Identification of a novel DNA molecule associated with Tobacco leaf curl virus

A circular DNA molecule, designated as DNAβ, was identified in tobacco plants infected with Tobacco leaf curl virus (TLCV) isolates Y5 and Y8 by PCR using primers based on the conserved region of the two reported DNAβ sequences of whitefly-transmitted geminiviruses (WTGs). The complete nucleotide sequences of DNAβ of Y5 and Y8 (TLCV DNAβ) were determined. Y5 DNAβ comprises 1333 nucleotides encoding 8 predicted ORFs with 4 ORFs in virion-sense DNA and 4 ORFs in complementary-sense DNA; Y8 DNAβ consists of 1338 nucleotides encoding 7 predicted ORFs with 4 ORFs in virion-sense DNA and 3 ORFs in complementary-sense DNA. TLCV DNAβ has little sequence homology to DNA-A of TLCV., except that it shares conserved TAATATTAC loop sequence with TLCV DNA-A. Sequence comparison showed that Y5 DNAβ shared 85% sequence homology with Y8 DNAβ, and both Y5 DNAβ and Y8 DNAβ had relatively low sequence identity (51%–65%) with the reported DNAβ molecules associated with Ageratum yellow vein virus and Cotton leaf curl virus. The immunotrapping PCR and whitefly transmission tests showed that DNAβ molecule could be encapsidated in virus particle and transmitted by Bemisia tabaci. This is the first report of DNAβ associated with WTGs in China.     

Analysis of components of conserved “backbone sequences” among genomes of<Emphasis Type="Italic">Shigella</Emphasis> spp. strains

Difference in the genomic compositions of prokaryotes is the basis of the diversity in their biological characters. However, besides their flora- or strain-specific genes, those floras with closer relationship in the evolution also have conserved “backbone sequences”, which reveal the marks of their origin and evolution, and these “backbone sequences” are just the basis of their elementary living abilities and common biological properties. Shigella is very closely related to E. coli in the origin and evolution, and may turn out to belong to the same genus. In this study, a microarray containing E. coli K-12 whole genome and SG01 specific ORFs is used to investigate the genomic components of four Shigella strains. The results indicate that 16%–22% K-12 ORFs sequences are not detected in the genome of Shigella strains while the genome of Shigella contains at least 2800 conserved ORFs, which compose the common “backbone sequences”. Advanced analysis indicated that the “backbone sequences” are the essential components in maintaining the normal physiological activities of intestinal bacteria. Furthermore, only 20% SGO1-specific ORFs exist in other strains simultaneously, which demonstrate the great genome heterogeneity and the genetic diversity among the strains. the first two authours made equal contribution to this work.     

高效木质素降解菌的筛选及降解性能研究

【目的】筛选纯化及鉴定木质素降解菌,对其降解性能进行初步研究。【方法】从某制浆造纸厂的造纸废水污泥中,筛选获得2株具有木质素降解能力的细菌LD-1和LD-2。通过形态观察和16SrRNA序列分析对菌株进行鉴定;采用苯胺蓝平板脱色法及以TC为指标分别定性定量测定2株细菌的木质素降解能力。【结果】LD-1和LD-2分别被鉴定为Sphingobacterium属和Bacillus属的菌株,命名为Sphingobacterium sp.LD-1和Bacillus sp.LD-2。通过苯胺蓝平板脱色实验,发现LD-1和LD-2均具有良好的木质素降解能力。经测定,两株菌种发酵7d对木质素的降解率分别达到52.23%和50.36%。【结论】成功筛选到2株能高效降解木质素的菌株LD-1和LD-2。     

Tobacco curly shoot virus isolated in Yunnan is a distinct species of Begomovirus

Virus isolate Y1 was obtained from tobacco showing curly shoot symptoms in Baoshan, Yunnan Province. Whitefly transmission test and virion morphology observation showed that it is a begomovirus. In reactions with 14 monoclonal antibodies raised against begomoviruses, Y1 was readily differentiated from begomoviruses reported in China, Pakistan and India. The complete nucleotide sequence of DNA-A was determined, it contains 2746 nucleotides, with two ORFs in virion-sense DNA and four ORFs in complementary-sense DNA. Comparisons with total DNA-A, intergenic region and deduced amino acid sequences of individual ORFs showed that Yl is a distinct Begomovirus species, for which the name Tobacco curly shoot virus (TCSV) is proposed. The total DNA-A of TCSV is most closely related to that of Tomato leaf curl virus from India (85% sequence identity). In contrast, the deduced coat protein of TCSV is most like that of Cotton leaf curl virus 72b isolate from Pakistan (98% amino acid sequence identity).     

水稻早熟大穗品系7-37二次枝梗数的QTL定位研究

通过水稻穗部性状的改良尤其是增加二次枝梗数更有助于实现水稻的大穗和高产。本研究以7-37作为二次枝梗数QTL定位的亲本材料,通过小穗广亲和品种02428与7-37杂交并自交获得02428/7-37F₂,然后对该F₂群体中随机选取的284个单株主茎穗的二次枝梗数进行遗传分析,结果表明二次枝梗数呈典型的正态分布,说明二次枝梗数受多基因控制,属数量性状,与前人的研究结果是一致的;在此基础上,利用从339对SSR引物中筛选出的均匀分布于12条染色体上的58对多态性引物对F₂群体中的284个单株进行PCR扩增分析,再利用QTL Icimapping作图软件,采用复合区间作图法对7-37的二次枝梗数进行了QTL分析和作图,结果在4号染色体25.0~30.5 Mb区间内和6号染色体6.6~30.8Mb区间内分别定位出了二次枝梗数相关QTL位点,LOD值分别为5.73和2.56,贡献率分别为8.95%和4.38%,加性效应分别为-5.71和-3.85,显性效应分别为-2.83和-1.30。这些研究结果为下一步二次枝梗数QTL位点的精细定位、克隆和功能分析提供了研究基础。     

Analysis of components of conserved “backbone sequences”among genomes of Shigella spp. strains

Difference in the genomic compositions of prokaryotes is the basis of the diversity in their biological characters. However, besides their flora-or strain-specific genes,those floras with closer relationship in the evolution also have conserved “backbone sequences”, which reveal the marks of their origin and evolution, and these “backbone sequences”are just the basis of their elementary living abilities and common biological properties. Shigella is very closely related to E. coli in the origin and evolution, and may turn out to belong to the same genus. In this study, a microarray containing E. coli K-12 whole genome and Sf301 specific ORFs is used to investigate the genomic components of four Shigella strains. The results indicate that 16%-22% K-12 ORFs sequences are not detected in the genome of Shigella strains while the genome of Shigella contains at least 2800 conserved ORFs, which compose the common “backbone sequences”.Advanced analysis indicated that the “backbone sequences”are the essential components in maintaining the normal physiological activities of intestinal bacteria. Furthermore,only 20% Sf301-specific ORFs exist in other strains simultaneously, which demonstrate the great genome heterogeneity and the genetic diversity among the strains.     

Inheritance of resistance toHelicoverpa armigera of 3 kinds of transgenicBt strains available in upland cotton in China

There are 3 kinds of transgenicBt strains, Shanxi 94-24, Zhongxin 94, and R19, in upland cotton in China. Their transgenicBt insect-resistance cultivars or hybrids have been developed and grown by farmers. Genetic studies indicate that the resistance of the 3 transgenicBt cotton strains toHelicoverpa armigera is controlled by one pair of non-allelic dominant genes. Linkage relationship between the resistant genes of R19 and Shanxi 94-24 transgenicBt strains shows that they may be inserted in the same chromosome. F₁ hybrids crossed among the 3 strains show that high levels of protection from feeding damage are the same as that of their parents. Therefore, there is no co-suppression phenomenon in many transgenic plants. The results presented here afford a fundamental reliance in developing transgenicBt insect-resistant cultivars and exploiting the heterosis of hybrids in upland cotton.     

多重耐药UPEC细菌毒力基因分布特征及进化分型分析

本研究对临床尿路感染病例病原菌耐药情况、毒力基因分布及其进化分型特征,以期为耐药性尿路感染病原防控提供参考。通过对收集的尿样进行细菌分离培养,结合革兰氏染色镜检、16S rDNA对细菌进行鉴定,利用K-B纸片扩散法对细菌进行药敏试验,并通过PCR扩增进行毒力基因及系统发育和进化分型分析。本研究成功检测出20株尿路致病性大肠杆菌（Uropathogenic Escherichia coli, UPEC）,药敏试验显示多数菌株具有多重耐药特征,该批UPEC对青霉素、红霉素、万古霉素耐药率达100%;对羧苄西林、氨苄西林、阿奇霉素耐药率达90%以上;对四环素、诺氟沙星、链霉素、耐药率达80%以上;对环丙沙星、 庆大霉素、卡那霉素、氟氧沙星、头孢曲松耐药率达70%以上;对头孢噻肟、呋喃妥因、氯霉素耐药率在35%以上;对阿莫西林与多粘菌素B耐药率低,分别仅为10%与5%。六个毒力基因（iutA、fimH、hly、fyuA、tsh、traT）检出率分别为85%、95%、85%、75%、25%、10%。其系统发育分型中,归属B2群的细菌最多,占比40%（n=8）;D群次之,占比35%(n=7);其次为A群,占比25%（n=5）;未检测到B1群菌株。通过MLST分型分析,20株大肠杆菌涉及10个ST型,其中ST131、ST648、ST744、ST1193型别较多。CRISPR序列扩增结果显示其中6株细菌含有CRISPR序列,提示不同菌株的进化差异。本研究通过对临床多重耐药UPEC进行毒力和分型特征分析,为临床有效防控耐药菌导致的尿路感染提供重要依据。     

耐碳青霉烯酶肺炎克雷伯菌的分离鉴定及生物学特性分析

以临床尿路感染患者尿液为研究对象,通过分离培养及16s rDNA进行肺炎克雷伯菌的分离鉴定;采用Kirby-Bauer纸片法进行药敏实验,并对分离株进行碳青霉烯酶表型筛选;通过PCR检测常见的碳青霉烯酶耐药基因、荚膜血清型和毒力基因分布情况;对分离的肺炎克雷伯菌株进行了生物被膜形成能力及其对小鼠致病力的分析。本研究从采取的86例尿液标本中分离检出11株耐碳青霉烯酶肺炎克雷伯菌,分离率为12.79%。耐碳青霉烯酶基因PCR检测结果显示,blaNDM、blaVIM、blaIMP和blaKPC基因在分离株中均呈现不同程度的分布。耐药性分析发现11株肺炎克雷伯菌对氨苄西林耐药率为90.91%,对头孢噻肟耐药率为63.64%,对链霉素、庆大霉素、氯霉素和诺氟沙星的耐药率较低。耐碳青霉烯类肺炎克雷伯菌荚膜分型结果显示,分离的11株细菌中10株均为强毒力型菌株（90.9%）,其中K57血清型4株（36.4%）,K1血清型1株（9.1%）,K2血清型1株（9.1%）,K5血清型1株（9.1%）,K20血清型3株（27.3%）,提示该批分离株具有较强的致病力。此外,毒力因子分布结果显示,其毒力因子rmpA（54.5%）、Aerobactin F（54.5%）在菌株中分布较为广泛。生物被膜形成能力检测及小鼠致病性试验结果显示,9株分离株均有较强的生物被膜形成能力,菌株致病力可能与荚膜血清型及生物被膜形成能力相关。综上所述,临床分离的致尿路感染病原肺炎克雷伯菌呈现多重耐药特征,强毒力菌株以K57荚膜型为主,K1、K2均有分布,提示对尿路感染病原应加强耐药监测,合理使用抗菌药物,有效防控多重耐药和强毒力菌株的感染与流行。     

从猪粪中分离抗铜大肠杆菌及其抗铜基因的初步定位

 从云南昆明周边的4个养猪场采集不同年龄段的猪粪样品,分离猪粪中的大肠杆菌.从分离到的大肠杆菌中发现了具有金属铜抗性的菌株并统计出抗性菌株的发生率.摸索了测定硫酸铜对抗铜性大肠杆菌的最低抑菌浓度(MIC)的方法,接合实验确定抗铜基因是否位于可移动的接合质粒上.实验结果初步表明抗铜大肠杆菌的发生率与饲料中添加硫酸铜的量成正相关性,且72%的抗性菌株中的抗铜基因位于可移动的接合质粒上.     

红树林土壤中假单胞菌群的重金属耐受活性

本研究从广西钦州茅尾海红树林保护区土壤中分离出的假单胞菌群着手，对其进行重金属耐受性能筛选，旨在获得可对重金属污染环境进行高效修复的菌株。选用传统稀释涂布法和16S rRNA基因序列的系统发育分析红树林土壤中的可培养假单胞菌；通过肉汤稀释法对菌株展开6种重金属耐受特性研究，对其进行耐受基因检测，并进一步测试重金属耐受活性显著菌株的重金属吸附性能。结果表明，从红树林土壤中共获得23株假单胞菌，18株菌对至少一种重金属表现出耐受活性，总阳性率为78.26%；10株菌的基因组DNA中检测出重金属耐受基因。其中，对铅和/或锌耐受活性显著的11株菌中，Y234、Y123、Y264、Y225和Y346具有显著的吸附性能，铅和/或锌的吸附率均大于50%。广西钦州茅尾海红树林保护区土壤中可培养假单胞菌群丰富，其重金属耐受活性显著，具有较大的挖掘潜力。     

High variability of the gvpA-gvpC region in Microcystis

Gas vesicles provide buoyancy to Microcystis and other common cyanobacterial bloom-forming species. gvpA and gvpC are structural genes encoding gas vesicle proteins. Phylogenetic analyses of 10 Microcystis strains/uncultured samples showed that gvpC and each intergenic segment of the gvpA-gvpC region can be divided into two types. The combination of different types of gvpC and intergenic segments is an important factor that diversifies this genomic region. Some Microcystis strains isolated in China possess a 172 to 176 bp sequence tag in the intergenic segment between gvpA and gvpC. The gvpA-gvpC region in Microcystis can be divided into at least 4 classes and more numbers of subclasses. Compared to rbcLX and other regions, the high variability of the gvpA-gvpC region should be more useful in identifying geographical isolates or ecotypes of Microcystis.     

Multiple transgenes Populus xeuramericana ＇Guariento＇ plants obtained by biolistic bombardment

A JERF36 regulation gene, a selection marker gene （NPT-Ⅱ）, and the foreign genes levansucrase （SacB）, Vitreoscilla hemoglobin （vgb）, and Binary coleopterus insect resistance （BtCry3A＋OC-I） were co-transferred into Populus xeuramericana ＇Guariento＇ using biolistic bombardment; 25 kanamycin resistant plants were obtained, The results of PCR and Southern hybridization showed that the foreign genes had been integrated into the genome of P, xeuramericana ＇Guariento＇ and 5 genes were all transferred into 7 poplar plants, The results of a BtCry3A ELISA experiment indicated that the BtCry3A gene was expressed in the 7 transgenic poplar plants, and these plants grew well on coastal saline land,     

A draft sequence of the rice (Oryza sativa ssp. indicd) genome

The sequence of the rice genome holds fundamental information for its biology, including physiology, genetics, development, and evolution, as well as information on many beneficial phenotypes of economic significance. Using a “whole genome shotgun” approach, we have produced a draft rice genome sequence ofOryza sativa ssp.indica, the major crop rice subspecies in China and many other regions of Asia. The draft genome sequence is constructed from over 4.3 million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-redundant sequences reached 409.76 Mb in length, based on 3.30 million successful sequencing traces with a total length of 1797.4 Mb from anindica variant cultivar93-11, giving an estimated coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage of the draft sequence, the randomness of the sequence distribution, and the consistency of BIG-ASSEMBLER, a custom-designed software package used for the initial assembly, were verified rigorously by comparisons against finished BAC clone sequences from bothindica andjapanica strains, available from the public databases. Over all, 96.3% of full-length cDNAs, 96.4% of STS, STR, RFLP markers, 94.0% of ESTs and 94.9% unigene clusters were identified from the draft sequence. Our preliminary analysis on the data set shows that our rice draft sequence is consistent with the comman standard accepted by the genome sequencing community. The unconditional release of the draft to the public also undoubtedly provides a fundamental resource to the international scientific communities to facilitate genomic and genetic studies on rice biology. These authors contributed equally to this work.     

青海柯柯盐湖16株细菌的ARDRA筛选及系统发育初步分析

 从青海柯柯盐湖泥样中分离的16株细菌,用2种限制性内切酶酶切进行ARDRA分析,其中12株菌的酶切带谱有较大差异.根据这12株菌的16SrDNA序列进行系统发育分析结果表明,12株菌有11株分布于芽孢杆菌科中的Halobacillus,Gracibacillus,Amphibacillus,Virgibacillus,Bacillus,Salibacillus和1个潜在的新属中,另1株属于Proteobacteria的Gamma亚群Halomonadaceae科,Halomonas属.而且16SrDNA系统发育分析提示这些菌株中存在3个新种和1个新属的可能.本研究得出的结论为:应用ARDRA来初步筛选菌株是可行的;青海柯柯盐湖这一极端环境中存在较丰富的新的芽孢菌种类.     

菠菜SoNAC转录因子家族的全基因组鉴定与分析

采用生物信息学分析方法,从菠菜基因组中筛选鉴定了57个菠菜NAC转录因子,并对其基因结构、编码蛋白和系统进化进行了分析;通过荧光定量聚合酶链式反应qRT-PCR分析,研究了高温和盐处理后菠菜叶片中NAC基因的表达模式.研究结果显示:菠菜NAC转录因子可以被归入2组17个亚组,GroupⅠ包含10个亚组,GroupⅡ包含...     

利用深黄伞形霉生产油脂的研究进展

总结了深黄伞型霉的不饱和脂肪酸含量高、品种多、易培养的优点.介绍了运用化学诱变和基因工程技术对深黄伞形霉菌种的选育和改造,以及深黄伞形霉产油脂的培养工艺和提取工艺的研究成果.研究表明,深黄伞型霉是产生油脂的优良菌种,为深黄伞形霉生产油脂和不饱和脂肪酸提供基础.     

雌核发育鲢各系及与普通鲢生长的比较研究

在相同池塘养殖条件下,迸行了雌核发育鲢各系(当年鱼)及与普通鲢的生长对比试验。结果表明:所选育的雌核发育鲢1系、2系间无显著差异,杂交系较1系、2系呈一般显著性差异(P<0.05);雌核发育鲢较普通鲢生长快,平均体长增长快7％以上,体重增长快14％以上,呈显著差异(P<0.01);其中雌核发育鲢杂交生长最快,其体重增长比普通鲢快23.8％,体长增长比普通鲢快12.4％,呈非常显著差异(P<0.005)。密度越稀,增长越快,雌核发育鲢各系成活率(83.4％以上)均高于普通鲢(64.8％),且雌核鲢体型较普通鲢肥厚。     

Malvastrum yellow vein virus,a new Begomovirus species associated with satellite DNA molecule

Virus isolate Y47 was obtained from Malvastrum coromandelianum showing yellow vein symptom in Honghe, Yunnan Province. The complete nudcotide sequence of DNA-A was determined, it contains 2731 nuclcotides,having typical genomic organiTation of a begomovirns, encoding 6ORFs with 2ORFs [AVI(CP) and AV2] in virionsense DNA and 40RFs (ACl-AC4) in complementary-sense DNA. Comparisons show that the total DNA-A of Y47 has the highest sequence identity (77%) with that of Okra yellow vein mosaic virus-[201] (AJ002451), while less than 76% identities are found when compared with other begomoviruses. The molecular data show that virus isolate Y47 is a distinct begomovirns species, for which the name Maivastrum yellow vein vorus is proposed. Satellite DNA molecule (Y47β) was found to be associated with Y47 using the primers (beta01 and beta02) specific for DNAβ Y47β consists of 1348 nuclcotides, with a functional ORF (CI) in complemen-tary-sense DNA.Y47β has 62%--67% sequence identity with DNAβ molecule associated with Cotton leaf curl Muitan virus or Cotton leaf curl Rajasthan virus, while lower than 46% sequence identities are found when compared with other reported DNA[~ molecules. Relationship dendrograms show that DNAβ molecules are co-evolved with their help begomoviruses.