昆虫水平基因转移及其研究进展

水平基因转移(horizontal gene transfer, HGT)是生物体获得遗传信息的方式之一,对生物体进化起重要作用。近年来,越来越多昆虫中的水平基因转移现象被报道,如在鳞翅目(如家蚕、甜菜夜蛾、小菜蛾、斜纹夜蛾)、半翅目(如柑橘粉蚧、烟粉虱)、鞘翅目(如咖啡果小蠹、米象、光肩星天牛)、膜翅目(如金小蜂)、双翅目(如果蝇、白纹伊蚊)等昆虫中广泛存在水平转移基因,且不同的水平转移基因对昆虫的营养合成与共生、吸收与消化、毒素产生与解毒、生长和发育、体色改变等方面有着重要作用。本文结合国内外专家学者的相关报道,就HGT的研究步骤与技术方法、评判HGT发生的方法、昆虫HGT的供体与功能几个方面进行了总结和讨论,以期更加深入地了解水平基因转移现象,为探究水平基因转移的作用机制、理解昆虫的进化、遗传和行为、并将水平基因转移应用到农业生产中为农业害虫的绿色防治提供更多思路。     

Analysis of protein function and its prediction from amino acid sequence

Understanding protein function is one of the keys to understanding life at the molecular level. It is also important in the context of human disease because many conditions arise as a consequence of alterations of protein function. The recent availability of relatively inexpensive sequencing technology has resulted in thousands of complete or partially sequenced genomes with millions of functionally uncharacterized proteins. Such a large volume of data, combined with the lack of high-throughput experimental assays to functionally annotate proteins, attributes to the growing importance of automated function prediction. Here, we study proteins annotated by Gene Ontology (GO) terms and estimate the accuracy of functional transfer from protein sequence only. We find that the transfer of GO terms by pairwise sequence alignments is only moderately accurate, showing a surprisingly small influence of sequence identity (SID) in a broad range (30-100%). We developed and evaluated a new predictor of protein function, functional annotator (FANN), from amino acid sequence. The predictor exploits a multioutput neural network framework which is well suited to simultaneously modeling dependencies between functional terms. Experiments provide evidence that FANN-GO (predictor of GO terms; available from http://www.informatics.indiana.edu/predrag) outperforms standard methods such as transfer by global or local SID as well as GOtcha, a method that incorporates the structure of GO.     

Causal transfer function analysis to describe closed loop interactions between cardiovascular and cardiorespiratory variability signals

Although the concept of transfer function is intrinsically related to an input–output relationship, the traditional and widely used estimation method merges both feedback and feedforward interactions between the two analyzed signals. This limitation may endanger the reliability of transfer function analysis in biological systems characterized by closed loop interactions. In this study, a method for estimating the transfer function between closed loop interacting signals was proposed and validated in the field of cardiovascular and cardiorespiratory variability. The two analyzed signals x and y were described by a bivariate autoregressive model, and the causal transfer function from x to y was estimated after imposing causality by setting to zero the model coefficients representative of the reverse effects from y to x. The method was tested in simulations reproducing linear open and closed loop interactions, showing a better adherence of the causal transfer function to the theoretical curves with respect to the traditional approach in presence of non-negligible reverse effects. It was then applied in ten healthy young subjects to characterize the transfer functions from respiration to heart period (RR interval) and to systolic arterial pressure (SAP), and from SAP to RR interval. In the first two cases, the causal and non-causal transfer function estimates were comparable, indicating that respiration, acting as exogenous signal, sets an open loop relationship upon SAP and RR interval. On the contrary, causal and traditional transfer functions from SAP to RR were significantly different, suggesting the presence of a considerable influence on the opposite causal direction. Thus, the proposed causal approach seems to be appropriate for the estimation of parameters, like the gain and the phase lag from SAP to RR interval, which have a large clinical and physiological relevance.     

Tracing lake trophic history with a chironomid–total phosphorus inference model

1. In the absence of historical water chemistry data, predictive biological indicator groups preserved in lake sediments can be employed to reconstruct the history of lake eutrophication. Diatoms are well established in this role, but to augment diatom‐based inferences of nutrient status we investigate the potential use of chironomid midges (Insecta: Chironomidae). 2. Canonical correspondence analysis (CCA) of modern chironomid assemblages in surface sediments from 44 lakes in the English Midlands and Wales, U.K., shows that five environmental variables (total phosphorus (TP), bottom dissolved oxygen, maximum lake depth, Secchi depth and surface water temperature) make a statistically significant (P < 0.05) contribution to explaining the variance in the chironomid data, of which TP makes the largest contribution (29%). 3. The relationship is used to develop a series of weighted averaging (WA) and partial least squares (PLS), (WA‐PLS) models to infer log₁₀TP. The models are evaluated by leave‐one‐out (jack‐knifing) cross‐validation. The simplest minimal adequate model is provided by WA with unweighted inverse deshrinking of root mean square error of prediction (RMSEP_jack=0.34 and r²_jack=0.60). 4. Using this model, the trophic history of Betton Pool, Shropshire, U.K., is reconstructed from the mid‐19th century to the present day and the results from the chironomid‐TP model are compared with inferences from a diatom‐TP model ( 13 ). Both reconstructions suggest that there was a gradual rise in TP since 1850 AD until about 1974, followed by a more pronounced and rapid increase that has continued until the present. Inferred TP values from the WA chironomid inference model agree with diatom‐inferred values. 5. The study demonstrates that fossil chironomid assemblages can be used to investigate quantitatively the trophic history of lakes.     

细菌自然转化的分子机制及生物学功能研究进展

基因的水平转移在细菌的进化中起着非常重要的作用。自然界中的细菌之间主要通过3种机制进行基因水平转移:由噬菌体介导的转导、接合转移和自然转化。自然转化是指自然感受态的细菌能够自发地从外界环境中摄取DNA分子并整合到自身基因组上的过程。该现象首先发现于肺炎链球菌,目前至少有83种细菌被发现具有发生自然转化的能力,其中革兰氏阳性菌以肺炎链球菌(Streptococcus pneumoniae,S. pneumoniae)为代表,革兰氏阴性菌以奈瑟氏菌(Neisseria)为代表,对其自然转化机制的研究和认识较为清楚,但不同细菌之间自然转化的机制有所差异。自然转化的生物学功能一直以来有以下几种推测:获取营养、修复DNA损伤、生物进化,而近年来对此认识争论不休。本文将详细描述细菌自然转化的分子机制,并对其主要的生物学功能争论焦点进行评述,以期对细菌自然转化有更深入的理解和认识。     

南黄海近岸底栖有孔虫分布与环境因子转换函数的建立

本文对南黄海西北陆架边缘的300个表层沉积物样品中的底栖有孔虫数据,与相应站位的水深、底层水温、盐度、沉积物粒度、有机碳含量等环境参数作了分析研究。除趋势对应分析(DCA)、典型对应分析(CCA)表明有孔虫种群分布与水深、夏季底层水温(Ts)和冬季底层水盐度(Sw)之间存在着显著的数值对应关系。利用加权平均偏最小二乘回归方法(WA-PLS)建立了底栖有孔虫数据与上述环境因子之间的数值转换函数。水深、Ts与Sw转换函数的预测均方根误差(RMSEP)分别是10.8%、11.5%和12.5%,与利用其他指标建立的此类转换函数水平(8%—20%)相当。利用此类统计建模方法建立近岸底栖有孔虫分布与浅海环境因子之间的数值关系是一项新的尝试,结果表明在我国近海底层水体古环境研究中底栖有孔虫转换函数是一种具有一定潜力的研究方法。     

On the Evaluation of Information Flow in Multivariate Systems by the Directed Transfer Function

The directed transfer function (DTF) has been proposed as a measure of information flow between the components of multivariate time series. In this paper, we discuss the interpretation of the DTF and compare it with other measures for directed relationships. In particular, we show that the DTF does not indicate multivariate or bivariate Granger causality, but that it is closely related to the concept of impulse response function and can be viewed as a spectral measure for the total causal influence from one component to another. Furthermore, we investigate the statistical properties of the DTF and establish a simple significance level for testing for the null hypothesis of no information flow.     

Accurate determination of local defocus and specimen tilt in electron microscopy

Accurate knowledge of defocus and tilt parameters is essential for the determination of three-dimensional protein structures at high resolution using electron microscopy. We present two computer programs, CTFFIND3 and CTFTILT, which determine defocus parameters from images of untilted specimens, as well as defocus and tilt parameters from images of tilted specimens, respectively. Both programs use a simple algorithm that fits the amplitude modulations visible in a power spectrum with a calculated contrast transfer function (CTF). The background present in the power spectrum is calculated using a low-pass filter. The background is then subtracted from the original power spectrum, allowing the fitting of only the oscillatory component of the CTF. CTFTILT determines specimen tilt parameters by measuring the defocus at a series of locations on the image while constraining them to a single plane. We tested the algorithm on images of two-dimensional crystals by comparing the results with those obtained using crystallographic methods. The images also contained contrast from carbon support film that added to the visibility of the CTF oscillations. The tests suggest that the fitting procedure is able to determine the image defocus with an error of about 10nm, whereas tilt axis and tilt angle are determined with an error of about 2 degrees and 1 degrees, respectively. Further tests were performed on images of single protein particles embedded in ice that were recorded from untilted or slightly tilted specimens. The visibility of the CTF oscillations from these images was reduced due to the lack of a carbon support film. Nevertheless, the test results suggest that the fitting procedure is able to determine image defocus and tilt angle with errors of about 100 nm and 6 degrees, respectively.     

Identification and categorization of horizontally transferred genes in prokaryotic genomes

Horizontal gene transfer （HGT）, a process through which genomes acquire genetic materials from distantly related organisms, is believed to be one of the major forces in prokaryotic genome evolution.However, systematic investigation is still scarce to clarify two basic issues about HGT： （1） what types of genes are transferred; and （2） what influence HGT events over the organization and evolution of biological pathways. Genome-scale investigations of these two issues will advance the systematical understanding of HGT in the context of prokaryotic genome evolution. Having investigated 82 genomes, we constructed an HGT database across broad evolutionary timescales. We identified four function categories containing a high proportion of horizontally transferred genes： cell envelope, energy metabolism, regulatory functions, and transport/binding proteins. Such biased function distribution indicates that HGT is not completely random;instead, it is under high selective pressure, required by function restraints in organisms. Furthermore, we mapped the transferred genes onto the connectivity structure map of organism-specific pathways listed in Kyoto Encyclopedia of Genes and Genomes （KEGG）. Our results suggest that recruitment of transferred genes into pathways is also selectively constrained because of the tuned interaction between original pathway members. Pathway organization structures still conserve well through evolution even with the recruitment of horizontally transferred genes. Interestingly, in pathways whose organization were significantly affected by HGT events, the operon-like arrangement of transferred genes was found to be prevalent. Such results suggest that operon plays an essential and directional role in the integration of alien genes into pathways.     

Automatic CTF correction for single particles based upon multivariate statistical analysis of individual power spectra

Three-dimensional electron cryomicroscopy of randomly oriented single particles is a method that is suitable for the determination of three-dimensional structures of macromolecular complexes at molecular resolution. However, the electron-microscopical projection images are modulated by a contrast transfer function (CTF) that prevents the calculation of three-dimensional reconstructions of biological complexes at high resolution from uncorrected images. We describe here an automated method for the accurate determination and correction of the CTF parameters defocus, twofold astigmatism and amplitude-contrast proportion from single-particle images. At the same time, the method allows the frequency-dependent signal decrease (B factor) and the non-convoluted background signal to be estimated. The method involves the classification of the power spectra of single-particle images into groups with similar CTF parameters; this is done by multivariate statistical analysis (MSA) and hierarchically ascending classification (HAC). Averaging over several power spectra generates class averages with enhanced signal-to-noise ratios. The correct CTF parameters can be deduced from these class averages by applying an iterative correlation procedure with theoretical CTF functions; they are then used to correct the raw images. Furthermore, the method enables the tilt axis of the sample holder to be determined and allows the elimination of individual poor-quality images that show high drift or charging effects.     

MITOCHONDRIA: Investigation of in vivo muscle mitochondrial function by 31P magnetic resonance spectroscopy

The most important function of mitochondria is the production of energy in the form of ATP. The socio-economic impact of human diseases that affect skeletal muscle mitochondrial function is growing, and improving their clinical management critically depends on the development of non-invasive assays to assess mitochondrial function and monitor the effects of interventions. ³¹P magnetic resonance spectroscopy provides two approaches that have been used to assess in vivo ATP synthesis in skeletal muscle: measuring P_i ⟶ ATP exchange flux using saturation transfer in resting muscle, and measuring phosphocreatine recovery kinetics after exercise. However, P_i ⟶ ATP exchange does not represent net mitochondrial ATP synthesis flux and has no simple relationship with mitochondrial function. Post-exercise phosphocreatine recovery kinetics, on the other hand, yield reliable measures of muscle mitochondrial capacity in vivo, whose ability to define the site of functional defects is enhanced by combination with other non-invasive techniques.     

Developing diatom-based transfer functions for Central Mexican lakes

This paper is the first attempt to produce diatom-based transfer functions for the northern tropical Americas. A dataset of 53 modern diatom samples and associated hydrochemical variables from 31 sites in the volcanic highlands of central Mexico is presented. The relationship between diatom species distribution and water chemistry is explored using canonical correspondence analysis (CCA) and partial CCA. Variance partitioning indicates that ionic strength and ion type both account for significant and independent portions of this variation. Transfer functions are developed for electrical conductivity (r ² = 0.91) and alkalinity (as a percentage of total anions) (r ² = 0.90), reflecting ionic strength and ionic composition respectively. Prediction errors, estimated using jack-knifing, are low for the conductivity model, but the carbonate transfer function performs less well. This study highlights the potential for diatom-based quantitative palaeoenvironmental reconstructions in central Mexico. However, a number of key diatom species found in fossil material are not represented in the modern flora. Sampling of additional sites may resolve this, but it is thought that the lack of modern analogues may reflect the high degree of anthropogenic disturbance in many of the catchments. This highlights the problem of trying to reconstruct pre-disturbance environmental changes in highly modified ecosystems. One possible solution is to merge the central Mexican data with the African dataset, which includes sites of similar chemical composition, but which have not suffered the same degree of disturbance.     

CTF determination and correction for low dose tomographic tilt series

The resolution of cryo-electron tomography can be limited by the first zero of the microscope’s contrast transfer function (CTF). To achieve higher resolution, it is critical to determine the CTF and correct its phase inversions. However, the extremely low signal-to-noise ratio (SNR) and the defocus gradient in the projections of tilted specimens make this process challenging. Two programs, CTFPLOTTER and CTFPHASEFLIP, have been developed to address these issues. CTFPLOTTER obtains a 1D power spectrum by periodogram averaging and rotational averaging and it estimates the noise background with a novel approach, which uses images taken with no specimen. The background-subtracted 1D power spectra from image regions at different defocus values are then shifted to align their first zeros and averaged together. This averaging improves the SNR sufficiently that it becomes possible to determine the defocus for subsets of the tilt series rather than just the entire series. CTFPHASEFLIP corrects images line-by-line by inverting phases appropriately in thin strips of the image at nearly constant defocus. CTF correction by these methods is shown to improve the resolution of aligned, averaged particles extracted from tomograms. However, some restoration of Fourier amplitudes at high frequencies is important for seeing the benefits from CTF correction.     

Object shape dependency of in-plane resolution for iterative reconstruction of computed tomography

The present study aimed to investigate whether the in-plane resolution property of iterative reconstruction (IR) of computed tomography (CT) data is object shape-dependent by testing columnar shapes with diameters of 3, 7, and 10 cm (circular edge method) and a cubic shape with 5-cm side lengths (linear edge method). For each shape, objects were constructed of acrylic (contrast in Hounsfield units [ΔHU] = 120) as well as a soft tissue equivalent material (ΔHU = 50). For each shape, we measured the modulation transfer functions (MTFs) of IR and filtered back projection (FBP) using two multi-slice CT scanners at scan doses of 5 and 10 mGy. In addition, we evaluated a thin metal wire using the conventional method at 10 mGy. For FBP images, the MTF results of the tested objects and the wire method showed substantial agreement, thus demonstrating the validity of our analysis technique. For IR images, the MTF results of different shapes were nearly identical for each object contrast and dose combination, and we did not observe shape-dependent effects of the resolution properties of either tested IR. We conclude that both the circular edge method and linear edge method are equally useful for evaluating the resolution properties of IRs.     

Effects of pulse ultrasonic irradiation on the lag phase of Saccharomyces cerevisiae growth

Aims: This paper presents an analysis of lag phase phenomena in Saccharomyces cerevisiae growth as a function of ultrasonic irradiation. Methods and Results: Pulse irradiation treatments were performed by a 20 kHz ultrasonic transducer with different durations and energies. Data obtained from experiments were then employed to estimate growth parameters by specific transfer function. The significance of the different lag times in response to ultrasonic irradiation was analysed. The results showed that the yeast growth in lag phase responded to the irradiated ultrasonic of 20 min more than the 10 min. The ultrasonic energies between 330 and 360 W s m^?3 could decrease lag time up to 1 h compared to the sample without ultrasonic irradiation. Conversely, the treatments with energies higher than 850 W s m^?3 were able to extend the lag time and decrease the yeast growth. Conclusions: The lag durations of S. cerevisiae were changed significantly by different ultrasonic irradiations, energies and durations. In particular, sufficient irradiation energies reduced the lag time, resulting in accelerated yeast growth. In contrast, high energy could inactivate growth by increasing the lag time. Significance and Impact of the Study: This work provides an alternative technique to either accelerate or inactivate the S. cerevisiae lag phase. The approach can be developed in experiment designed to control the yeast growth by ultrasonic irradiation as assistance in the environments.     

Comparison of transient and asymptotic perturbation analyses of three epiphytic orchid species growing in coffee plantations in Mexico: effect on conservation decisions

Background: Epiphyte removal forms part of routine management in shade coffee plantations.

Aims: Assess the current status of three population orchids growing in Mexican shaded coffee plantations and evaluate the effect of perturbing the transient behaviour of different life stages.

Methods: We modelled the short-term response of eliminating I) non-reproductive juveniles, or II) reproductive adult plants from coffee bushes, on populations of Oncidium poikilostalix, Lepanthes acuminata and Telipogon helleri (Orchidaceae). First, we calculated the transient dynamics per se and second, we made a perturbation analysis on population inertia. Finally, we made a comparison with a traditional sensitivity analysis.

Results: All three species showed different positive asymptotic growth rate: O. poikilostalix (λmax = 1.106), L. acuminata (λmax = 1.209), and T. helleri (λmax = 1.012). The effect of eliminating the major part of the juvenile or adult orchids gave population inertia in relation to steady state, respectively, (+19%, -24%) for O. poikilostalix, (+17%, -28%) for T. helleri and (+57%, -35%) for L. acuminata.

Conclusions: Eliminating juveniles or adults affects in different ways the short-term dynamics due to differential impact on size stages that have the non-linear effects associated with important disturbances that currently affect orchids growing in coffee plantations.     

Molecular determination by electron microscopy of the actin filament end structure

In eukaryotic cells, actin filaments play various crucial roles by altering their spatial and temporal distributions in the cell. The distribution of actin filaments is regulated by the binding of end-binding proteins, including capping protein (CapZ in muscle), the Arp2/3 complex, gelsolin, formin and tropomodulin, to the end of the actin filament. In order to determine the nature of these regulations, structural elucidations of actin filament-end-binding protein complexes are crucially important. Here, we have developed new procedures on the basis of single-particle analysis to determine the structure of the end of actin filaments from electron micrographs. In these procedures, the polarity of the actin filament image, as well as the azimuth orientation and the axial position of each actin protomer within a short stretch near the filament end, were determined accurately. This improved both the stability and accuracy of the structural determination dramatically. We tested our procedures by reconstructing structures from simulated filament images, which were obtained from 24 model structures for the actin-CapZ complex. These model structures were generated by random docking of the atomic structure of CapZ to the barbed end of an atomic model of the actin filament. Of the 24 model structures, 23 were recovered correctly by the present procedures. We found that our analysis was robust against local aberrations of the helical twist near the end of the actin filament. Finally, the procedures were applied successfully to determine the structure of the actin-CapZ complex from real cryo-electron micrographs of the complex. This is the first method for elucidating the detailed 3D structures at the end of the actin filament.     

Epilithic algal communities and their relationship to environmental variables in lakes of the English Lake District

1. The relationship between epilithic algal communities and 17 environmental variables from 17 oligo- to eutrophic lakes in the English Lake District was explored using canonical correspondence analysis (CCA). Total phosphorus (TP) and calcium (Ca) concentration were the most important variables accounting for species distribution.
2. Weighted-averaging regression and calibration models with tolerance downweighting and classical deshrinking were developed to infer TP, Ca, dissolved inorganic carbon (DIC) and conductivity from the relative abundance of 138 epilithic algal taxa.
3. The ranges of the environmental variables covered by the models are 0.8-49.2 μg L−1 for TP, 2.2–13.0 mg L−1 for Ca, 0.5–8.6 mg L−1 for DIC and 38–124 μS cm−1 for conductivity. Within these limits the models can be used to infer chemical properties of lakes from epilithic communities in the English Lake District.
4. The major advantages of using transfer functions based on epilithic communities are the low logistic requirements and the integrative character of algal samples compared to direct point measurements of chemical parameters of the lakes.     

Surface sediment diatom assemblages and epilimnetic total phosphorus in large, shallow lakes of the Yangtze floodplain: their relationships and implications for assessing long-term eutrophication

1. The Yangtze floodplain (SE China) is characterized by a number of large shallow lakes, many of which have undergone eutrophication due to the intensification of agriculture and urban growth over recent decades. As monitoring data are limited and in order to determine lake baseline nutrient concentrations, 49 lakes were sampled, covering a total phosphorus (TP) gradient (c. 30–550 μg L⁻¹) to develop a diatom-based inference model. 2. There are three dominant diatom assemblages in these shallow lakes with a marked change in assemblage structure near the boundary between eutrophic and hypereutrophic nutrient levels (as indicated by their TP value). Canonical correspondence analysis indicated that TP was the most important and significant variable in explaining the diatom distributions, independently accounting for 9.5% variance of diatoms. 3. Forty-three lakes were used to generate a transfer function using weighted averaging (WA) with inverse deshrinking. This model had low predictive error (root mean squared error of prediction; RMSEP_jack = 0.12) and a high coefficient of prediction (R²_jack = 0.82), comparable with regional TP models elsewhere. The good performance of this TP model may reflect the low abundance of benthic diatom species which are commonly regarded as the main error source in European shallow lake WA models. 4. The WA model was used to reconstruct the past-TP concentrations for Taibai Lake, a shallow hypereutrophic lake in Hubei province. The results showed that TP concentration varied slightly (43–62 μg L⁻¹) prior to the 1920s, indicating an eutrophic state since the 1800s. A period of sustained eutrophication occurred after 1950, because of the development of agriculture, reflecting by maximum values of Aulacoseira alpigena and increased abundance of Cyclotella meneghiniana, C. atomus and Cyclostephanos dubius. The steep increase in nutrient concentration after 1970 was related to the overuse of chemical fertilizer and fish farming in the catchment. 5. The shift in fossil diatoms from epiphytic to planktonic forms in the lake sediment core during 1950–70 provides useful information on the transformation from macrophyte-dominated to alga-dominated states. It is plausible that the TP concentration of 80–110 μg L⁻¹ observed in this study is the critical range for switching between the two stable states in the lake. 6. The regional diatom-TP model developed in this study allows, therefore, the possibility of reconstructing historical background nutrient concentrations in lakes. It will provide an indication of the onset and development of eutrophication at any site. This is particularly important for the many lakes in the Yangtze floodplain where information about historical changes in water quality is lacking.