Abstract:In the early 1990s, focusing on the total sequencing and annotation of the complete human genome as its core mission, the Human Genome Project (HGP) was initiated under the leadership of the USA. Since China joined the HGP in 1999, the genomics in China developed rapidly in the past ten years, establishing several genome centers with advanced technology platform, and organizing many grand scientific projects. The development of genomics lead to an unprecedented development in life science research and biotechnology development in China. To display the progress of genomics research in China, the first issue of Sci China Ser C-Life Sci (2009) organized a series of reviews focusing on this special topic. Some reviews analyze the future trend of genomics research and its scientific impact based on the technical perspectives of genomic sequencing, genotyping and functional genomics, while the others present the significant change of research strategy and technology brought in by the HGP with respect to liver cancer, immunology, and medical, environmental and industrial microbiology.

Abstract:Kindlins are a group of newly identified focal adhesion proteins, including Kindlin-1, Kindlin-2, and Kindlin-3. Kindlins possess high homogeneity and conservation evolutionarily, involving in the regulation of many important cellular physiological functions, such as cell migration, liferation, and differentiation. Through the interaction with the cytoplasmic domain of β integrin, Kindlins play important roles in cell-extracellular matrix adhesion, cell-cell junctions, cytoskeleton remodeling, and integrin-mediated bidirectional signaling. Abnormities of Kindlins are associated with the etiology and progression of some genetic diseases, cardiovascular diseases, and cancers. The further elucidation of the mechanisms regulating the cellular functions mediated by the interaction between Kindlins and integrins will not only improve our knowledge about cell adhesion and migration, but also the therapeutics of Kindlins-related diseases.

Abstract:The sirtuins are a highly conserved family of NAD⁺-dependent deacetylase enzymes. Recently, the mammalian sirtuins have been connected to an ever widening circle of activities that encompass cellular stress resistance, genomic stability, tumorigenesis and energy metabolism. The research progress of sirtuin and its relationship with aging were summarized.

Abstract:High-throughput mass spectrometry-based proteomics is developing rapidly in recent years. A key and essential issue in proteomics data processing is to identify proteins via tandem mass spectra. De novo peptide sequencing approach is database independent, which is a distinct advantage compared to database searching approach, so it can be used to analyze the data of new organisms or unsequenced organisms. De novo peptide sequencing problem is briefly described at first, and then the state-of-the-art of this problem is introduced from different aspects, which include the strategies with their advantages and disadvantages, frequently used algorithms and tools, criteria for algorithm assessment, and frequently used datasets for algorithm comparison. At last, the characteristics of some algorithms are summarized and some possible improvements of de novo peptide sequencing algorithm design are proposed.

Abstract:Six internal protein gene segments of attenuated, cold-adapted(ca), temperature -sensitive (ts) influenza A/Ann Arbor/6/60 ca (H2N2) and HA, NA gene segments of A/California/07/2009ca were introduced to plasmid pAD3000 carrying polⅠ and polⅡ promoters, and rescued the reassortant virus from Vero cell using reverse genetics technology. The reassortant has the attenuate characters, ca and ts, the TCID₅₀ is 7.5, HA titer maintain at 1∶256 and EID₅₀ is 8 which was detected using SPF eggs. The stable of reassortant is determined by RT-PCR gene segments from virus which were propagated in eggs. The morphology of reassortant conform the wild type virus. In order to test the immunogenicity, the reassortant viruses were purified. Mice were intranasally immunized and intramuscular injected with inactive whole virus as control. The high HI titer can be detected in both groups, seems hinger in i.m.(intramuscular) immunized groups (P=0.044), but higher IgA titer can only detected in i.n.(intranasal) immunized group. Compared with i.m. immunized group, higer pro-inflammation cytokines IL-1β, TNFα, IFN-α were tested in i.n. groups, means faster and stronger mucosal immune response was induced. Virus load were detected in lung, brain, spleen 4 days after immunization to determine the safety of reassortant as vaccine candidate, no detectable virus were found. All results show that the vaccine candidate can be used for vaccine production.

Abstract:In order to study the effects of extracellular matrix (ECM) protein micropatterns on biomaterials surfaces fabricated by microcontact printing (μCP) on human chondrocytes adhesion, spread and protein expression, the bone morphogenetic protein 2 (BMP-2) was printed onto polystyrene (PS) surface to fabricate the ECM protein micropatterns by μCP. Three kinds of excellent micropattern were obtained successfully according to the fluorescent images. The human chondrocytes were seeded on PS (control samples), BMP-2 coated PS surface and PS surface with BMP-2 micropatterns, respectively. As compared with control samples, the human chondrocytes on BMP-2 coating exhibited better growth and spread behavior, at the same time, the BMP-2 coating also cannot promote expression of collagenⅡ and Ⅵ. On the other side, the results concerning BMP-2 micropattens indicated that the protein micropattern surfaces have significant influence on cell adhesion, spread, alignment and functions. The cells preferentially adhered on micropattern protein zones. The micropattern shape and its sizes affected not only the cell adhesion morphology and spread degree but also the typeⅡ and Ⅵ collagen expression. The spread behavior of cell has some positive connections with protein expression and the cell with more spread expressed more typeⅡ and Ⅵ collagen. These results suggested that the ECM protein micropatterns can effectively regulate human chondrocytes growth and functions.

Abstract:Alveoli are the key functional units of the lungs where gas exchange take place. But the regulation of alveolar morphogenesis is not completely understood. The basic strategies of mammalian lung development can be generally divided into two stages: epithelial branching morphogenesis, and septal formation. P311 was identified previously as a gene that specifically expressed during lung septal formation. In order to further explore the potential effects of P311 during lung development, a yeast two-hybrid screen was performed to identify P311 interacting partners. A recombinant P311 fused with the Gal4 DNA binding domain was used as the bait protein to screen a cDNA library constructed from developing mouse lungs. After confirmed by coimmunoprecipitation (CoIP) and bimolecular fluorescence complementation (BiFC) experiments, SPARC (secreted protein, acidic and rich in cysteine) was identified as a P311 binding protein. In further studies, it was found that SPARC showed similar temporal expression pattern with P311 during lung development. Double immunostaining indicated SPARC and P311 colocalized in alveolar epithelium and myofibroblast in P11 mouse lung sections. Taken together, the data suggested that P311 might have a close connection with SPARC on its influences on lung development.

Abstract:Pseudolaric acid B (PAB), a major biologically active component of "TuJinPi" (the root bark of Pseudolarix kaemferi Gordon), exhibited cytotoxicity in many human tumor cell lines. High content analysis (HCA) is a fluorescence microscopy-based automated technology used for quantitative analysis of multiple targets in cells. HCA could yield rich information about the temporal-spatial dynamics of the fluorescence-labeled cell constituents. The mechanism of inhibitory effects of pseudolaric acid B on human breast cancer MCF-7 cells was explored by high content analysis and flow cytometry. As shown by sulforhodamine B assay, PAB inhibited the proliferation of MCF-7 cells in a dose-dependent and time-dependent manner, and the 50% inhibition concentration (IC₅₀) for 72 h was (1.80±0.33) μmol/L. Flow cytometry (propidium iodide staining) showed that, after treatment with PAB for 24 h, the proportion of MCF-7 cells at G2/M phase could increase to about 93%. Flow cytometry (annexin V-FITC and propidium iodide staining) showed that, PAB induced apoptosis of MCF-7 cells. High content analysis showed that: after treatment with PAB for 16 h, the mitotic index of MCF-7 could increase to about 40%, and cyclin B1 was upregulated; PAB caused dose-dependent disassembly of microtubules and inhibited the formation of mitotic bipolar spindles; PAB induced increase of mitochondrial mass; PAB induced grape-like giant nuclei indicating mitotic slippage in MCF-7 cells. These results suggest that PAB inhibits MCF-7 cell proliferation and induces apoptosis, these inhibitory effects may be related to disassembly of microtubules, spindle abnormalities, mitotic arrest and increase of mitochondrial mass.

Abstract:The cDNA of UCP5 gene was obtained by 3′ and 5′ RACE, the length was 1 611 bp. One A→T mutation was found at -1 567 bp of UCP5 gene. The mutation resulted in the change of transcript factors CdxA, HNF-1, Sox-5, GATA-2. Different genotypes were detected in 524 Jinhua× Pietrain pigs using PCR-RFLP, and the relationships between the genotypes and live weight, muscle weight of hind leg, fat weight of hind leg, average back-fat thickness, back-fat thickness in the 6th～7th rib, area of loin and leaf fat weight were analyzed. The statistical analysis showed that animals of the AA genotype had the highest live weight, which was significantly higher than that of BB genotype and obviously higher than that of AB genotype. For muscle weight of hind leg and hind leg fat weight, AA genotype was also higher than AB and BB genotype. By Real-time quantitative PCR, UCP5 expression was analyzed in heart, liver, spleen, lung, kidney, loin, abdominal adipose and cerebral tissues. The results showed that UCP5 existed in all tissues, and the expression of UCP5 was the majority in cerebral tissue and lung. The result of t-test showed that the distribution of UCP5 in loin of Dalan pigs was significantly higher than that of Jinhua.

Abstract:Prediction of protein folding rate is one of the most important challenges in contemporary biophysics. Over the past few years, many researchers have devoted great efforts to reveal the major determinants of protein folding rate, and many parameters and methods have been proposed successively. However, the interaction of amino acids and the sequence order information have never been considered as a property for predicting protein folding rates. It was proposed a novel method, which adopted Chou's pseudo-amino acid composition to extract the sequence order information, used Monte Carlo method to choose the optimal feature factors, and established the linear regression model to predict the protein folding rate. This novel method can predict protein folding rate from amino acid sequence without any knowledge of the tertiary or secondary structure, or structural class information. Using the Jackknife cross validation test, for the largest dataset yet studied including 99 proteins, it was found that the predicted folding rates correlated well with the experimental values; the correlation coefficient is 0.81, and the standard error is 2.54. The prediction quality is excelled with most existing sequence-based methods. The result implies that the sequence order information plays an important role in protein folding.

Abstract:Timing of the first zygotic cleavage is related to the developmental potential of mammalian embryos. This phenomenon in porcine parthenogenetically activated (PA) and somatic cell nuclear transfer (SCNT) embryos was documented. In vitro matured pig oocytes were either activated parthenogenetically or microinjected with a somatic cell, followed by electro-fusion. At 24 h post activation(hpa), PA and SCNT embryos were assessed visually, and cleaved embryos were moved into new culture wells. This process was repeated at 36 hpa or 48 hpa. Embryos in different groups were allowed to develop for 6 days in culture. The relationship between embryo developmental competence and the first zygotic cleavage at different timing (early-cleaving, 20～24 h; mid-cleaving, 25～36 h; late-cleaving, 37～48 h and unselected controls, 20～48 h) was evaluated by the proportions of cleaved embryos developed to blastocysts and expanded blastocysts (EB), and blastocyst total cell number. For PA embryos, the proportion of early-cleaving embryos that developed to blastocysts was significantly higher than that of mid-cleaving, late-cleaving and controls (P < 0.05; 54.0% vs. 19.6%, 5.4% and 18.7%, respectively); a similar pattern was noted for the formation of EB. For SCNT embryos, the proportion of early-cleaving embryos developing to blastocysts was not significantly higher than that of mid-cleaving embryos (32.2% vs. 23.5%), but the late-cleaving embryos had poor developmental competence to blastocysts (6.3%). Early-cleaving SCNT embryos showed a significant higher competence developing to expanded blastocysts than the mid-, late-cleaving and unselected control embryos (P < 0.05; 18.9% vs. 5.9%, 3.1%, 7.4%, respectively). Total cell number in the blastocysts declined across the three cleavage-timed groups. Developmental potential of SCNT cloned embryos was assessed in vivo by transferring early-cleaving (< 24 h) and unselected (time of cleavage up to 48 h not determined) embryos into recipient gilts. Litter size and cloning efficiency (piglets born/transferred embryos) in recipients of early-cleaving embryos were significantly higher than those in recipients of unselected embryos (4.7 vs. 2.1 piglets; 3.9% vs. 0.9%). The data demonstrate that the developmental potential of early-cleaving SCNT embryos is higher than that of later-cleaving embryos, thus suggesting that timing of the first zygotic cleavage can be utilized as a useful parameter for indicating developmental potential of porcine cloned embryos.