穿龙薯蓣、黄山药和盾叶薯蓣psbA-trnH片段序列分析

为研究薯蓣叶绿体psbA-trnH片段遗传多样性,探讨该片段用于中药穿龙薯蓣、黄山药和盾叶薯蓣种间分子鉴别和系统学研究中的意义,我们对不同类群薯蓣种的叶绿体psbA-trnH基因间区进行PCR扩增并测序,获得了该区间的完整序列,所得序列用软件MEGA3.0进行相关分析.穿龙薯蓣的psbA-trnH片段全长274bp,黄山药全长279bp,盾叶薯蓣植物个体内的叶绿体DNA则有两种psbA-trnH片段,长度分别为241bp和503bp.经MEGA3.0软件分析,3种薯蓣种间psbA-trnH片段序列的遗传距离(p-distance)为0.00350~0.04545,各个薯蓣种内的不同类群该序列无差异.用UPGMA法根据psbA-trnH序列的遗传距离建立系统发生树,聚类结果和形态分类相符.所得结果显示,psbA-trnH片段序列在所研究的3种薯蓣种内保守,在种间具有明显的较大差异,而3种薯蓣及薯蓣属的系统发生关系尚须进一步研究.图3表2参6     

CMS高粱保持系叶绿体基因ps1A1和ps1A2片段的克隆与序列比对

以15种包括同质异核和同核异质高粱材料的总：DNA为模板进行RAPD分析，196个随机引物中，引物Y-19扩增得到一个很有规律的差异片段SAY-192300。该片段只出现在4个保持系(B)和3个恢复系(R)中，而不出现在6个不育系(A)和2个杂种F1中，进一步对cms—Al、cms—A2两套8个材料(A／B／R／F1)的总DNA、mtDNA和cpDNA用引物Y-19进行扩增，发现片段SAY-192300仅在cpDNA得到，Southern杂交结果证实了片段SAY-192300的叶绿体来源，同时也表明在cms胞质中该片段所在区未发生插入、缺失等大的结构变异,DNA序列测定结果表明，该片段为叶绿体ps1A1和ps1A2基因的部分序列。图6表2参19。     

长链烷烃降解菌alkB片段的分离和鉴定

分离并鉴定了长链烷烃降解菌Pseudomonasaeruginosa1785和P.marginata766烃羟化酶基因alkB片段.根据烃羟化酶的保守氨基酸序列,设计兼并引物,扩增P.aeruginosa1785和P.marginata766的alkB片段,获得了目标产物.经DNA测序和氨基酸序列分析,证实目标片段编码的肽段含有烃羟化酶的特征基序.由此确认采用该方法分离到了长链烷烃降解基因的alkB同源体片段.DNA序列比对结果表明,P.aeruginosa1785和P.marginata766的alkB片段与P.aeruginosaPAO1的alkB1和alkB2的相似性分别达到95.7%和94.8%.这些alkB片段可用于分析烃降解微生物群落结构.图3表2参11     

利用TAIL-PCR和RT-PCR技术克隆云芝植酸酶基因

从采绒革盖菌(Coriolus versicolor,常被称为杂色云芝)中筛选到产植酸酶基因.根据植酸酶基因的保守序列设计引物P1、P2,从云芝中分离克隆植酸酶基因的片段.再在分离到的已知序列的5′端和3′端设计嵌套的特异引物SP1、SP2、SP3和SP1′、SP2′、SP3′,利用TAIL-PCR技术进行分离已知序列的侧翼序列.结合Blastn、ORF和Primer5.0软件,在侧翼序列上设计特异引物P3、P4,最终从云芝中分离克隆到全长的植酸酶基因B4.再在B4序列的基础上设计引物phyP rt1、phyP rt2,利用这两个引物通过RT-PCR技术从云芝中克隆到全长的植酸酶基因B5.通过分析,分离克隆到的植酸酶基因可能是新的基因.图4参12     

用单个特异引物扩增桃ACC氧化酶cDNA及其在大肠杆菌中的表达

用单个特异引物和通用引物ｏｌｉｇｏ（ｄＴ）１５从桃受伤叶片ｃＤＮＡ中扩增出１．３ｋｂ左右大小的片段．将该扩增产物克隆并对重组克隆作酶切分析发现至少可分为３类．用桃ＡＣＣ氧化酶基因组ＤＮＡ为探针进行点杂交表明,４,７,９,１０,１１,１２重组质粒能与之杂交,其中７,９,１０,１１,１２号重组质粒酶切图谱与已报导的桃果实成熟相关的ＡＣＣ氧化酶ｃＤＮＡ基因基本一致,而４号克隆则不同．ＤＮＡ序列分析和ＰＣＲ鉴定表明,插入片段均由５′端特异引物单个引物扩增出来,对７号重组克隆插入片段ＤＮＡ全序列分析表明,７号重组克隆插入片段全长１１４６ｂｐ,包含了除启始密码子外的全部编码区和１９２ｂｐ的３′端非编码区．通过补上起始密码子ＡＴＧ构建重组表达载体,在大肠杆菌中表达出３５×１０３的非融合蛋白     

基于EST-SSR标记的沙棘品种鉴定及指纹图谱构建

以沙棘(Hippophae rhamnoides)优良品种“实优1号”为材料,对其叶片进行转录组测序,利用微卫星识别软件(microsatellite identification tool, MISA)和Primer 3(version 2.3.4)对获得的序列进行简单重复序列(simple sequence repeat, SSR)位点挖掘和引物设计,以收集的42份沙棘品种为研究材料,开展聚合酶链式反应(PCR)和毛细管电泳检测,旨在开发一套多态性高、稳定性好和通用性强的表达序列标签微卫星(express sequence tags from simple sequence repeat, EST-SSR)引物,构建沙棘指纹图谱,从而实现沙棘品种的快速准确鉴定,并对沙棘品种间亲缘关系进行分析。“实优1号”转录组测序共获得6 196个SSR位点,其中,重复基元类型为182种,SSR基序长度主要分布在10～21 bp区间,占全部SSR的81.58%,主要SSR重复类型为单核苷酸重复(48.72%)、二核苷酸重复(22.68%)和三核苷酸重复(18.85%)。利用筛选出的28对引物在42...     

汕头海域几丁质酶产生菌的筛选及其几丁质酶编码基因研究

在汕头海域表层沉积物中分离得到69株高产几丁质酶的菌株,对其中6株形态特征差异比较明显、几丁质酶活力比较高的菌株SWCH-1、SWCH-2、SWCH-3、SWCH-5、SWCH-6和SWCH-9进行了16S rDNA序列鉴定,发现它们分别归属于5个属.即短芽孢杆菌属(Brevibacillus)、类芽孢杆菌属(Paenibacillus)、芽孢杆菌属(Bacillus)、气单胞菌属(Aeromonas)和寡养单胞菌属(Stenotrophomonas).采用兼并引物对6株菌几丁质酶编码基因的催化保守区片段进行了PCR扩增和序列分析,发现菌株均含有18家族几丁质酶编码基因;但是其编码的蛋白序列与NCBI收录的蛋白序列存在着差异,其中菌株SWCH-1和SWCH-3的蛋白序列与数据库中序列的相似性比较低,分别为85%和81%,菌株含有比较新的几丁质酶编码基因,其全基因序列的克隆和酶蛋白的纯化分析尚在进一步研究中.图6参18     

生长温度对盾叶薯蓣POD活性等生理特性的影响

研究了15℃、20℃、25℃、30℃和35℃五个不同温度条件下盾叶薯蓣一些生理参数的变化.结果显示,盾叶薯蓣叶片的POD活性和MDA含量的变化呈V字形,其中在25℃时处于最低点;可溶性蛋白含量的变化呈M字形,可溶糖含量的变化呈W字形.在15℃、20℃、30℃和35℃下, 5d内,随着时间的延长,MDA含量增加,POD活性、可溶性蛋白和可溶性糖的含量下降;在25℃下,盾叶薯蓣的POD活性以及MDA、可溶性蛋白和可溶性糖的含量变化较小,相对稳定,所以25℃是最为适宜的生长温度. 图1表1参20     

用简并引物扩增与克隆D.radiodurans超氧化物歧化酶和过氧化氢酶基因片段

依据超氧化物歧化酶（ＳＯＤ） 和过氧化氢酶（Ｃａｔ） 的保守性氨基酸序列,设计简并引物,自Ｄ．ｒａｄｉｏｄｕｒａｎｓ 基因组ＤＮＡ扩增并克隆了ＳＯＤ和Ｃａｔ 基因片段．ＳＯＤ 和Ｃａｔ 基因片段分别长４５３ ｂｐ 和６７３ ｂｐ,各编码１５１和２２４ 个氨基酸,氨基酸序列与不同生物来源的ＳＯＤ或Ｃａｔ 具有高度同源性     

非纯培养物细菌蛋白酶DNA片段的克隆与表达

为了构建更多的蛋白酶基因工程菌,以及进行蛋白酶基因的直接进化研究,从非纯培养细菌总DNA中扩增各种编码蛋白酶的DNA片段.根据MEROPS和GenBank数据库中的枯草杆菌类蛋白酶的编码区和成熟肽编码序列设计并合成了10条引物.富集培养胞外蛋白酶产生菌并提取了12个总DNA样品,分别用每对引物在降落PCR (TouchdownPCR, TD-PCR)条件下进行蛋白酶编码序列的扩增.选择了19个长800 ~1 200 bp的扩增片段测序,其结果为: 8个是蛋白酶DNA片段,它们应属于4种不同的蛋白酶基因序列;同一对引物扩增到的基因序列差异性可达到32%,说明只使用基于已知序列的PCR方法从混合菌中获得新蛋白酶基因是可行的.将克隆到的1个与碱性蛋白酶E (GenBank No.AJ539133)的编码区99%相似的蛋白酶DNA片段插入pTWIN1载体,在大肠杆菌ER2566中进行表达.结果表明,表达的成熟蛋白酶可分泌到培养基中,能在牛奶平板上产生水解圈,对大肠杆菌有致死作用.图5表3参14     

Porphyrobacter sp.D22F的降解特性及其在石油降解菌群中的生态位

为揭示多环芳烃(Polycyclic aromatic hydrocarbons,PAHs)降解微生物资源的多样性和石油降解菌群的优势菌,研究了从南海沉积物中分离得到的一株PAHs降解菌D22F的降解特性及其在石油降解菌群D22-1中的生态位.对菌株D22F进行16S rRNA基因同源性分析及透射电镜观察以初步确定其种属,通过培养法、气相色谱质谱联用(GC-MS)测定其多环芳烃降解范围和降解率,通过简并引物PCR扩增其PAHs双加氧酶大亚基基因片段并进行系统发育分析,采用变性梯度凝胶电泳(DGGE)监测石油降解菌群中的优势菌.结果表明,与菌株D22F的16S rRNA基因相似度最高的模式株为产卟啉杆菌属Porphyrobacter tepidarius DSM 10594T(AF465839;98.55%).该菌株能降解萘、甲基萘、苊、硫芴、菲、蒽等;对初始浓度为0.2 g/L菲10 d后的降解率可达90%以上.从其基因组DNA中克隆到的PAHs起始双加氧酶大亚基基因phnAc与Novosphingobium aromaticivorans DSM 12444中的质粒pNL1(CP000676)上的bphA1f基因相似度最高,达到99.41%.DGGE谱图显示,菌株D22F是石油降解菌群中的3种优势菌之一,在传代菌群中可稳定存在.Porphyrobacter sp.D22F为产卟啉杆菌属(Porphyrobacter)中首株以低分子量PAHs为唯一碳源和能源的菌株,是石油降解菌群的优势菌.     

Comparative Population Genetic Structure of the Rare Woodland Shrub Daviesia suaveolens and Its Common Congener D. mimosoides

Genetic (allozyme) variation and population genetic structure of the rare shrub Daviesia suaveolens , found in only a few large populations on the eastern escarpment of the southern tablelands of New South Wales, were compared to those of its abundant and widespread relative D. mimosoides at both spatially equivalent and rangewide scales. We hypothesized that the rare species is genetically depauperate relative to the common one. We also generated baseline data on D. suaveolens to provide management recommendations for its conservation. Both species had high variation relative to other widespread woody angiosperms. Rangewide, the rare species exhibited lower species-level genetic variation than its common relative but a similar level of variation to that found in D. mimosoides over an equivalent spatial scale. Population-level genetic variation was similar for the two species. Over its small geographic range, D. suaveolens populations were three times as genetically differentiated as D. mimosoides over the same scale, showing a clear northsouth genetic disjunction and as much interpopulation divergence as the common species exhibited rangewide. These results confirm that not all types of rarity have the same genetic implications. Conservation strategies for D. suaveolens need not be concerned about low population-level variation unless populations become significantly smaller than is currently typical. Of more importance is to maintain the high interpopulation differentiation by conserving populations from both the north and south of the species' range.     

Upper temperature tolerances of some European molluscs II. Donax vittatus,D. semistriatus and D. trunculus

The upper temperature tolerances of 3 European species of Donax [D. vittatus (da Costa), D. semistriatus Poli, D. trunculus L.] are compared by means of median lethal temperatures (LT₅₀) and median burial temperature (BT₅₀) determinations for periods of exposure up to 96 h. The influence of previous acclimation temperatures on these determinations is also considered. D. trunculus shows the greatest thermal tolerance, reflecting its distribution in shallower water; D. vittatus and D. semistriatus display much closer thermal tolerances, although D. semistriatus which has a more southerly geographical distribution has a slightly higher thermal tolerance. All 3 species exhibit a significant effect of previous acclimation temperature, the effect on the burrowing responses being greater than that on LT₅₀.     

Observations on the biology of Donax trunculus and D. vittatus at Ile d'Oléron (French Atlantic coast)

Observations have been made on the biology of two species of the bivalve genus Donax, on two beaches, Vertbois and St. Trojan, on the Ile d'Oléron, French Atlantic coast. The two species displayed different vertical distribution: D. trunculus Linné in the intertidal; and D. vittatus (da Costa) between low-water spring tide (LWST) and 5 to 6m depth, with only the fringe of the population extending to the shore. D. trunculus also showed differential distribution by size or age, the youngest individuals being highest on the shore, and the oldest near LWST. The two species exhibited a similar pattern of seasonal recruitment and growth, but in both there were differences in growth characteristics between the two beaches, individuals at St. Trojan growing to a larger size than those at Vertbois. The mean pattern of mortality in the two areas was similar, and productivity per 100 recruits surviving to the first winter following settlement was greater at St. Trojan than at Vertbois. For D. trunculus the mean population density at Vertbois was higher and the production per unit area on the two beaches was similar. Production to biomass (B) and elimination to biomass (B) ratios were similar for the two beaches for both species, and while production was greater for D. trunculus at both beaches, the B and B ratios were higher for D. vittatus. Comparisons with other published data reveal that the rate of growth of D. trunculus is similar throughout its range from Brittany to the Mediterranean Sea, while that of D. vittatus shows more variation. In both species, there is a trend of increasing P/B and E/B ratios from north to south throughout the geographical range.     

Mitochondrial DNA analysis of the genetic relationships among populations of scad mackerel (Decapterus macarellus, D. macrosoma, and D. russelli) in South-East Asia

The genetic relationships among South-East Asian populations of the scad mackerels Decapterus macarellus, D. macrosoma and D. russelli (Pisces: Carangidae) were investigated. In 1995 and 1996, 216 fish were sampled in seven localities spanning the seas of Indonesia and were examined for restriction-site polymorphisms using ten restriction enzymes for the mitochondrial (mt) DNA control region, amplified by the polymerase chain-reaction. The inferred phylogeny of haplotypes led to the recognition of three distinct mitochondrial lineages or phylads consistent with the distinctions of current taxonomy. All 15 mtDNA haplotypes found in D. macarellus and all 9 haplotypes found in D. macrosoma were arranged as star-like clusters, suggesting recent evolutionary history. In contrast, the phylad formed by 6 haplotypes in D. russelli from the Sulawesi Sea exhibited diffuse topology, suggesting that ancestral lineages of this species have been retained to the present. Average nucleotide-divergence estimates between haplotypes of different phylads were between 0.042 and 0.135, suggesting ancient separation, in consistency with published allozyme data. High levels of haplotype diversity, but no geographical heterogeneity, was detected within D. macarellus from the Molucca Sea and the Banda Sea. Populations of D. macrosoma exhibited both significant differences between adjacent regions (Sunda Strait and Java Sea), and broadscale genetic homogeneity from the South China Sea to the Sulawesi Sea via the Java Sea and Makassar Strait. The geographic isolation of the D. macrosoma population sampled in the Sunda Strait suggests that this region constitute a sharp transition zone between the Indian Ocean and the Sunda Shelf. Near-monomorphism of haplotypes and low nucleotide diversity (d _X) were observed in the samples of D. macrosoma from the continental shelf (haplotype-diversity estimates, h, = 0.00 to 0.25 ± 0.08 and d _X = 0.000 to 0.002). This was in contrast to the comparatively high haplotype and nucleotide diversities observed in other pelagic fish species including D. macarellus (h = 0.82 ± 0.05, d _X = 0.012 to 0.015) and D. russelli (h = 0.63 ± 0.12, d _X = 0.016), and in the oceanic D. macrosoma population sampled in the Sunda Strait (h = 0.67 ± 0.31, d _X = 0.005). We hypothesise that this may be the consequence of recent and perhaps repeated bottleneck events that have affected the D. macrosoma population sampled on the continental shelf. Received: 29 September 1997 / Accepted: 3 September 1999     

The ecology of two sandy beaches in south west India. III. Observations on the population of Donax incarnatus and D. spiculum

The biology of two species of Donax, D. incarnatus Gmelin and D. spiculum Reeve on two beaches in south west India is described. Two year groups of D. incarnatus were present on both beaches, from settlements during the monsoon period in 1967 and 1968. At Shertallai, both groups were studied through the year, and data on growth, mortality and production are presented. At Cochin, the rate of growth was slower and the maximum size attained smaller, but mortality during the early monsoon precluded study of D. incarnatus through a full year. D. spiculum occurred at Cochin mainly during the pre-monsoon period, and at Shertallai during the post-monsoon. The species has a shorter life-span than D. incarnatus, but its irregular occurrence did not allow detailed production estimates.     

Digit ratio (2D:4D) and dominance rank in female rhesus macaques (Macaca mulatta)

Female rhesus macaques exhibit matrilineal dominance structures, and high dominance rank confers fitness benefits across a lifetime and across generations. Rank effects are “inherited” through social processes that are well understood; however, biological mechanisms that might impact these processes are not well known. Recently, it has been shown that prenatal androgens appear to be implicated in supporting dominance rank hierarchies in some mammals. In humans, interindividual differences in the second (index) to fourth (ring) digit ratio (2D:4D) have been linked indirectly to variation in prenatal androgens, with low 2D:4D in both sexes associated with higher inferred prenatal androgen effects. 2D:4D has also been related to dominant social behavior and has been shown to co-vary with social systems across nonhuman primate species. Here, we investigate how 2D:4D co-varies with socially inherited dominance rank in female rhesus macaques. Low 2D:4D was associated with higher-ranking females, while higher 2D:4D was associated with lower-ranking females. Similar relationships were also shown between ranked families within matrilines. This is the first study to show such a relationship between 2D:4D and dominance rank in a nonhuman primate and suggests that prenatal androgen effects could be involved in the maintenance of dominance rank in female cercopithecine primates.     

Inf luence of Season and a Sympatric Congener on Habitat Use by Stephens' Kangaroo Rat

We examined habitat use by the endangered Stephens' kangaroo rat ( Dipodomys stephensi) in different seasons and assessed whether this may be influenced by a sympatric congener, the Pacific kangaroo rat (Dipodomys agilis). Trapping on three plots over 2 years revealed these species were rarely captured at the same trap stations. Spatial segregation was highly significant when both species were at high density. The spatial distribution of these species was temporally stable where both species were relatively abundant, but where D. agilis was relatively uncommon the distribution of D. stephensi varied from one census to another. The abundance of three microhabitats (grass, debris, and bare ground) followed a regular seasonal pattern of variation that was consistent across 2 years of substantially different rainfall. A canonical discriminant analysis showed that the five quantified microhabitats (those above and bush and rock cover) provided highly significant discrimination between the trap stations occupied by the two species. Dipodomys stephensi was associated with trap stations where grass cover and bare ground were abundant but where bush and rock were uncommon. Dipodomys agilis was associated with stations that had large amounts of bare ground and average abundances of bush and rock cover. The spatial segregation of these species appears to be mediated by habitat preferences; D. stephensi prefers grassland and D. agilis prefers sage scrub. This suggests that habitat management for D. stephensi should include (1) controlling the spread of shrubs into grassland and (2) creating dispersal corridors of open habitat to link areas of suitable habitat where none presently exist. Each of these options may be needed to maintain viable populations in all reserves designated for the conservation of D. stephensi.     

Genetic structure and allozyme variation of sea bass (Dicentrarchus labrax and D. punctatus) in the Mediterranean Sea

This paper reports data on 28 allozyme loci in wild and artificially reared sea bass (Dicentrarchus labrax) samples, originating from either coastal lagoon or marine sites in the Mediterranean Sea. F _ST analysis (θ estimator) indicated strong genetic structuring among populations; around 34% of the overall genetic variation is due to interpopulation variation. Pairwise θ estimates showed that, on average, the degree of genetic structuring was much higher between marine populations than between samples from lagoons. Six polymorphic loci showed differences in allele frequencies between marine and lagoon samples. Multivariate analyses of individual allozymic profiles and of allele frequencies suggested that different arrays of genotypes prevail in lagoons compared to marine samples, particularly at those loci that, on the basis of previous acclimation experiments, had been implicated in adaptation to freshwater. On the other hand, variation at “neutral” allozyme loci reflects to a greater extent the geographic location of populations. Allozyme differentiation was also studied in a D. labrax population from the Portuguese coast. Average genetic distance between this population and the Mediterranean populations was quite high (Nei's D = 0.236) and calls into question the taxonomic status of the Portuguese population. Finally, genetic relationships between D. labrax and D. punctatus were evaluated. Average Nei's D was 0.648, revealing high genetic differentiation between the two species, even for two sympatric populations of these species in Egypt; thus gene flow was not indicated between species. Received: 24 October 1996 / Accepted: 27 November 1996