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.

Chemical and biological flocculation process to treat municipal sewage and analysis of biological function

The pilot scale experimental apparatus and the procedure of the chemical and biological flocculation process to verify the feasibility in treating Shanghai municipal sewage were introduced in this paper. In addition, the biological function of the process was discussed. The results of optimal running showed that in the reaction tank, the concentration of mixed liquor suspended solid(MLSS) was 2 g/L, hydraulic retention time(HRT) was 35 min, dosage of liquid polyaluminium chloride(PAC) was 60 mg/L, and the concentration of polyacrylamide(PAM) was 0 5 mg/L. The effluent average concentrations of COD Cr , TP, SS and BOD 5 were 50 mg/L, 0 62 mg/L, 18 mg/L, and 17 mg/L, respectively. These were better than the designed demand. In addition, the existence of biological degradation in this system was proven by several methods. The removal efficiencies of the chemical and biological flocculation process were 20% higher than that of the chemical flocculation process above at the same coagulant dosage. The treatment process under different situations was evaluated on a pilot scale experiment, and the results provided magnificent parameters and optimal condition for future operation of the plant.

Effect of Ferric Chloride on the Properties of Biological Sludge in Co-precipitation Phosphorus Removal Process

This paper studied the effect of ferric chloride on waste sludge digestion,dewatering and sedimentation under the optimized doses in co-precipitation phosphorus removal process.The experimental results showed that the concentration of mixed liquid suspended solid(MLSS) was 2436 mg.L-1 and 2385 mg.L-1 in co-precipitation phosphorus removal process(CPR) and biological phosphorous removal process(BPR),respectively.The sludge reduction ratio for each process was 22.6% and 24.6% in aerobic digestion,and 27.6% and 29.9% in anaerobic digestion,respectively.Due to the addition of chemical to the end of aeration tank,the sludge content of CPR was slightly higher than that of BPR,but the sludge reduction rate for both processes had no distinct difference.The sludge volume index(SVI) and sludge specific resistance of BPR were 126 ml.g-1 and 11.7×1012 m.kg-1,respectively,while those of CPR were only 98 ml.g-1 and 7.1×1012 m.kg-1,indicating that CPR chemical could improve sludge settling and dewatering.

Optimal Size for Maximal Energy Efficiency in Information Processing of Biological Systems Due to Bistability

Energy efficiency is closely related to the evolution of biological systems and is important to their information processing. In this work, we calculate the excitation probability of a simple model of a bistable biological unit in response to pulsatile inputs, and its spontaneous excitation rate due to noise perturbation. Then we analytically calculate the mutual information, energy cost, and energy efficiency of an array of these bistable units. We find that the optimal number of units could maximize this array＇s energy efficiency in encoding pulse inputs, which depends on the fixed energy cost. We conclude that demand for energy efficiency in biological systems may strongly influence the size of these systems under the pressure of natural selection.

Uptake and Storage of Anthropogenic CO_2 in the Pacific Ocean Estimated Using Two Modeling Approaches

A basin-wide ocean general circulation model （OGCM） of the Pacific Ocean is employed to estimate the uptake and storage of anthropogenic CO2 using two different simulation approaches. The simulation （named BIO） makes use of a carbon model with biological processes and full thermodynamic equations to calculate surface water partial pressure of CO2, whereas the other simulation （named PTB） makes use of a perturbation approach to calculate surface water partial pressure of anthropogenic CO2. The results from the two simulations agree well with the estimates based on observation data in most important aspects of the vertical distribution as well as the total inventory of anthropogenic carbon. The storage of anthropogenic carbon from BIO is closer to the observation-based estimate than that from PTB. The Revelle factor in 1994 obtained in BIO is generally larger than that obtained in PTB in the whole Pacific, except for the subtropical South Pacific. This, to large extent, leads to the difference in the surface anthropogenic CO2 concentration between the two runs. The relative difference in the annual uptake between the two runs is almost constant during the integration processes after 1850. This is probably not caused by dissolved inorganic carbon （DIC）, but rather by a factor independent of time. In both runs, the rate of change in anthropogenic CO2 fluxes with time is consistent with the rate of change in the growth rate of atmospheric partial pressure of CO2.

Differential gene expression in proximal and distal nerve segments of rats with sciatic nerve injury during Wallerian degeneration

Wallerian degeneration is a subject of major interest in neuroscience. A large number of genes are differentially regulated during the distinct stages of Wallerian degeneration： transcription factor activation, immune response, myelin cell differentiation and dedifferentiation. Although gene expression responses in the distal segment of the sciatic nerve after peripheral nerve injury are known, differences in gene expression between the proximal and distal segments remain unclear. In the present study in rats, we used microarrays to analyze changes in gene expression, biological processes and signaling pathways in the proximal and distal segments of sciatic nerves under- going Wallerian degeneration. More than 6,000 genes were differentially expressed and 20 types of expression tendencies were identified, mainly between proximal and distal segments at 7-14 days after injury. The differentially expressed genes were those involved in cell differentiation, cytokinesis, neuron differentiation, nerve development and axon regeneration. Furthermore, 11 biological processes were represented, related to responses to stimuli, cell apoptosis, inflammato- ry response, immune response, signal transduction, protein kinase activity, and cell proliferation. Using real-time quantitative PCR, western blot analysis and immunohistochemistry, microarray data were verified for four genes： aquaporin-4, interleukin 1 receptor-like 1, matrix metallopro- teinase-12 and periaxin. Our study identifies differential gene expression in the proximal and distal segments of a nerve during Wallerian degeneration, analyzes dynamic biological changes of these genes, and provides a useful platform for the detailed study of nerve injury and repair during Wallerian degeneration.

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.

Treatment of a dyeing wastewater from a woolen mill using an A/O membrane bio-reactor

An anaerobic/oxic membrane bioreactor (A/O MBR) was used for treatment of dyeing wastewater from a woolen mill. COD and color of the wastewater were 54—473 mg/L and 40—400 dilution time (DT) respectively. The ratio of BOD 5/COD was less than 0.13. By the A/O MBR process, the average removal of COD, BOD 5, color and turbidity was 82%, 96%, 71% and 99%, respectively. The average COD, BOD 5, color and turbidity of effluent was 37 mg/L, 0.8 mg/L, 40 DT and 0.44 NUT respectively. The effluent COD met the local standard of reuse water in Beijing, China. The average COD volume load of the anaerobic biological tank was 0.0483 kgCOD/(m 3·d) and that of the aeration tank of the MBR was 0.3589 kgCOD/(m 3·d). The sludge load of the MBR was 0.19 kgCOD/(kg·MLSS·d) on average and the maximum of that was 0.4 kgCOD/(kg·MLSS·d). The flux of the A/O membrane bioreactor could be remained at larger than 50 L/(h·m 2·0.1MPa). The results indicated that A/O membrane bioreactor has technical feasibility for treatment of woolen mill wastewater.

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.

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.

Test of membrane bioreactor for waste water treatment of a petrochemical complex

Membrane bioreactor (MBR) used in water and waste water treatment is a developing technique for water pollution control and water reuse. This paper described a membrane bioreactor for treatment of waste water in a petrochemical complex. The experimental MBR was a lab scale one composed of an activated sludge bioreactor unit and an ultrafiltration membrane unit. The relationship of COD removal with MLSS and HRT in this MBR was studied. The effects of crossflow velocity, backwash interval and volume of flush liquid on the flux were discussed. The results showed that average removal of COD, oil, SS and turbidity in petrochemical waste water by the MBR was 91%, 86%, 92% and 99%, respectively. The average removal of NH 3 N and total phosphorous was 85% and 82% respectively. A coefficient of COD removal, k , was 0017—0080 L/(mg.d). The membrane flux maintained higher than 60 L/hm 2 bar for 34 days without chemical cleaning when the velocity of crossflow was 35—39 m/s and the backwash interval was 30 minutes and backwash duration at 20 seconds. The results indicated that it is feasible for MBR technology to be used in petrochemical waste water treatment. The treated water could be considered as a source of to make up water for industrial cooling system or to be reused for other purposes.

Identification of key genes responsible for cytokine-induced erythroid and myeloid differentiation and switching of hematopoietic stem cells by RAGE

We utilized a unique culture system to analyze the expression patterns of gene, protein, and cell surface antigen, and the biological process of the related genes in erythroid and myeloid differentiation and switching of hematopoietic stem cells （HSCs） in response to cytokine alterations. Gene-specific fragments （266） identified from five populations of cytokine-stimulated HSCs were categorized into three groups： （1） expressed specifically in a single cell population; （2） expressed in two cell populations, and （3） expressed in three or more populations. Of 145 defined cDNAs, three （2%） were novel genes. Protein two-dimensional gel electrophoresis and flow cytometry analyses showed overlapped and distinguished protein expression profiles in the cell populations studied. Biological process mapping of mRNAs expressed in erythroid and myeloid lineages indicated that mRNAs shared by both lineages attended ＇core processes,＇ whereas genes specifically expressed in either lineage alone were related to specific processes or cellular maturation. Data from this study support the hypothesis that committed HSCs （El4 or G14） cells can still be redirected to develop into myeloid or erythroid cells when erythropoietin （EPO） is replaced with granulocyte-colony stimulating factor （G-CSF） under erythroid-cultured condition or G-CSF with EPO in myeloid-cultured environment, respectively. Our results suggest that genes or proteins co-expressed in erythroid and myeloid lineages may be essential for the lineage maintenance and switching in hematopoiesis.

Automatic Verification of Biochemical Network Using Model Checking Method

This study focuses on automatic searching and verifying methods for the teachability, transition logics and hierarchical structure in all possible paths of biological processes using model checking. The automatic search and verification for alternative paths within complex and large networks in biological process can provide a considerable amount of solutions, which is difficult to handle manually. Model checking is an automatic method for verifying if a circuit or a condition, expressed as a concurrent transition system, satisfies a set of properties expressed in a temporal logic, such as computational tree logic （CTL）. This article represents that model checking is feasible in biochemical network verification and it shows certain advantages over simulation for querying and searching of special behavioral properties in biochemical processes.

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.

Effect of ozone on the performance of a hybrid ceramic membrane-biological activated carbon process

Two hybrid processes including ozonation-ceramic membrane-biological activated carbon （BAC） （Process A） and ceramic membrane-BAC （Process B） were compared to treat polluted raw water. The performance of hybrid processes was evaluated with the removal efficiencies of turbidity, ammonia and organic matter. The results indicated that more than 99% of particle count was removed by both hybrid processes and ozonation had no significant effect on its removal. BAC filtration greatly improved the removal of ammonia. Increasing the dissolved oxygen to 30.0 mg/L could lead to a removal of ammonia with concentrations as high as 7.80 mg/L and 8.69 mg/L for Processes A and B, respectively. The average removal efficiencies of total organic carbon and ultraviolet absorbance at 254 nm （UV254, a parameter indicating organic matter with aromatic structure） were 49% and 52% for Process A, 51% and 48% for Process B, respectively. Some organic matter was oxidized by ozone and this resulted in reduced membrane fouling and increased membrane flux by 25%-30%. However, pre-ozonation altered the components of the raw water and affected the microorganisms in the BAC, which may impact the removals of organic matter and nitrite negatively.

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.

The next decade of SET:from an oncoprotein to beyond

This year marks the fourth decade of research into the protein SET,which was discovered in 1992.SET was initially identified as an oncoprotein but later shown to be a multifaceted protein involved in regulating numerous biological processes under both physiological and pathophysiological conditions.SET dysfunction is closely associated with diseases,such as cancer and Alzheimer's disease.With the increasing understanding of how SET works and how it is regulated in cells,targeting aberrant SET has emerged as a potential strategy for disease intervention.In this review,we present a comprehensive overview of the advancements in SET studies,encompassing its biological functions,regulatory networks,clinical implications,and pharmacological inhibitors.Furthermore,we provide insights into the future prospects of SET research,with a particular emphasis on its promising potential in the realm of immune modulation.

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.