Multiplex PCR assay for the simultaneous detection and differentiation of Olpidium bornovanus, O. brassicae, and O. virulentus

A multiplex PCR method has been developed to detect, differentiate, and confirm the morphological identification of three root infecting Olpidium spp.: O. bornovanus, O. brassicae, and O. virulentus. Of the 132 root samples examined, 101 samples were infected by Olpidium spp.. Based on the morphology of resting spores, the presence of O. bornovanus was confirmed in 20.5 % of the samples, whereas species identity could not be determined for the remaining samples because they failed to reproduce sexually. With multiplex PCR, it was possible to determine the Olpidium identity of all the infected samples, even when resting spores were not formed. This method was also effective for detecting Olpidium spp. in water samples. In addition, the specificity and sensitivity of multiplex PCR were evaluated. The multiplex PCR method was validated with samples of 9 different crops from 11 countries of America, Europe, and Africa.     

粤港澳大湾区生态系统服务识别、分类及制图

海岸带生态系统服务识别、分类与制图是合理利用海岸带自然资源,协调海岸带开发与保护矛盾的重要基础。现有生态系统服务分类方法在海岸带应用存在一定的局限性。在前人研究的基础上,以我国城市化和工业化水平较高的粤港澳大湾区为研究区,对该区域海岸带生态系统服务进行识别、分类,并在此基础上使用地图大数据与遥感解译的土地利用数据对海岸带生态系统服务进行了制图。共识别出35种海岸带生态系统服务,并对其中的31种服务进行制图。结果表明,建立的这套方法能较为系统地展示粤港澳大湾区生态系统服务的类型及空间分布特征。具体而言,该区域供给服务和文化服务在城市中心区较为集中,而调节服务多分布于城市周边。对识别的生态系统服务进行综合叠加分析,可将研究区分为文化服务主体区、供给服务主体区、调节服务主体区。建立的海岸带生态系统服务识别、分类体系和制图方法可操作性强,能为我国海岸带生态系统的保育、修复和重建提供科学基础。     

Group‐specific primers for amplifying DNA sequences that identify Amphipoda,Cephalopoda, Echinodermata,Gastropoda, Isopoda,Ostracoda and Thoracica

We describe seven group‐specific primer pairs that amplify small sections of ribosomal RNA genes suitable for identification of animal groups of major importance as prey items in marine ecosystems. These primer sets allow the isolation of DNA from the target animal groups from mixed pools of DNA, where DNA‐based identification using universal primers is unlikely to succeed. The primers are designed for identifying prey in animal diets, but could be used in any situation where these animal groups are to be identified by their DNA.     

一株马冠状病毒的分离鉴定及遗传演化分析

马冠状病毒病是由马冠状病毒(equine coronavirus, ECoV)引起的一种马新发胃肠道病毒病,成年马感染后主要出现发烧、腹痛和腹泻等症状。1975年,马冠状病毒感染首次在美国出现,此后在多个国家和地区均有流行,此前我国仅从山东腹泻驴的小肠样品中分离得到了一株重组马冠状病毒。【目的】了解ECoV中国毒株的基因组成、亲缘关系以及生物学特性,可以为我国ECoV流行现状和遗传演化趋势提供依据,为ECoV防控产品的研发提供材料。【方法】对湖北省武汉市黄陂区腹泻马匹的粪便样品进行RT-PCR检测,对检测阳性样品进行病毒分离,并利用靶向ECoV S1蛋白的单克隆抗体通过间接免疫荧光试验(indirect immunofluorescence assay, IFA)对分离的病毒进行验证。根据ECoV-JL株全基因组测序结果,对全基因组、N基因和NS2基因进行了基因组系统发育分析和同源性比较。【结果】成功分离到一株ECoV,并命名为ECoV-JL。透射电镜(transmission electron microscopy, TEM)观察分离到的病毒颗粒呈球状,且具有囊膜和冠状病毒典型的纤突结构。该分离株感染HRT-18细胞72 h后病毒滴度可到达峰值,半数组织培养感染剂量(tissue culture infectious dose 50%, TCID₅₀)约为10^6.16 TCID₅₀/mL。ECoV-JL毒株可以在人回盲肠癌(human ileocecal cancer-18, HRT-18)细胞、人结直肠腺癌(human colorectal adenocarcinoma-2, Caco-2)细胞和人肝癌(human liver cancer cells, Huh7)细胞上稳定传代。ECoV-JL株与GenBank中现有的ECoV全基因组序列相似性为97.9%-99.0%,系统发育分析发现ECoV-JL株属于单独的演化分支,与其他毒株的亲缘关系较远,说明ECoV-JL株可能是重组变异而来,其中NS2基因突变较多,NS2基因编码的差异是造成ECoV-JL株与其他毒株同源性较差的主要原因。【结论】本研究从腹泻马的粪便样品中成功分离并鉴定了一株ECoV,将其命名为ECoV-JL株,对该毒株生物学特性和亲缘关系的研究反映了湖北地区流行毒株的特点,为我国ECoV流行现状和演化趋势提供重要依据。     

A new species and new records of the leafhopper genus Taperus Li & Wang, 1994 (Hemiptera,Cicadellidae, Evacanthinae) from China

The paper deals with the species of the Oriental leafhopper genus Taperus Li & Wang. A new species, Taperus daozhenensissp. n., from Guizhou Province, China is described and new records for other Chinese species are given together with a key for their separation. The type specimens of the new species are deposited in the Institute of Entomology, Guizhou University (GUGC).     

Variation in number of vertebrae and gill rakers of sockeye salmon,Oncorhynchus nerka,in North America

Synopsis The latitudinal, regional, and annual variation in number of vertebrae and number of gill rakers present in sockeye salmon, Oncorhynchus nerka, stocks in North America was examined. Stocks in more northern areas had higher numbers of vertebrae and gill rakers than did those in more southern ones. Significant annual variability in the frequencies of these meristic characters within stocks was observed. When stocks were grouped into three regions (southern, central, and northern), heterogeneity in vertebral and gill raker frequencies was greater among regions than among stocks within the regions. Similarly, heterogeneity was greater among stocks than among sampling years within stocks. Differences in vertebral and gill raker frequencies are only useful for stock identification of sockeye salmon on a broad regional basis.     

Phylogeny, evolution, and taxonomy of vannellid amoebae

We sequenced 18S rRNA genes from 21 vannellid amoebae (Amoebozoa; Vannellidae), including nearly all available type cultures, and performed a comprehensive phylogenetic analysis for 57 Vannellidae sequences. The results show that species of Vannella and Platyamoeba are completely mixed and do not form distinct clades. Several very closely related species pairs exist, each with a Vannella and a Platyamoeba species differing in only a few nucleotides. Therefore, presence (Vannella) or absence (Platyamoeba) of glycostyles in the cell surface coat is an invalid generic distinction; the genera must be merged. As Vannella has priority, we formally transferred Platyamoeba species into Vannella, except for the non-vannellid P. stenopodia, here renamed Stenamoeba stenopodia gen. n. comb. n. and transferred to the family Thecamoebidae. Our trees show that Vannella glycostyles were probably easily and repeatedly evolutionarily lost. We have established a new genus Ripella, with distinct morphology and sequence signatures for Vannella platypodia and morphologically similar species that form a clearly separate clade, very distant from other Vannellidae. Vannellids form four well-separated single-genus clades: Vannella sensu stricto, Ripella, Clydonella, and Lingulamoeba. Species of the revised genus Vannella comprise four closely related, well-supported subclades: one marine and three freshwater. Here, we provide an illustrated checklist for all 40 known Vannellidae species.     

应用荧光、水试和紫外吸收法鉴别伪劣中药材

为了建立快速鉴别多种中药材真伪优劣的方法,利用荧光鉴别、水试和紫外吸收法对多种中药材进行鉴别、检查。实验结果表明,法半夏、金银花、木香、柴胡、巴戟天等可通过紫外激发荧光、水试或紫外吸收图谱来快速鉴别药材真伪。本研究结果表明,以上三种方法快速、简便,可应用于有荧光反应、水试反应和紫外吸收特性的中药材的快检筛查。     

Biometrics, identification and surveillance

Governing by identity describes the emerging regime of a globalizing, mobile world. Governance depends on identification but identification increasingly depends on biometrics. This 'solution' to difficulties of verification is described and some technical weaknesses are discussed. The role of biometrics in classification systems is also considered and is shown to contain possible prejudice in relation to racialized criteria of identity. Lastly, the culture of biometric identification is shown to be limited to abstract data, artificially separated from the lived experience of the body including the orientation to others. It is proposed that creators of national ID systems in particular address these crucial deficiencies in their attempt to provide new modes of verification.     

一株产丙烯酸和一株耐高浓度丙烯酸细菌的筛选与鉴定

从广西大学农场、养猪场排水沟、奶牛场的排水沟、屠宰场的废液池及鱼塘的污泥和废水中分离到1株能产丙烯酸和1株耐高浓度丙烯酸的菌株。经高效气相色谱检测其培养提取物,能产丙烯酸的菌株在培养物中丙烯酸的摩尔浓度达到3．5mmoL／L;耐高浓度丙烯酸的菌株其耐受丙烯酸的摩尔浓度可以达到2moL／L,对这2个菌株进行16S rDNA鉴定,它们分别属于Cellulosimicrobium属和Brevundimonas属。     

Identification of proteins encoded in Escherichia coli hydA, hydB and analysis of the hydA locus

The hydB gene of Escherichia coli, which is related with the expression of hydrogenase activity, was cloned into the plasmid (pES1). Using the maxicell protein-labeling method, the molecular weight of hydB gene product was estimated. Comparing between the gene products from the mutant strains and that of the hydB genes cloned strains, the molecular weight of the gene product was 35,000 Mr. Similarly, the molecular weight of the gene product of hydA, which had been previously cloned, was determined by maxicell analysis. The molecular weight of hydA gene product was estimated to be 80,000 Mr. Using deletion analysis and Tn1000 insertional inactivation of hydA's function, the hydA coding region was estimated between 2.2 kb and 2.8 kb in a 3.1 kb EcoRI-MluI fragment on the recombinant plasmid pEH3.     

A standardized microsatellite marker panel for parentage and kinship analyses in channel catfish,Ictalurus punctatus

This research was designed to produce a standardized set of microsatellite loci for parentage and kinship analyses in channel catfish, the leading species of US aquaculture. Three panels of five to six markers each were developed that contained a total of two dinucleotide‐, eight trinucleotide‐ and seven tetranucleotide‐microsatellite loci respectively. The loci had a range of nine to 31 alleles per locus in an outbred population. Based on the allele frequencies measured in commercial randomly bred broodstock, the combined probability of non‐exclusion of an unrelated candidate parent pair was 5.36e‐18. The combined probability of non‐exclusion of unrelated identical genotypes was 2.58e‐08. The microsatellite panels were validated by parentage and kinship evaluation in three populations. A total of 697 spawns were collected from matings of outbred broodstock over three spawning seasons, and parents were determined unambiguously for all but three spawns. Genotype analysis also enabled the identification of half‐sibling and full‐sibling families produced by pond spawning. In a second experiment, parentage was unambiguously determined in nine spawns from a population consisting of broodstock derived from only four families. A third experiment demonstrated that all but one of 374 individuals from 10 full‐sibling families could be assigned to a family after coculture in an earthen pond for 1 year. The standardized microsatellite panels enable the development of pedigreed catfish populations and large‐scale performance evaluations in common environments to support the genetic improvement of cultured catfish through selective breeding.     

Aegilops (Poaceae) in Italy: taxonomy,geographical distribution,ecology, vulnerability and conservation

ABSTRACT

Aegilops L. includes wild species from which, over millennia, man has cultivated forms of Triticum L. Ten species of Aegilops occur in Italy. Three species are allochthonous and eight out of ten species are recorded in the Apulia region. Five out of the ten species have been included in Red Lists. Each taxon is presented and discussed, citing old and new sites of occurrence, by examining specimens from many different herbaria, and describing their ecology and habitats, according to the Directive 92/43 EEC. A new taxonomic key, for the identification of all Aegilops species growing in Italy, is provided. The occurrence of Aegilops caudata L., A. peregrina (Hack. in J. Fraser) Maire & Weiller and A. speltoides Tausch in Italy is doubtful.     

脱氮除硫菌株的分离鉴定和功能确认

从长期稳定运行的脱氮除硫反应器污泥中,分离获得两株具有脱氮除硫功能的芽孢杆菌。经形态观察、生理试验和16SrDNA序列比对,将两菌株归入芽孢杆菌属,菌株CB归类于Bacillus pseudofirmus,菌株CS则与Bacillus hemicellulosilytus和Bacillus halodurans最为接近。以Biolog板检测,菌株CB的基质多样性不明显,菌株CS则可利用Biolog板中多种碳源。菌株CB和菌株CS都能以硝酸盐氧化硫化物,其中菌株CB对硝酸盐、硫化物的转化能力大于CS,菌株CB对硝酸盐的亲和力也大于菌株CS。     

广东中山地区气单胞菌环境株的分离、鉴定及系统发生关系

从广东省中山市的池塘水样、底泥、健康鱼、肠道及稻田土样中用Aeromonas的选择培养基分离到10株气单胞菌。通过生理生化测试、16S rDNA序列测定、与气单胞菌典型菌株的16S rDNA序列进行比对和聚类分析,对它们进行了鉴定,并研究了它们之间的系统发生关系。结果显示该地区环境中气单胞菌的优势种除A.hydrophila(HG1组)外,还有A.caviae(HG4组)、A.jandaei(HG9组)和A.veronii(HG10组),其中后两种是国内新记录。这是国内首次对环境中气单胞菌多样性进行研究。     

重组人源脑红蛋白的高效表达、纯化及鉴定

脑红蛋白(Neuroglobin,NGB)是新发现的主要表达于脊椎动物神经元及视网膜中的第三类携氧珠蛋白。已有诸多报道认为脑红蛋白在缺氧缺血性脑损伤的神经保护过程中,作为活性氧簇(ROS)的清除剂或缺氧信号的感受器起重要作用,但其神经保护作用的具体机制不明。显然,实现该蛋白的制备对于研究其功能具有重要作用。基于此,通过RT-PCR从人胎脑中扩增出脑红蛋白cDNA并克隆到原核表达载体pBV220,通过测序鉴定正确后转化至大肠杆菌HB101中诱导表达,表达产物超声破碎后经凝胶过滤柱Sephacryl S-200和阴离子交换柱Q Sepharose FF纯化,最后通过Sephadex G-25脱盐。经15% SDS-PAGE和Western blot检测及质谱和蛋白序列分析鉴定制备的蛋白样品为脑红蛋白。本文采用两步法实现了脑红蛋白高效特异性纯化,为后期基于脑红蛋白神经保护作用的功能及机制研究奠定了重要基础。     

Identification, morphometries and cytogenetics of green geckos (Phelsuma) from Praslin, Seychelles (with notes on P. longinsulae, Mahé)

The three species of green geckos (Phelsuma) on the granitic Seychelles can be identified by colour pattern, snout shape and the occurrence of keeled belly scales. There is no difference in chromosome number (2n=S6) between species but multivariate morphometries analysis, based on body proportions and scalation, can distinguish between the species on Praslin Island.     

Comparison of morphological,DNA barcoding,and metabarcoding characterizations of freshwater nematode communities

Biomonitoring approaches and investigations of many ecological questions require assessments of the biodiversity of a given habitat. Small organisms, ranging from protozoans to metazoans, are of great ecological importance and comprise a major share of the planet's biodiversity but they are extremely difficult to identify, due to their minute body sizes and indistinct structures. Thus, most biodiversity studies that include small organisms draw on several methods for species delimitation, ranging from traditional microscopy to molecular techniques. In this study, we compared the efficiency of these methods by analyzing a community of nematodes. Specifically, we evaluated the performances of traditional morphological identification, single‐specimen barcoding (Sanger sequencing), and metabarcoding in the identification of 1500 nematodes from sediment samples. The molecular approaches were based on the analysis of the 28S ribosomal large and 18S small subunits (LSU and SSU). The morphological analysis resulted in the determination of 22 nematode species. Barcoding identified a comparable number of operational taxonomic units (OTUs) based on 28S rDNA (n = 20) and fewer OTUs based on 18S rDNA (n = 12). Metabarcoding identified a higher OTU number but fewer amplicon sequence variants (AVSs) (n = 48 OTUs, n = 17 ASVs for 28S rDNA, and n = 31 OTUs, n = 6 ASVs for 18S rDNA). Between the three approaches (morphology, barcoding, and metabarcoding), only three species (13.6%) were shared. This lack of taxonomic resolution hinders reliable community identifications to the species level. Further database curation will ensure the effective use of molecular species identification.