes may also be influenced.Recently,more evidence has suggested that ER stress participates in the pathogenesis of melanoma.Many biological functions of melanoma can be affected by the disturbance of ER stress.We herein review the network of ER stress and its role in melanoma and discuss several chemicals or drugs that may act as tumor inhibitors by influencing ER stress.