Abstract:Based on the maturity of the researches of various kinds of Omics networks, integrated cell network which integrates Omics networks will greatly improve the prediction ability of biological phenotype, and will become a powerful weapon of metabolic engineering decisions. After expounding that integrated cell network should be considered in the design of cell factory, we gave a review about reconstruction, analysis, and design methods of integrated cell network. We also introduced several aspects of databases, software platforms, parallel computing which involved in the research of integrated cell network.

Abstract:Molecular network research is an important means to reveal the structure and function of biological systems from a global point of view. The existing analysis methods are mostly based on the static network. In fact, the biological networks change all the time with the environmental conditions, tissue types, disease status, growth and differentiation. Researchers have proposed some bioinformatics methods for the dynamic analysis of molecular networks, such as the dynamic classification of the hub nodes, the prediction of dynamic protein complexes, the construction of condition specific subnetworks, and the simulation of dynamic behavior of networks. In this paper, we reviewed these methods for the dynamic molecular network analysis. Predictable, dynamic network analysis will become the standard mode of the future network research.

Abstract:Ubiquitination is one of the pervasively studied ways of post-transcriptional modifications (PTMs)， which orchestras a plethora of physiological events，including cell mitosis，cell differentiation，cell growth， transcriptional controls，DNA damage repair and immune responses. Recently，a constitutive member of "The Ubiquitin Kingdom" called DUB (deubiquitylating enzymes) has come into the center of the stage. As an iso-peptidase，DUBs govern distinct structures and various functions. Meanwhile，the topic of gene expression control has always been the cutting edge of life sciences. It is of great importance to summarize the relationships between DUBs and gene expression regulations. In this review，we summarize the roles that DUBs play in three fields: First，chromatin regulation. Second，cell cycle control. Third，DNA damage response. Finally，we discussed and predicted the potential perspectives.

Abstract:The Ribonuclease-4 (RNase-4) is one member of the ribonuclease A superfamily. RNase-4 displays the highest level of inter-species sequence similarity (approximately 90%) among the whole family, and unique uridine-specificity enzymatic properties, which relates to its three-dimensional (3D) structure. The biological functions of RNase-4 have not been well characterized to documents, although it is possibly associated with host defence by degrading polymeric RNA released from specific pathogens. Recently studies have revealed that RNase-4 protects neuron degeneration diseases through promoting angiogenesis, neurogenesis, and neuronal survival under stress in neurodegeneration diseases. This review summarizes the molecular characterization, three-dimensional structure, enzymatic properties, and biological functions of RNase-4, and gives fresh perspectives on further investigation and clinical application of RNase-4.

Abstract:The crowding effect refers to the fact that observers' ability to recognize an object in the periphery deteriorates when the target object is flanked by other items, especially if the target and flankers are similar. Here, a reduction of the crowding effect was caused by a topological difference between target and flankers. In three experiments using a number of different stimulus patterns (e.g., triangles and arrows; digits and letters and geometrical shapes), results showed that the crowding effect was significantly reduced when the target and the flankers were topologically different. Control experiments showed that such a reduction of the crowding effect was not due to differences in subjective similarity, or differences in geometrical features such as area and shape. This finding suggests that topological properties play an important role in perceptual grouping which influences the crowding effect.

Abstract:Recently, we sequenced the transcriptomes of a hepatocellular carcinoma biopsy and a normal liver tissue using the RNA-Sequencing (RNA-Seq) strategy based on the Next Generation Sequencing (NGS) technique, and identified several adjacent high RNA-Seq signal peaks on chromosome 11q13.1 in the hepatocellular carcinoma biopsy, while not in the normal control tissue. In this chromosome region, there is no characterized genes have been identified, implying that these RNA-Seq peaks may represent one or more novel genes. Further study was confirmed that these RNA-Seq peaks were transcribed by one novel gene. Through cloning the full length of this novel gene, we found that this novel gene transcribed many splicing isoforms, and the longest isoform is 3 562 bp. Then we deposited twelve representative RNA isoforms into the GenBank database of the National Center for Biotechnology Information (NCBI), and created the GenBank IDs from KC136297 to KC136308 for these isoforms. None significant open reading fragment (ORF) was found in any transcripts of this novel gene, implying that this gene may encodes long non-coding RNAs (lncRNAs). To further elucidate the potential transcriptional regulation mechanism of this lncRNA gene, we predicted the promoter from the upstream sequence of the lncRNA gene using bioinformatic tools, and found that there is one potential promoter in -719 to -469 bp from the transcript start site of the lncRNA gene, and there are seven Sp1, one STAT5 and one EGR1 transcription factor binding sites in the promoter region. The molecular mechanisms of the lncRNA gene in carcinogenesis and progression of hepatocellular carcinoma are worthful for further investigation.

Abstract:Activity-dependent synaptic structural plasticity underlies the learning and memory. Mammals, especially the rodents, are very sensitive to odorants, and have considerable capability of odor learning and memory. Here, the activity-dependent synaptic structural plasticity in the olfactory bulb (OB) of the CNGA2 knock-out transgenic mice (CNGA2 KO), which is anosmic, was investigated. Using immunohistochemistry for specific presynaptic and postsynaptic markers, it was found that deficits of peripheral inputs induced significant decreases in the expression of synaptophysin, a general marker for synapses, and gephyrin, a marker for inhibitory synapses, in the external plexiform layer (EPL) and the granule cell layer (GCL), but the vesicular glutamate transporters 1 (VGluT1) decreased only in EPL, not in GCL. Western-blots showed the decreases in the expression of gephyrin in the OB of CNGA2 KO mice, but not in the expression of the VGluT1. The results of immunohistochemistry and Western blot revealed that the excitatory and inhibitory synapses may have changed after deficits of peripheral inputs. GCs were the main participants in the EPL and GCL in the OB. Dendritic spines are the postsynaptic sites of the majority of excitatory synapses in the mammalian central nervous system, and the morphology and dynamics of dendritic spines change in response to novel experiences and neuropathologies. In the OB, spines on mature GCs are recipients of glutamatergic synapses in the GCL and reciprocal synapses in the EPL. Almost all study related to structural plasticity of GCs concentrated on the adult-born GCs, but the number of new-born granule cells in the OB is negligible compared with the number of preexisting GCs. In order to further reveal the quantitive changes of glutamatergic synapses on GCs, in vivo adult brain plasmid electroporation to label mature GCs in the OB directly were adopted. Here, the spines in EPL were defined as distal spines and the spines in GCL as proximal spines. It was revealed that the density of spines on granule cells decreased significantly in EPL (distal spines) of CNGA2 KO mice, but did not change significantly in GCL (proximal spines), as same as the result of optical density analysis in the VGluT1 immunolabeling. These data suggest that the structural plasticity of the distal dendrodendritic synapses, rather than the proximate axon-dendritic synapses on granular cells of the OB, are significantly affected by the peripheral olfactory inputs.

Abstract:Orientation selectivity is an important property of neurons in the primary visual cortex (area 17 or V1) and plays significant roles in the perception for object shape. V1 neurons also show clear responses to the Onset and Offset of a stimulus that lasts more than 100 ms, called as Onset and Offset responses, respectively. Previous studies have focused on Onset responses, while Offset responses were neglected. We investigated orientation selectivity of both Onset and Offset responses by presenting the stimuli of oriented gratings for 200 ms and showed that the preferred orientations of Offset responses are similar to that of Onset responses for most neurons. Moreover, the orientation tuning widths of Offset responses of most cells tended to be narrower than that of Onset responses, and the response latencies of Offset oriented responses significantly were longer than those of Onset responses. The strong orientation selectivity and long response latency of Offset responses relative to those of Onset responses suggest that the intracortical feedback inputs may contribute to the enhancement in orientation tuning of Offset responses. The orientation selectivity of Offset responses provides a neural substrate for the more precise discrimination and consecutive representation of the orientated borders of a shape over time.

Abstract:In the present work, we applied mechanical stimulus to study the propagations of intercellular calcium waves among BV-2 microglial cells by the fast fluorescence microscopy imaging system in vitro. The results showed that calcium signaling responded to mechanical stimulus and propagated to neighboring cells in isolated BV-2 microglial cells, suggesting that the paracrine pathway mediated intercellular calcium waves. Further data indicated that gap junction was involved in mechanically-induced intercellular calcium waves when the cells had physical contact with each other. More importantly, tunneling nanotubes (TNTs)-like structure between BV-2 microglial cells was found in vitro and mediated the propagation of intercellular calcium wave. Taken together, our studies demonstrated that three distinct pathways, including paracrine, gap junction and TNTs-like structures, could mediate the intercellular calcium waves in BV-2 microglial cells.

Abstract:In previous study, our group have found that there is a significant increased level of miR-122 in the serum of ob/ob mice, an animal model of type 2 diabetes. Here, we further investigated the role of miR-122 targeting AldoA in the liver of ob/ob mice. First, a significant decrease of miR-122 level and a notable increase of AldoA expression was found in the liver of the ob/ob mice. Second, mature miR-122 was transfected into 293T cells and then MVs isolated from 293T cells were collected; qRT-PCR was applied to confirm that miR-122 was rich in MVs. Third, specific fluorescent dye DiI-C₁₈-labeled MVs were injected intravenously into BALB/c mice; the frozen section of liver was observed through fluorescent microscopy. Finally, miR-122 targeting AldoA in the metabolism of ob/ob mice was confirmed by qRT-PCR and Western blotting. AldoA mainly catalysed the transformation between dihydroxyacetone phosphate, glyceraldehyde-3- phosphate and fructose 1, 6 - bisphosphate in glycolytic pathway. MiR-122 may play an important role in the pathologenesis of ob/ob mice through AldoA pathway.

Abstract:Budding yeast (Saccharomyces cerevisiae) protein kinase Sch9 is homologous to the mammalian kinase S6K1. S6K1 is a substrate of mammalian target of rapamycin (mTOR) and phosphatidylinositol-3 kinase (PI3K) and relates to many diseases, including obesity, diabetes and cancer. Both Sch9 and S6K1 are important to the regulation of cell growth in response to different nutrient and stress factors. The residue T570 is a conserved phosphorylation site in the activation loop of Sch9, also called PDK1 site. Whereas another conserved phosphorylation site, T737, in the hydrophobic motif of C terminus is called PDK2 site. The phosphorylation of these two sites are important to Sch9 kinase activity. Upstream kinases Pkh1/2 phosphorylate the PDK1 site, while the Target of Rapamycin Complex 1 (TORC1) phosphorylates the PDK2 site. To better understand the intracellular function of protein kinase Sch9, it is important to elucidate the dynamics and regulation of the phosphorylation of PDK1 and PDK2 sites in Sch9 under different environmental condition. Using antibody that is specific for T570 site phosphorylated Sch9 or T737 site phosphorylated Sch9, we studied the regulation of the phosphorylation of PDK1 and PDK2 sites in Sch9 under different environmental factors and during chronological aging. Our results demonstrate the regulatory model of the phosphorylation of PDK1 and PDK2 sites in Sch9 during nutrient sensing, stress response, calorie restriction and chronological aging. The results also suggest a novel mechanism by which calorie restriction extends chronological lifespan that involves the regulation of the phosphorylation of Sch9 PDK1 site.

Abstract:Camptothecin derivatives have an obvious inhibitory effect on keloid fibroblasts proliferation. In order to improve the utilization rate of drug and provide a transdermal drug treat method, a non-alcoholic hyaluronic acid O/W type nanoemulsion without any chemical enhancers was made to encapsulate 10,11-methylenedioxycamptothecin (MD-CPT). We used transmission electron microscopy (TEM) and laser particle size instrument to survey the HA-GMS nanoemulsion morphology observation, and measured the particle size of (177.32±27.11) nm, the zetaelectric potential of -15.6±1.7, the PdI of 0.55±0.01 and the encapsulation efficiency of (77.85±1.29)%. Determination by MTT method was used to research the effect of biomaterial HA-GMS on HSF cells and HUVECs cells, and the relative cell viability range from 75%～95%, having good biocompatibility, and for keloid fibroblasts culture, growth inhibition rate was 28.2%.The transdermal effect of HA-GMS nanoemulsion carrying MD-CPT was obviously better than that of the control group (CPT MD-CPT ethanol solution), treating for 4 h, the cumulative drug permeation was (660.72±20.54) μg/cm² and (102.73±13.81) μg/cm² respectively, the HA-GMS nanoemulsion significantly increased the efficiency of MD-CPT through skin, which may provide a good drug delivery approach.