植物分枝模型

从生物体总是最有效地利用物质的思想出发,对植物分枝形状建立了一个数学模型,该模型认为,当主干与侧枝的截面积之间存在类似平行四边形法则的关系时,分枝的体积取极小值。该模型揭示植物分枝形态不仅符合力学平衡的原则,在进化上也有显著生物学意义。     

SNObase,a database for S-nitrosation modification

S-Nitros(yl)ation is a ubiquitous redox-based posttranslational modification of protein cysteine thiols by nitric oxide or its derivatives, which transduces the bioactivity of nitric oxide (NO) by regulation of protein conformation, activity, stability, localization and protein- protein interactions. These years, more and more S-nitrosated proteins were identified in physiological and pathological processes and the number is still growing. Here we developed a database named SNObase (http://www.nitrosation.org), which collected S-nitrosation targets extracted from literatures up to June 1st, 2012. SNObase contained 2561 instances, and provided information about S-nitrosation targets, sites, biological model, related diseases, trends of S-nitrosation level and effects of S-nitrosation on protein function. With SNObase, we did functional analysis for all the SNO targets: In the gene ontology (GO) biological process category, some processes were discovered to be related to S-nitrosation (“response to drug”, “regulation of cell motion”) besides the previously reported related processes. In the GO cellular component category, cytosol and mitochondrion were both enriched. From the KEGG pathway enrichment results, we found SNO targets were enriched in different diseases, which suggests possible significant roles of S-nitrosation in the progress of these diseases. This SNObase means to be a database with precise, comprehensive and easily accessible information, an environment to help researchers integrate data with comparison and relevancy analysis between different groups or works, and also an SNO knowledgebase offering feasibility for systemic and global analysis of S-nitrosation in interdisciplinary studies.     

Agrobacterium-mediated genetic transformation and regeneration of transgenic plants using leaf midribs as explants in ramie [Boehmeria nivea (L.) Gaud]

In this study, leaf midribs, the elite explants, were used for the first time to develop an efficient regeneration and transformation protocol for ramie [Boehmeria nivea (L.) Gaud.] via Agrobacterium-mediated genetic transformation. Sensitivity of leaf midribs regeneration to kanamycin was evaluated, which showed that 40 mg l^?1 was the optimal concentration needed to create the necessary selection pressure. Factors affecting the ramie transformation efficiency were evaluated, including leaf age, Agrobacterium concentration, length of infection time for the Agrobacterium solution, acetosyringone concentration in the co-cultivation medium, and the co-cultivation period. The midrib explants from 40-day-old in vitro shoots, an Agrobacterium concentration at OD₆₀₀ of 0.6, 10-min immersion in the bacteria solution, an acetosyringone concentration of 50 mg l^?1 in the co-cultivation medium and a 3-day co-cultivation period produced the highest efficiencies of regeneration and transformation. In this study, the average transformation rate was 23.25 %. Polymerase chain reactions using GUS and NPTII gene-specific primers, Southern blot and histochemical GUS staining analyses further confirmed that the transgene was integrated into the ramie genome and expressed in the transgenic ramie. The establishment of this system of Agrobacterium-mediated genetic transformation and regeneration of transgenic plants will be used not only to introduce genes of interest into the ramie genome for the purpose of trait improvement, but also as a common means of testing gene function by enhancing or inhibiting the expression of target genes.     

Draft Genome Assembly and Annotation for Cutaneotrichosporon dermatis NICC30027, an Oleaginous Yeast Capable of Simultaneous Glucose and Xylose Assimilation

The identification of oleaginous yeast species capable of simultaneously utilizing xylose and glucose as substrates to generate value-added biological products is an area of key economic interest. We have previously demonstrated that the Cutaneotrichosporon dermatis NICC30027 yeast strain is capable of simultaneously assimilating both xylose and glucose, resulting in considerable lipid accumulation. However, as no high-quality genome sequencing data or associated annotations for this strain are available at present, it remains challenging to study the metabolic mechanisms underlying this phenotype. Herein, we report a 39,305,439 bp draft genome assembly for C. dermatis NICC30027 comprised of 37 scaffolds, with 60.15% GC content. Within this genome, we identified 524 tRNAs, 142 sRNAs, 53 miRNAs, 28 snRNAs, and eight rRNA clusters. Moreover, repeat sequences totaling 1,032,129 bp in length were identified (2.63% of the genome), as were 14,238 unigenes that were 1,789.35 bp in length on average (64.82% of the genome). The NCBI non-redundant protein sequences (NR) database was employed to successfully annotate 11,795 of these unigenes, while 3,621 and 11,902 were annotated with the Swiss-Prot and TrEMBL databases, respectively. Unigenes were additionally subjected to pathway enrichment analyses using the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG), Clusters of orthologous groups for eukaryotic complete genomes (KOG), and Non-supervised Orthologous Groups (eggNOG) databases. Together, these results provide a foundation for future studies aimed at clarifying the mechanistic basis for the ability of C. dermatis NICC30027 to simultaneously utilize glucose and xylose to synthesize lipids.     

氧胁迫对人肝癌细胞生长分化和凋亡的影响

采用不同浓度的抗坏血酸(50—800μmol/L)和硫酸亚铁(2.5—40μmol/L)系统生成以羟自由基为主的各种程度氧胁迫,使之作用于人肝癌细胞。本文所采用的不同程度的氧胁迫均能抑制癌细胞的生长。低水平氧胁迫可使肝癌细胞失去某些恶性特征,趋向分化,表现为细胞表面对Con-A的凝集力、甲胎蛋白含量、γ-谷氨酰转肽酶和酪氨酸-α-酮戊二酸转氨基酶活性都朝着分化方向变化,差异显著。分化后的细胞克隆形成能力显著降低。在分化过程中,出现一定量的凋亡细胞。随着氧胁迫程度的增高,凋亡细胞增多,表现为非贴壁细胞增多,细胞体积变小,染色质凝缩在核膜边缘,呈新月形,核碎裂,但质膜完整。细胞核中DNA降解成大约21.2kbp大小的大片段DNA。有望通过严格控制氧胁迫程度来减慢肝癌细胞增殖,促进分化和凋亡,使恶性细胞逆转成良性细胞。     

Characterization of two Bacillus thuringiensis plasmids whose replication is thermosensitive in B. subtilis

Abstract Two cryptic plasmids of 8.6 and 15 kb, originating from Bacillus thuringiensis , have been cloned in Escherichia coli . The determination of their physical map shows that the 8.6-kb plasmid harbors the transposon Tn 4430 and that the 15-kb plasmid carries Tn 4430 plus one copy of the IS 231 element. The replication regions were identified on the restriction maps and the segregational stability of derived plasmids containing these regions was analyzed in B. subtillis . The results indicate that the stability of these plasmids is negatively correlated to the temperature. After 30 generations, without selective pressure at 51°C, the two types of plasmids are lost.     

Changes of soil organic and inorganic carbon in relation to grassland degradation in Northern Tibet

The effect of livestock grazing on grassland degradation and the resulting impact on soil carbon concentration is an important factor in carbon estimation. We addressed this issue using field observations and laboratory analysis of samples from Tibetan grassland. Based on the field measurements, we investigated the soil organic carbon (SOC) and soil inorganic carbon (SIC) under two contrasting degradation states: lightly or non-degraded grasslands (LDG) and heavily degraded grasslands (HDG). We assessed their relationships with environmental factors using data collected from 99 sites across Northern Tibet during 2011–2012. Data were analyzed using a linear mixed-effects model and one-way ANOVA. The results showed that: (1) SOC concentration decreased and SIC concentration increased following grassland degradation, especially at soil depths in the range of 0–10 cm (P < 0.05); (2) the major environmental factors affecting SOC and SIC were soil pH and plant biomass; (3) spatially, the SOC density increased with the mean annual temperature and mean annual precipitation, whereas SIC exhibited the opposite trend; (4) the SOC density increased at first and then decreased with increasing grazing intensity, with an opposite trend in SIC; and (5) soil carbon storage in this region was 0.14 Pg smaller in the HDG than in the LDG. This study suggests that grassland degradation can significantly affect the vertical distribution and storage of SOC and SIC. The carbon sequestration capacity of the top 100 cm of soil in Northern Tibet was estimated as 0.14 Pg.     

Shifts in priming partly explain impacts of long‐term nitrogen input in different chemical forms on soil organic carbon storage

Input of labile organic carbon can enhance decomposition of extant soil organic carbon (SOC) through priming. We hypothesized that long‐term nitrogen (N) input in different chemical forms alters SOC pools by altering priming effects associated with N‐mediated changes in plants and soil microbes. The hypothesis was tested by integrating field experimental data of plants, soil microbes and two incubation experiments with soils that had experienced 10 years of N enrichment with three chemical forms (ammonium, nitrate and both ammonium and nitrate) in an alpine meadow on the Tibetan Plateau. Incubations with glucose–¹³C addition at three rates were used to quantify effects of exogenous organic carbon input on the priming of SOC. Incubations with microbial inocula extracted from soils that had experienced different long‐term N treatments were conducted to detect effects of N‐mediated changes in soil microbes on priming effects. We found strong evidence and a mechanistic explanation for alteration of SOC pools following 10 years of N enrichment with different chemical forms. We detected significant negative priming effects both in soils collected from ammonium‐addition plots and in sterilized soils inoculated with soil microbes extracted from ammonium‐addition plots. In contrast, significant positive priming effects were found both in soils collected from nitrate‐addition plots and in sterilized soils inoculated with soil microbes extracted from nitrate‐addition plots. Meanwhile, the abundance and richness of graminoids were higher and the abundance of soil microbes was lower in ammonium‐addition than in nitrate‐addition plots. Our findings provide evidence that shifts toward higher graminoid abundance and changes in soil microbial abundance mediated by N chemical forms are key drivers for priming effects and SOC pool changes, thereby linking human interference with the N cycle to climate change.     

The Shanghuang Mammalian Fauna, Middle Eocene of Jiangsu:History of Discovery and Significance

APaleogenemammalianfauna,herenamedtheShanghuangfauna,wasdiscoverednearthevillageofShanghuang,closetoLiyangCity,JiangsuProvince,China(Fig.1).Atpresent,rouglilysixtyspeciesoffossilmammalshavebeenrecogniedintheShanghuangfauna.Manyofthesemammaltaxaarenewtoscience,andothersrepresentnewoccurrencesfortheEoceneofChina.ParticularlywellrepresentedintheShanghuangfaunaaremicromammals(includingmarsupials,insectivores,rodents,lagomorphs,primates,andbats)thathaveseldomifeverbeenfoundinotherEoceneAsianl…     

Association of Per3 length polymorphism with susceptibility of Alzheimer disease (AD) in Chinese population

Objectives: The association of Per3 length polymorphism with susceptibility of Alzheimer Disease (AD) was examined in the present study. Methods: This study was constructed using the case-control method and investigated the association of Per3 length polymorphism with susceptibility of AD. Genotypes of APOE and Per3 length were determined by a PCR restriction fragment length polymorphism detection method. Results: In this study, we gathered 130 unrelated AD patients and 188 controls in performing an analysis the association of Per3 length polymorphism with susceptibility of AD. In the whole sample or APOE ε4 non-carriers, an increased prevalence of five repeat homozygotes of Per3 length in AD patients had significant higher than that in controls (in the whole sample: χ² = 7.261,= 0.0176; in APOE ε4 non-carriers: χ² = 6.086, p = 0.030). And, among APOE ε4 carriers, an increased prevalence of five repeat homozygotes of Per3 length in AD patients had also significant higher than that in controls (χ² = 3.893, p = 0.0319). Conclusions: Among APOE ε4 non-carriers, five repeat homozygotes of Per3 length was associated with a high susceptibility of AD among APOE ε4 carriers and non-carriers.