Abstract:With the rapid advancement of the high resolution mass spectrometry, top-down proteomics becomes the reality. Proteome research on the intact protein level will provide more precise and more abundant biological information. For example, it can detect the relationship between the multiple post-translational modifications. Due to the genetic mutation, alternative splicing of RNA and various post-translational modifications, one gene may produce multiple protein forms, now called 'proteoforms'. Top-down proteomics will help identify the proteoforms. The three pillar technologies in top-down proteomics are separation, mass spectrometry and bioinformatics from the point of view on the entire proteins. This paper reviews these technologies and puts more emphases on the bioinformatics related topics, including the mass spectral preprocessing, the database searching algorithms and the localization of post-translational modifications.

Abstract:Disease similarity studies for understanding the pathogenesis of complex diseases, diagnosis, prognosis and drug development are important. Recently, researchers constructed Disease Ontology disease (DO) by integrating a variety of disease terms, which builds up the foundation of disease similarity measurement based on DO. We summary disease similarity calculation methods based on DO-related information in this paper and discuss the issues and challenges in disease similarity measurement, offer helpful reference for further research.

Abstract:Protein directed evolution is widely used to improve enzymes, particularly for industrial biocatalytic processes and construction of cell factories. It is an efficient and powerful tool to improve and optimize natural proteins in order to generate robust biocatalysts for practical applications. In addition, optimization of metabolic pathways, regulation of functional regulatory systems, and development of desired complex phenotypes in industrial host organisms have all been achieved by way of protein directed evolution. Numerous in vivo and in vitro methods have been developed for the efficient evolutionary effects, especially in high mutation rate and rapidly high-throughput screening capabilities. Some of the methods have only recently been applied for general use and are just beginning to find greater application. In this review, we summarize some of the new methods for mutant libraries generation, including random evolution, semi-rational evolution and rational evolution. And current state-of-the-art screening techniques in protein directed evolution are also reviewed. Advancements are discussed with respect to the state of the art in diversity generation and high-throughput screening capabilities. Meanwhile, limitations and remaining challenges are also pronounced.

Abstract:Glucose metabolism is one of essential biochemical processes for the survival of living species. In mammals, glucose is utilized in different ways among the different types of cells under different situations. The cells under plenty of oxygen can use oxidative phosphorylation during aerobic respiration. Under hypoxic condition, cells repress oxidative phosphorylation and ferment glucose to lactate. However, some cells choose “Warburg effect”, an activated glycolytic flux even under normoxia, as a way to metabolise glucose. It is known that Warburg effect is favored by tumor cells. Recently, accumulating evidences show that Warburg effect is also involved in mammalian reproduction. Here we summarize the advances on Warburg effect in mammalian reproduction and fertility-related diseases.

Abstract:RNA processing and degradation are essential steps in gene expression regulation that influences many aspects of development and growth. In eukaryotes, virtually all RNAs are processed from longer precursors to generate mature RNAs. After completing their functions, these RNAs enter to the decay pathway. 3′- exoribonucleases, 5′ -exoribonucleases and endonucleases were involved in RNAs decay. In eukaryotic cells, part of 3′-exoribonucleases activity is contributed by the exosome, a complex composed of nine core subunits and several auxiliary components. The exosome has been shown to play an important role in processing and decaying of various RNA in animals, yeast and plants. In this paper, we briefly review the research advance of exosome in eukaryotes, and focus on the function mechanism of the exosome.

Abstract:P53 pulses refer to the fluctuation of the p53 protein levels in the cells in a periodic or repetitive manner. The mechanisms for triggering P53 pulses lie in several kinds of the positive and negative feedback loops in the p53 network. Two core feedback loops include the p53-Mdm2 negative feedback loop and Wip1-ATM-p53 negative feedback loop. Owing to the existence of these feedback loops, a limit cycle and a given number of P53 pulses were generated when the p53 system entered the limit cycle region. Pro-apoptotic regulator and P53 existing in different form are gradually accumulated as the number of P53 pulses increases and then the irreversible cell fate is determined by opening apoptotic "switch" above the threshold level. The cell fate can be determined by the number of P53 pulses partly, but it also has close relationship with its frequency, amplitude and wave form. Therefore, it is of great significance for the mechanism investigation of diseases development, prevention and treatment.

Abstract:The biological function of a protein depends not only on the correct primary amino acid sequence, but also on achieving its native three-dimensional structure. Thus, correct folding of a protein is of great significance to life activities. Due to the complex and crowded intracellular environment, the folding of many proteins is often difficult in vivo. One category of proteins, called chaperones, help other proteins to fold correctly. Chaperones can recognize and stabilize other instable protein to assist its folding. Recent studies showed that, the ring-shaped chaperone GroEL can repetitively unfolding kinetically trapped protein folding intermediate, giving the intermediate another chance to refold, thus increases its overall folding rate. The detailed mechanism of GroEL assisted folding is still under controversy. In this review, we briefly summarize the recent progress in the study of the latter mechanism.

Abstract:Cellular repressor of E1A-stimulated genes (CREG) has been shown to be ubiquitously expressed in human and mouse tissues. However, its physiological functions and possible involvement in pathological processes remain unknown. To explore pathogenesis of vascular remodeling and possible role of CREG, we established an injury model of the mouse carotid artery in the present study. High-resolution small-animal ultrasound, Masson staining, immunohistochemistry, RT-PCR and Western-blot were used to detect the intima-media thickness, collagen content, the change of collagen typeⅠ and CREG expression of arterial wall at different time after arterial injury. CREG was expressed in normal arteries. The expression of CREG mRNA and protein of the arterial wall was markedly down-regulated after injury of mouse carotid artery, and reached its lowest value on the third day after arterial injury, with close correlation to the process of vascular remodeling (increase in mRNA and protein level of collagen typeⅠ). CREG expression was gradually restored on the seventh day, and almost returned to normal levels on fourteenth day and twenty-eighth day after arterial injury. In contrast, injured arteries developed marked vascular remodeling after 7 days as manifested by increase in intima-media thickness, narrowing of the vascular lumen, collagen content as well as mRNA and protein level of collagen typeⅠ. There were negative relationships between CREG expression and vascular remodeling at the early time of artery injuries. The expression of CREG was decreased at beginning and then increased, but the degree of vascular remodeling was continued to exacerbate. These data strongly suggest that CREG is involved in the development of vascular remodeling after arterial injury, and that injury-induced CREG down-regulation may contribute to the progression of vascular remodeling.

Abstract:To investigate the proliferative effects and the synergistic mechanism of irinotecan combined with norcantharidin in human gastric cancer cell line BGC-823. BGC-823 cells were treated with CPT-11 30, 60, 90, 120, 150 μmol/L and NCTD 30, 60, 90, 120, 150 μmol/L alone or in combination with the fixed constant ratio (1∶1) and with the complete cross-over concentrations (as show above) for 24, 48 and 72 h, and the combination of CPT-11 and NCTD with a sequential schedule were combined for culturing BGC-823 cells for 24 h. Cell proliferation was investigated by MTT assay, and the combination effect was evaluated by Chou-Talalay method. Cell cycle and apoptosis in BGC-823 cells treated with CPT-11 60 μmol/L and NCTD 60 μmol/L alone or in combination (60∶60) μmol/L and combination with a sequential schedule for 24 h were determined by Flow cytometry. The expression of Pdcd4 and p53 in BGC-823 cells treated with CPT-11 30, 60 μmol/L and NCTD 30, 60 μmol/L alone or in combination (30∶30, 60∶60) μmol/L for 24 h was detected by Western blotting. Compared with treatment with CPT-11 and NCTD alone, the combination of them increased the proliferation inhibition, and the IC₅₀ were significantly decreased (P < 0.05). The IC₅₀ values of the combination for 24, 48 and 72 h were 2.83, 3.15, 2.19 fold and 2.66, 3.11, 2.45 fold respectively compared to BGC-823 cells treated with CPT-11 and NCTD alone. The results indicated synergistic effect. The sequence of CPT-11 followed by NCTD showed a stronger inhibition than the sequence of NCTD followed by CPT-11 (P < 0.05), and it was superior to co-administration (P < 0.05). For 24 h, CPT-11 60 μmol/L triggered both S and G2-M phase arrest (P < 0.01) in the BGC-823 cells, and NCTD 60 μmol/L induced cell cycle arrest at G2-M phases and apoptosis (P < 0.05) in the BGC-823 cells. The combination of CPT-11 and NCTD (60∶60) μmol/L increased the G2-M phase arrest. Compared with the sequence of NCTD 6 h first followed by CPT-11 and co-administration, the sequence of CPT-11 6 h first followed by NCTD increased the S phase arrest (P < 0.05) and apoptosis in the BGC-823 cells. CPT-11 30，60 μmol/L up-regulated the expression of Pdcd4 (P < 0.05) and down-regulated the expression of p53(P < 0.05) after 12 h; NCTD 30，60 μmol/L down-regulated the expression of Pdcd4 (P < 0.05) and up-regulated the expression of p53(P < 0.05) after 12 h; The combination (30∶30, 60∶60) μmol/L up-regulate the expression of Pdcd4 and p53(P < 0.05). The combination of CPT-11 and NCTD has a synergistic effect mainly due to the fact that it can induce the G2-M phase arrest, and up-regulate the expression of Pdcd4 and p53 as the tumor suppressor. The combination of CPT-11 and NCTD with a sequential schedule has some impacts on the growth of BGC-823 cells. The sequence of CPT-11 followed by NCTD shows a stronger inhibition than the sequence of NCTD followed by CPT-11 and co-administration, and it may be related to the increase of S phase arrest and apoptosis. Pdcd4 and p53 protein may have a negative regulation in BGC-823 cells.

Abstract:We have examined the orientation, direction selectivity and receptive field size by extracellular recording for 82 V1 neurons of cat. Based on the area-summation measurements, 82 units were classified as 52 suppressive surround cells (SSCs) and 30 non-suppressive surround cells (nSSCs). Our results showed nSSCs have much sharper orientation selectivity and narrower tuning width than SSCs. No significant difference was found in direction selectivity between SSCs and nSSCs. SSCs have larger peak firing rates than the nSSCs. Two methods were used in measuring the receptive field size, but arises different results in comparison of SSCs and nSSCs.

Abstract:In this paper, to analyze the functional influence of the early stage of global ischemia on cardiac electrical activity and subsequently on ventricular arrhythmia, we take into account of three main pathophysiological consequences of ischemia: hyperkalaemia, acidosis, and anoxia, and develop a human ventricular cell and tissue ischemic model that combines a detailed biophysical description of the excitation kinetics of human ventricular cells. Based on the model, the APDR curves, ERPR curves, vulnerable window, and CVR curves under control and ischemic condition are computed separately. The experimental results show that global ischemia can reduce APD, and slow down CV. Meanwhile since global ischemia decreases slope of APDR and increases ERP, the induced re-entry can be maintained stably which is not prone to degenerate into ventricular fibrillation. And due to a comparatively longer ectopic stimulation length to ensure the formation of reentry, global ischemia decreases the probability to arrhythmia in some extent although the increased tissue vulnerability.

Abstract:The incidence rate of epithelial ovarian cancers ranks third among female reproductive system cancers, and its mortality rate stands first among the list of gynecologic tumors. The standard mode of treatment is cytoreductive surgery (debulking) plus the administration of platinum-based chemotherapy drugs. About 70% of advanced patients who receive standard treatments can achieve clinical remission. However, a certain percentage of patients with clinical remission will still experience tumor recurrence, metastasis, and drug resistance. this study focuses on the occurrence process of EMT in SKOV3 cells, which is mediated by RAC1 activation, as well as the relationship between the process of cell sensitivity and cisplatin (CDDP), and the ability of invasion and metastasis.