白编《近代汉语词典》“B”组词小校

出版于2015年12月的《近代汉语词典》,一经问世,便引起了学界的广泛关注。其在义项漏收、释义不确、引例时限等方面略存瑕疵。通过对该词典"B"组词的梳理,可窥全豹之一斑。略成此文,以补智者千虑之失。

白编《近代汉语词典》“L”组词辨正

2015年12月出版的《近代汉语词典》,其专业权威的内容为学林研究近代汉语打开了一片新天地。然工作量的巨大导致其在义项收录、释义明确、引例时限和释词注音等方面仍存在一些疏失。文章通过对"L"组词的梳理、描写和分析,得出一些结论,希望能为《近代汉语词典》的修订提供点滴参考。

翟灏《通俗编》吴方言词疏证举隅

翟灏《通俗编》具有汉语词源学研究价值、汉语词汇史研究价值、汉语方言词汇史研究价值、汉语语汇史研究价值。研究古今方言词时需要注意方言词的性质、方言词研究的路径、方言词的古今变化等问题。《通俗编》中的“浜”“孛相”“我侬”“艮头”“豆凑”是典型的吴方言词。作“浦名”解的“浜”即为“滨”之俗体,此俗体又发展成为表“安船沟”义的专用字。“白相”则可以理解为“说说看看”发展出“嬉戏”义,也可以说得通。在古今不同时代不同区域方言中,“侬”作单音词,可以用作第一人称、第二人称代词,“我侬”可以用同“我”是同义复词,用同“我们”是附加式合成词,“侬”成了复数标记。“浜”与“滨”、“白相”与“孛相”、“豆凑”与“斗凑”属于词形的变化以及古今方言、南北方言的异同与发展。

Effects of Mapping Methods on Accuracy of Protein Coding Regions Prediction

[Objective] To discuss the effects of major mapping methods for DNA sequence on the accuracy of protein coding regions prediction,and to find out the effective mapping methods.[Method] By taking Approximate Correlation（AC） as the full measure of the prediction accuracy at nucleotide level,the windowed narrow pass-band filter（WNPBF） based prediction algorithm was applied to study the effects of different mapping methods on prediction accuracy.[Result] In DNA data sets ALLSEQ and HMR195,the Voss and Z-Curve methods are proved to be more effective mapping methods than paired numeric（PN）,Electron-ion Interaction Potential（EIIP） and complex number methods.[Conclusion] This study lays the foundation to verify the effectiveness of new mapping methods by using the predicted AC value,and it is meaningful to reveal DNA structure by using bioinformatics methods.

Correlation Analysis of Differences of Photoinhibitory Sensitivity of D1 Proteins in Oryza sativa ssp. japonica and indica and Structural Features of the Sequences of the Coding Genes

Oryza sativa L. ssp. japonica and indica exhibit different sensitivity to photoinhibition and they show different stability of their core proteins D1 in the chloroplast photosystem Ⅱ. Using in situ hybridization, psbA, the gene encoding D1 protein of O. sativa ssp. japonica cv. 9516, and that of O. sativa ssp. indica cv. Shanyou 63 was cloned. As revealed by homology comparison of their sequences, the sequences are identical in the regions of promoter and 5′-UTR; differences are found in individual bases in the coding region all of which, being in the third position of respective codons, however, do not affect the amino acids coded finally; a difference is noted in the length of the oligo-U sequence in the region of 3′-UTR. It is thus apparent that, rather than a result of any difference in the amino acid sequences, the differences in the sensitivity to photoinhibition of D1 proteins between japonica and indica rice may be related to the upstream factors that regulate expression of psbA or to differences of photoprotective mechanisms.

The Full-length Genome Analysis of a Street Rabies Virus Strain Isolated in Yunnan Province of China

The epidemic of rabies has rapidly increased and expanded in Yunnan province in recent years. In order to further analyze and understand the etiological reasons for the rapid expansion of rabies in Yunnan, a strain of rabies virus CYN1009D in Yunnan was isolated, and the complete genomic sequencing was carried out, and the bioimfomative analysis on genes/encoded proteins and phylogeny with reference to sequences in GenBank was performed. The complete genome of CYN1009D was 11923 nt in length and belonged to genotype I. The genes encoding different structural proteins were all conserved in their lengths, in comparison to other strains in China. The amino acid sequence was conserved at different antigen sites of NP, but the variation was detected at the secondary phosphorylation site of position 375; variations were also detected in the phosphorylation sites at positions 63-63 and 162 of PP; the sites playing important roles in virus synthesis, budding and viral morphology in MP were conserved; two glycosylation sites were detected at Asn37 and Ash319 in GP, the neutralizing antigen sites in GP were conserved; the initial amino acid of LP （ML） was different from that of most of the strains in China （MM）; the variations in G-L region in the intergenic region were significant. The phylogenic tree showed that CYN1009D has a closer genetic relationship to the strains in Southeast Asia, indicating that prevention and control on rabies in borderland areas should be reinforced meanwhile efforts are made to control rabies in China.

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.

A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand

Recent transcription profiling studies have revealed an unexpectedly large proportion of antisense transcripts in eukaryotic genomes. These antisense genes seem to regulate gene expression by interacting with sense genes. Previ- ous studies have focused on the non-coding antisense genes, but the possible regulatory role of the antisense protein is poorly understood. In this study, we found that a protein encoded by the antisense gene ADF1 acts as a transcription suppressor, regulating the expression of sense gene MDF1 in Saccharomyces cerevisiae. Based on the evolutionary, ge- netic, cytological and biochemical evidence, we show that the protein-coding sense gene MDF1 most likely originated de novo from a previously non-coding sequence and can significantly suppress the mating efficiency of baker＇s yeast in rich medium by binding MATa2 and thus promote vegetative growth. These results shed new light on several im- portant issues, including a new sense-antisense interaction mechanism, the de novo origination of a functional gene, and the regulation of yeast mating pathway.

Relationship between Epstein-Barr virus-encoded proteins with cell proliferation,apoptosis,and apoptosis-related proteins in gastric carcinoma

AIM: To investigate the interrelationship between Epstein-Barr virus (EBV)-encoded proteins and cell proliferation, apoptosis and apoptosis-related proteins in gastric carcinoma, and to explore their role in gastric carcinogenesis. METHODS: Tissues from 13 cases of EBV-associated gastric carcinoma (EBVaGC) and 45 cases of matched EBV-negative gastric carcinoma (EBVnGC) were collected, and then subjected to analysis for apoptotic index (AI) using the terminal deoxynucleotidyl transferase (TdT)-mediated dUTP-biotin nick end-labeling (TUNEL) assay. Nuclear cell proliferation-associated antigen ki-67 index (KI), bcl-2, and p53 expression were examined by immunohistochemistry.p53 mutation in exons 5-8 of 13 EBVaGC cases was determined by single-strand conformation polymorphism (SSCP) and DNA sequencing.RT-PCR and Southern hybridization were used to detect the expression of nuclear antigens (EBNAs) 1 and 2, latent membrane protein (IMP) 1, immediately early gene BZLF1 and early genes BARF1 and BHRF1 in 13 EBVaGC cases. RESULTS: The percentage of AI, KI and p53 overexpression was significantly lower in the EBVaGC group than in the EBVnGC group. However, bcl-2 expression did not show significant difference between the two groups. p53 gene mutations were not found in 13 EBVaGCs. Transcripts of EBNA1 were detected in all 13 EBVaGCs, while both EBNA2 and LMP1 mRNA were not detected. Six of the thirteen cases exhibited BZLF1 transcripts and two exhibited BHRF1 transcripts. BARF1 mRNA was detected in six cases. CONCLUSION: Lower AI and KI may reflect a low biological activity in EBVaGC. EBV infection is associated with p53 abnormal expression but not bcl-2 protein in EBVaGC. BZLF1,BARF1,and BHRF1 may play important roles in inhibiting cell apoptosis and tumorigenesis of EBVaGC through different pathways.

Correlation of Epstein-Barr virus and its encoded proteins with Helicobacter pylori and expression of c-met and c-myc in gastric carcinoma

AIM： To investigate the interrelationship of Epstein-Barr virus （EBV） and EBV- encoded proteins with Helicobacter pylori （H pylor/~ infection and the expression of c-met and c-myc oncogene proteins in gastric carcinoma, and to explore their role in gastric carcinogenesis. METHODS： One hundred and eighty-five gastric carcinoma tissues were detected by polymerase chain reaction （PCR）-Southern blot for EBV genome and in situ hybridization （ISH） for EBV-encoded small RNA 1 （EBER1）. Gastric carcinoma with positive EBER1 signals was confirmed EBV-associated gastric carcinoma （EBVaGC）. The status of Hpylori infection in 185 gastric carcinomas was assessed by rapid urease test and PCR. The samples with positive PCR and urease test were defined as H pylorl infection. The expression of c-met and c-myc oncogene proteins in tissues of EBVaGC and matched EBV-negative gastric carcinoma （EBVnGC） were examined by immunohistochemistry. RT-PCR and Southern hybridization were used to detect the expression of nuclear antigens （EBNAs） 1 and 2, latent membrane protein （LMP） 1, early genes BARF1 and BHRF1 in EBVaGC cases. RESULTS： The positive rate of H pylori and EBV in 185 gastric carcinomas was 59.45% （110/185） and 7.03% （13/185） respectively. No difference was found in sex, age, pathological differentiation, clinical stages and lymph node metastasis between H pylori-positive and H pylori-negative gastric carcinomas. However, the positive rate of H pylori infection in the antrum gastric carcinomas was higher than that of cardia and body gastric carcinomas. In our series, age, pathological differentiation, clinical stages, lymph node metastasis and location of cancer were not different between EBVnGC and EBVaGC, while the positive rate of EBV in male patients was significantly higher than that of female patients. The positivity of Hpylori in EBV-associated and EBV-negative gastric carcinomas was 46.15% （6/13） and 81.40%（104/172） respectively. There was no significant correlation between EBV and H pylori infection. The c-met overexpression was significantly higher in the EBVaGC group than in the EBVnGC group. However, c-met and c-myc expression did not show significant difference between the two groups. Transcripts of EBNA1 were detected in all 13 EBVaGCs, while both EBNA2 and LMP1 mRNA were not detected. Six of the 13 cases exhibited BARF1 transcripts and 2 exhibited BHRF1 transcripts. CONCLUSION： The positivity of H pylori in EBVnGCs is higher than that of EBVaGCs, but no significant correlation is found between EBV infection and H pylori infection. H pylori-positive gastric carcinoma is predominant in antrum location, while EBVaGC has a tendency of predominance in cardia/body location. EBV infection is associated with c-met abnormal expression but not with c-myc protein in EBVaGC. c-met overexpression is not induced by LMP1. BARF1 and BHRF1 may play important roles in the tumorigenesis of EBVaGC through different pathways.

LEAFY HEAD2,which encodes a putative RNA-binding protein,regulates shoot development of rice

During vegetative development, higher plants continuously form new leaves in regular spatial and temporal patterns. Mutants with abnormal leaf developmental patterns not only provide a great insight into understanding the regulatory mechanism of plant architecture, but also enrich the ways to its modification by which crop yield could be improved. Here, we reported the characterization of the rice leafy-head2 （lhd2） mutant that exhibits shortened plastochron, dwarfism, reduced tiller number, and failure of phase transition from vegetative to reproductive growth. Anatomical and histological study revealed that the rapid emergence of leaves in lhd2 was resulted from the rapid initiation of leaf primordia whereas the reduced tiller number was a consequence of the suppression of the tiller bud outgrowth. The molecular and genetic analysis showed that LHD2 encodes a putative RNA binding protein with 67% similarity to maize TEl. Comparison of genome-scale expression profiles between wild-type and lhd2 plants suggested that LHD2 may regulate rice shoot development through KNOXand hormone-related genes. The similar phenotypes caused by LHD2 mutation and the conserved expression pattern of LHD2 indicated a conserved mechanism in controlling the temporal leaf initiation in grass.

The initial results of Epstein-Barr virus (EBV)-encoded latent membrane protein-1 (LMP-1) for screening nasopharyngeal carcinoma (NPC)

Objective: Early diagnosis of nasopharyngeal carcinoma (NPC) is an important method to improve the survival rate.However,the sensitivity and specificity of the screening protocols which was widely used in clinic now are considered to be unsatisfactory.Epstein-Barr virus (EBV)-encoded latent membrane protein-1 (LMP-1) is one of the proteins that have been suggested to be a classic oncogene with transformation properties.The current study set out to discuss the clinical significance of LMP-1 on the screening of NPC.Methods: Three hundred patients who visited our institution (Department of Radiation Oncology,Fujian Provincial Cancer Hospital,Fuzhou,China) with ENT symptoms between 2007 and 2008 were involved in this study,and all of them were agreed to be involved in this investigation.Not only did they undergo nasopharyngeal swab to obtain cells for the LMP-1 polymerase chain reaction (PCR) analysis,but also nasopharyngeal biopsy were taken to identify the diagnosis.Results: An amount of DNA that was sufficient for PCR was extracted from 243 (81%) swab samples,the positive rate of LMP-1 of those with non-nasopharyngeal carcinoma was 3.85% (4/108),which was much lower than those with nasopharyngeal carcinoma (P < 0.05).By detecting LMP-1 in nasopharyngeal swabs,NPC was diagnosed with a sensitivity of 88.15% (119 of 135 patients),specificity of 96.30% (104 of 108 patients),a positive predictive value of 95.2% (119 of 123 patients),a negative predictive value of 86.67% (104 of 120 patients),accuracy of 91.77%,and Youden index of 84.45%.Conclusion: The nasopharyngeal swab coupled with PCR-based EBV LMP-1 detection have high sensitivity and specificity,and also good repeatability,it could serve as part of the screening program for high-risk populations.

The complete mitochondrial genome of Triuncina daii(Lepidoptera:Bombycidae) and its phylogenetic implications

The bombycid moth, Triuncina daii Xing Wang ＆ Zolotuhin, 2015, plays an important role for analyzing the phylogenetic relationships of the family Bombycidae （Lepidoptera： Bombycoidea）. Here we first describe the complete mitochondrial genome （mitogenome） of T. daii, which includes thirteen protein-coding genes （PCGs）, twenty-two transfer RNA genes, two ribosomal RNA genes and an A＋T-rich region, and we find the mitogenome is 15,482 bp in length （GenBank no. KY091643）. The genes order and orientation in the T. daii mitogenome are similar to other sequenced lepidopteran species. Except for cox1, all of the PCGs started with ATN. Twelve PCGs stopped at TAA except for cox1 which stops at a single T. Thirteen PCGs of available species are used to demonstrate the inner phylogenetic relationships of Bombycoidea. The bombycid species form a monophyletic clade with a bootstrap value of 100% and a posterior probability of 1.00.

Genomic Imprinting—The Story of the Other Half and the Conflicts of Silencing

G-enomic imprinting is an epigenetic mechanism that produces functional differences between the paternal and mammal genomes and plays an essential role in mammalian development and growth. There are a number of genes in our genomes that are subject to genomic imprinting where one parent＇s copy of the gene is expressed while the other is silent. Silencing of one allele predetermines that any function ascribed to that gene are now dependant on the single active copy. Possession of only a single active allele can lead to deleterious health consequences in humans. If imprinted genes are crucial in mammalian development, one would also expect mutations in these genes to cause diseases. Since imprinting is an epigenetic mechanism, mistakes in maintaining epigenetic mark also cause imprinting disorders. Here we in this review focus on the current understanding of this unique genetic mechanism more than two decades after the first description of the imprinting phenomenon was given by McGrath and Solter. Although the possible molecular mechanisms by which imprinting is imposed and maintained are being identified, we have a long way to go in understanding the molecular mechanisms that regulate the expression of these oddly behaving genes, the function of imprinting and the evolution. Post genomic technologies might ultimately lead to a better understanding of the ＇imprinting effects＇.

Isolation and functional analysis of a Brassica juncea gene encoding a com-ponent of auxin efflux carrier

Polar auxin transport plays a divergent role in plant growth and developmental processes including root and embryo development, vascular pattern formation and cell elongation. Recently isolated Arabidopsis pin gene family was believed to encode a component of auxin efflux carrier (G(?)lweiler et al, 1998). Based on the Arabidopsis pin1 sequence we have isolated a Brassica juncea cDNA (designated Bjpin1), which encoded a 70-kDa putative auxin efflux carrier. Deduced BjPIN1 shared 65% identities at protein level with AtPINl and was highly homologous to other putative PIN proteins of Arabidopsis (with highest homology to AtPIN3). Hydrophobic analysis showed similar structures between BjPINl and AtPIN proteins. Presence of 6 exons (varying in size between 65 bp and 1229 bp) and 5 introns (sizes between 89 bp and 463 bp) in the genomic fragment was revealed by comparing the genomic and cDNA sequences. Northern blot analysis indicated that Bjpin1 was expressed in most of the tissues tested, with a relatively higher level of transcript in flowers and a lower level in root tissues. Promoter-reporter gene fusion studies further revealed the expression of Bjpin1 in the mature pollen grains, young seeds, root tip, leaf vascular tissue and trace bundle, stem epidermis, cortex and vascular cells. BjPINl was localized on the plasma membrane as demonstrated through fusion expression of green fluorescent protein (GFP). Auxin efflux carrier activity was elevated in transgenic Arabidopsis expressing BjPIN1.

Cloning and expression of prion protein encoding gene of flounder (Paralichthys olivaceus)

The prion protein (PrP) encoding gene of flounder (Paralichthys olivaceus) was cloned. It was not interrupted by an intron. This gene has two promoters in its 5' upstream, indicating that its transcription may be intensive, and should have an important function. It was expressed in all 14 tissues tested, demonstrating that it is a house-keeping gene. Its expression in digestion and reproduction systems implies that the possible prions of fish may transfer horizontally.

Preliminary analysis of the mitochondrial genome evolutionary pattern in primates

Since the birth of molecular evolutionary analysis, primates have been a central focus of study and mitochondrial DNA is well suited to these endeavors because of its unique features. Surprisingly, to date no comprehensive evaluation of the nucleotide substitution patterns has been conducted on the mitochondrial genome of primates. Here, we analyzed the evolutionary patterns and evaluated selection and recombination in the mitochondrial genomes of 44 Primates species downloaded from Genl3ank. The results revealed that a strong rate heterogeneity occurred among sites and genes in all comparisons. Likewise, an obvious decline in primate nucleotide diversity was noted in the subunit rRNAs and tRNAs as compared to the protein-coding genes. Within 13 protein-coding genes, the pattern of nonsynonymous divergence was similar to that of overall nucleotide divergence, while synonymous changes differed only for individual genes, indicating that the rate heterogeneity may result from the rate of change at nonsynonymous sites. Codon usage analysis revealed that there was intermediate codon usage bias in primate protein-coding genes, and supported the idea that GC mutation pressure might determine codon usage and that positive selection is not the driving force for the codon usage bias. Neutrality tests using site-specific positive selection from a Bayesian framework indicated no sites were under positive selection for any gene, consistent with near neutrality. Recombination tests based on the pairwise homoplasy test statistic supported complete linkage even for much older divergent primate species. Thus, with the exception of rate heterogeneity among mitochondrial genes, evaluating the validity assumed complete linkage and selective neutrality in primates prior to phylogenetic or phylogeographic analysis seems unnecessary.

The Arabidopsis PARAQUAT RESISTANT2 gene encodes an S-nitrosoglutathione reductase that is a key regulator of cell death

Metabolism of S-nitrosoglutathione （GSNO）, a major biologically active nitric oxide （NO） species, is catalyzed by the evolutionally conserved GSNO reductase （GSNOR）. Previous studies showed that the Arabidopsis GSNOR1/ HOT5 gene regulates salicylic acid signaling and thermotolerance by modulating the intracellular S-nitrosothiol level. Here, we report the characterization of the Arabidopsisparaquat resistant2-1 （par2-1） mutant that shows an anti-cell death phenotype. The production of superoxide in par2-1 is comparable to that of wild-type plants when treated by paraquat （1,1＇-dimethyl-4,4＇-bipyridinium dichloride）, suggesting that PAR2 acts downstream of superoxide to regulate cell death. PAR2, identified by positional cloning, is shown to be identical to GSNOR1/HOT5. The par2-1 mutant carries a missense mutation in a highly conserved glycine, which renders the mutant protein unstable. Compared to wild type, par2-1 mutant has a higher NO level, as revealed by staining with 4,5-diaminofluorescein diacetate. Consistent with this result, wild-type plants treated with an NO donor display resistance to paraquat. Interestingly, the GSNOR1/HOT5/PAR2 protein level, other than its steady-state mRNA level, is induced by paraquat, but is reduced by NO donors. Taken together, these results suggest that GSNOR1/HOT5/PAR2 plays an important role in regulating cell death in plant cells through modulating intracellular NO level.

Identification and Analysis of SSRs Derived from Protein-coding Genes in Grape

SSR(Simple Sequence Repeats), also known as microsatellites or STRs(short tandem repeats), are a type of PCRbased markers. So far, the version of grape genome has been updated constantly, but SSRs derived from protein-coding genes in grape have not yet been identified. In this study, 4 337 SSR-containing genes were found among 29 971 protein-coding genes in grape(Vitis vinifera L.), and 5 384 SSRs were found. There were 96 types of repeat motifs in SSRs derived from protein-coding genes in grape, and the most frequently occurring repeat motif was A/T. Among various repeat motifs in dinucleotide SSRs, the most frequently occurring repeat motif was AG/CT. Moreover, many genes exhibited codon usage bias, which was affected by the mutation pressure. GO annotation, KEGG annotation and domain analysis of these genes were performed.Several genes were found to be closely related to the synthesis and metabolism of secondary metabolites, synthesis of flavones or anthocyanins, development and morphology of plant organs, and tolerance to biotic or abiotic stresses, including transcription factors in MYB, Hsf, NBS and TPC families. This study laid a solid foundation for the development of SSR markers and research of QTLs controlling complex agronomic traits in grape.

Interleukin-2 gene-encoded stromal cells inhibit the growth of metastatic cholangiocarcinomas

AIM： To demonstrate bone marrow stromal cells （BMSCs） can be used as an attractive target for genetic modification in the treatment of malignant diseases. METHODS： Using a hamster model of biliary cancer, we investigated the therapeutic effects of interleukin-2 （IL-2） gene-modified BHSCs. Syrian golden hamsters were injected via the femoral vein with 5×10^5 cells of the KIGB-5 biliary cancer cell line （n=20）. One week later, the hamsters were injected intraperitoneally with BMSCs containing Ad/hIL-2 and Ad/△E1, unmodified BHSCs, or RPHI only （control） and observed for 12 wk （n=5/each group）. RESULTS： All hamsters treated with BMSCs containing Ad/hIL-2 survived with no evidence of the disease during this period. In contrast, hamsters in the other three groups showed disseminated metastases involving the lungs as eady as 4 wk.CONCLUSION： Ad/IL-2 therapy is effective in the treatment of biliary cancer.