Chlorella virus SC-1A encodes at least five functional and one nonfunctional DNA methyltransferases

Chlorella virus SC-1A encodes at least six DNA methyltransferases (MTases): four N⁶-methyldeoxyadenine (m⁶A) MTases, M- CviSI (TGC^mA), M· CviSII C^mATG), M· CviSIII (TCG^mA) and M^mCviSIV (G^mATC), one 5-methyldeoxycytosine (m⁵C) MTase, M· CviSV (RC^mCG), and one nonfunctional m⁵C MTase, M· CviSVI, which is homologous to the MTase M· CviJI [RG^mC(T/C/G)] produced by another chlorella virus IL-3A. Genes encoding three of the SC-1A m⁶A MTases (M·CviSI, M· CviSII, and M· CviSIII) and the nonfunctional m⁵C MTase were cloned and sequenced. Neither M· CviSI nor M· CviSIII genes hybridized to genes for their respective isomethylomers, M· CviRI and M· CviBIII, from other chlorella viruses. However, the M· CviSII gene hybridized strongly to its M· CviAII isomethylomer gene from virus PBCV-1. Like the prototype chlorella virus PBCV-1, the SC-1A genome contains inverted terminal repeats, one of which is adjacent to the nonfunctional m⁵C MTase. The three cloned m⁶A MTase genes are distributed throughout the approx. 345 kb SC-1A genome.     

Endostatin inhibits VEGF-induced endothelial cell migration and tumor growth independently of zinc binding.

Endostatin, produced as recombinant protein in human 293-EBNA cells, inhibits the migration of human umbilical vein endothelial cells (HUVECs) in response to vascular endothelial growth factor (VEGF) in a dose-dependent manner and prevents the subcutaneous growth of human renal cell carcinomas in nude mice at concentrations and in doses that are from 1000- to 100 000-fold lower than those previously reported. The inhibition of migration is not affected by mutations which eliminate Zn or heparin binding and inhibition of tumor growth does not depend on Zn binding. The results of the migration assays suggest that endostatin causes a block at one or more steps in VEGF-induced migration, while VEGF in turn can cause a block of the inhibition by endostatin of VEGF-induced migration of HUVECs.     

西双版纳种子植物物种多样性的垂直格局及机制

物种多样性海拔分布格局及其形成机制的研究是生物地理学和宏观生态学的重要议题之一。本文利用西双版纳植物专著资料, 结合高分辨率的地形和气候等数据, 探讨了面积、边界限制和现代气候对西双版纳野生种子植物物种丰富度及物种密度海拔分布格局的影响。结果表明: (1)物种丰富度呈单峰分布格局, 面积(81.9%)、边界限制(17.5%)和气候(60.0-69.3%)都不同程度地解释了物种丰富度的单峰格局; (2)利用幂函数种-面积关系计算的物种密度沿海拔大致呈减小的分布趋势, 气候的解释率降低为32.6-40.6%, 与边界限制无显著相关关系; (3)利用等面积高度带划分得到的物种密度沿海拔呈单峰变化趋势, 物种密度与边界限制无显著相关性, 但气候对物种密度的解释率为81.6-89.9%。研究结果有助于准确全面地理解物种多样性的海拔分布格局及其成因机制, 为西双版纳生物多样性保护提供理论支撑和实践指导。     

Comparison of 1D and 2D NMR spectroscopy for metabolic profiling

High-resolution, liquid state nuclear magnetic resonance (NMR) spectroscopy is a popular platform for metabolic profiling because the technique is nondestructive, quantitative, reproducible, and the spectra contain a wealth of biochemical information. Because of the large dynamic range of metabolite concentrations in biofluids, statistical analyses of one-dimensional (1D) proton NMR data tend to be biased toward selecting changes in more abundant metabolites. Although two-dimensional (2D) proton-proton experiments can alleviate spectral crowding, they have been mainly used for structural determination. In this study, 2D total correlation spectroscopy NMR was used to compare the global metabolic profiles of urine obtained from wild-type and Abcc6-knockout mice. The 2D data were compared to an improved 1D experiment in which signal contributions from macromolecules and the urea peak have been spectroscopically removed for more accurate quantitation of low-abundance metabolites. Although statistical models from both 1D and 2D data could differentiate samples acquired from the two groups of mice, only the 2D spectra allowed the characterization of statistically relevant changes in the low-abundance metabolites. While acquisition of the 2D data require more time, the data obtained resulted in a more meaningful and comprehensive metabolic profile, aided in metabolite identifications, and minimized ambiguities in peak assignments.     

Visualisation and Quantitative Analysis of the Rodent Malaria Liver Stage by Real Time Imaging

The quantitative analysis of Plasmodium development in the liver in laboratory animals in cultured cells is hampered by low parasite infection rates and the complicated methods required to monitor intracellular development. As a consequence, this important phase of the parasite''s life cycle has been poorly studied compared to blood stages, for example in screening anti-malarial drugs. Here we report the use of a transgenic P. berghei parasite, PbGFP-Luc_con, expressing the bioluminescent reporter protein luciferase to visualize and quantify parasite development in liver cells both in culture and in live mice using real-time luminescence imaging. The reporter-parasite based quantification in cultured hepatocytes by real-time imaging or using a microplate reader correlates very well with established quantitative RT-PCR methods. For the first time the liver stage of Plasmodium is visualized in whole bodies of live mice and we were able to discriminate as few as 1–5 infected hepatocytes per liver in mice using 2D-imaging and to identify individual infected hepatocytes by 3D-imaging. The analysis of liver infections by whole body imaging shows a good correlation with quantitative RT-PCR analysis of extracted livers. The luminescence-based analysis of the effects of various drugs on in vitro hepatocyte infection shows that this method can effectively be used for in vitro screening of compounds targeting Plasmodium liver stages. Furthermore, by analysing the effect of primaquine and tafenoquine in vivo we demonstrate the applicability of real time imaging to assess parasite drug sensitivity in the liver. The simplicity and speed of quantitative analysis of liver-stage development by real-time imaging compared to the PCR methodologies, as well as the possibility to analyse liver development in live mice without surgery, opens up new possibilities for research on Plasmodium liver infections and for validating the effect of drugs and vaccines on the liver stage of Plasmodium.     

Effects of elevated atmospheric CO2 on soil enzyme activities at different nitrogen application treatments

It has been predicted that elevated atmospheric CO₂ will increase enzyme activity as a result of CO₂-induced carbon entering the soil. The objective of this study was to investigate the effects of elevated atmospheric CO₂ on soil enzyme activities under a rice/wheat rotation. This experiment was conducted in Wuxi, Jiangsu, China as part of the China FACE (Free Air Carbon Dioxide Enrichment) Project. Two atmospheric CO₂ concentrations (580±60) and (380±40) μmol·mol^-1) and three N application treatments (low-150, normal-250 and high-350 kg N·hm^-2) were included. Soil samples (0-10 cm) were collected for analysis of β-glucosidase, invertase, urease, acid phosphates and β-glucosaminidase activities. The results revealed that with elevated atmospheric CO₂ β-glucosidase activity significantly decreased (P < 0.05) at low N application rates; had no significant effect with a normal N application rate; and significantly increased (P < 0.05) with a high N application rate. For urease activity, at low and normal N application rates (but not high N application rate), elevated atmospheric CO₂ significantly increased (P < 0.05) it. With acid phosphatase elevated atmospheric CO₂ only had significant higher effects (P < 0.05) at high N application rates. Under different CO₂ concentration, effects of N fertilization are also different. Soil β-glucosidase activity at ambient CO₂ concentration decreased with N fertilization, while it increased at elevated CO₂ concentration. In addition, invertase and acid phosphatase activities at elevated CO₂ concentration, significantly increased (P < 0.05) with N treatments, but there was no effect with the ambient CO₂ concentration. For urease activity, at ambient CO₂ concentration, N fertilization increased it significantly (P < 0.05), whereas at elevated CO₂ concentration it was not significant. Additionally, with β-glucosaminidase activity, there were no significant effects from N application. In general, then, elevated atmospheric CO₂ increased soil enzyme activity, which may be attributed to the following two factors: (1) elevated atmospheric CO₂ led to more plant biomass in the soil, which in turn stimulated soil microbial biomass and activity; and (2) elevated atmospheric CO₂ increased plant photosynthesis, thereby increasing plant-derived soil enzymes.     

Knock out of the annexin gene <Emphasis Type="Italic">OsAnn3</Emphasis> via CRISPR/Cas9-mediated genome editing decreased cold tolerance in rice

Plant annexins are Ca²⁺-dependent phospholipid-binding proteins and exist as multigene families in plants. They are implicated in the regulation of plant development as well as protection from environmental stresses. In this study, the rice annexin gene OsAnn3 knockout was performed via the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR associated proteins) mediated genome editing. Thus, mutant plantlets were successfully obtained. We identified cold tolerance phenotype of T₁ mutant lines from T0 biallelic mutants using the 4～6°C for 3 days cold treatment. The results showed that REC (the relative electrical conductivity) of T₁ mutant lines was increased, and the survival ratio of T₁ mutant lines was decreased dramatically compared with the wild type after the exposure to cold treatment. It was suggested that OsAnn3 was involved in cold tolerance of rice.     

Gene identification and expression analysis of 86,136 Expressed Sequence Tags (EST) from the rice genome

Expressed Sequence Tag (EST) analysis has pioneered genome-wide gene discovery and expression profiling. In order to establish a gene expression index in the rice cultivar indica, we sequenced and analyzed 86,136 ESTs from nine rice cDNA libraries from the super hybrid cultivar LYP9 and its parental cultivars. We assembled these ESTs into 13,232 contigs and leave 8,976 singletons. Overall, 7,497 sequences were found similar to the existing sequences in GenBank and 14,711 are novel. These sequences are classified by molecular function, biological process and pathways according to the Gene Ontology. We compared our sequenced ESTs with the publicly available 95,000 ESTs from japonica, and found little sequence variation, despite the large difference between genome sequences. We then assembled the combined 173,000 rice ESTs for further analysis. Using the pooled ESTs, we compared gene expression in metabolism pathway between rice and Arabidopsis according to KEGG. We further profiled gene expression pattern