Four Pathogenic Candida Species Differ in Salt Tolerance

The virulence of Candida species depends on many environmental conditions, including extracellular pH and concentration of alkali metal cations. Tests of the tolerance/sensitivity of four pathogenic Candida species (C. albicans, C. dubliniensis, C. glabrata, and C. parapsilosis) to alkali metal cations under various growth conditions revealed significant differences among these species. Though all of them can be classified as rather osmotolerant yeast species, they exhibit different levels of tolerance to different salts. C. parapsilosis and C. albicans are the most salt-tolerant in general; C. dubliniensis is the least tolerant on rich YPD media and C. glabrata on acidic (pH 3.5) minimal YNB medium. C. dubliniensis is relatively salt-sensitive in spite of its ability to maintain as high intracellular K⁺/Na⁺ ratio as its highly salt-tolerant relative C. albicans. On the other hand, C. parapsilosis can grow in the presence of very high external NaCl concentrations in spite of its high intracellular Na⁺ concentrations (and thus lower K⁺/Na⁺ ratio) and thus resembles salt-tolerant (halophilic) Debaryomyces hansenii.     

Genome-Wide Analyses of Recombination Suggest That Giardia intestinalis Assemblages Represent Different Species

Giardia intestinalis is a major cause of waterborne enteric disease in humans. The species is divided into eight assemblages suggested to represent separate Giardia species based on host specificities and the genetic divergence of marker genes. We have investigated whether genome-wide recombination occurs between assemblages using the three available G. intestinalis genomes. First, the relative nonsynonymous substitution rates of the homologs were compared for 4,009 positional homologs. The vast majority of these comparisons indicate genetic isolation without interassemblage recombinations. Only a region of 6 kbp suggests genetic exchange between assemblages A and E, followed by gene conversion events. Second, recombination-detecting software fails to identify within-gene recombination between the different assemblages for most of the homologs. Our results indicate very low frequency of recombination between the syntenic core genes, suggesting that G. intestinalis assemblages are genetically isolated lineages and thus should be viewed as separated Giardia species.     

四种嗜热真菌的分离与鉴定

目的:在对嗜热真菌的资源调查中,分离到嗜热真菌20株。方法:通过形态学比较研究并结合分子分析方法。结果:鉴定出嗜热真菌4种,即杜邦青霉Penicillium dupontii、疏绵状嗜热丝孢菌Thermomyceslanuginosus、嗜热子囊菌Thermoascus aurantiacus、嗜热革节孢Scytalidium thermophilum。此外,还分离到耐热真菌1种,鉴定为不规则头梗霉Cephaliophora irregularis,为中国新记录种。结论:这些研究结果新增了嗜热真菌在中国的分布记载,丰富了我国西南地区嗜热真菌的菌种资源库,另外对分离获得的嗜热真菌进行木聚糖酶活性测试,发现嗜热子囊菌为高产木聚糖酶活力的菌株。     

Fast Technology Analysis Enables Identification of Species and Genotypes of Latent Microsporidia Infections in Healthy Native Cameroonians

Several enteric microsporidia species have been detected in humans and other vertebrates and their identifications at the genotype level are currently being elucidated. As advanced methods, reagents, and disposal kits for detecting and identifying pathogens become commercially available, it is important to test them in settings other than in laboratories with “state‐of‐the‐art” equipment and well‐trained staff members. In the present study, we sought to detect microsporidia DNA preserved and extracted from FTA (fast technology analysis) cards spotted with human fecal suspensions obtained from Cameroonian volunteers living in the capital city of Yaoundé to preclude the need for employing spore‐concentrating protocols. Further, we tested whether amplicon nucleotide sequencing approaches could be used on small aliquots taken from the cards to elucidate the diversity of microsporidia species and strains infecting native residents. Of 196 samples analyzed, 12 (6.1%) were positive for microsporidia DNA; Enterocytozoon bieneusi (Type IV and KIN‐1), Encephalitozoon cuniculi, and Encephalitozoon intestinalis were identified. These data demonstrate the utility of the FTA cards in identifying genotypes of microsporidia DNA in human fecal samples that may be applied to field testing for prevalence studies.     

Genome-Wide Comparative Analyses of Microsatellites in Papaya

Microsatellites, or simple sequence repeats (SSRs), are highly polymorphic and universally distributed in eukaryotes. SSRs have been used extensively as sequence tagged markers in genetic studies. Recently, the functional and evolutionary importance of SSRs has received considerable attention. Here we report the mining and characterization of the SSRs in papaya genome. We analyzed SSRs from 277.4 Mb of whole genome shotgun (WGS) sequences, 51.2 Mb bacterial artificial chromosome (BAC) end sequences (BES), and 13.4 Mb expressed sequence tag (EST) sequences. The papaya SSR density was one SSR per 0.7 kb of DNA sequence in the WGS, which was higher than that in BES and EST sequences. SSR abundance was dramatically reduced as the repeat length increased. According to SSR motif length, dinucleotide repeats were the most common motif in class I, whereas hexanucleotides were the most copious in class II SSRs. The tri- and hexanucleotide repeats of both classes were greater in EST sequences compared to genomic sequences. In class I SSR, AT and AAT were the most frequent motifs in BES and WGS sequences. By contrast, AG and AAG were the most abundant in EST sequences. For SSR marker development, 9,860 primer pairs were surveyed for amplification and polymorphism. Successful amplification and polymorphic rates were 66.6% and 17.6%, respectively. The highest polymorphic rates were achieved by AT, AG, and ATG motifs. The genome wide analysis of microsatellites revealed their frequency and distribution in papaya genome, which varies among plant genomes. This complete set of SSRs markers throughout the genome will assist diverse genetic studies in papaya and related species.     

厚朴基原植物及其4个近缘种的花粉鉴定

采用扫描电镜对2种厚朴基原植物(厚朴Magnolia officinalis Rehd.et Wils.、凹叶厚朴M.officinalis Rehd.et Wils.var.biloba Rehd.et Wils.)及4种近缘植物(玉兰M.denudata Desr.、紫玉兰M.liliiflora Desr.、望春玉兰M.biondii Pampan.、荷花玉兰M.grandiflora L.)的花粉形态、表面纹饰和大小进行了观察研究。结果显示:(1)6种植物的花粉粒均为单粒,具远极单萌发沟,沟长,直达两端,左右对称,异极;侧面观均为舟形,两端较尖,赤道面观为椭圆形或近椭圆形,极面观均为近圆形;外壁均具小穴状或网状纹饰。(2)厚朴的小穴状纹饰小而浅,不明显;凹叶厚朴的小穴状纹饰小但较深,也不甚明显;相比之下,紫玉兰、玉兰、望春玉兰和荷花玉兰的花粉粒表面密布不规则隆起及深穴点,明显。(3)6种植物花粉粒由大至小依次为:荷花玉兰凹叶厚朴厚朴玉兰紫玉兰望春玉兰。3种不同的花粉处理方法中,自然干燥法能清晰地观察到花粉的扫描电镜特征,此方法优于戊二醛固定法和叔丁醇真空冷冻干燥法。本研究结果为厚朴中药资源的基原植物及其近缘种鉴定提供了新的证据,也为现代植物从种及亚种级水平分类提供了参考。     

4种薯蓣属植物的分子鉴别和亲缘关系研究

为揭示薯蓣属植物的亲缘关系,根据叶绿体matK、rbcL、trnL-F和psbA-trnH序列片段,对小花盾叶薯蓣(Dioscorea sinopatviflora)、盾叶薯蓣(D.zingibiernsis)、黄独(D.bulbifera)和山药(D.polystachya)进行种间分子鉴别研究,并探讨这4个片段在薯蓣属植物系统发育上的意义。结果表明,4种薯蓣属植物共22份材料的matK、rbcL、trnL-F和psbA-trnH序列片段的长度分别为1026~1142 bp、1156~1178 bp、744~822 bp和355~599 bp。用PAUP 4.0b10和贝叶斯推断构建的系统发育树分析表明,云南的黄独与盾叶薯蓣的亲缘关系较近;小花盾叶薯蓣与盾叶薯蓣的亲缘关系很近;而非洲的黄独与云南的黄独的亲缘关系很远。但仅用这4个cpDNA片段还不能完全区分小花盾叶薯蓣和盾叶薯蓣,这说明基于这4个序列片段的系统发育证据与4种薯蓣属植物属内的分类划分并不十分吻合。     

Identification and Phylogenetic Relationships of Microsporidia by Riboprinting

ABSTRACT. The SSUrDNA and the ITS of different microsporidia from eight fishes, four insects and a shrimp were amplified and digested with restriction enzymes. The generated riboprints suggest a close evolutionary relationship between Glugea americanus and Spraguea lophii suggesting that Glugea americanus should be renamed Spraguea americanus and that the tissue infected and host origin should be considered of greater taxonomic importance for defining a genus than previously considered. Phylogenetic analysis of the riboprints demonstrates an unidentified microsporidium from a bumper fish ( Chloroscombrus chrysurus ) is related although not identical to Microgemma oviodea , a parasite from red band fish. We were also able to distinguish between Glugea anomala and Glugea atherinae and Glugea stephani but were not able to differenciate among the latter two. Insects isolates, Nosema costelytrae, N. bombycis, N. trichoplusiae, Nosema sp. and a shrimp isolate, Agmasoma penaei , are not related to the fish isolates.     

Genome-Wide Identification,Biochemical Characterization,and Expression Analyses of the YTH Domain-Containing RNA-Binding Protein Family in Arabidopsis and Rice

RNA-binding proteins are critical to RNA metabolism in cells and, thus, play important roles in diverse biological processes. In the present study, we identified the YTH domain-containing RNA-binding protein (RBP) family in Arabidopsis thaliana and rice at the molecular and biochemical levels. A total of 13 and 12 genes were found to encode YTH domain-containing RBPs in Arabidopsis and rice and named as AtYTH01–13 and OsYTH01–12, respectively. The phylogeny, chromosomal location, and structures of genes and proteins were analyzed. Electrophoretic mobility shift assays demonstrated that recombinant AtYTH05 protein could bind to single-stranded RNA in vitro, demonstrating that the YTH proteins have RNA-binding activity. Analyses of publicly available microarray data, gene expression by qRT-PCR, and AtYTH05 promoter activity indicate that the Arabidopsis AtYTHs and rice OsYTHs genes have distinct and diverse expression patterns in different tissues and developmental stages, showing tissue- and developmental-specific expression patterns. Furthermore, analyses of publicly available microarray data also indicate that many of the Arabidopsis AtYTHs and rice OsYTHs genes might be involved in responses to various abiotic and biotic stresses as well as in response to hormones. Our data demonstrate that the YTH family proteins are a novel group of RBPs and provide useful clues to define their biological functions of this RBP family in plants.     

四株抗荔枝病原菌的芽孢杆菌的分离鉴定

荔枝果树根际土壤中筛选出4株芽孢杆菌OR-1、OR-2、OR-3、ON-6,都显示出抗荔枝病原菌的活性。采取对该菌株形态特征、培养特征、生理生化特征和遗传特性进行研究的方法,结果表明菌株与枯草芽孢杆菌(Bacillus subtilis)的特征一致;将4菌株的16S rDNA序列在GenBank中进行序列比对,结果亦显示其与Bacillus subtilis的16S rDNA的序列片段的相似性均达99%以上;以相似性为基础构建系统进化树,分析表明菌株与Bacillus subtilis同源关系最近。最终得出结论为菌株OR-1、OR-2、OR-3、ON-6为枯草芽孢杆菌。     

4种模式植物LRR VIII-2亚家族基因的鉴定和进化历史分析

全基因组重复与串联重复是发生基因重复的重要机制, 也是基因组和遗传系统多样化的重要动力。LRR-RLK编码富含亮氨酸重复的类受体蛋白激酶, 是被子植物进化史上发生大规模扩张而形成的多基因家族。拟南芥(Arabidopsis thaliana) AtLRR-RLK包含15个亚家族, AtLRR VIII-2是其中发生串联重复比例最高的亚家族。通过分析拟南芥、杨树(Populus trichocarpa)、葡萄(Vitis vinifera)和番木瓜(Carica papaya) 4种模式植物中LRR VIII-2亚家族基因的扩张及差异保留情况, 结果显示, LRR VIII-2在杨树中的扩张程度最高, 在拟南芥和葡萄中的扩张程度居中, 但在番木瓜中发生丢失。拟南芥、杨树和葡萄LRR VIII-2亚家族具有旁系同源基因对, 但在番木瓜中未发现旁系同源基因。除杨树中的1对旁系同源基因外, 4种模式植物中LRR VIII-2亚家族的旁系和直系同源基因都受到较强的纯化选择作用。对LRR VIII-2亚家族进化历史的深入分析有助于理解基因重复在植物进化中的作用和意义, 可为预测同源基因功能及解析其它基因家族进化历史提供参考。     

nrDNA ITS和cpDNA rpl16基因测序法对六种鼠尾草的检测

为从鼠尾草属植物中鉴别丹参品种,采用基因测序方法,用核糖体核酸内转录间隔区基因(nrDNA ITS),编码核蛋白体大亚基多肽L16的基因(rpl16)及叶绿体DNA上包含trnL以及trnL和trnF间隔区的区域基因(trnL-trnF)的序列,检测六种鼠尾草属新鲜植物.由于nrDNA ITS和rpl16突变率较高,可以做为6种鼠尾草的基源鉴定标记,依此设计了两对特异引物,从6种鼠尾草中鉴定出丹参(Salvia miltiorrhiza)和云南鼠尾草(S.yunnanensis).但trnL-trnF突变率太低,未能用于鉴别.商品干燥中药材因加工和储藏的方式致使DNA降解严重,基因测序法难于应用.     

Identification of Sources of Resistance to Four Species of Root-knot Nematodes in Tobacco

Resistance to the southern root-knot nematode, Meloidogyne incognita races 1 and 3, has been identified, incorporated, and deployed into commercial cultivars of tobacco, Nicotiana tabacum. Cultivars with resistance to other economically important root-knot nematode species attacking tobacco, M. arenaria, M. hapla, M. javanica, and other host-specific races of M. incognita, are not available in the United States. Twenty-eight tobacco genotypes of diverse origin and two standard cultivars, NC 2326 (susceptible) and Speight G 28 (resistant to M. incognita races 1 and 3), were screened for resistance to eight root-knot nematode populations of North Carolina origin. Based on root gall indices at 8 to 12 weeks after inoculation, all genotypes except NC 2326 and Okinawa were resistant to M. arenaria race 1, and races 1 and 3 of M. incognita. Except for slight root galling, genotypes resistant to M. arenaria race 1 responded similarly to races 1 and 3 of M. incognita. All genotypes except NC 2326, Okinawa, and Speight G 28 showed resistance to M. javanica. Okinawa, while supporting lower reproduction of M. javanica than NC 2326, was rated as moderately susceptible. Tobacco breeding lines 81-R-617A, 81-RL- 2K, SA 1213, SA 1214, SA 1223, and SA 1224 were resistant to M. arenaria race 2, and thus may be used as sources of resistance to this pathogen. No resistance to M. hapla and only moderate resistance to races 2 and 4 of M. incognita were found in any of the tobacco genotypes. Under natural field infestations of M. arenaria race 2, nematode development on resistant tobacco breeding lines 81-RL-2K, SA 1214, and SA 1215 was similar to a susceptible cultivar with some nematicide treatments; however, quantity and quality of yield were inferior compared to K 326 plus nematicides.