Abstract:Transfer RNAs (tRNAs) with classic clover structure, have been researched as a key component of cellular protein synthesis machine for decades. However, the pace of progress in the understanding of tRNA function is still staggering, especially in the role of tRNA as the precursor of potential molecules to regulate gene expression globally. Several recent studies suggest that some tRNA-derived small RNAs have been detected in many cell lines by deep sequencing. These cleavage products of tRNAs are indicated to interact with some important protein factors like Dicer and Ago family in microRNA processing system. In additional, luciferase reporter assay results implied that the small RNAs derived from tRNA might play some roles in response to the stress as regulatory molecules with microRNA-like features. If their regulatory functions were to be confirmed by more evidence, these newly revealed RNAs would provide expanding insight into the repertoire of small noncoding RNAs.

Abstract:Gamma band oscillation ranges from 30 to 100 Hz. It can be recorded in many brain areas such as somotosensory cortex, hippocampus and thalamus. The gamma band oscillation can be detected at different levels such as microscopic (spikes), mesoscopic (local field potentials, LFP) and macroscopic (electroencephalogram, EEG) level. GABAergic inhibitory interneuron network is considered as the main source of the gamma oscillation generation, and the cortical gamma oscillation is also related with the interaction of thalamo-cortical system. Gamma band oscillation is associated with sensory and cognition functions, in particular the feature binding, selective attention and memory processing.

Abstract:The present paper reviewed the evidence for scene consistency effect accumulated recently. Behavioral studies showed that participants performed better in naming, categorizing, searching and recognizing consistent objects (which appeared in usual context) than inconsistent objects (which appeared in unusual context). ERP studies demonstrated that inconsistent objects, compared with consistent objects, induced a larger negative-going wave (N390) especially in centro-parietal sites. fMRI studies revealed that PHC/PPA and RSC played important roles in scene processing. Theories proposed to explain the scene consistency effect were also discussed.

Abstract:Neuroscience research in China has stepped into the development of "golden period" in 21st century. As Prof. Poo pointed out, "Improving funding for research on neuroscience, a larger number of returning researchers with professional training abroad, a variety of international academic exchange", all of these created conducive environment for scientific research, promoted the development of neuroscience in China. 12 interesting reviews were published in the 2010 edition No.3 of Science in China Series C-life Sciences (SCLS), which summarized the progress from 2000 to 2009 and perspectives in four different directions of neuroscience research in China: developmental neuroscience, cellular and molecular neuroscience, mechanisms of neural disorders, and systems and computational neuroscience.

Abstract:Increase in nuclear calcium concentration has several biological effects which include controlling calcium-activated gene transcription. Using extracellular ATP to induce intracellular calcium transient as a model, Western blotting, immunofluorescence, real-time PCR as well as Ca²⁺ image studies were carried out. It was found that inositol 1, 4, 5-trisphosphate receptors (IP₃Rs) and endoplasmic reticulum protein 44 (ERp44) co-localized on the nuclear envelope and endoplasmic reticulum (ER). Extracellular ATP induced nuclear calcium transient via IP₃Rs and subsequently increased the cAMP response element binding protein (CREB) phosphorylation and the expression of c-Myc. However, all these were inhibited by 2-aminoethoxydiphenyl borate (2-APB), an IP₃Rs inhibitor, and by over-expression of ERp44. These results suggest that ERp44 inhibits gene transcription via IP₃Rs in HeLa cells.

Abstract:NPCEDRG is an NPC associated suppressive gene cloned by positional candidate cloning strategy. Its transcriptional down-expression has been shown in the cell lines and primary tumor tissues of NPC. Reintroduction of NPCEDRG into CNE2, a cell line derived from NPC, was effective to induce cell differentiation, control cell growth, and regulate the cell cycle. To uncover the molecular mechanisms underlying down-expression of NPCEDRG in NPC cells, bioinformatics approaches and functional assays in different tumor cell lines were used to identify and characterize the NPCEDRG core promoter and cis-acting elements. The conserved region from -180 to +235 bp was found in the potential promoter among 6 vertebrate species by the ECR browser, and there have several potential binding sites for transcription factors, such as CCAAT/NFY, STAT1 and SP1. To characterize the NPCEDRG core promoter, transient luciferase and/or EGFP reporter assay were carried out with the construct pGL3-en138. The results demonstrated that the core promoter is located at the conserved region from -146 to -8 nucleotides. Gel shift assay revealed the specific binding of some nuclear proteins to probes containing a putative CCAAT/NFY site，suggesting that the CCAAT/NFY site contributes to the regulation of NPCEDRG gene expression.

Abstract:To explore the possibility of foreign gene expression in transgenic silkworm mediated by non-transposon vector, a hIL-28A gene was inserted into the insect cells expression vector pIZT-V5-His to generate recombinant vector pIZT/V5-His-hIL-28A, the vector was transferred into silkworm eggs by sperm mediated gene transfer, screening for gfp gene and verified by PCR and Dot blot hybridization. Transgenic silkworms were obtained after a specific band with the molecular mass of 25 ku could be detected in transgenic silkworm by Western blotting using an goat anti-hIL-28A antibody, and the content of hIL-28A in the G3 generation transgenic silkworms estimated by ELISA was approximately 0.198, 0.32, 0.238 ng/g in freeze-dried whole bodies, posterior silk glands and fat bodies, respectively. These results suggested that a heterologous gene could be integrated into silkworm genome by non-transposon vector and expressed successfully.

Abstract:To explore the effects of the death receptor (mouse killer, MK) of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) on decidualization of mouse uterine stromal cells, both of the over-expression and siRNA of MK gene recombinant adenovirus were applied to infect the primary culture of mouse uterine stromal cells followed by decidualization induction with estrogen, progesterone plus cAMP. Seventy-two hours later, immunocytochemical assay and flow cytometry were used to detect the prolactin protein expression and apoptosis of decidualized cells, which were transfected with MK recombinant adenovirus (overexpression and RNAi). Moreover, each MK recombinant adenovirus was injected into the uterine horns of mice on the early morning of d4 of pregnancy. The number of implanting embryos was counted on d8 of pregnancy. The results showed that the levels of prolactin protein decreased significantly, but the apoptosis rate increased in the decidualized cells transfected with MK over-expression adenovirus. In the MK siRNA group, the prolatin levels were increased while the apoptosis rate was downregulated markedly. However, uterine injection of either the over-expression or the siRNA adenovirus led to dramatic decline the numbers of the implanting embryos. These results suggested that MK was involved in modulating the decidulization of mouse uterine stromal cells possibly through balancing proliferation and apoptosis of the decidualized cells.

Abstract:Mucin O-glycosylation plays important roles in many carcinogenic events, and it is initiated by the enzymes: UDP-GalNAc∶polypeptide N-acetylgalactosaminyltransferases (ppGalNAc-Ts). The association of ppGalNAc-T2 expression and Jurkat cells proliferation and migration was investigated. The RNAi and negative control shRNA were synthesized and then inserted into lentivirus vector YH1. After enzyme digestion and sequencing confirmation, each of the recombinant vectors and packaging vectors were cotransducted into 293T cells, and the recombinant lentivirus were packaged. Then Jurkat cells were infected by purified lentivirus, RT-PCR and Western blot showed that ppGalNAc-T2 mRNA and protein expression were remarkably decreased after RNA interference. Furthermore, the proliferation and migration abilities of Jurkat cells were detected. In conclusion, the recombinant lentivirus interfering vector was constructed targeting on ppGalNAc-T2 gene, and decreased expression of ppGalNAc-T2 gene inhibit proliferation and migration of Jurkat cells.

Abstract:MicroRNAs(miRNAs) are a class of small non-coding RNAs that regulate gene expression at post-transcriptional level. They play important roles in multiple physiological and pathological processes, including development, cell proliferation，apoptosis，metabolism and tumorigenesis, etc. Mouse B cell at different development stages were isolated by FACS and analyzed the miRNAs profile using TaqMan® Low Density Array. The data showed that 9 miRNAs were significantly up-regulated in the pre-B cells. Functional clustering and pathway analysis of 1102 predicted target genes of these miRNAs showed that about 4% of the genes involved in immune system processes, including Bcl2, Kit, etc. A dual luciferase reporter system and Western blot were used to validate the interaction between foxO1 and miR-19b, miR-142-3p, miR-106b, miR-182, miR-133b. The results show that miR-133b can directly regulate the expression of foxO1. According to the foxO1 expression profile of human and mouse, the expression pattern is negatively correlated with that of miR-133b, indicating that miR-133b may be involved in the regulation of foxO1 in B cell development.

Abstract:To get a better optimization expression of the Ustilago maydis CYP51 (P450-14DM, UmCYP51) protein in E. coli BL21(DE3), the different lengths of UmCYP51 gene that lacked the coding region for the putative membrane-spanning segment of the N-terminus were truncated. The first one is the wild type, the second one with 20 amino acids (60 base pairs) in N-terminus was truncated and the third one with 35 amino acids (105 base pairs) was truncated. Then these genes were incorporated into different expression vectors (pET28, pET32 and pGEX-KG) to construct nine recombinant expression plasmids (pET28-Um, pET28-Um-20, pET28-Um-35,pET32-Um, pET32-Um-20, pET32-Um-35, pGEXKG-Um, pGEXKG-Um-20 and pGEXKG-Um-35). The expression of recombinant plasmids were performed using 0.5 mmol/L of isopropyl β-D-thiogalactoside (IPTG) at 30℃. The culture harvested every 2 h up to 8 h. It was found that only recombinant plasmid pET32-Um-35 was expressed in E. coli BL21(DE3). Codon usage database (http//:www.kazusa.or.jp/coden) was used for the analysis of rare codon and software RNAStructure 4.5 was employed to study the mRNA secondary structure of translation initiation region. The results showed that rare codons rate in UmCYP51 gene is only 4.63%, the Rosetta (DE3) strain expressing some rare codons is not suitable for the protein expression of UmCYP51. Only the lowest energy of mRNA structure for pET32-Um-35 can obtained protein expression. These results are compatible with the experiments. Moreover, to design novel antifungal compounds against UmCYP51, based on the recently determined X-ray crystal structure human CYP51, a three-dimensional structure model of UmCYP51 was built through homology modeling using MODELLER 9V7 program. After refinement of the energy minimization and MD simulation using GROMACS 4.0.3 package, the UmCYP51 model was evaluated by PROCHECK Ramachandran plot statistics that indicated the designed model was in good quality. Commercial fungicide tebuconazole was docked into the model protein using Autodock 4.2.3 program to form the binding pattern of inhibitor with UmCYP51. The docking conformation of tebuconazole in the active site of UmCYP51 showed that the N-4 of the triazole ring was bound to heme iron with a distance about 0.245 nm. The hydroxy group of tebuconazole formed hydrogen-bonding interaction with the oxygen atom of carbonyl group for Ala265 with a distance about 0.245 nm. The mechanism of inhibitory activity of tebuconazole against UmCYP51 obtained from this study could aid in designing new antifungal compounds targeting this enzyme.

Abstract:Kinetic modeling of large-scale metabolic network require a generic enzymatic rate equation. In the generic form, kinetic parameters are clear and precise enough to correlate to experimental data and construct a database. Such a uniform form is easy to deal with arbitrary number of substrates and products in computation of dynamic modeling. The generic rate equation is symmetrical in both directions of reversible reaction and formally exact under the quasi-steady state condition. Here presented the rigorous derivation of generic rate equation from further three classical enzymatic rate equations and discussed the characters and uses of the generic form.

Abstract:In order to study the variation, dynamic equation of DNA sequences was established by the homology in nucleotide sequences, and further evolution distance d_y(selected evolutionary distance) between species was obtained. Selected evolutionary distance d_y was calculated in 4 nucleotide substitution models, and indicated the relationship among p-distance, d-distance and Г distance d_G. According to the characteristics of dynamic equations, selection model can be transformed into a linear regression problem. Then both of the parameter b and the average substitution ratio of nucleotide each year r were obtained by the Least Square Method. Take the mitochondrial DNA sequences of 16 species for example to illustrate the new evolution distance, and then evolution trees are constructed in order to compare different evolution distance. The results indicate that the new distance d_y is an efficient evolution distance to analyze DNA sequence.