棉花细菌人工染色体的荧光原位杂交(BAC-FISH)技术

细菌人工染色体荧光原位杂交(BAC-FISH)技术是植物染色体识别、物理作图等分子细胞遗传学研究的重要工具,但对于某些物种尤其是多倍体植物,由于大量重复序列的存在等问题,使得该技术应用受到很大的限制.通过选择棉花分子遗传图中高重组区的微卫星位点(simple sequence repeats,SSR)标记的策略,筛选到不含或含有少量重复序列的细菌人工染色体(BAC)克隆,同时,在通用FISH技术程序基础上,通过改进发根、变性、洗脱条件等步骤,构建出适合于棉花的BAC-FISH技术,简化了操作流程的同时,获得稳定的杂交结果及较高的检出率;并通过将一随机获得的BAC进行染色体的物理定位,进一步引入双探针、双色及重复杂交技术,显示了该技术的成熟与良好的应用前景和价值.     

Improvements in cytogenetic slide preparation: controlled chromosome spreading, chemical aging and gradual denaturing

BACKGROUND: Metaphase spreading is an essential technique for clinical and molecular cytogenetics. Results of classical banding techniques as well as complex fluorescent in situ hybridization (FISH) applications, such as comparative genomic hybridization (CGH) or multiplex FISH (M-FISH), are greatly influenced by the quality of chromosome spreading and pretreatment of the slide prior to hybridization. Materials and Methods Using hot steam and a metal plate with a temperature gradient across its surface, a reproducible protocol for slide preparation, aging, and hybridization was developed. RESULTS: This protocol yields good chromosome spreads from even the most difficult cell suspensions and is unaffected by the environmental conditions. Chromosome spreads were suitable for both banding and FISH techniques common to the cytogenetic laboratory. Chemical aging is a rapid slide pretreatment procedure for FISH applications, which allows freshly prepared cytogenetic slides to be used for in situ hybridization within 30 min, thus increasing analytical throughput and reducing benchwork. Furthermore, the gradually denaturing process described allows the use of fresh biologic material with optimal FISH results while protecting chromosomal integrity during denaturing. CONCLUSION: The slide preparation and slide pretreatment protocols can be performed in any laboratory, do not require specialized equipment, and provide robust results.     

A novel fluorescence-based array biosensor: principle and application to DNA hybridization assays

A novel fluorescence-based array biosensor targeted for field applications, such as environmental monitoring, has been developed, and successfully applied to DNA hybridization assays. The purpose was to meet the demand for automated, portable but easy-to-maintain systems allowing continuous flow monitoring of surface reactions. The biosensor presented here can be distinguished from the existing systems by the optical method used, which provides an enhanced simplicity and robustness, and enables a simple maintenance by potentially unskilled personnel. The system is based on a conventional microscope slide which acts both as transducer and biological array sensor. The excited fluorescence is guided by total internal reflection into the slide to the detector which is directly interfaced to the slide. Each region of the sensor array is successively optically interrogated, and the detection of the corresponding fluorescent emission synchronized. A real-time three-analyte analysis is thus feasible without any mechanical scanning movement or optical imaging systems as generally used in the existing instruments. The ability of the biosensor to operate in continuous flow for several tens of hours has been demonstrated. The biosensor has been assessed in terms of stability, and slide-to-slide reproducibility, which is found to be less than 3.7%, thus far below the standard biological reproducibility. DNA hybridization assays were performed to estimate a limit of detection, which was found to be 16 mol/microm(2), and to determine the reaction kinetics associated to the DNA model used. The developed biosensor is thus shown to be able to predict reaction kinetics, and to monitor in real time surface reactions between targets and probes.     

Canine cytogenetics--from band to basepair

Humans and dogs have coexisted for thousands of years, during which time we have developed a unique bond, centered on companionship. Along the way, we have developed purebred dog breeds in a manner that has resulted unfortunately in many of them being affected by serious genetic disorders, including cancers. With serendipity and irony the unique genetic architecture of the 21st century genome of Man's best friend may ultimately provide many of the keys to unlock some of nature's most intriguing biological puzzles. Canine cytogenetics has advanced significantly over the past 10 years, spurred on largely by the surge of interest in the dog as a biomedical model for genetic disease and the availability of advanced genomics resources. As such the role of canine cytogenetics has moved rapidly from one that served initially to define the gross genomic organization of the canine genome and provide a reliable means to determine the chromosomal location of individual genes, to one that enabled the assembled sequence of the canine genome to be anchored to the karyotype. Canine cytogenetics now presents the biomedical research community with a means to assist in our search for a greater understanding of how genome architectures altered during speciation and in our search for genes associated with cancers that affect both dogs and humans. The cytogenetics 'toolbox' for the dog is now loaded. This review aims to provide a summary of some of the recent advancements in canine cytogenetics.     

Making the biodiversity monitoring system sustainable: Design issues for large‐scale monitoring systems

Abstract There is strong demand for information about the status of, and trends in, Australia's biodiversity. Almost inevitably, this demand for information has led to demand for a broad‐scale monitoring system. However, the decision to embark on a monitoring system should only be made once it has been established that a monitoring system is the optimal way to inform management. We stress the need to invest resources in assessing whether a monitoring system is necessary before committing resources to the design and implementation of the system. Current debate associated with the design of a biodiversity monitoring system has similarities to the debate within the range management profession in the early 1970s. The experience with range monitoring shows that large‐scale monitoring systems such as those being proposed will require considerable resources, recurrently expended into the distant future, but with only a limited ability to adapt to new demands. Those involved in any biodiversity monitoring system will need to understand the implications of investing in a long‐term monitoring programme. Monitoring sustainability will only be possible if the monitoring system is itself sustainable. We discuss a number of issues that need to be addressed before the system is at all sustainable. These attributes are a mix of biophysical, social and institutional attributes and highlight the view that monitoring systems of the type being suggested comprise an unusual mixture of attributes not found in typical scientific activity. The present paper is not a technical manual, but rather considers some of the design issues associated with designing and implementing large‐scale monitoring systems.     

Current status and future directions of post-marketing vaccine safety monitoring with focus on USA and Europe

Vaccine safety research is a key component of public health programs. Regulatory agencies need to be able to make informed decisions. Public health authorities need to respond to vaccine concerns before they turn into large scale scares reducing vaccine uptake and derailing immunization programs. Several post-licensure vaccine safety monitoring systems have been established in the USA and Europe, and methods such as rapid cycle analysis have been developed for real-time detection and analysis of safety issues. Accurate and reliable vaccine product testing and monitoring requires high quality data of populations of 100 million and above depending on the frequency of the event, vaccine coverage, and the time pressure during which data need to be generated. This requires post-licensure safety studies utilizing large linked population based databases of exposure and outcomes. Harmonized methods for development and linkage of these databases across countries need to be further developed, validated and implemented. Concerted action between the US and Europe could move vaccine safety monitoring to today's level of requirements globally and should be pursued.     

A simplified technique for the short-term tissue culture of rabbit corneal cells

Summary A technique for the short-term culture of pure populations of rabbit corneal endothelial and epithelial cells has been developed. Rabbit corneas were placed on concave agarose surfaces, treated briefly with a solution of trypsin and ethylenediamine tetracetic acid, and transferred, either epithelial cell surface or endothelial cell surface down, to microscope slide culture chambers. Within 6 to 12 h the epithelial cells or endothelial cells attached to the slide chamber surface and the cornea was removed, leaving behind a pure population of cells which spread out and grew to fill the surface of the slide chamber. This technique provides a simple and economic means for the reproducible initiation of primary cultures of rabbit corneal epithelial and endothelial cells for us in a variety of experiments. This study was supported in part by Public Health Service grants EY03150, EY02580, and EY02377 from the National Eye Institute, National Institutes of Health, Bethesda, MD, and a Foreign Fellowship (Dr. Xie) from Research to Prevent Blindness, Inc., New York, NY.     

河流生境的评估方法及应用的研究进展

河流生境是水生生物赖以生存的物理、化学和生物环境的综合体,是河流生态系统的重要组成部分。河流生境评价有助于掌握河流的生态健康状况,识别河流退化的原因,为河流的生态修复提供依据。文章梳理总结了20世纪80年代至2018年文献中报道的全球范围内河流生境评估的方法,然后根据每种方法的侧重点和目标,将它们分为预测模型法和多指标综合评估法两种类型,并比较了它们各自的优势和不足。预测模型法适于长期的生境动态监测,但该方法需要以自然无干扰的河流为参照,并且需要大量历史数据,统一评估不易实现;多指标综合评估法评估相对快速方便,但评估过程复杂,且评价标准不一,结果有一定的局限性。这些方法的适用范围从中小型的可涉水河流到较大的不可涉水河流,但适用于大型不可涉水河流的生境评估方法和案例非常有限。通过分类整理,发现我国河流生境评估方法多是参考国外几种常用的河流评估方法,种类单一,而且多是针对个别河流,并且未对这些河流所在的流域的生境状况进行深入研究,广适性较差。因此,文章从以下几个方面对我国河流生境评估体系的发展提出几点建议:(1)确定科学和标准化的评分指标,因地制宜,以满足不同河流特征;(2)扩大评估范围,...     

Quantitative trait locus (QTL) isogenic recombinant analysis: a method for high-resolution mapping of QTL within a single population

In the quest for fine mapping quantitative trait loci (QTL) at a subcentimorgan scale, several methods that involve the construction of inbred lines and the generation of large progenies of such inbred lines have been developed (Complex Trait Consortium 2003). Here we present an alternative method that significantly speeds up QTL fine mapping by using one segregating population. As a first step, a rough mapping analysis is performed on a small part of the population. Once the QTL have been mapped to a chromosomal interval by standard procedures, a large population of 1000 plants or more is analyzed with markers flanking the defined QTL to select QTL isogenic recombinants (QIRs). QIRs bear a recombination event in the QTL interval of interest, while other QTL have the same homozygous genotype. Only these QIRs are subsequently phenotyped to fine map the QTL. By focusing at an early stage on the informative individuals in the population only, the efforts in population genotyping and phenotyping are significantly reduced as compared to prior methods. The principles of this approach are demonstrated by fine mapping an erucic acid QTL of rapeseed at a subcentimorgan scale.     

Image analysis as a simple and useful tool for evaluating the constitutive heterochromatin (C-banding) in human chromosomes

Image analysis can contribute to those fields of cytogenetics that are influenced most by subjectivity, especially evaluation of chromosome regions that are histochemically polymorphic. C-banding of human or primate chromosomes may be used as a typical example of this concept. In addition, using it quantitatively it is useful in studies of population cytogenetics of man and Primates. Therefore, the aim of this study was to determine the best conditions for measurement by image analysis of C-positive regions in a sample of 29 normal subjects. We looked for relationships of chromosomal C-positive areas with the dimensions of the corresponding metaphases. Finally, we suggest some criteria for potential use of C-banding in population and comparative studies.     

Can site and landscape‐scale environmental attributes buffer bird populations against weather events?

Projected impacts of climate change on the populations and distributions of species pose a challenge for conservationists. In response, a number of adaptation strategies to enable species to persist in a changing climate have been proposed. Management to maximise the quality of habitat at existing sites may reduce the magnitude or frequency of climate‐driven population declines. In addition large‐scale management of landscapes could potentially improve the resilience of populations by facilitating inter‐population movements. A reduction in the obstacles to species’ range expansion, may also allow species to track changing conditions better through shifts to new locations, either regionally or locally. However, despite a strong theoretical base, there is limited empirical evidence to support these management interventions. This makes it difficult for conservationists to decide on the most appropriate strategy for different circumstances. Here extensive data from long‐term monitoring of woodland birds at individual sites are used to examine the two‐way interactions between habitat and both weather and population count in the previous year. This tests the extent to which site‐scale and landscape‐scale habitat attributes may buffer populations against variation in winter weather (a key driver of woodland bird population size) and facilitate subsequent population growth. Our results provide some support for the prediction that landscape‐scale attributes (patch isolation and area of woodland habitat) may influence the ability of some woodland bird species to withstand weather‐mediated population declines. These effects were most apparent among generalist woodland species. There was also evidence that several, primarily specialist, woodland species are more likely to increase following population decline where there is more woodland at both site and landscape scales. These results provide empirical support for the concept that landscape‐scale conservation efforts may make the populations of some woodland bird species more resilient to climate change. However in isolation, management is unlikely to provide a universal benefit to all species.     

Concentrating and Staining Bone Marrow; An On-the-Slide Technique

A 0.5-1 ml sample of bone marrow is aspirated into a syringe containing 3 drops of 15% K₂-EDTA and an additional 1-2 drops of the EDTA solution previously placed on a slide, is then drawn into the syringe. All of the contents are ejected onto this slide, which is carefully tilted 2 or 3 times to an angle of 5-10°, and the edge brought to the center of another slide. The slide with the aspirate is then slowly tilted to 80-90°. Most of the blood and part of the marrow will drain off, leaving spicules of marrow and some blood on the original slide. A small drop of this concentrated marrow is dragged off with the edge of a third slide and deposited about 2 cm from the edge of a fourth slide on which the smear is to be made. The smear is made by bringing a clean (smearing) slide to the slide with the deposited marrow with flat surfaces parallel and the edges at a 90° angle. With gentle pressure, the smearing slide is pushed toward the empty end of the slide upon which the smear is made. This separates the marrow from the circulating blood. Before staining the smear is air dried and heated in an oven at 120-125 C for 2 min; or alternately for satisfactory but less uniform results the smear is heated over a microburner for 10 sec; then the smear is covered with 1 part of undiluted Wright's stain for 30—45 sec which is then diluted with 2 parts of a solution of 0.1-0.2 gm of Na₂S₂O₃ in 1 liter of distilled water and stained for 10-13 min with this diluted stain. Smears made in this manner have 3 concentric zones; the central zone contains the myeloid tissue; the middle, erythropoetic tissue; the outer, a mixture of blood and marrow.     

Corals and starfish devastation of the great barrier reef: Aggregation methods

Aggregation methods allow one to replace a large scale dynamical system (micro-system) by a reduced dynamical system (macro-system) governing a small number of global variables. This aggregation of variables can be performed when two time scales exist, a fast time scale and a slow time scale. Perturbation theory allows to obtain an approximated aggregated dynamical system which describes the behaviour of a few number of slow time varying variables which are constants of motion of the fast part of the micro-system. Aggregation methods are applied to the case of the devastation of the great barrier reef by the starfishes. We recall the Antonelli/Kazarinoff model which implies a stable limit cycle for the corals and starfish populations. This prey-predator model describes the interactions between two species of corals and the starfish. Then, we generalize the Antonelli/Kazarinoff model to the case of two spatial patches with a fast part describing the starfish migration on the patches and the human manipulation of the communities by divers and, a slow part describing the growth and the interactions between the populations. We obtain an aggregated model governing the total coral densities on the patches and the total starfish population. This model can exhibit stable limit cycle oscillations and a Hopf bifurcation. The critical value of the bifurcation parameter is expressed in terms of the proportions of coral species and starfish on the two patches. This implies for example that rather than random killing of starfish by the Australian military, it may be better to send teams of divers to outbreaking reefs when they first occur who will then manipulate the community structure to increase protection.     

Learning to karyotype in the university environment: a computer-based virtual laboratory class (KaryoLab) designed to rationalize time for the tutor/researcher and to encourage more students to engage in cytogenetics

The ability to karyotype G-banded chromosome preparations is an essential skill for chromosome biologists. For this reason, the teaching of the rudiments of G banding analysis forms an integral part of the curriculum in many biology and genetics degree courses. The way in which karyotyping is usually taught involves providing the students with a photograph of G-banded chromosomes, a pair of scissors and some glue from which they can cut out the chromosomes and build the karyotype. This has the disadvantage that large amounts of time are taken in cutting and pasting and comparatively little in learning pattern recognition of individual chromosomes. In this paper we describe the development of a computer-based student practical class "KaryoLab". To the best of our knowledge, this is the first report of a teaching tool that combines instruction in cytogenetic analysis with both formative and summative feedback to the student and a virtual elimination of marking time for the tutor. Chromosome research and diagnostics will only continue while there are sufficiently motivated and trained individuals to perform it. We see the software developed here as a significant step towards training and motivating students in cytogenetics.     

Laser Capture Microdissection - A Demonstration of the Isolation of Individual Dopamine Neurons and the Entire Ventral Tegmental Area

Laser capture microdissection (LCM) is used to isolate a concentrated population of individual cells or precise anatomical regions of tissue from tissue sections on a microscope slide. When combined with immunohistochemistry, LCM can be used to isolate individual cells types based on a specific protein marker. Here, the LCM technique is described for collecting a specific population of dopamine neurons directly labeled with tyrosine hydroxylase immunohistochemistry and for isolation of the dopamine neuron containing region of the ventral tegmental area using indirect tyrosine hydroxylase immunohistochemistry on a section adjacent to those used for LCM. An infrared (IR) capture laser is used to both dissect individual neurons as well as the ventral tegmental area off glass slides and onto an LCM cap for analysis. Complete dehydration of the tissue with 100% ethanol and xylene is critical. The combination of the IR capture laser and the ultraviolet (UV) cutting laser is used to isolate individual dopamine neurons or the ventral tegmental area when using PEN membrane slides. A PEN membrane slide has significant advantages over a glass slide as it offers better consistency in capturing and collecting cells, is faster collecting large pieces of tissue, is less reliant on dehydration and results in complete removal of the tissue from the slide. Although removal of large areas of tissue from a glass slide is feasible, it is considerably more time consuming and frequently leaves some residual tissue behind. Data shown here demonstrate that RNA of sufficient quantity and quality can be obtained using these procedures for quantitative PCR measurements. Although RNA and DNA are the most commonly isolated molecules from tissue and cells collected with LCM, isolation and measurement of microRNA, protein and epigenetic changes in DNA can also benefit from the enhanced anatomical and cellular resolution obtained using LCM.     

The importance of within-year repeated counts and the influence of scale on long-term monitoring of sage-grouse

Long-term population monitoring is the cornerstone of animal conservation and management. The accuracy and precision of models developed using monitoring data can be influenced by the protocols guiding data collection. The greater sage-grouse (Centrocercus urophasianus) is a species of concern that has been monitored over decades, primarily, by counting the number of males that attend lek (breeding) sites. These lek count data have been used to assess long-term population trends and for multiple mechanistic studies. However, some studies have questioned the efficacy of lek counts to accurately identify population trends. In response, monitoring protocols were changed to have a goal of counting lek sites multiple times within a season. We assessed the influence of this change in monitoring protocols on model accuracy and precision applying generalized additive models to describe trends over time. We found that at large spatial scales including >50 leks, the absence of repeated counts within a year did not significantly alter population trend estimates or interpretation. Increasing sample size decreased the model confidence intervals. We developed a population trend model for Wyoming greater sage-grouse from 1965 to 2008, identifying significant changes in the population indices and capturing the cyclic nature of this species. Most sage-grouse declines in Wyoming occurred between 1965 and the 1990s and lek count numbers generally increased from the mid-1990s to 2008. Our results validate the combination of monitoring data collected under different protocols in past and future studies—provided those studies are addressing large-scale questions. We suggest that a larger sample of individual leks is preferable to multiple counts of a smaller sample of leks. © 2011 The Wildlife Society.     

Cytogenetic diversity in primary human tumors

Cytogenetic patterns from primary short-term culture of breast cancer, renal carcinoma, and tumors of the central nervous system are presented to illustrate the range of karyotypic diversity of human solid tumors as well as their biologic differences in culture systems that support their growth. These studies have illustrated several major issues. 1) Results vary with the tissue of origin: primary cultures from breast are almost uniformly diploid, while renal tumors are near-diploid, mosaic, and show clonal aberrations; and CNS tumors are heterogeneous: some diploid, some near-diploid and some highly aneuploid. 2) Results after short-term culture are selective, representing subpopulations from the heterogeneous cells that are detected on direct analysis of fresh tumors by cytogenetics or flow cytometry (FCM). It is not yet clear whether prognosis depends on the dominant population of the primary tumor or alternatively should be influenced by detection of small aneuploid subpopulations. 3) Evidence from all three tumor types supports the interpretation that cytogenetically normal diploid cells constitute part of some tumor populations, and may be better adapted to routine growth in culture than aneuploid subpopulations from the same primary tumors. These cells may also compose a major portion of the viable population of tumors in vivo and, therefore, could represent a useful model for studies of tumorigenesis and therapeutic regimens.     

Evaluation de deux méthodes de lutte intégrée contre les ravageurs en vergers d'agrumes

Abstract:  Evaluation of two IPM methods to control main pests in citrus orchards This study aims to the consolidation of the acquired knowledge regarding integrated pest management (IPM) against the main pests in citrus orchards. We provide evidence that the principles of this method already tested on small scales, are quite applicable on larger ones. In addition to this aspect, the purpose of our work has been the evaluation of two IPM methods: the first one, has been tested in Morocco for 3 years in areas not exceeding 1.2 ha; the second one originating from Australia, is presently recommended by the Plant Protection Authorities in Morocco. The results obtained confirm the complementarity between these two methods which are not mutually exclusive, despite some advantages recorded in favour of this method or the other. Our results show that the Moroccan method is more efficient in monitoring aphids and citrus leaf miner (CLM) population as it leads to the same results while reducing by half the number of the samples inspected. In contrast, mites monitoring is more convenient with the Australian method, allowing a good evaluation of the numbers of phytoseiid predators. Moreover, this method enabled us to reduce the quantity of pesticides used against Mediterranean fruit fly through treatment by lured spots reducing pulp volume by more than 92.8% and costs by 20%. These two methods gave the same results for monitoring population dynamics of California red scale and Mediterranean fruit fly but, fruit infestation at harvest was higher with the Australian method than the method developed locally (70.95% against 74.75 for California red scale and 2.35 against 3.35 for Mediterranean fruit fly).     

Quantifying the importance of geographic replication and representativeness when estimating demographic rates,using a coastal species as a case study

Demographic rates are rarely estimated over an entire species range, limiting empirical tests of ecological patterns and theories, and raising questions about the representativeness of studies that use data from a small part of a range. The uncertainty that results from using demographic rates from just a few sites is especially pervasive in population projections, which are critical for a wide range of questions in ecology and conservation. We developed a simple simulation to quantify how this lack of geographic representativeness can affect inferences about the global mean and variance of growth rates, which has implications for the robust design of a wide range of population studies. Using a coastal songbird, saltmarsh sparrow Ammodramus caudacutus, as a case study, we first estimated survival, fecundity, and population growth rates at 21 sites distributed across much of their breeding range. We then subsampled this large, representative dataset according to five sampling scenarios in order to simulate a variety of geographic biases in study design. We found spatial variation in demographic rates, but no large systematic patterns. Estimating the global mean and variance of growth rates using subsets of the data suggested that at least 10–15 sites were required for reasonably unbiased estimates, highlighting how relying on demographic data from just a few sites can lead to biased results when extrapolating across a species range. Sampling at the full 21 sites, however, offered diminishing returns, raising the possibility that for some species accepting some geographical bias in sampling can still allow for robust range‐wide inferences. The subsampling approach presented here, while conceptually simple, could be used with both new and existing data to encourage efficiency in the design of long‐term or large‐scale ecological studies.