PSDS 2.0: 一个基于GIS和多个模型的生物潜在分布地预测系统

根据对生物分布地预测模型和软件发展现状的分析和总结, 本研究在PSDS 1.0的基础上提出并实现一个基于GIS且具有多个代表性模型的生物分布地预测系统(PSDS 2.0)。PSDS 2.0系统继承了1.0的环境包络和聚类包络模型, 进一步引入了限制因子包络、马氏距离、支持向量机等新模型, 并针对本领域中模型比较与选择的难点增加了迭代交叉验证的多模型选择功能。系统还实现了灵活定制和评估伪负样本的功能, 通过用只需要正样本的I类模型预测的结果对随机产生的伪负样本进行评估, 减小其落入适宜地区的概率, 进一步提高需要正负样本的II类模型的准确率。GIS功能在PSDS 2.0中也得到加强, 被应用于数据准备及结果分析等重要环节。文章最后以白冠长尾雉(Syrmaticus reevesii)为例, 运用PSDS 2.0系统预测其在中国范围内的潜在分布地, 并对各种模型的预测结果进行评估和比较。     

Hybrid scanning ion conductance and scanning near-field optical microscopy for the study of living cells

We have developed a hybrid scanning ion conductance and scanning near-field optical microscope for the study of living cells. The technique allows quantitative, high-resolution characterization of the cell surface and the simultaneous recording of topographic and optical images. A particular feature of the method is a reliable mechanism to control the distance between the probe and the sample in physiological buffer. We demonstrate this new method by recording near-field images of living cells (cardiac myocytes).     

Real time quantitative analysis of lipid storage and lipolysis pathways by confocal spectral imaging of intracellular micropolarity

Organisms store fatty acids in triacylglycerols in the form of lipid droplets, or hydrolyze triacylglycerols in response to energetic demands via activation of lipolytic or storage pathways. These pathways are complex sets of sequential reactions that are finely regulated in different cell types. Here we present a high spatial and temporal resolution-based method for the quantification of the turnover of fatty acids into triglycerides in live cells without introducing sample preparation artifacts.We performed confocal spectral imaging of intracellular micropolarity in cultured insulin secreting beta cells to detect micropolarity variations as they occur in time and at different pixels of microscope images. Acquired data are then analyzed in the framework of the spectral phasors technique.The method furnishes a metabolic parameter, which quantitatively assesses fatty acids - triacylglycerols turnover and the activation of lipolysis and storage pathways. Moreover, it provides a polarity profile, which represents the contribution of hyperpolar, polar and non-polar classes of lipids. These three different classes can be visualized on the image at a submicrometer resolution, revealing the spatial localization of lipids in cells under physiological and pathological settings.This new method allows for a fine-tuned, real-time visualization of the turnover of fatty acids into triglycerides in live cells with submicrometric resolution. It also detects imbalances between lipid storage and usage, which may lead to metabolic disorders within living cells and organisms.     

A Technique for Continuous Observation of the Infection Process in Cucumber Anthracnose

A new light microscope preparation technique for high magnification observation of living plant tissue and fungal penetration is described. Agar immersion is used in differential interference contrast microscopy (DIC) instead of coverslips (lens 40) or instead of coverslips and oil (lens 100).
This technique is suitable for
(a) longtime observation of living tissue, because the tissue to be observed remains on the plant, and for
(b) thick and uneven samples, as no coverslips are required.
With this technique it was possible to observe the dynamics of penetration of Colletotrichum lagenarium into epideral cells of cucumber cotyledons for 72 hours.
A time lapse film using this technique is in preparation.     

Biomarker discovery across annotated and unannotated microarray datasets using semi-supervised learning

The growing body of DNA microarray data has the potential to advance our understanding of the molecular basis of disease. However annotating microarray datasets with clinically useful information is not always possible, as this often requires access to detailed patient records. In this study we introduce GLAD, a new Semi-Supervised Learning (SSL) method for combining independent annotated datasets and unannotated datasets with the aim of identifying more robust sample classifiers. In our method, independent models are developed using subsets of genes for the annotated and unannotated datasets. These models are evaluated according to a scoring function that incorporates terms for classification accuracy on annotated data, and relative cluster separation in unannotated data. Improved models are iteratively generated using a genetic algorithm feature selection technique. Our results show that the addition of unannotated data into training, significantly improves classifier robustness.     

Retrospective Markov chain Monte Carlo methods for Dirichlet process hierarchical models

Inference for Dirichlet process hierarchical models is typicallyperformed using Markov chain Monte Carlo methods, which canbe roughly categorized into marginal and conditional methods.The former integrate out analytically the infinite-dimensionalcomponent of the hierarchical model and sample from the marginaldistribution of the remaining variables using the Gibbs sampler.Conditional methods impute the Dirichlet process and updateit as a component of the Gibbs sampler. Since this requiresimputation of an infinite-dimensional process, implementationof the conditional method has relied on finite approximations.In this paper, we show how to avoid such approximations by designingtwo novel Markov chain Monte Carlo algorithms which sample fromthe exact posterior distribution of quantities of interest.The approximations are avoided by the new technique of retrospectivesampling. We also show how the algorithms can obtain samplesfrom functionals of the Dirichlet process. The marginal andthe conditional methods are compared and a careful simulationstudy is included, which involves a non-conjugate model, differentdatasets and prior specifications.     

Progeny from sperm obtained after ectopic grafting of neonatal mouse testes

Ectopic grafting of testicular tissue is a promising new approach that can be used to preserve testicular function. This technique has been used recently to differentiate the neonatal testes of different species, up to the level of complete spermatogenesis. This approach can be applied successfully to generate live progeny using sperm extracted from grafts originating from testes of newborn donors. The sperm are capable of supporting normal development and producing fertile male and female offspring after intracytoplasmic injection into mouse oocytes and embryo transfer into surrogate mothers. The grafted tissue was also capable of significantly normalizing reproductive hormone levels in the castrated recipients. This technique presents new avenues for experimentation. The recipient mouse can be regarded as a living incubator and a culture system of testicular tissue, allowing the experimental manipulation of several aspects of testis development and spermatogenesis. The successful generation of pups indicates that this technique can be used to study the testicular phenotype and to breed mutant or transgenic mouse strains with lethal postnatal phenotypes. The ability to generate sperm from the germ line ex vivo also paves the way for the development of new strategies for preserving fertility in boys undergoing cancer therapy.     

Visual perception and social foraging in birds

Birds gather information about their environment mainly through vision by scanning their surroundings. Many prevalent models of social foraging assume that foraging and scanning are mutually exclusive. Although this assumption is valid for birds with narrow visual fields, these models have also been applied to species with wide fields. In fact, available models do not make precise predictions for birds with large visual fields, in which the head-up, head-down dichotomy is not accurate and, moreover, do not consider the effects of detection distance and limited attention. Studies of how different types of visual information are acquired as a function of body posture and of how information flows within flocks offer new insights into the costs and benefits of living in groups.     

Determination of complexation capacity using coulometric stripping analysis

Abstract

Complexation capacity is a measure of the ability of a water sample to complex metal ions. In this work, a new method which involves coulometrically plating copper on to a glassy carbon electrode and then completely stripping it into a vigorously stirred sample solution has been used to determine the complexation capacity. We have called this technique coulometric stripping analysis (CSA). A technique which uses several electrodes with different amounts of plated copper can be used to determine the complexation capacity. The accuracy of the method was examined using EDTA standard solutions and the method was applied to analyse some water samples.     

Multiphoton imaging of host-pathogen interactions

Studying the events that occur when a pathogen comes into contact with its host is the basis of the field of infection biology. Over the years, work in this area has revealed many facets of the infection process, including attachment, invasion and colonization by the pathogen, and of the host responses, such as the triggering of the immune system. Recent advancements in imaging technologies, such as multiphoton microscopy (MPM), mean that the field is in the process of taking another big leap forward. MPM allows for cellular-level visualization of the real-time dynamics of infection within the living host. The use of live animal models means that all the interplaying factors of an infection, such as the influences of the immune, lymphatic and vascular systems, can be accounted for. This review outlines the developing field of MPM in pathogen-host interactions, highlighting a number of new insights that have been ‘brought to light’ using this technique.     

Sibship reconstruction from genetic data with typing errors

Likelihood methods have been developed to partition individuals in a sample into full-sib and half-sib families using genetic marker data without parental information. They invariably make the critical assumption that marker data are free of genotyping errors and mutations and are thus completely reliable in inferring sibships. Unfortunately, however, this assumption is rarely tenable for virtually all kinds of genetic markers in practical use and, if violated, can severely bias sibship estimates as shown by simulations in this article. I propose a new likelihood method with simple and robust models of typing error incorporated into it. Simulations show that the new method can be used to infer full- and half-sibships accurately from marker data with a high error rate and to identify typing errors at each locus in each reconstructed sib family. The new method also improves previous ones by adopting a fresh iterative procedure for updating allele frequencies with reconstructed sibships taken into account, by allowing for the use of parental information, and by using efficient algorithms for calculating the likelihood function and searching for the maximum-likelihood configuration. It is tested extensively on simulated data with a varying number of marker loci, different rates of typing errors, and various sample sizes and family structures and applied to two empirical data sets to demonstrate its usefulness.     

Myoblast-mediated fusion-injection: a new technique for introduction of macromolecules specifically into living skeletal muscle cells

A new technique for the introduction of macromolecules specifically into living skeletal muscle cells has been developed by a modification of the red blood cell ghost-mediated fusion-injection technique [M. Furusawa (1980) Int. Rev. Cytol. 62, 29-67]. Fluorescein-labeled bovine serum albumin (FITC-BSA) was introduced into chicken skeletal muscle myoblasts by the human red blood cell-mediated fusion-injection method in the presence of polyethylene glycol. Myoblasts loaded with FITC-BSA were then purified by a fluorescence cell sorter and cocultured with myotubes. Specific cell fusion between myoblasts and myotubes occurred under normal culture conditions and BSA was successfully introduced into living myotubes. This technique may provide a new method not only for the study of a given macromolecule's function in living muscle cells but also for therapeutic purposes such as muscle-specific drug delivery.     

Numerical investigation of the intravascular coronary stent flexibility

Nowadays stent therapy is widely adopted to treat atherosclerotic vessel diseases. The high commercial value of these devices and the high prototypation costs require the use of finite element analyses, instead of classical trial and error technique, to design and verify new models. In this paper, we explore the advantages of the finite element method (FEM) in order to investigate new generation stent performance in terms of flexibility. Indeed, the ability of the stent to bend in order to accommodate curvatures and angles of vessels during delivery is one of the most significant prerequisites for optimal stent performance. Two different FEM models, resembling two new generation intravascular stents, were developed. The main model dimensions were obtained by means of a stereo microscope, analyzing one Cordis BX-Velocity and one Carbostent Sirius coronary stent. Bending tests under displacement control in the unexpanded and expanded configuration were carried out. The curvature index, defined as the ratio between the sum of rotation angles at the extremes and the length of the stent, yielded comparative information about the capability of the device to be delivered into tortuous vessels and to conform to their contours. Results, expressed in terms of the bending moment-curvature index, demonstrated a different response for the two models. In particular the Cordis model showed a higher flexibility. Lower flexibility in the expanded configurations for both models was detected. However this flexibility depends on how the contact takes place between the different parts of the struts.     

Analysis of intracellular state based on controlled 3D nanostructures mediated surface enhanced Raman scattering

Near-infrared surface-enhanced Raman spectroscopy (SERS) is a powerful technique for analyzing the chemical composition within a single living cell at unprecedented resolution. However, current SERS methods employing uncontrollable colloidal metal particles or non-uniformly distributed metal particles on a substrate as SERS-active sites show relatively low reliability and reproducibility. Here, we report a highly-ordered SERS-active surface that is provided by a gold nano-dots array based on thermal evaporation of gold onto an ITO surface through a nanoporous alumina mask. This new combined technique showed a broader distribution of hot spots and a higher signal-to-noise ratio than current SERS techniques due to the highly reproducible and uniform geometrical structures over a large area. This SERS-active surface was applied as cell culture system to study living cells in situ within their culture environment without any external preparation processes. We applied this newly developed method to cell-based research to differentiate cell lines, cells at different cell cycle stages, and live/dead cells. The enhanced Raman signals achieved from each cell, which represent the changes in biochemical compositions, enabled differentiation of each state and the conditions of the cells. This SERS technique employing a tightly controlled nanostructure array can potentially be applied to single cell analysis, early cancer diagnosis and cell physiology research.     

Life, self-reproduction and information: beyond the machine metaphor

The problem of representing information in automation models of self-replication is considered. It is shown that, unlike in the natural reproduction process, in a computable model the reproduced entities do not contain all the information necessary for guiding the process. Current theoretical understanding of life and its replication, based on such models, is argued to be essentially inadequate. The solution to this problem is claimed to require recognition of the theoretical fact that information in living systems is different from that subsumed under the category of "knowledge", which is representable as computer programs or triggers of state transitions. A discussion of fundamentals of a new theory of information and its relationship to replication models is given and a new direction of further developments of biological theories is envisioned.     

Alignment and defect structures in oriented phosphatidylcholine multilayers.

The alignment of dilauryl-, dimyristoyl-, and dipalmitoylphosphatidylcholine at various water concentrations into large oriented monodomain multilayers by annealing at elevated temperatures (Powers and Clark, 1975, Proc. Natl. Acad. Sci. U.S.A. 72:840; Powers and Pershan. 1977. Biophys. J. 20:137) is accompanied by the formation and subsequent dissolution of various defect structures. Some of these defects appear similar to those observed in thermotropic and other lyotropic liquid crystals, reflecting the lamellar structure of these materials. The formation and evolution of defects during the alignment of the lipids into the defect-free, monodomain, multilamellar geometry is studied using polarized microscopy. A combination of polarized and dark-field microscopy facilitated characterization of the defects; specific structural models are proposed. A new alignment technique involving compression and dilation of the lipid, which effects sample alignment at temperatures that are lower than those required by the Powers technique, is described. Lower temperature alignment avoids thermal decomposition that will sometimes occur if the lipid is maintained at elevated temperatures for prolonged periods. With this technique, samples (80 micrometer thick) of dilaurylphosphatidylcholine with 20% water by weight were aligned at room temperature.     

Two-color STED microscopy of living synapses using a single laser-beam pair

The advent of superresolution microscopy has opened up new research opportunities into dynamic processes at the nanoscale inside living biological specimens. This is particularly true for synapses, which are very small, highly dynamic, and embedded in brain tissue. Stimulated emission depletion (STED) microscopy, a recently developed laser-scanning technique, has been shown to be well suited for imaging living synapses in brain slices using yellow fluorescent protein as a single label. However, it would be highly desirable to be able to image presynaptic boutons and postsynaptic spines, which together form synapses, using two different fluorophores. As STED microscopy uses separate laser beams for fluorescence excitation and quenching, incorporation of multicolor imaging for STED is more difficult than for conventional light microscopy. Although two-color schemes exist for STED microscopy, these approaches have several drawbacks due to their complexity, cost, and incompatibility with common labeling strategies and fluorophores. Therefore, we set out to develop a straightforward method for two-color STED microscopy that permits the use of popular green-yellow fluorescent labels such as green fluorescent protein, yellow fluorescent protein, Alexa Fluor 488, and calcein green. Our new (to our knowledge) method is based on a single-excitation/STED laser-beam pair to simultaneously excite and quench pairs of these fluorophores, whose signals can be separated by spectral detection and linear unmixing. We illustrate the potential of this approach by two-color superresolution time-lapse imaging of axonal boutons and dendritic spines in living organotypic brain slices.     

Infrared surface plasmon resonance: a novel tool for real time sensing of variations in living cells

We developed a novel surface plasmon resonance (SPR) method, based on Fourier transform infrared (FTIR) spectroscopy, as a label-free technique for studying dynamic processes occurring within living cells in real time. With this method, the long (micrometer) infrared wavelength produced by the FTIR generates an evanescent wave that penetrates deep into the sample. In this way, it enables increased depth of sensing changes, covering significant portions of the cell-height volumes. HeLa cells cultivated on a gold-coated prism were subjected to acute cholesterol enrichment or depletion using cyclodextrins. Cholesterol insertion into the cell plasma membrane resulted in an exponential shift of the SPR signal toward longer wavelengths over time, whereas cholesterol depletion caused a shift in the opposite direction. Upon application of the inactive analog alpha-cyclodextrin (alpha-CD), the effects were minimal. A similar trend in the SPR signal shifts was observed on a model membrane system. Our data suggest that FTIR-SPR can be implemented as a sensitive technique for monitoring in real time dynamic changes taking place in living cells.     

High-Q dynamic force microscopy in liquid and its application to living cells.

We present a new dynamic force microscopy technique for imaging in liquids in the piconewton regime. The low quality factor (Q) of the cantilever is increased up to three orders of magnitude by the implementation of a positive feedback control. The technique also includes a phase-locked loop unit to track the resonance of the cantilever. Experiments and computer simulations indicate that the tip-sample forces are below 100 pN, about two orders of magnitude lower than in conventional tapping mode atomic force microscopy. Furthermore, the spectroscopic ability is greatly enhanced. Either the phase shift or the resonant frequency shows a high sensitivity to variations in either the energy dissipation or conservative interactions between the tip and the sample, respectively. The potential of this technique is demonstrated by imaging living cells.