Complete Genome Sequence of Staphylococcus aureus Strain JKD6008, an ST239 Clone of Methicillin-Resistant Staphylococcus aureus with Intermediate-Level Vancomycin Resistance

We report here the complete 2.92-Mb genome sequence of a clinical isolate of methicillin-resistant Staphylococcus aureus subsp. aureus that demonstrates intermediate-level vancomycin resistance. The strain, named JKD6008, belongs to multilocus sequence type 239 and was isolated from the bloodstream of a patient in New Zealand in 2003.We have previously described the in vivo evolution of low-level vancomycin resistance in Staphylococcus aureus through comparative and functional genomic assessment of a pair of isogenic methicillin-resistant Staphylococcus aureus (MRSA) strains. The vancomycin-susceptible S. aureus (VSSA) strain JKD6009 was a patient wound isolate, whereas vancomycin-intermediate S. aureus (VISA) strain JKD6008 was recovered from the bloodstream of the same patient after 42 days of vancomycin treatment (5). Comparison of the partially assembled genomes of the two isolates revealed a single-point mutation in the sensor region of the two-component regulatory gene graS, which caused a significant reduction in the vancomycin susceptibility of JKD6008 (6). Here we report the fully assembled and annotated genome of S. aureus JKD6008.The genome sequence of S. aureus strain JKD6008 was determined by whole-genome shotgun sequencing using single-read 454 GS20 (Roche Diagnostics, Basel, Switzerland), Sanger (Applied Biosystems), and SOLiD (Applied Biosystems) sequencing technologies, producing approximately 20 times, 4 times, and 225 times coverage of the genome, respectively. GS20 reads were assembled using gsAssembler v2.0 software, resulting in 131 contigs (≥500 bp) totaling 2.83 Mbp (6, 10). Sanger paired-end reads (clone insert size, 3 to 5 kb) were combined with the GS20 contigs using Gap4 v4.11 software (3). Mate-pair SOLiD reads (3 to 5 kb) were aligned to the contigs using SHRiMP 1.3.2 software to identify and correct sequencing errors (11). Optical mapping produced a high-resolution XbaI chromosome restriction map, to which the contigs were aligned using MapSolver 2.1.1 (Opgen) to determine misassemblies. Gap closures were performed by PCR, followed by Sanger sequencing and primer walking of amplification products (3730S DNA Analyzer sequencer; Applied Biosystems). The assembly of the completed genome was confirmed to be correct by reference to the XbaI optical map.Protein-coding regions were predicted using GeneMarkS 4.6b software, tRNA genes using tRNAscan-SE 1.23, and rRNA genes using RNAmmer 1.2 (2, 8, 9). Gene products were assigned using HMMER 3.0 against the Pfam database (release 23) and BLAST 2.2.23 against RefSeq proteins (April 2010) and the Conserved Domain Database (v2.22) (1, 4). These automated analyses were followed by manual curation and comparisons with other completed S. aureus genomes.The genome of S. aureus strain JKD6008 consists of a circular 2,924,344-bp chromosome with a 34% G+C content and no extrachromosomal elements. A total of 2,766 coding DNA sequences, 82 tRNA genes, and 5 rRNA loci were detected. Over 70% of genes were assigned to specific Clusters of Orthologous Groups (COG) functional groups, and 42% were assigned an enzyme classification number (12).Initial analysis of the whole-genome sequence of JKD6008 confirmed it as a member of the ST239 complex, sharing 2,504 orthologous coding sequences (CDSs) with the recently described ST239 member TW20 (EMBL accession no. {"type":"entrez-nucleotide","attrs":{"text":"FN433596.1","term_id":"269939526","term_text":"FN433596.1"}}FN433596.1). There are 17 copies of IS256 and a type III staphylococcal cassette chromosome mec element (SCCmec). Comparisons with 19 published S. aureus genomes revealed 20 CDS not present in any other S. aureus genome, although some of these 20 CDS have orthologs in other Staphylococcus species. JKD6008 also harbors a 28-kb integrated pSK1-like plasmid that is predicted to confer resistance to aminoglycosides and trimethoprim, as well as efflux-mediated antiseptic and disinfectant resistance (7).Nucleotide sequence accession number. The complete genome sequence has been deposited in NCBI GenBank under accession number {"type":"entrez-nucleotide","attrs":{"text":"CP002120","term_id":"302749911","term_text":"CP002120"}}CP002120.     

县域生态资产核算研究——以云南省屏边县为例

生态资产(Eco-Assets)是生产与提供生态产品和服务的自然资源。以国家重点生态功能区县——屏边苗族自治县为例,研究了县域生态资产核算的指标和方法,以生态资产综合指数、负债表和损益表,开展屏边县生态资产实物量核算,以期能够切实反映出生态系统实物量的变化和生态补偿成效,结合生态补偿分析屏边县生态资产变化的原因和趋势,给生态补偿政策和离任干部审计提供技术支撑。结果表明:(1)屏边县生态资产核算可以分为森林、灌丛、草地、湿地自然生态系统和农田、城镇和荒漠人工生态系统实物量的核算。(2)2015年,屏边县生态资产指数为1.09,森林和灌丛占据主要位置,二者总和占当年生态资产的95.48%。15年来,屏边县生态资产综合指数降低了16.48%,其中森林和草地降低明显,分别减少了20.10%和6.67%,湿地指数增长了57.11%。(3)2000年以来,生态保护工程和城镇扩张是生态资产变化的主要原因,生态补偿投入持续增加为生态保护工程顺利建设实施提供了保障。本研究表明,现有的土地利用数据和生态环境监测数据基本可以支撑县域生态资产的核算,同时县域生态资产的变化能够体现出生态保护工程实行成效,并为实...     

阿帕替尼对人肝癌细胞增殖及凋亡的作用机制研究

目的:探讨阿帕替尼抑制肝癌细胞增殖促进凋亡的作用机制。方法:选取肝癌细胞系SNU739、HepG2,以CCK-8细胞增殖实验、平板克隆实验测定阿帕替尼对肝癌细胞增殖及克隆形成能力的影响;流式细胞术检测阿帕替尼对肝癌细胞凋亡的影响;蛋白免疫印迹法检测阿帕替尼影响肝癌细胞凋亡相关蛋白Bax、Bcl-2及Caspase3的表达情况。结果:与对照组相比,阿帕替尼可显著抑制肝癌细胞增殖(P0.05)。平板克隆实验提示与对照组相比,10μM和20μM阿帕替尼组肝癌细胞克隆数明显减少(P0.05)。流式细胞术结果提示10μM和20μM阿帕替尼处理组细胞凋亡率明显增加(P0.05)。蛋白免疫印迹法结果显示经阿帕替尼处理的肝癌细胞,促凋亡蛋白Bax及Caspase3的活性片段Cleaved-caspase3表达水平显著上调,抗凋亡蛋白Bcl-2显著下调(P0.01)。结论:阿帕替尼通过调节肝癌细胞凋亡相关蛋白从而抑制肝癌细胞增殖、促进其凋亡。     

Quantifying landscape‐level methane fluxes in subarctic Finland using a multiscale approach

Quantifying landscape‐scale methane (CH₄) fluxes from boreal and arctic regions, and determining how they are controlled, is critical for predicting the magnitude of any CH₄ emission feedback to climate change. Furthermore, there remains uncertainty regarding the relative importance of small areas of strong methanogenic activity, vs. larger areas with net CH₄ uptake, in controlling landscape‐level fluxes. We measured CH₄ fluxes from multiple microtopographical subunits (sedge‐dominated lawns, interhummocks and hummocks) within an aapa mire in subarctic Finland, as well as in drier ecosystems present in the wider landscape, lichen heath and mountain birch forest. An intercomparison was carried out between fluxes measured using static chambers, up‐scaled using a high‐resolution landcover map derived from aerial photography and eddy covariance. Strong agreement was observed between the two methodologies, with emission rates greatest in lawns. CH₄ fluxes from lawns were strongly related to seasonal fluctuations in temperature, but their floating nature meant that water‐table depth was not a key factor in controlling CH₄ release. In contrast, chamber measurements identified net CH₄ uptake in birch forest soils. An intercomparison between the aerial photography and satellite remote sensing demonstrated that quantifying the distribution of the key CH₄ emitting and consuming plant communities was possible from satellite, allowing fluxes to be scaled up to a 100 km² area. For the full growing season (May to October), ~ 1.1–1.4 g CH₄ m^?2 was released across the 100 km² area. This was based on up‐scaled lawn emissions of 1.2–1.5 g CH₄ m^?2, vs. an up‐scaled uptake of 0.07–0.15 g CH₄ m^?2 by the wider landscape. Given the strong temperature sensitivity of the dominant lawn fluxes, and the fact that lawns are unlikely to dry out, climate warming may substantially increase CH₄ emissions in northern Finland, and in aapa mire regions in general.     

Genetic polymorphism of mitochondrial DNA HVS-I and HVS-Ⅱ of Chinese Tu ethnic minority group

We analyzed the two hypervariable segments HVS-Ⅰ and HVS-Ⅱ of 108 Chinese Tu ethnic minority group samples for forensic and population genetics purposes.Comparing with Anderson sequence,79 polymorphic loci in HVS-Ⅰ and 40 in HVS-Ⅱ were found in Chi-nese Tu ethnic minority group mtDNA sequences,and 90 and 64 haplotypes were then defined.Haplotype diversity and the mean pair-wise differences were 0.9903:±0.0013 and 5.7785 in HVS-Ⅰ,and 0.9777±0.0013 and 3.5819 in HVS-Ⅱ,respectively.By analyzing the hypervariable domain from nucleotide 1,6180 to 1,6193 in HVS-Ⅰ,we defined some new types of sequence variations.We also compared the relationship between Tu population and other populations using mtDNA HVS-Ⅰ sequences.According to Rst genetic distances,the phylogenetic tree showed that the Tu population,the Xi'an Han population,the Chinese Korean,and the Mongol ethnic group were in a clade.This indicated a close genetic relationship between them.There were far relations between the Tu population and other Chinese southern Han populations,Siberian,European,African,and other foreign populations.The results suggest that Tu population has a multi-origin and has also merged with other local populations.     

Oral and parenteral immunization with synthetic retro-inverso peptides induce antibodies that cross-react with native peptides and parent antigens

The objective of this study was to determine whether certain retro-inverso peptides have the potential to act as synthetic vaccines in mice, when immunized by injection or orally. Immunization of mice parenterally with conjugates of three such retro-inverso peptides and orally with the unconjugated peptides elicited generally high titres of anti-peptide antibodies. Antibodies against the same three peptides cross-reacted by binding strongly in ELISA to the native peptides and vice versa, regardless of the mode of immunization. Antibodies against a retro-inverso diphtheria peptide also reacted strongly with diphtheria toxin. Seven of 8 mice, immunized by injection of the conjugate of a retro-inverso derivative of robustoxin [a lethal spider (Atrax robustus) venom toxin] were protected from challenge involving injection with twice the minimum lethal dose of A. robustus venom containing the toxin.     

中脑导水管周围灰质内注射抗阿片肽血清对神经降压素增强电针镇痛的影响

本工作以钾离子透入引起大鼠甩尾反应作为痛反应指标,观察纳洛酮（ＮＸ）和抗阿片肽血清对大鼠中脑导水管周围灰质（ＰＡＧ）内微量注射神经降压素（ＮＴ）增强电针镇痛作用的影响。结果显示：（１）ＰＡＧ内微量注射ＮＴ后,大鼠电针镇痛效应明显提高;（２）ＰＡＧ内注射大剂量ＮＸ,可以显著减弱ＮＴ增强电针镇痛效应;（３）ＰＡＧ内微量注射抗甲脑啡肽血清和抗β内啡肽血清后,ＮＴ增强电针镇痛的作用明显降低;而ＰＡＧ内微量注射抗强啡肽Ａ１１３血清,对于ＮＴ增强电针镇痛的作用并无明显影响。提示：ＰＡＧ内ＮＴ在针刺镇痛过程中发挥重要作用,ＮＴ增强电针镇痛的作用与甲脑啡肽和β内啡肽有较密切的关系。