Abstract:先生垂风范　来者当勉之(《生物化学与生物物理进展》编委会、编辑部)
      贝时璋院士生平
      百年耕耘 功绩卓著
      继承和发扬贝老师的精神遗产(杨福愉)
      秉承贝老治学理念 推动我国生物物理学持续发展(徐 涛 杨星科)
      百岁寿星　科学巨擘(梁栋材 王书荣)

Abstract:Developmental dyslexia is a specific learning disability. The cerebral mechanism of development dyslexia is an important topic that has fascinated many researchers. With the introduction of brain imaging in studies of cerebral mechanism of development dyslexia, many achievements have been made. Studies of developmental dyslexia structure image found that development dyslexia showed brain structure abnormal in the parietotemporal region, occipitotemporal cortex, inferior frontal gyrus, and cerebellum et al, manifesting either in one specific area or by the asymmetry of one area; the functional image studies revealed that development dyslexia showed activity abnormal in most regions that proved to display structure abnormality; studies of brain functional connectivity demonstrates that the abnormality of development dyslexia happened not only in the connection between front-back part in one cerebral hemisphere, but also in the connection between the two hemispheres. In addition, some studies indicate Chinese development dyslexia has different brain mechanisms compared to that of alphabetic languages. These findings provide valuable insight for future developmental cerebral mechanisms research and for the expansion of Chinese development dyslexia research.

Abstract:Gold nanorods is a capsule-shaped gold nanoparticles. Gold nanorods give rise to two absorption peaks corresponding to their plasmonic modes, transverse mode and longitudinal mode, corresponding to light absorption and scattering along the short and long axis, respectively. The longitudinal surface plasmon resonance can be tuned by adjusting their aspect ratio from the visible to the NIR region and extremely sensitive to changes in the dielectric properties of the surroundings including solvents, adsorbates, and the interparticle distance of the gold nanorods. This unique optical property of gold nanorods opens up fascinating applications in biological and chemical sensors. Optical properties and biomedical application of gold nanorods are introduced, and its future research prospects are discussed.

Abstract:Agrobacterium tumefaciens can transfer a DNA fragment (T-DNA) from its Ti plasmid to host plant and integrate the T-DNA fragment into host cell nuclear genome. Agrobacterium-mediated T-DNA transfer is the most widely used genetic transformation method for plant. The T-DNA is delivered in the form of single-stranded T-DNA-protein complex (T-complex) by the polar-located Agrobacterium type Ⅳ secretion system (T4SS) to the host cell. T4SS is ancestrally related to bacterial conjugation machines and still used by many plasmids as conjugation channel. Moreover, T4SS is also the secretion channel that used by many human bacterial pathogens to inject the effector proteins to host cells, thus contributing directly to the bacterial pathogenicity. Therefore, in addition to the technical application as a gene vector to create transgenic plants, Agrobacterium-mediated T-DNA transfer also provides a fascinating model system to study the intercellular transfer of macromolecules. The study on the molecular mechanism of T-DNA transfer arouses extensive interest and progresses rapidly in recent years. Here the recent advances in research on T-complex formation and T-complex transfer in Agrobacterium cell are reviewed.

Abstract:Tumor genesis and development often result from deregulation of important biological pathways at the gene expression level. Although there has been much work focused on searching gene sets using gene expression data or other prior information, proper statistical testing of the gene sets is still an open question. Most studies have expanded the testing method of a single gene into the gene sets. Parametric statistical analysis of gene sets ( p-SAGE ) was presented for determining the significant gene sets or pathways associated with a phenotype of interest. The method was applied to brain tumor experiments to identify many gene sets. Some of the newly discovered gene sets were related to signal transduction and immunity. This simple and effective method gives useful biologically meaningful results.

Abstract:Nuclear factor κB(NF-κB) is an important cellular transcription factor. The important role of NF-κB-mediated cell signal transduction pathway in apoptosis is a hot topic at home and abroad. In order to discover new regulators in NF-κB signaling pathway, a high-throughput cell-based screening model based on dual luciferase reporters system was established, a number of genes that can activate NF-κB signal pathway were obtained by screening of 439 novel function genes. Among them, TMEM9B can obviously activate NF-κB signaling pathway. Further experiments showed that TMEM9B activated NF-κB signaling pathway in a dose-dependent pattern. Western blotting and EMSA experiments confirmed that TMEM9B can promote the degradation of IκBα (a cytoplasm inhibitor of NF-κB), and cause NF-κB shift from the cytoplasm to nucleus. At the same time, flow cytometry result demonstrated TMEM9B can induce apoptosis in HEK293T and HeLa cells. In short, a stable and effective screening system for NF-κB has been established, through which TMEM9B was identified to be able to significantly activate NF-κB signal transduction pathway and thus cause cells apoptosis.

Abstract:Human ribosomal DNA (hrDNA) targeting vector pHr is a homologous recombinant plasmid for human genome which developed in the State Key Laboratory of Medical Genetics. pHr was used to construct a recombinant plasmid pHr-CMG expressing mda-7/GFP fusion gene and its efficacy in the hepatocellular carcinoma cell line Bel-7402 was investigated. The expression of mda-7/GFP fusion gene was detected by fluorescent microscope, RT-PCR and Western blotting, and its function was detected by cell-cycle analyses, MTT assay and Hoechst33258 staining. The results demonstrated that pHr-CMG vector could express MDA-7/GFP fusion protein effectually and the mda-7 gene could induce cell apoptosis and proliferation suppression in Bel-7402 cell line, which might be caused by the G2/M cell cycle arrest. These results also suggested that human ribosomal DNA targeting vector system and the pHr-CMG vector may be applied in further gene therapy researches for hepatocellular carcinoma.

Abstract:Conditional forebrain-specific presenilin-1 and presenilin-2 double knockout mice (dKO mice) exhibit several neurodegenerative phenotypes of Alzheimer’s disease (AD) pathology, such as tau hyperphosphorylation, neuron loss, forebrain cortical shrinkage and memory impairment. By using capillary electrophoresis assay, monoamine neurotransmitters in forebrain cortex, hippocampus and other forebrain region of dKO mice aged at 6, 9 and 12 months were measured to illustrate the relationship among presenilins function deficiency, neurodegenerative phenotypes and monoamine neurotransmitters. Data showed that levels of monoamine neurotransmitters in forebrain cortex of dKO mice were significantly decreased at 6 months when compared to controls, while as mice getting older, levels of monoamine neurotransmitters increased to that of controls, or even higher. In hippocampus, 5-hydroxytryptamin and epinephrine in dKO mice had a significant increase at 6 months, followed with a significant increase of each monoamine neurotransmitter at 12 months age. In other forebrain region, 5-hydroxytryptamin and dopamine had a similar level between control and dKO mice at 6 and 9 months but a significant decrease at 12 months; however, level of norepinephrine and epinephrine were significantly decreased at 6 and 12 months except epinephrine of 6 months. These results demonstrated that knockout of presenilins genes could lead to the variation of monoamine neurotransmitters, and the variation profiles were different among forebrain cortex, hippocampus and other forebrain region. However, whether presenilins deficiency caused the variation of monoamine neurotransmitter directly or not, and how about the effects of variation of monoamine neurotransmitters on AD-like pathology need to be further analyzed.

Abstract:In order to investigate the interactions between first- and second-order motion perception systems, 14 adult subjects with normal or correct to normal visual acuity were recruited and divided into two groups. Then these two groups were trained, in their parafovea, to discriminate the direction of first- and second-order motion gratings respectively. The spatial frequency of the gratings used in study was fixed at 2 cycles/degree and the temporal frequency was fixed at 8 Hz during training. Contrast sensitivity of subjects in these two training groups for first- and second- order motion was measured before and after 7 days’ training to estimate the effects of training. In addition, the differences between the two training groups(14 subjects) and another control group (11 subjects) were studied. The results showed that: 1) the training with first-order motion gratings can improve subjects’ performance in first-order motion direction discrimination but the improvement can’t be transferred to the performance in second-order motion task; 2) the training with second-order motion gratings can improve subjects’ performance in both first- and second-order motion direction discrimination tasks. In conclusion, an “asymmetric transfer” occurred between the training effect of first- and second-order motion gratings. These results indicate that there are two mechanisms for perceiving first- and second-order motion respectively. However, they are not completely different from each other but only partly separated.

Abstract:TLR4-MD-2 complex plays a key role in LPS recognition and its signal transduction. These steps are the vital elements of the host’s defensive reaction. Studying the functional domain of TLR4 and MD-2 is very important to further understand the mechanism of LPS signal transduction. It was studied the interaction domain of TLR4 and MD-2 in living cells based on gene mutation, gene transfection and fluorescence resonance energy tramsfer(FRET) which is considered as one of the best methods used for intracellular protein-protein interaction study. CY-15P which was fused by CFP and YFP through 15 neutral amino acids was used as positive control, while co-expressed CFP and YFP proteins were used as negative control. The results showed that the ability of TLR4 binding to MD-2 decreased dramatically after the deletion of Glu²⁴～Met⁴¹ in N terminal of TLR4. Aggregation of TLR4 to LPS stimulation was observed, however, TLR4 without the Glu²⁴～Met⁴¹ mutation did not aggregate. All these results indicated that TLR4 Glu²⁴～Met⁴¹ might be the interaction domain of TLR4 binding to MD-2 and participate in the aggregation effect of TLR4 upon LPS stimulation.

Abstract:Dorsal root ganglion (DRG) neurons are primary sensory neurons that conduct neuronal impulses related to pain, touch and temperature senses. To comprehensively identify proteins of plasma membrane (PM) from small amount of dorsal root ganglion (DRG) neurons, a proteomics strategy that utilizes aqueous polymer two-phase partition in combination with differential velocity centrifugation was adopted to enrich the PM, followed by SDS-PAGE, CapLC-MS/MS and bioinformatics analysis. Western blot analysis showed that the concentration of PM in purified plasma membrane(PPM) was 2.3 times higher than that in crude plasma membrane(CPM), 15 times higher than that in whole tissue lysate (WTL). By searching against the rat IPI protein sequence database, a total of 729 non-redundant proteins were identified from the PM preparation, of which 547 had a gene ontology (GO) annotation indicating a cellular component, and 159 (21.8%) were unambiguously identified as PM proteins. A data set of plasma membrane proteins of DRG as well as a tool to study PM proteins were provided in a small amounts of sample.

Abstract:Whole mount in situ hybridization with BHC80 RNA probe showed that BHC80 was expressed in zebrafish central nervous system. Morpholino-modified antisense oligonucleotide was injected into zebrafish zygotes to knock down BHC80 expression. BHC80 knockdown resulted in striking decrease of erythrocytes and accumulation of erythrocytes at PBI. Further investigation of embryonic erythrocytes marker βe3 globin and hematopoiesis transcription factors gata1, c-myb and lmo2 by in situ hybridization showed that the erythroid progenitors marked with gata1 in BHC80 knockdown embryos were high proliferation and their differentiation were delayed, which led to decrease of erythrocytes and accumulation of erythrocytes at PBI. Both in situ hybridization and microangiography indicated that vasculature pattern of BHC80 knockdown embryos were almost normal.

Abstract:ATP-binding cassette protein E (ABCE1) has been annotated as an RNase L inhibitor in eukaryotes. Previous study showed that the overexpression of ABCE1 was related with the occurrence and clinical stage of lung adenocarcinoma. As an initial investigation into the novel functions of ABCE1, siRNA-expressing vectors targeting sites of the ABCE1 gene were constructed from RNAi-Ready pSIREN-DNR-DsRed-Express vector. Cultured 95-D and NCI-H446 lung carcinoma cells were transfected with the siRNA-expressing vectors using FuGENE 6 and transfection efficiency was determined by using fluorescence microscopy. The expression level of ABCE1 protein was determined by Western blot and immunofluorescence staining. Cell viability was determined by MTT, cell cycle was analysed by flow cytometry.The apoptotic rate was observed by ELISA. Fluorescence microscopy showed a satisfactory transfection efficiency which was about 42.70%. Cell viability and the growth fraction were markedly suppressed,whereas the apoptosis was significantly increased in SiRNA-95-D and SiRNA-NCI-H446 cells than controls(P < 0.05). It can be concluded that the siRNA targeting ABCE1 gene shows a dramatic inhibitory effect on RNA transcription and protein expression and a promoting effect on the apoptosis in 95-D/NCI-H446 cells, which offers a reliable base for the further in vivo experiment.

Abstract:The female sheep reproductive tracts were freshly collected from a local meat processing plant and used as experimental materials. Two antibacterial peptides were isolated and characterized from female sheep reproductive tracts by two consecutive chromatographic steps. The peptide isolation procedures included acetic acid extraction, dialyzed, gel filtration chromatography on Sephadex G-50, and reverse phase high-performance liquid chromatography (RP-HPLC). Their molecular mass were 4 820.47 u and 4 012.5 u, respectively, analyzed by MALDI-TOF-MS. The partial N-terminal amino acid sequences of two peptides were determined as AYVLDEPKP and YDSGA, respectively, by Edman degradation. The antimicrobial activity was tested during each purification step by the radial diffusion plate assay and broth microdilution method. These two peptides showed good antimicrobial activities against reference strains of G⁺(S. aureus ATCC2592 and Streptococcu ATCC55121), G-(E. coli ATCC25922) and fungi(C. albicans ATCC2002). The peptides did not show active hemolytic activity against rabbit blood red cells and had no significant effects on human blood coagulation system. The discovery of antibacterial peptides in sheep reproductive system reveals that antibacterial peptides may play a role in innate immunity against microorganisms in a wide range of animal species.

Abstract:A novel PCR-based mutagenesis method was reported, in which there is no need to purify megaprimers or design a special flanking primer. This method used one mutagenic primer and two sequencing primers (T_m≤58℃) as flanking primers. After first round PCR, 12.5 μl first PCR production was directly added into 50 μl second PCR system as template and megaprimer, and 10 rounds of asymmetrical PCR at high temperature of annealing (68℃) was to add in initiation of second PCR. This additional step greatly has increased the efficiency of mutagenesis via 600 bp or 800 bp long megaprimer. The results demonstrated that this method can achieve high fidelity, 97%～98% efficiency, high yield.

Abstract:Retrieval of ancient DNA (aDNA) sequences from organism remains provide direct view of their evolutionary history. However, researches on aDNA have suffered from lots of technical problems. Specifically, discredited sequences were generated from damaged aDNA templates, and expensive and time-consuming methods were employed. Here, a method which could recover the endogenous aDNA as well as to reduce the cost and research period is described. This is achieved by improving the ancient DNA extraction method of isopropanol precipitation, and reevaluating the method of PCR after N-glycosylase (UNG) treatment, which could remove the damaged DNA from the aDNA extract. The efficiency of these methods were tested by comparing with traditional methods using ancient specimens of pig teeth aged between 4 300 years before present (BP) and 3 900 BP. The results showed that: firstly, the extraction efficiency of the improved method of isopropanol precipitation and current method with silica-based spin column were all 60%. Furthermore, the research period at least could be reduced by half with the application of the improved methods and the cost to 1/10 of the current method. Secondly, sequences obtained through the method of PCR after UNG treatment were 100% authentic. In contrast, 66%～88% sequences were authentic based on the results obtained with the method of multiple PCRs without UNG treatment. And the research cost and period needed by the method with UNG treatment were only half of the later one. These results demonstrate that the improved extraction method of isopropanol precipitation combined with the method of PCR after UNG treatment could increase the success rate of authentic DNA amplified and at least reduce the research cost and period by half. Therefore, this method can be applied in the large-scale detection of ancient specimens.