DNA聚合酶对PCR方法检测基因点突变的干扰分析

以野生型斑马鱼p53基因外显子7为目的片段,运用变性高效液相色谱(DHPLC),比较分析三种常用的商品DNA聚合酶对聚合酶链式反应(PCR)技术检测基因点突变的影响.DHPLC检测结果显示,Promega Shanghai公司Taq DNA聚合酶,Promega公司Taq DNA聚合酶和BD Biosciences公司高保真酶Advantage-HF2的分子突变频率分别为14.3%,5.95%和0.76%.通过DNA直接测序法确认表明,Promega公司Taq DNA聚合酶和BD Biosciences公司高保真酶Advantage-HF2的碱基突变频率分别为3.61×10-4和7.69×10-5.研究表明,不同的DNA聚合酶对PCR技术的检测结果有明显影响,高保真酶Advantage-HF2所造成的碱基错配率明显低于其它两种商业化Taq酶.     

费氏中华根瘤菌15142的cysDN基因克隆及其相关功能

为确定cysDN操纵子的功能及对根瘤菌结瘤的影响,通过三亲本接合,将质粒转座子pTnMod-RKm′随机插入费氏中华根瘤菌15142中,建成随机插入突变体库,随后通过含有不同硫源的MM培养基的筛选得到一株不能利用硫酸盐但能够利用半胱氨酸的突变体.进一步克隆和测序分析后发现该操纵子与已报道的Sinorhizobium sp.strain BR816的cysDN在核苷酸水平上有92%的相似性,在氨基酸水平上有96%的相似性.用自杀质粒pK18mob分别构建含有cysD部分片段和cysN部分片段的重组质粒,通过三亲本接合导入出发菌株15142中,经过同源单交换,分别获得cysD的pK18mob正反向插入突变株cysDF/15142以及cysDR/15142和cysN的pK18mob正反向插入突变株cysNF/15142与cysNR/15142.用广谱宿主质粒pLAFRJ载体连接完整操纵子cysDN构建互补质粒cysDN+pLAFRJ,将该质粒通过三亲本接合导入突变株中,获得互补菌株.用不同硫源的液体MM培养基培养,发现互补菌株能够补回突变菌株不能利用硫酸盐作为唯一硫源的缺陷,说明cysDN操纵子确实与硫酸盐同化途径有关;植株试验表明突变株比出发菌株推迟结瘤1~2 d,固氮酶活也比出发菌株稍低;竞争结瘤试验表明突变菌株占瘤率较差,但在平均瘤数、平均瘤重、平均植株干重上则无差异.     

费氏中华根瘤菌lrp基因的克隆、突变与功能

通过分子克隆技术,从费氏中华根瘤菌(Sinorhizobium fredii)HN01基因组文库中克降到一个lrp基因.该基因与已报道的苜蓿中华根瘤菌(Sinorhizobium meliloti)1021的lrp基因在核苷酸水平上有89%相似性,在氨基酸水平上有99%相似性.利用自杀质粒pK18mob构建含有lrp基因部分片段的重组质粒,通过三亲本结合后导入原始菌株HN01中,经过同源单交换,获得发生正向插入突变的突变株GXHNLTA和反向插入突变的突变株GXHNLTB.将lrp基因ORF连接到载体pLAFR3上,获得用于互补的质粒pGXHNL100,将该质粒通过三亲本接合导入突变株中,获得互补株GXHNWA、GXHNWB.对野生型菌株、突变株、互补株进一步研究发现,在以脯氨酸、亮氨酸、丝氨酸等氨基酸为唯一碳、氮源的MM培养基中培养时,突变体GXHNLTA、GXHNLTB的生长均滞后于出发菌株HN01.植株试验表明,突变菌株GXHNLTA、GXHNLB比野生菌株HN01开始结瘤的时间提前1 d,在结瘤效率、单株瘤数、瘤重、固氮酶活性方面并无显著差别.     

采用高通量测序技术检测肺癌致病突变及靶向药物突变位点

Ion Torrent高通量测序平台可通过测序癌症病人的基因组,找出致病突变位点进而选择对应的靶向药物以更加有效地治疗并减少毒副作用.利用Ion Torrent平台共检测了55例非小细胞肺癌组织的甲醛固定石蜡包埋样本(FFPE样本),对测序结果进行分析并找出致病突变位点.其中,30(54.5%)例样本有抑癌基因TP53的突变,突变类型一共包括36种,是突变频率最高的一个基因.突变频率次高的基因是EGFR,检测到17(30.9%)例病人共8种突变类型.突变频率第三高的是ERBB4(HER4,与EGFR同属HER家族),检测到14(25.5%)例病人共两类突变.此外,还有其他突变频率较高的基因,如MLH1(8例,14.5%)、KRAS(6例,10.9%)、PIK3CA(5例,9.1%)等.本研究表明通过提取肺癌病人FFPE样本中的DNA并使用Ion Torrent平台测序可以找到致病突变,可用于指导医生进行更好的靶向药物治疗.     

东亚飞蝗mariner转座子片段的克隆和序列分析

mariner转座子在昆虫中广泛存在,转座时不需要宿主特异因子的作用,是昆虫种系转化的有力工具.以mariner转座酶的保守序列设计的简并引物从东亚飞蝗Locusta migratoria manilensis(Meyen)基因组中扩增出7个序列有差异的片段,其中的1个片段能够翻译成为连续的氨基酸序列,另外6个片段中均含有终止子或移码突变.经同源性比对、序列特征分析,证实东亚飞蝗基因组中存在mariner类元件,但大部分都是无功能的假基因;系统进化分析发现东亚飞蝗基因组中的mariner类元件有可能属于新的mariner次级家族.     

全氟辛烷磺化物(PFOS)诱导斑马鱼胚胎p53基因的点突变

将斑马鱼胚胎于0μg·1-1(空白对照),5μg·l-1,16μg·l-1和50μg·l-1全氟辛烷磺化物(PFOS)溶液中暴露染毒5h,采用变性高效液相色谱方法对PCR扩增的含斑马鱼胚胎p53基因外显子7的173 bp的目标片段进行突变分析.结果显示,16μg·l-1和50μg·l-1两个处理组与对照组相比均有显著性差异,表明PFOS可以诱导斑马鱼胚胎p53基因外显子7的点突变.     

乳酸杆菌食品级表达系统的构建与鉴定

以LacF为选择标记,构建了乳杆菌食品级表达系统.首先克隆了Latobacillus caseiATCC393乳糖操作子LacF和LacG基因片段,将LacF克隆至载体pRV300上后,利用T4DNA聚合酶消除了LacF片段的SphI位点,构建LacF基因编码区移码突变的质粒pRV△lacf随后将LacG片段与质粒pRV△lacf接后获得了质粒pRvg△lacf.同时将没有移码突变的LacF和LacG基因片段克隆至载体pRV300上,构建了整合型载体pRVgf.将质粒pRVg△lacf电导入L.casei ATCC393中,筛选到不能在乳糖平板上生长的突变菌株.经PcR分析表明,该菌株的LacF基因被移码突变基因Lac△F取代,命名为L.casei MBL25(LacF).为了鉴定此系统的可行性,将豆豉溶栓酶基因成熟肽编码片段插入到整合型载体pRVgf中,成功构建了质粒pRVgf-badfe,将其导L.casei MBL25(LacP)后,筛选LacF 菌株.PcR分析结果显示,豆豉溶栓酶基因已经整合到L.casei染色体巾并且表型已经得到恢复.表明MBL25(LacF-)中LacF基因的功能能被pRVgf-bafe上的LacF基因互补.经0.5%乳糖过夜诱导后,SDS-PAGE电泳显示成功表达了相对分子质量(M)28x103大小的特异蛋白.图3参22     

BnGID1基因过量表达对甘蓝型油菜矮化突变体NDF-1株高的恢复

在正常株高油菜中克隆了与拟南芥矮化突变相关基因AtGID1同源的BnGID1基因全长cDNA目的片段,将其正向插入表达载体pFGC5941上的CaMV35S启动子下游,构成该基因过量表达载体pFGC5941-BnGID1.经根癌农杆菌介导,导入甘蓝型油菜矮化突变体NDF-1基因组,通过PCR及半定量RT-PCR检测,确定得到抗性转基因植株23株.移至大田生长,观察结果显示,转基因植株明显高于对照矮化突变体NDF-1,平均高出49.05cm.结果表明,BnGID1基因过量表达能够使甘蓝型油菜矮化突变体NDF-1株高得到较大程度的恢复.图7表2参16     

甘蓝型油菜脂肪酸链延长酶基因FAE1的克隆与原核表达

脂肪酸延长酶1(FAE1)是广泛存在于植物中并定位于内质网上的一种能催化脂肪酸碳链延长的酮脂酰CoA合成酶.根据Genbank上已知的植物FAE1基因设计引物,以从甘蓝型油菜叶片中提取的总DNA为模板,进行PCR扩增,获得了1380bp的片段.回收该片段,并连接到pMD18-T载体测序.序列比对结果说明了该片段与植物中已知的FAE1序列有极高的相似性,并且不存在内含子序列.将该片段通过高保真酶扩增,EcoRⅠ酶切消化后定向克隆到pGEX-2T表达载体中,在IPTG诱导下于28℃表达出Mr76×103的蛋白质条带.用兔抗GST多克隆抗体做第一抗体进行Western-blot检测,并获得阳性检测结果.这为甘蓝型油菜脂肪酸链延长酶基因FAE1功能的进一步研究奠定了基础.图4表1参14     

Bt肠毒素基因与plcR基因的相关性及肠毒素对小鼠的急性毒性

用PCR方法检测溶血肠毒素BL、肠毒素T和肠毒素S三种肠毒素基因(hblA、becT、entS)及毒素调控基因plcR在30株苏云金芽胞杆菌株(Bt)中的分布.结果表明,含有hblA基因、entS基因、becT基因及plcR基因片段的Bt菌株分别占66.7%、70%、70%和73.3%.其中,含有plcR基因的菌株都至少含有一种肠毒素基因,不含肠毒素基因的菌株也未检测到plcR基因,说明plcR基因与肠毒素基因有着密切的关系.用3个Bt菌株WB9、HD2和HD9(都含有hblA、becT、entS和plcR基因片段,HD2和HD9经RPLA与TECRA肠毒素检测试剂盒检测具有高滴度)对小白鼠进行口服急性毒性试验.结果表明,所有3种供试菌株的发酵上清液对小白鼠行为和健康没有明显影响,对内部器官(心、肝、肺等)也没有产生病理现象.图5表3参14     

Representation of the world's biophysical conditions by the global protected area network

Protected areas (PAs) are often implemented without consideration of already existing PAs, which is likely to cause an overrepresentation of certain biophysical conditions. We assessed the representativeness of the current PA network with regard to the world's biophysical conditions to highlight which conditions are underprotected and where these conditions are located. We overlaid terrestrial and marine PAs with information on biophysical conditions (e.g., temperature, precipitation, and elevation) and then quantified the percentage of area covered by the PA network. For 1 variable at a time in the terrestrial realm, high temperature, low precipitation, and medium and very high elevation were underrepresented. For the marine realm, low and medium sea surface temperature (SST), medium and high sea surface salinity (SSS), and the deep sea were underrepresented. Overall, protection was evenly distributed for elevation across the terrestrial realm and SST across the marine realm. For 2 variables at a time, cold and very dry terrestrial environments had mostly low protection, which was also the case for low SST and low and medium SSS across most depths for marine environments. Low protection occurred mostly in the Sahara and the Arabian Peninsula for the terrestrial realm and along the Tropic of Capricorn and toward the poles for the marine realm. Although biodiversity measures are of prime importance for the design of PA networks, highlighting biophysical gaps in current PAs adds a frequently overlooked perspective. These gaps may weaken the potential of PAs to conserve biodiversity. Thus, our results may provide useful insights for researchers, practitioners, and policy makers to establish a more comprehensive global PA network.     

Quantitative composition of the defensive secretion ofBledius species (Coleoptera: Staphylinidae: Oxytelinae) is adapted to naturally occurring predators

Summary The adaptation of defensive secretions to their target organisms was examined for the abdominal gland secretions ofBledius furcatus, B. spectabilis andB. arenarius. Therefore the target organisms of the secretion of theseBledius species (i.e. their predators) had to be identified. At the collection sites examined these were the earwigLabidura riparia, the antCataglyphis bicolor, the flyLispe candicans, different carabids of the generaPogonus, Dichirotrichus, Dyschirius, Bembidion andCalathus and the wading birdsHaematopus ostralegus andCalidris alba. The secretion of the abdominal glands contains the toxin ptoluquinone dissolved in either-dodecalactone and 1-undecene (B. furcatus andB. spectabilis) or in octanoic acid and octyloctanoate (B. arenarius). The ratio of these solvents is species-specific. Application experiments using some of the natural insect predators (L. riparia, C. bicolor, Pogonus, Di. gustavii, Dyschirius) revealed that these solvent ratios provided a more effective deterrent than other possible ratios. Thus by combining the solvents in certain ratios, the capability of cuticular penetration and therefore the effectiveness of the defensive secretions are adapted to their natural targets.     

Democracy versus development: New urban debates

The politics of development includes subtexts of choice, as underpinned by community consensus (or lack of it), against the larger backdrop of a liberal democracy, with its intricate power structures that influence the choice of concepts and often lead to complicity rather than consent. A dilemma exists between the understanding of field-level practitioners and that of academics, whose understandings of progress differ. Progress can (and often does) imply long-term change across generations whereas development is often more a matter of crisis management and delivering tangible results to end-users. This makes it a bone of contention across political systems, irrespective of local or global dynamics. Development can emerge as a tool to be wielded for power and further political mileage at the expense of progress. Progress cannot be studied as a counterpoint to development as the sense of history is often missing in development interventions. Development tends to be piecemeal as its very logic often stems from the rationale of power. This is not to suggest, however, that development is only about politics; it is definitely more than the politics of everyday life and involves all of civil society that requires its critical and immediate attention. In this sense, it has become a priority for politicians with an underlying agenda designed to out-manouevre dissent and all statements of protest.     

A framework to measure the wildness of managed large vertebrate populations

As landscapes continue to fall under human influence through habitat loss and fragmentation, fencing is increasingly being used to mitigate anthropogenic threats and enhance the commercial value of wildlife. Subsequent intensification of management potentially erodes wildness by disembodying populations from landscape-level processes, thereby disconnecting species from natural selection. Tools are needed to measure the degree to which populations of large vertebrate species in formally protected and privately owned wildlife areas are self-sustaining and free to adapt. We devised a framework to measure such wildness based on 6 attributes relating to the evolutionary and ecological dynamics of vertebrates (space, disease and parasite resistance, exposure to predation, exposure to limitations and fluctuations of food and water supply, and reproduction). For each attribute, we set empirical, species-specific thresholds between 5 wildness states based on quantifiable management interventions. We analysed data from 205 private wildlife properties with management objectives spanning ecotourism to consumptive utilization to test the framework on 6 herbivore species representing a range of conservation statuses and commercial values. Wildness scores among species differed significantly, and the proportion of populations identified as wild ranged from 12% to 84%, which indicates the tool detected site-scale differences both among populations of different species and populations of the same species under different management regimes. By quantifying wildness, this framework provides practitioners with standardized measurement units that link biodiversity with the sustainable use of wildlife. Applications include informing species management plans at local scales; standardizing the inclusion of managed populations in red-list assessments; and providing a platform for certification and regulation of wildlife-based economies. Applying this framework may help embed wildness as a normative value in policy and mitigate the shifting baseline of what it means to truly conserve a species.     

Achieving Open Access to Conservation Science

Conservation science is a crisis discipline in which the results of scientific enquiry must be made available quickly to those implementing management. We assessed the extent to which scientific research published since the year 2000 in 20 conservation science journals is publicly available. Of the 19,207 papers published, 1,667 (8.68%) are freely downloadable from an official repository. Moreover, only 938 papers (4.88%) meet the standard definition of open access in which material can be freely reused providing attribution to the authors is given. This compares poorly with a comparable set of 20 evolutionary biology journals, where 31.93% of papers are freely downloadable and 7.49% are open access. Seventeen of the 20 conservation journals offer an open access option, but fewer than 5% of the papers are available through open access. The cost of accessing the full body of conservation science runs into tens of thousands of dollars per year for institutional subscribers, and many conservation practitioners cannot access pay‐per‐view science through their workplace. However, important initiatives such as Research4Life are making science available to organizations in developing countries. We urge authors of conservation science to pay for open access on a per‐article basis or to choose publication in open access journals, taking care to ensure the license allows reuse for any purpose providing attribution is given. Currently, it would cost $51 million to make all conservation science published since 2000 freely available by paying the open access fees currently levied to authors. Publishers of conservation journals might consider more cost effective models for open access and conservation‐oriented organizations running journals could consider a broader range of options for open access to nonmembers such as sponsorship of open access via membership fees. Obtención de Acceso Abierto a la Ciencia de la Conservación     

Sexual Predators,Energy Development,and Conservation in Greater Yellowstone

Abstract: In the United States, as elsewhere, a growing debate pits national energy policy and homeland security against biological conservation. In rural communities the extraction of fossil fuels is often encouraged because of the employment opportunities it offers, although the concomitant itinerant workforce is often associated with increased wildlife poaching. We explored possible positive and negative factors associated with energy extraction in the Greater Yellowstone Ecosystem (GYE), an area known for its national parks, intact biological diversity, and some of the New World's longest terrestrial migrations. Specifically, we asked whether counties with different economies—recreation (ski), agrarian (ranching or farming), and energy extractive (petroleum)—differed in healthcare (gauged by the abundance of hospital beds) and in the frequency of sexual predators. The absolute and relative frequency of registered sex offenders grew approximately two to three times faster in areas reliant on energy extraction. Healthcare among counties did not differ. The strong conflation of community dishevel, as reflected by in‐migrant sexual predators, and ecological decay in Greater Yellowstone is consistent with patterns seen in similar systems from Ecuador to northern Canada, where social and environmental disarray exist around energy boomtowns. In our case, that groups (albeit with different aims) mobilized campaigns to help maintain the quality of rural livelihoods by protecting open space is a positive sign that conservation can matter, especially in the face of rampant and poorly executed energy extraction projects. Our findings further suggest that the public and industry need stronger regulatory action to instill greater vigilance when and where social factors and land conversion impact biological systems.     

Comparison of the insecticidal effects of water extracted and intact aromatic plants onAcanthoscelides obtectus,a bruchid beetle pest of kidney beans

Summary Acanthoscelides obtectus (Say) is one of the most damaging pests of kidney beans,Phaseolus vulgaris L. worldwide. However, aromatic plants from the families Lamiaceae, Lauraceae, Myrtaceae and Poaceae can protect kidney beans by direct or delayed insecticidal effect, through increased adult mortality and inhibition of beetle reproduction (both oviposition and adult emergence). The efficiency of hydrodistillated and intact plants fromThymus vulgaris andT. serpyllum, Mentha piperata, Rosmarinus officinalis, Satureia hortensis, Eucalyptus globulus, Laurus nobilis, Origanum vulgare, andCymbopogon nardus was compared. For both extracts,Origanum vulgare had the best effect. The insecticidal effect was induced by more than the essential oils because no significant difference was noticed between distilled and intact plants extract. Inhibition of reproduction was particularly important. These results suggest that lipidic as well as non lipidic, allelochemicals, such as phenolics, or non-protein amino-acids, or flavonoids may be involved in the toxicity of aromatic plants to this beetle.     

Rapid,recurring, structured survey versus bioblitz for generating biodiversity data and analysis with a multispecies abundance model

A bioblitz inexpensively and quickly generates biodiversity data, but bioblitzes are often conducted with haphazard, unreplicated sampling. Results tend to be taxonomically, geographically, or temporally biased, lack metadata, and consist of lists of observed taxa that do not enable further analyses or correction for imperfect detection. A rapid, recurring, structured survey (RRSS) uses a structured sampling design and temporal and spatial replication to survey randomly selected sites on a conservation property. We participated in a loosely structured bioblitz and a subsequent RRSS at Big Canoe Creek Nature Preserve in Springville (St. Clair County), Alabama (USA) to compare observed richness derived from the 2 survey approaches. The RRSS data structure enabled us to fit models that accounted for imperfect detection to estimate abundances, occupancy probabilities, and habitat associations. The loosely structured bioblitz data could not be used in such models. We present a new integrated multispecies abundance model that we applied to avian RRSS data. Our model extension enables estimation for the community, employs data augmentation to estimate the number of undetected species, and incorporates covariates. The RRSS generated a more comprehensive and less biased list of observed taxonomic richness than the loosely structured bioblitz (e.g., 73 vs. 45 bird species and 104 vs. 63 insect families from the RRSS vs. loosely structured bioblitz, respectively). Models fit to the RRSS data identified seasonal patterns in avian community composition and allowed for estimation of habitat–occupancy relationships for insect taxa. The RRSS protocol has potential for broad transferability as a standardized, quick, and inexpensive way to inventory biodiversity and estimate ecological parameters while providing an outreach opportunity.     

Compliance with and ecosystem function of biodiversity offsets in North American and European freshwaters

Land-use change via human development is a major driver of biodiversity loss. To reduce these impacts, billions of dollars are spent on biodiversity offsets. However, studies evaluating offset project effectiveness that examine components such as the overall compliance and function of projects remain rare. We reviewed 577 offsetting projects in freshwater ecosystems that included the metrics project size, type of aquatic system (e.g., wetland and creek), offsetting measure (e.g., enhancement, restoration, and creation), and an assessment of the projects’ compliance and functional success. Project information was obtained from scientific and government databases and gray literature. Despite considerable investment in offsetting projects, crucial problems persisted. Although compliance and function were related to each other, a high level of compliance did not guarantee a high degree of function. However, large projects relative to area had better function than small projects. Function improved when projects targeted productivity or specific ecosystem features and when multiple complementary management targets were in place. Restorative measures were more likely to achieve targets than creating entirely new ecosystems. Altogether the relationships we found highlight specific ecological processes that may help improve offsetting outcomes.     

Some polyphagous Homoptera gain protection from their natural enemies by feeding on the toxic plantsSpartium junceum andErythrina corallodendrum (Leguminosae)

Summary Interactions were studied among alkaloid-containing legumes (Erythrina corallodendrum andSpartium junceum) and non-toxic plants (Citrus sinensis, Cucurbita moschata andEuphorbia tirucalli), several polyphagous homopterans,Aphis craccivora (Aphididae),Icerya purchasi, I. aegyptiaca (Margarodidae),Lepidosaphes ulmi (Diaspididae) andPlanococcus citri (Pseudococcidae), and some major natural enemies of these homopterans. Significant reductions in survival due to negative effects of alkaloid containing as compared with non-alkaloidal plants were recorded for the predatorsRodolia cardinalis andChilocorus bipustulatus, but not forCryptolaemus montrouzieri (Coleoptera: Coccinellidae),Chrysoperla carnea (Neuroptera: Chrysopidae) andSympherobius sanctus (Neuroptera: Sympherobiidae). The development time of the larvae or pupae ofR. cardinalis, C. carnea andS. sanctus was longer on the toxic plants than on the non-toxic ones. The percentage of parasitism ofA. craccivora collected from the non-alkaloidal plantsVicia palaestina andMelilotus albus was much higher than that onS. junceum. The parasitoid complexes ofA. craccivora differed between both plant groups. The nutritive value of honeydew ofI. purchasi andA. craccivora, as expressed by the life span ofEncyrtus infelix (Hymenoptera: Encyrtidae) adults, was also investigated. Life spans were significantly longer when the wasps fed on honeydew produced on non-alkaloidal plants (C. sinensis andPittosporum tobira) than on alkaloid containing plants whenI. purchasi — but notA. craccivora — was the producer. It is suggested that the chemical defense ofE. corallodendrum andS. junceum is exploited by polyphagous phytophages to reduce predation. In nature, population growth and density of four of the investigated homopterans are conspicuously high when they developed on the alkaloid containing plant species, and very low on non-alkaloid plants. The efficiency of their natural enemies may be reduced by sequestration of alkaloids (or other toxic plant compounds) or their transfer into excreted honeydew. Therefore it is assumed that a generalist phytophagous homopteran may be protected from its natural enemies, although at different rates of efficiency, if it can safely sequester the host allelochemical when it develops on toxic species within its host range.