近代藏书家张之铭的表谱学实践

张之铭是近代科学中国化的实践者,上海宁波帮商人、有名的藏书家。他的表谱学实践是对中国传统纪年法的继承与发展,其工作主要有采用黄帝纪年,推敲《历代帝王中西纪元彙考》,出版《历代甲子纪年表》与《历代帝王纪元表》,编纂其他纪年研究著作,其价值主要为中外纪年对照,即中西对照和东亚文化圈中的宗主和藩属对照。

Ultra-soft Desorption Assisted Mass Spectrometry using Picosecond Infrared Laser for the Detection of lons in the Liquid Surface

To identify the species in liquid surface using mass spectrometry,we must eliminate or reduce interferences during the vaporization or desorption of the species from the liquid surface.It is much more challenging to isolate the ionic,larger species from the liquid surface,because of the frangible structures and the higher solvation energies of those species.Here we demonstrate a new mass spectrometry in which the ionic species at the liquid surface can be desorbed with ultrasoft infrared picosecond laser pulses while the liquid surface is not breached.This laser desorption assisted mass spectrometry is not only a powerful tool to detect the fragile species but also promising to investigate vibrational energy transfer dynamics in the liquid surface.

《史記》諸表“邪上”新探

《梁書》卷五十《劉杳傳》引桓譚《新論》云:"太史《三代世表》,旁行邪上,並效周譜。""邪上"所指,學界缺乏確切的認識。本文在檢討已有研究基礎上,通過分析、比較,在《史記》之《三代世表》以及《十二諸侯年表》《秦楚之際月表》《漢興以來將相名臣年表》等篇中找到多處可以理解爲"邪上"的實例;進而認爲"邪上"實指斜向而前的書寫或閲讀樣式,狹義上的"邪上"、"邪下"均爲其涵蓋。"邪上"在《漢書》諸表和秦漢簡牘中亦有所見,屬於秦漢時期表譜類文獻中習見的表現形式。

Generation of Antibodies Against DMRT1 and DMRT4 of Oreochromis aurea and Analysis of Their Expression Profile in Oreochromis aurea Tissues

Sex determination is composed of somatic and germ-line sex differentiation hierarchies whose interaction is poorly understood. A single gene known to control somatic sex determination, the DM-domain containing （Doublesex/Mab-3 DNA-binding motif） gene, is highly conserved across species. Vertebrate DMRT1 （DM-related transcription factor 1） expression occurs predominantly in the testis. Here, however, isolated two distinct DM-domain cDNA from Oreochromis aurea ovary and testis have been named DMRT4 （DM-related transcription factor 4） and DMRT1 by BLAST, respectively. Despite high homology in the DM-domain there is little similarity outside the DM-domain.To better understand the structure, function, and possible roles of DMRT4 and DMRT1 as potential candidates for sex differentiation and sex determination, the intact regions encoding DMRT4 and DMRT1 obtained by PCR were sub-cloned into the vector pMAL-c2x and introduced into the Escherichia coli TB1 cell for efficient fusion expression. After purification and cleavage, DMRT4 and DMRT1 proteins were used to immunize adult rabbits following standard protocols. Consequently, it was found by using Western blot analysis that polyclonal antibodies against DMRT4 and DMRT1 had high specificity. The relative expression levels of DMRT4 and DMRT1 mRNA were determined by fluorescent Real-time RT-PCR in female and male Oreochromis aurea with 13-actin as the internal standard. DMRT1 was expressed only in testis, whereas DMRT4 was over expressed in the ovary, but in both female and male, a slight expression in the brain was also detected. Statistical analysis showed that in the brain, mean DMRT4 mRNA levels in female were significantly higher than in male. Meanwhile, the expression of DMRT4 and DMRT1 protein was also analyzed using the purified antibodies through Western blot and immunohistochemistry. It was found that DMRT4 was exclusively expressed in the ovary and DMRT1 in the testis. Study on DMRT4 and DMRT1 expression facilitated the elucidation of their roles and the understanding of sex differentiation of fish.

Screening of the Metastasis-Associated Genes by Gene Chip in High Metastatic Human Ovarian Cancer Cell Lines

Affymetrix U133A oligonucleotide microarrays were used to study the differences of gene expressions between high （H） metastatic ovarian cancer cell line, HO-8910PM, and normal ovarian tissues （C）. Bioinformatics was used to identify their chromosomal localizations. A total of 1,237 genes were found to have a difference in expression levels more than eight times. Among them 597 were upregulated [Signal Log Ratio （SLR） ≥3], and 640 genes were downregulated （SLR≤-3）. Except one gene, whose location was unknown, all these genes were randomly distributed on all the chromosomes. However, chromosome 1 contained the most differentially expressed genes （115 genes, 9.3%）, followed by chromosome 2 （94 genes, 7.6%）, chromosome 12 （88 genes, 7.1%）, chromosome 11 （76 genes, 6.1%）, chromosomes X （71 genes, 5.7%）, and chromosomes l7 （69 genes, 5.6%）. These genes were localized on short-arm of chromosome （q）, which had 805 （65.1%） genes, and the short arms of No.13, 14, 15, 21, and 22 chromosomes were the only parts of the chromosomes where the differentially expressed genes were localized. Functional classification showed that most of the genes （306 genes, 24.7%） belonged to the enzymes and their regulator groups. The subsequent group was the nucleic acid binding genes （144 genes, 11.6%）. The rest of the top two groups were signal transduction genes （137 genes, 11.1%） and proteins binding genes （116 genes, 9.4%）. These comprised 56.8% of all the differentially expressed genes. There were also 207 genes whose functions were unknown （16.7 %）. Therefore it was concluded that differentially expressed genes in high metastatic ovarian cancer cell were supposed to be randomly distributed across the genome, but the majority were found on chromosomes 1, 2, 12, 11, 17, and X. Abnormality in four groups of genes, including in enzyme and its regulator, nucleic acid binding, signal transduction and protein binding associated genes, might play important roles in ovarian cancer metastasis. Those genes need to be further studied.

Hyperspectral image classification based on spatial and spectral features and sparse representation

To minimize the low classification accuracy and low utilization of spatial information in traditional hyperspectral image classification methods, we propose a new hyperspectral image classification method, which is based on the Gabor spatial texture features and nonparametric weighted spectral features, and the sparse representation classification method（Gabor–NWSF and SRC）, abbreviated GNWSF–SRC. The proposed（GNWSF–SRC） method first combines the Gabor spatial features and nonparametric weighted spectral features to describe the hyperspectral image, and then applies the sparse representation method. Finally, the classification is obtained by analyzing the reconstruction error. We use the proposed method to process two typical hyperspectral data sets with different percentages of training samples. Theoretical analysis and simulation demonstrate that the proposed method improves the classification accuracy and Kappa coefficient compared with traditional classification methods and achieves better classification performance.

Expression Profile Changes of Genes Involved in Lipid Metabolism Pathway During Liver Regeneration in Mice

[ Objective ] The aim of the research was to study the expression profile changes of genes involved in lipid metabolism pathway during liver regeneration in mice. [ Method] The CCI4 induced mouse model of liver regeneration was established and the total RNA was isolated from liver tissue of mouse. Then the changes of genes involved in lipid metabolism pathway during different stages of liver regeneration were detected through micro-array chip gene technique and their specific functions were also analyzed. [ Result] Dudng the process of liver regeneration, the expression level of 98 genes involved in lipid metabolism pathway changed, which were divided into eight groups according to change trend. In the mass, the expression of genes was inhibited in the early stage and up-regulated in the late phase. And the gene expression associated with fatty acid synthesis pathway was mainly up-regulated while the catabolic pathway did not change significantly. Most of genes involved in bile acid synthesis pathway were suppressed before 4.5 d and up-regulated after 4.5 d or 7 d. [ Conclusion] During the process of liver regeneration, the genes associated with lipid metabolism are expressed in different trends, and this data should provide a specific range of genes for further studying the regulation effect of lipid metabolism related pathway on liver regeneration.

Genes Expression Profile Difference in Peripheral Blood Between Esophageal Carcinoma Patients and Normal Subjects

Objective： To study the genes expression profile differences in the peripheral blood between esophageal carcinoma patients and normal subjects using the gene chip technique and screen out the esophageal early conceration associated genes. Methods： The total RNA was extracted and purified in the peripheral blood obtained from the patients with esophageal carcinoma and normal subjects. The first strand of cDNA was synthesized through retro-transcription and labeled with Cy5 and Cy3 fluorescence as probes. The mixed probes were hybridized with a piece of 4096 double dot human whole gene chip. The acquired image was analyzed by microarrav suite software using a digital computer, and the intensity of ttuorescence signal and its ratio were calculated. Results： A total of 92 genes were screened out and its expression difference was more than 2 times in the peripheral blood between the patients with esophageal carcinoma and normal subjects. Among these, the expression difference of 36 genes was more than 3 times. Two human urokinase plasminogen activator surface receptor （UPAR） genes, 80K-L protein gene, human protein tyrosine-phosphatase gent arid proto-oncogene protein mRNA were significantly up-regulated, while the collagen V type （α-2 gene was markedly down-regulated. Conclusion： 80K-L protein gene, tyrosinephophatase gene, proto-oncogene protein arid the collagen V type α-2 gene might be associated with the ontogenesis, development and its metastasis in the esophageal carcinoma. The UPAR gene may play important roles in the diagnosing the micrometastasis in the peripheral blood of esophageal carcinoma.

Tomographic inversion of near-surface Q factor by combining surface and cross-hole seismic surveys

The estimation of the quality factor Q plays a fundamental role in enhancing seismic resolution via absorption compensation in the near-surface layer.We present a new geometry that can be used to acquire field data by combining surface and cross-hole surveys to decrease the effect of geophone coupling on Q estimation.In this study,we drilled number of receiver holes around the source hole,each hole has different depth and each geophone is placed geophones into the bottom of each receiver hole to avoid the effect of geophone coupling with the borehole wall on Q estimation in conventional cross-hole seismic surveys.We also propose a novel tomographic inversion of the Q factor without the effect of the source signature,and examine its stability and reliability using synthetic data.We estimate the Q factors of the near-surface layer in two different frequency bands using field data acquired in the Dagang Oilfield.The results show that seismic absorption in the nearsurface layer is much greater than that in the subsurface strata.Thus,it is of critical practical importance to enhance the seismic solution by compensating for near-surface absorption.In addition,we derive different Q factors from two frequency bands,which can be treated,to some extent,as evidence of a frequency-dependent Q.

AFM and XPS Study on the Surface and Interface States of CuPc and SiO_2 Films

A CuPc/SiO2 sample is fabricated. Its morphology is characterized by atomic force microscopy, and the electron states are investigated by X-ray photoelectron spectroscopy. In order to investigate these spectra in detail, all of these spectra are normalized to the height of the most intense peak,and each component is fitted with a single Gaussian function. Analysis shows that the O element has great bearing on the electron states and that SiO2 layers produced by spurting technology are better than those produced by oxidation technology.

Molecular Detection of Healthiness of Bombyx mori

[Objective] The paper was to explore the regularity between heat shock protein expression and the healthiness changes of Bombyx moil materials. [Method] The representative heat shock protein gene Bmhsp24.3 was screened by bioinfor- matic analysis method, and carried out real-time PCR expression analysis. [Result] The target gene Bmhsp24.3 expressed in different B. mori materials, but the expres- sion level in different materials significantly varied. The relative expression level of the gene had different degrees of changes under different rearing conditions. With the increase of rearing temperature, the gene expression was upregulated. The ma- terials with better healthiness had remarkable increase in expression of target gene, while the materials with poorer healthiness had less increase in expression of target gene. The expression difference of target gene Bmhsp24.3 was exactly consistent with the healthiness of breeds. [Conclusion] The healthiness of materials had rela- tionship with expression of target gene Bmhsp24.3. the higher the expression of tar- get gene Bmhsp24.3 was, the better the healthiness of materials was; conversely, the lower the expression of target gene Bmhsp24.3 was, the poorer the healthiness of materials was.

Triangular Au-Ag framework nanostructures prepared by multi-stage replacement and their spectral properties

Triangular Au-Ag framework nanostructures （TFN） were synthesized via a multi-step galvanic replacement reaction （MGRR） of single-crystalline triangular silver nanoplates in a chlorauric acid （HAuCl4） solution at room temperature. The morphological, compositional, and crystal structural changes involved with reaction steps were analyzed by using transmission electron microscopy（TEM）, energy-dispersive X-ray spectrometry （EDX）, and X-ray diffraction. TEM combined with EDX and selected area electron diffraction confirmed the replacement of Ag with Au. The in-plane dipolar surface plasmon resonance （SPR） absorption band of the Ag nanoplates locating initially at around 700 nm gradually redshifted to 1 100 nm via a multi-stage replacement manner after 7 stages. The adding amount of HAuCl4 per stage influenced the average redshift value per stage, thus enabled a fine tuning of the in-plane dipolar band. A proposed formation mechanism of the original Ag nanoplates developing pores while growing Au nanoparticles covering this underlying structure at more reaction steps was confirmed by exploiting surface-enhanced Raman scattering （SERS）.

Comparative Analysis of Five Different Homologous Feeder Cell Lines in the Ability to Support Rhesus Embryonic Stem Cells

In our previous study, five homologous feeder cell lines, Monkey ear skin fibroblasts （MESFs）, clonally derived fibroblasts from the MESFs （CMESFs）, monkey oviductal fibroblasts （MOFs）, monkey follicular granulosa fibroblast-like （MFGs） cells, monkey follicular granulosa epithelium-like （MFGEs） cells, were developed for the maintenance of rhesus embryonic stem cells （rESCs）. We found that MESFs, CMESFs, MOFs and MFGs, but not MFGEs, support the growth of rhesus embryonic stem cells. Moreover, we detected some genes that are upregulated in supportive feeder cell lines by semi-quantitative PCR. In the present study, we applied the GeneChip Rhesus Macaque Genome Array of Affymetrix Corporation to study the expression profiles of these five feeder cell lines, in purpose to find out which cytokines and signaling pathways were important in maintaining the rESCs, mRNAs of eight genes, including GREM2, bFGF, KITLG, DKK3, GREM1, AREG, SERPINF1 and LTBP1, were found to be upregulated in supportive feeder cell lines, but not in MFGE. The results indicate that many signaling pathways may play redundant roles in supporting the undifferentiated growth and maintenance of pluripotency in rESCs.

Aquaporin-8 expression is reduced in ileum and induced in colon of patients with ulcerative colitis

AIM： To study susceptibility genes which may play a potential role in the pathogenesis and etiology of inflammatory bowel disease （IBD）. METHODS： To identify potential susceptibility genes we performed global gene expression profiling in patients with IBD and control specimens. For determination of an intrinsic gene expression profile in ulcerative colitis （UC） and Crohn＇s disease （CD） compared to normal subjects, mucosal biopsies of non-inflamed regions of the colon and the terminal ileum were subjected to DNA microarray analysis. Real-time RT-PCR and immunohistochemistry were used for verification of selected regulated candidate genes and a genetic analysis was performed. RESULTS： We could show that aquaporin-8 （AQP8） mRNA and protein levels were significantly increased in the colon of UC patients compared to controls. Genetic analysis of the six exons and the promoter region of AQPS, however, revealed no mutations or polymorphisms in IBD patients. CONCLUSION： Our results suggest that upregulation of AQP8 in the colon of UC patients represents a secondary phenomenon which may, due to altered water exchange of the distal intestinal mucosa, disturb the physiologic colonic mucus barrier and thus lead to chronic inflao mmation and ulceration.

DNA chip-based expression profile analysis indicates involvement of the phosphatidylinositol signaling pathway in multiple plant responses to hormone and abiotic treatments

The phosphatidylinositol (PI) metabolic pathway is considered critical in plant responses to many environmental factors,and previous studies have indicated the involvement of multiple PI-related gene families during cellular responses.Through a detailed analysis of the Arabidopsis thaliana genome,82 polypeptides were identified as being involved in PI signaling. These could be grouped into different families including PI synthases (PIS),PI-phosphate kinases (PIPK),phospholipases (PL),inositol polyphosphate phosphatases (IPPase),inositol polyphosphate kinases (IPK),PI transfer proteins and putative inositol polyphosphate receptors. The presence of more than 10 isoforms of PIPK,PLC,PLD and IPPase suggested that these genes might be differentially expressed during plant cellular responses or growth and development. Accordingly,DNA chip technology was employed to study the expression patterns of various isoforms.In total,79 mRNA clones were amplified and used for DNA chip generation. Expression profile analysis was performed using samples that represented multiple tissues or cellular responses. Tested samples included normal leaf,stem and flower tissues,and leaves from plants treated with various hormones (auxin,cytokinin,gibberellin,abscisic acid and brassinosteroid) or environmental factors (temperature,calcium,sodium,drought,salicylic acid and jasmonic acid).Results showed that many PI pathway-related genes were differentially expressed under these experimental conditions.In particular,the different isoforms of each family were specifically expressed in many cases,suggesting their involvement in tissue specificity and cellular responses to environmental conditions. This work provides a starting point for functional studies of the relevant PI-related proteins and may help shed light onto the role of PI pathways in development and cellular responses.

MiRNA profile in esophageal squamous cell carcinoma:Downregulation of miR-143 and miR-145

AIM:To investigate the expression profile of miRNA in esophageal squamous cell carcinoma(ESCC).METHODS:The expression profile of miRNA in ESCC tissues was analyzed by miRNA microarray.The expression levels of miR-143 and miR-145 in 86 ESCC patients were determined by real-time polymerase chain reaction(PCR) using TaqMan assay.The mobility effect was estimated by wound-healing using esophageal carcinoma cells transfected with miRNA expression plasmids.RESULTS:A set of miRNAs was found to be deregulated in the ESCC tissues,and the expression levels of miR-143 and-145 were significantly decreased in most of the ESCC tissues examined.Both miR-143 and miR-145 expression correlated with tumor invasion depth.The transfection of human esophageal carcinoma cells with miR-143 and miR-145 expression plasmids resulted in a greater inhibition of cell mobility,however,the protein level of the previously reported target of miR-145,FSCN1,did not show any significant downregulation.CONCLUSION:These findings suggest that the deregulation of miRNAs plays an important role in the progression of ESCC.Both miR-143 and miR-145 might act as anti-oncomirs common to ESCC.

Discovery and validation of prognostic markers in gastric cancer by genome-wide expression profiling

AIM: To develop a prognostic gene set that can predict patient overall survival status based on the whole genome expression analysis. METHODS: Using Illumina HumanWG-6 BeadChip followed by semi-supervised analysis, we analyzed the expression of 47 296 transcripts in two batches of gastric cancer patients who underwent surgical resection. Thirty-nine samples in the first batch were used as the training set to discover candidate markers correlated to overall survival, and thirty-three samples in the second batch were used for validation. RESULTS: A panel of ten genes were identified as prognostic marker in the first batch samples and classified patients into a lowand a high-risk group with significantly different survival times (P = 0.000047). This prognostic marker was then verified in an independent validation sample batch (P = 0.0009). By comparing with the traditional Tumor-node-metastasis (TNM) staging system, this ten-gene prognostic marker showed consistent prognosis results. It was the only independent prognostic value by multivariate Cox regression analysis (P = 0.007). Interestingly, six of these ten genes are ribosomal proteins, suggesting a possible association between the deregulation of ribosome related gene expression and the poor prognosis. CONCLUSION: A ten-gene marker correlated with overall prognosis, including 6 ribosomal proteins, was identified and verified, which may complement the predictive value of TNM staging system.

Expression profiles of two small heat shock proteins and antioxidant enzyme activity in Mytilus galloprovincialis exposed to cadmium at environmentally relevant concentrations

Small heat shock proteins encompass a widespread but diverse class of proteins, which play key roles in protecting organisms from various stressors. In the present study, the full-length cDNAs of two small heat shock proteins （MgsHSP22 and MgsHSP24.1） were cloned from Mytilus galloprovincialis, which encoded peptides of 181 and 247 amino acids, respectively. Both MgsHSP22 and MgsHSP24.1 were detected in all tissues examined by real-time PCR, with the highest expression being observed in muscle and gonad tissues. The real-time PCR results revealed that Cd significantly inhibited MgsHSP22 expression at 24 h and MgsHSP24.1 at 24 and 48 h under 5 ug/L Cd2＋ exposure. MgsHSP24.1 expression was also significantly inhibited after 50 ug/L Cd2＋ exposure for 48 h. With regard to antioxidant enzymes, increased GPx and CAT activity were detected under Cd2＋ stress （5 and 50 ug/L）, while no significant difference in SOD activity was observed throughout the experiment. Overall, both MgsHsps and antioxidant enzymes revealed their potential as Cd stress biomarkers in M. galloprovincialis.

Role of H3K27 methylation in the regulation of IncRNA expression

Once thought to be transcriptional noise, large non-coding RNAs （IncRNAs） have recently been demonstrated to be functional molecules. The cell-type-specific expression patterns of lncRNAs suggest that their transcription may be regulated epigenetically. Using a custom-designed microarray, here we examine the expression profile of IncRNAs in embryonic stem （ES） cells, lineage-restricted neuronal progenitor cells, and terminally differentiated fibroblasts. In addition, we also analyze the relationship between their expression and their promoter H3K4 and H3K27 methyla- tion patterns. We find that numerous lncRNAs in these cell types undergo changes in the levels of expression and promoter H3K4me3 and H3K27me3. Interestingly, lncRNAs that are expressed at lower levels in ES cells exhibit higher levels of H3K27me3 at their promoters. Consistent with this result, knockdown of the H3K27me3 methyltransferase Ezh2 results in derepression of these IncRNAs in ES cells. Thus, our results establish a role for Ezh2-mediated H3K27 methylation in lncRNA silencing in ES cells and reveal that lncRNAs are subject to epigenetic regulation in a similar manner to that of the protein-coding genes.

Study on differential gene expression profile of serum exosomes in patients with acute cerebral infarction

Objective To analyze the differential gene expression profile of serum exosomes in patients with acute cerebral infarction(ACI)and clarify the changes in gene expression related to cerebral infarction injury and the potential serum markers.Methods Four patients with ACI and five healthy people were enrolled in the PhaseⅠstudy.After serum isolation from peripheral blood,exosomes were extracted with exosomes kits,highthroughput detection of m RNA was performed with gene chips,and differentially expressed m RNAs were screened.Gene Ontology(GO)functional analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis were performed simultaneously.Furthermore,real-time polymerase chain reaction(q RT-PCR)was used to verify the expression levels of the screened differential m RNAs in the serum exosomes collected in PhaseⅡfrom 32 patients each in the ACI case and normal control groups.Results In the PhaseⅠstudy,there were 248 differentially expressed m RNAs(fold change≥2.0,P<0.05)among five patients in the normal control group and four patients in the case group,of which the expression of 242 was upregulated and that of six was downregulated.The results of GO functional enrichment analysis mainly included behavior regulation,cell connection,and antioxidant activity.The results of KEGG pathway enrichment analysis mainly included ribosomes,proteasomes,oxytocin signaling pathways,and oxidative phosphorylation.After researching and screening based on relevant literature,it was found that among the genes with significant differential expression,H3 F3 B m RNA may be associated with and might play an important role in ACI.The q RT-PCR method was used to detect the H3 F3 B mRNA expression in serum exosomes of 32 patients each in the normal control and case groups in PhaseⅡ;the expression was significantly higher in serum exosomes of the case group than in those of the normal control group(P<0.001).H3 F3 B mRNA expression in serum exosomes of the case group positively correlated with age,the National Institutes of Health Stroke Scale(NIHSS)score,and the maximum infarct size(P<0.05).Conclusion ACI can lead to changes in the serum exosomes mRNA expression profile,which may be closely related to the occurrence,development,and prognosis of this condition.These findings will provide direction for research on the molecular mechanism,diagnostic markers,and therapeutic targets of ACI.