Minimum data requirements for designing a set of marine protected areas, using commonly available abiotic and biotic datasets

Marine protected areas (MPAs) can be an effective tool for marine biodiversity conservation, yet decision-makers usually have limited and biased datasets with which to make decisions about where to locate MPAs. Using commonly available abiotic and biotic datasets, I asked how many datasets are necessary to achieve robust patterns of conservation importance. I applied a decision support tool for marine protected area design in two regions of British Columbia, Canada, and sequentially excluded the datasets with the most limited geographic distribution. I found that the reserve selection method was robust to some missing datasets. The removal of up to 15 of the most geographically limited datasets did not significantly change the geographic patterns of the importance of areas for conservation. Indeed, including abiotic datasets plus at least 12 biotic datasets resulted in a spatial pattern similar to including all available biotic datasets. It was best to combine abiotic and biotic datasets in order to ensure habitats and species were represented. Patterns of clustering differed according to whether I used one set alone or both combined. Biotic datasets served as better surrogates for abiotic datasets than vice versa, and both represented more biodiversity features than randomly selected reserves. These results should provide encouragement to decision-makers engaged in MPA planning with limited spatial data.     

基于VTK和MFC的医学图像三维重建研究与实现

VTK是医学可视化领域的主流工具,MFC是Windows平台下的应用程序框架。尝试将两者进行结合编程,以实现二维医学图像的三维重建。实现医学图像三维重建的主要方法是面绘制和体绘制。将利用多组医学图像数据进行三维重建研究,其中面绘制用移动立方体法,体绘制用光线投射法、最大密度投影法和合成体绘制法实现。最后比较两种绘制技术的结果并讨论了它们的特点。结果表明,VTK作为一种图像处理和三维可视化工具其功能是十分强大的。     

In silico comparison of marine, terrestrial and synthetic compounds using ChemGPS-NP for navigating chemical space

Nature represents a vast source of chemical diversity, which is supposed to cover broader areas of chemical space than synthetically obtained substances typical of medicinal chemistry. With regard to drug discovery from nature, the terrestrial environment has been the most and longest studied source, while the investigation of compounds produced by marine organisms is still in its infancy. With the objective of demonstrating the enormous chemical diversity of nature, in particular that of the marine environment, we used the chemical space navigation tool ChemGPS-NP to compare sets of marine, terrestrial and synthetic compounds with respect to physico-chemical properties and their occupation of the biologically relevant chemical space. Despite considerable overlap, the three datasets clearly differ from each other by occupying and extending into different, specific, regions in chemical space. Synthetic compounds are e.g. comparably small, with some of them being highly flexible, while marine and terrestrial products are larger and characterised by higher and lower molecular flexibility, respectively, with increasing size. Moreover, the three datasets differ to some degree in polarity, aromaticity and heteroatom content. Taken together, ChemGPS-NP has been proven to be a useful tool for navigating large volumes of biologically relevant chemical space. In this study we demonstrated the chemical uniqueness and differences of large sets of natural products, with particular emphasis on marine substances. The hence de-veiled differences further underline the relevance of natural products, of both marine and terrester origin, for future drug discovery.     

Registration of 2D histological sections with 3D micro-CT datasets from small animal vertebrae and tibiae

The aim of this study was the registration of digitized thin 2D sections of mouse vertebrae and tibiae used for histomorphometry of trabecular bone structure into 3D micro computed tomography (μCT) datasets of the samples from which the sections were prepared. Intensity-based and segmentation-based registrations (SegRegs) of 2D sections and 3D μCT datasets were applied. As the 2D sections were deformed during their preparation, affine registration for the vertebrae was used instead of rigid registration. Tibiae sections were additionally cut on the distal end, which subsequently undergone more deformation so that elastic registration was necessary. The Jaccard distance was used as registration quality measure. The quality of intensity-based registrations and SegRegs was practically equal, although precision errors of the elastic registration of segmentation masks in tibiae were lower, while those in vertebrae were lower for the intensity-based registration. Results of SegReg significantly depended on the segmentation of the μCT datasets. Accuracy errors were reduced from approximately 64% to 42% when applying affine instead of rigid transformations for the vertebrae and from about 43% to 24% when using B-spline instead of rigid transformations for the tibiae. Accuracy errors can also be caused by the difference in spatial resolution between the thin sections (pixel size: 7.25 μm) and the μCT data (voxel size: 15 μm). In the vertebrae, average deformations amounted to a 6.7% shortening along the direction of sectioning and a 4% extension along the perpendicular direction corresponding to 0.13–0.17 mm. Maximum offsets in the mouse tibiae were 0.16 mm on average.     

Seascape genetics: a coupled oceanographic-genetic model predicts population structure of Caribbean corals

Population genetics is a powerful tool for measuring important larval connections between marine populations [1-4]. Similarly, oceanographic models based on environmental data can simulate particle movements in ocean currents and make quantitative estimates of larval connections between populations possible [5-9]. However, these two powerful approaches have remained disconnected because no general models currently provide a means of directly comparing dispersal predictions with empirical genetic data (except, see [10]). In addition, previous genetic models have considered relatively simple dispersal scenarios that are often unrealistic for marine larvae [11-15], and recent landscape genetic models have yet to be applied in a marine context [16-20]. We have developed a genetic model that uses connectivity estimates from oceanographic models to predict genetic patterns resulting from larval dispersal in a Caribbean coral. We then compare the predictions to empirical data for threatened staghorn corals. Our coupled oceanographic-genetic model predicts many of the patterns observed in this and other empirical datasets; such patterns include the isolation of the Bahamas and an east-west divergence near Puerto Rico [3, 21-23]. This new approach provides both a valuable tool for predicting genetic structure in marine populations and a means of explicitly testing these predictions with empirical data.     

4D confocal microscopy of Dictyostelium discoideum morphogenesis and its presentation on the Internet

 Methods to present three-dimensional (3D) and time series of 3D datasets (4D) are demonstrated using the recent advances in confocal microscopy and computer visualization. The process of cell sorting during tip formation in the slime mould Dictyostelium discoideum is examined as an example by in vivo confocal microscopy of spectrally different green fluorescent protein (GFP) variants as reporters of cell-type specific gene expression. Also, cell sorting of the co-aggregating slime mould species D. discoideum and D. mucoroides is observed using a GFP variant and a spectrally distinguishable fluorescent vital stain. The confocal data are handled as 3D and 4D datasets, their processing and the advantages of different methods of visualization are discussed step by step. Selected sequences of the experiments can be viewed on the Internet, giving a much better impression of the complex cellular movements during Dictyostelium morphogenesis than printed photographs. Received: 17 February 1998 / Accepted: 14 June 1998     

Estimating herbaceous aboveground biomass in Sahelian rangelands using Structure from Motion data collected on the ground and by UAV

Herbaceous aboveground biomass (HAB) is a key indicator of grassland vegetation and indirect estimation tools, such as remote sensing imagery, increase the potential for covering larger areas in a timely and cost‐efficient way. Structure from Motion (SfM) is an image analysis process that can create a variety of 3D spatial models as well as 2D orthomosaics from a set of images. Computed from Unmanned Aerial Vehicle (UAV) and ground camera measurements, the SfM potential to estimate the herbaceous aboveground biomass in Sahelian rangelands was tested in this study. Both UAV and ground camera recordings were used at three different scales: temporal, landscape, and national (across Senegal). All images were processed using PIX4D software (photogrammetry software) and were used to extract vegetation indices and heights. A random forest algorithm was used to estimate the HAB and the average estimation errors were around 150 g m⁻² for fresh mass (20% relative error) and 60 g m⁻² for dry mass (around 25% error). A comparison between different datasets revealed that the estimates based on camera data were slightly more accurate than those from UAV data. It was also found that combining datasets across scales for the same type of tool (UAV or camera) could be a useful option for monitoring HAB in Sahelian rangelands or in other grassy ecosystems.     

Digit ratio (2D:4D) and handgrip strength in subjects of Han ethnicity: Impact of sex and age

The ratio of the length of the second finger to the fourth finger (2D:4D) is considered to be a putative proxy of prenatal exposure to testosterone, and has been increasingly used as a promising tool to evaluate the impact of prenatal androgenization in humans in such traits as physical performance. In this study, for the first time, we present 2D:4D data on adult participants of Han ethnicity. We consider the sexual dimorphism of 2D:4D and handgrip strength, and also report the relationship between 2D:4D and handgrip strength of males and females. The sample consisted of 54 males and 55 females recruited from a remote village in the Qinling Mountains, China. We found sexual dimorphism of both 2D:4D and handgrip strength, i.e., males had lower 2D:4D and right‐left 2D:4D than females and greater handgrip strength than females. There was a sex‐specific correlation between 2D:4D and handgrip strength, i.e., 2D:4D in the right hand was negatively correlated with handgrip strength in males but not in females. This relationship may be driven by sexual selection operating on fetal programming. Am J Phys Anthropol 149:266–271, 2012. © 2012 Wiley Periodicals, Inc.     

Illuminating the dark depths inside coral

The ability to observe in situ 3D distribution and dynamics of endosymbionts in corals is crucial for gaining a mechanistic understanding of coral bleaching and reef degradation. Here, we report the development of a tissue clearing (TC) coupled with light sheet fluorescence microscopy (LSFM) method for 3D imaging of the coral holobiont at single‐cell resolution. The initial applications have demonstrated the ability of this technique to provide high spatial resolution quantitative information of endosymbiont abundance and distribution within corals. With specific fluorescent probes or assays, TC‐LSFM also revealed spatial distribution and dynamics of physiological conditions (such as cell proliferation, apoptosis, and hypoxia response) in both corals and their endosymbionts. This tool is highly promising for in situ and in‐depth data acquisition to illuminate coral symbiosis and health conditions in the changing marine environment, providing fundamental information for coral reef conservation and restoration.     

Organization of marine phenology data in support of planning and conservation in ocean and coastal ecosystems

Among the many effects of climate change is its influence on the phenology of biota. In marine and coastal ecosystems, phenological shifts have been documented for multiple life forms; however, biological data related to marine species' phenology remain difficult to access and is under-used. We conducted an assessment of potential sources of biological data for marine species and their availability for use in phenological analyses and assessments. Our evaluations showed that data potentially related to understanding marine species' phenology are available through online resources of governmental, academic, and non-governmental organizations, but appropriate datasets are often difficult to discover and access, presenting opportunities for scientific infrastructure improvement. The developing Federal Marine Data Architecture when fully implemented will improve data flow and standardization for marine data within major federal repositories and provide an archival repository for collaborating academic and public data contributors. Another opportunity, largely untapped, is the engagement of citizen scientists in standardized collection of marine phenology data and contribution of these data to established data flows. Use of metadata with marine phenology related keywords could improve discovery and access to appropriate datasets. When data originators choose to self-publish, publication of research datasets with a digital object identifier, linked to metadata, will also improve subsequent discovery and access. Phenological changes in the marine environment will affect human economics, food systems, and recreation. No one source of data will be sufficient to understand these changes. The collective attention of marine data collectors is needed—whether with an agency, an educational institution, or a citizen scientist group—toward adopting the data management processes and standards needed to ensure availability of sufficient and useable marine data to understand marine phenology.     

Z曲线的理论研究

DNA序列与正四面体(RT)中的映象点(D格点)具有对应关系．一系列D格点形成晶格(D晶格)．D晶格证明是面心立方晶格,并揭示了D格点的空间分布规律．在此基础上得到Z曲线的一些特性,如Z曲线束具有S4群的对称性。Z曲线均在最大正四面体的内切球内等等．     

Imaging mass spectrometry to visualize biomolecule distributions in mouse brain tissue following hemispheric cortical spreading depression

MALDI mass spectrometry can simultaneously measure hundreds of biomolecules directly from tissue. Using essentially the same technique but different sample preparation strategies, metabolites, lipids, peptides and proteins can be analyzed. Spatially correlated analysis, imaging MS, enables the distributions of these biomolecular ions to be simultaneously measured in tissues. A key advantage of imaging MS is that it can annotate tissues based on their MS profiles and thereby distinguish biomolecularly distinct regions even if they were unexpected or are not distinct using established histological and histochemical methods e.g. neuropeptide and metabolite changes following transient electrophysiological events such as cortical spreading depression (CSD), which are spreading events of massive neuronal and glial depolarisations that occur in one hemisphere of the brain and do not pass to the other hemisphere , enabling the contralateral hemisphere to act as an internal control. A proof-of-principle imaging MS study, including 2D and 3D datasets, revealed substantial metabolite and neuropeptide changes immediately following CSD events which were absent in the protein imaging datasets. The large high dimensionality 3D datasets make even rudimentary contralateral comparisons difficult to visualize. Instead non-negative matrix factorization (NNMF), a multivariate factorization tool that is adept at highlighting latent features, such as MS signatures associated with CSD events, was applied to the 3D datasets. NNMF confirmed that the protein dataset did not contain substantial contralateral differences, while these were present in the neuropeptide dataset.     

The second to fourth digit ratio and variation in the androgen receptor gene

The second to fourth digit ratio (2D:4D) is sexually dimorphic, with lower mean values in males compared to females. It has been suggested that the sex difference in 2D:4D is determined prenatally, 2D:4D is negatively related to prenatal testosterone and positively to prenatal oestrogen, and that 2D:4D is a marker for levels of sex steroids during brain organisation. There is growing evidence that many sex-dependent behaviours are correlated with 2D:4D. However, there is no direct evidence for an effect of prenatal sex steroids on the digit ratio. The response to prenatal testosterone is dependent on the amount produced and the foetal sensitivity to the hormone. Variation in the X-linked androgen receptor gene (AR) determines sensitivity to testosterone. Alleles of AR with low numbers of CAG triplets respond to testosterone with high transactivational activity, while high numbers of CAG's are associated with increased insensitivity to testosterone. We show in a sample of 50 men (49 Caucasian subjects, 1 Caucasian/Chinese subject) that 2D:4D is a phenotypic correlate of AR structure. Right-hand 2D:4D was positively correlated with CAG number and individuals with low 2D:4D in their right hand compared to left hand had AR alleles with low CAG numbers. We discuss the implications of our findings for our understanding of the aetiology of 2D:4D, its relationships with sex-dependent behaviours, and the evolutionary implications of variation in 2D:4D and AR.     

FOCAL3D: A 3-dimensional clustering package for single-molecule localization microscopy

Single-molecule localization microscopy (SMLM) is a powerful tool for studying intracellular structure and macromolecular organization at the nanoscale. The increasingly massive pointillistic data sets generated by SMLM require the development of new and highly efficient quantification tools. Here we present FOCAL3D, an accurate, flexible and exceedingly fast (scaling linearly with the number of localizations) density-based algorithm for quantifying spatial clustering in large 3D SMLM data sets. Unlike DBSCAN, which is perhaps the most commonly employed density-based clustering algorithm, an optimum set of parameters for FOCAL3D may be objectively determined. We initially validate the performance of FOCAL3D on simulated datasets at varying noise levels and for a range of cluster sizes. These simulated datasets are used to illustrate the parametric insensitivity of the algorithm, in contrast to DBSCAN, and clustering metrics such as the F1 and Silhouette score indicate that FOCAL3D is highly accurate, even in the presence of significant background noise and mixed populations of variable sized clusters, once optimized. We then apply FOCAL3D to 3D astigmatic dSTORM images of the nuclear pore complex (NPC) in human osteosaracoma cells, illustrating both the validity of the parameter optimization and the ability of the algorithm to accurately cluster complex, heterogeneous 3D clusters in a biological dataset. FOCAL3D is provided as an open source software package written in Python.     

Carbon source utilization by the marine Dendryphiella species D. arenaria and D. salina

Carbon utilization by the marine Dendryphiella species, D. arenaria and D. salina, was investigated to detect differences in utilization and traits associated with their adaptation to the marine habitat. Fifty-four strains were isolated world-wide and tested for the utilization of various carbon sources using BIOLOG phenotype MicroArray (PM) and for the production of extracellular enzymes on solid culture media and on API ZYM assay strips. PM analysis showed that the fastest growth occurred on several monosaccharides and amino acids, 2-keto-d-gluconic acid, succinamide and turanose. Some polyols were poor carbon sources. However, the two species differed in their utilization rates of carbon sources, forming three major clusters: two separate clusters for D. arenaria and D. salina and a third cluster in which strains of the two species formed separate subclades that correlated with geographic origin. Several carbon sources were also found useful in differentiating the two speices. Dendryphiella salina did not utilize xylitol and quinic acid, whereas D. arenaria grew well on these substrates. The latter failed to grow on sorbitol and grew slowly on mannitol, both were good substrates for the former. There were also no qualitative differences between the extracellular enzymes produced, although laccase and peroxidase activities were confined only to some strains. The physiological similarities exhibited by the two species support the close relationship between D. arenaria and D. salina.     

ProSAT: functional annotation of protein 3D structures

ProSAT (for Protein Structure Annotation Tool) is a tool to facilitate interactive visualization of non-structure-based functional annotations in protein 3D structures. It performs automated mapping of the functional annotations onto the protein structure and allows functional sites to be readily identified upon visualization. The current version of ProSAT can be applied to large datasets of protein structures for fast visual identification of active and other functional sites derived from the SwissProt and Prosite databases.     

Covariance NMR in higher dimensions: application to 4D NOESY spectroscopy of proteins

Elucidation of high-resolution protein structures by NMR spectroscopy requires a large number of distance constraints that are derived from nuclear Overhauser effects between protons (NOEs). Due to the high level of spectral overlap encountered in 2D NMR spectra of proteins, the measurement of high quality distance constraints requires higher dimensional NMR experiments. Although four-dimensional Fourier transform (FT) NMR experiments can provide the necessary kind of spectral information, the associated measurement times are often prohibitively long. Covariance NMR spectroscopy yields 2D spectra that exhibit along the indirect frequency dimension the same high resolution as along the direct dimension using minimal measurement time. The generalization of covariance NMR to 4D NMR spectroscopy presented here exploits the inherent symmetry of certain 4D NMR experiments and utilizes the trace metric between donor planes for the construction of a high-resolution spectral covariance matrix. The approach is demonstrated for a 4D (13)C-edited NOESY experiment of ubiquitin. The 4D covariance spectrum narrows the line-widths of peaks strongly broadened in the FT spectrum due to the necessarily short number of increments collected, and it resolves otherwise overlapped cross peaks allowing for an increase in the number of NOE assignments to be made from a given dataset. At the same time there is no significant decrease in the positive predictive value of observing a peak as compared to the corresponding 4D Fourier transform spectrum. These properties make the 4D covariance method a potentially valuable tool for the structure determination of larger proteins and for high-throughput applications in structural biology.     

Finding distinct biclusters from background in gene expression matrices

Biclustering, or the discovery of subsets of samples and genes that are homogeneous and distinct from the background, has become an important technique in analyzing current microarray datasets. Most existing biclustering methods define a bicluster type as a fixed (predefined) pattern and then trying to get results in some searching process. In this work, we propose a novel method for finding biclusters or 2-dimensional patterns that are significantly distinct from the background without the need for pre-defining a pattern within the bicluster. The method named Distinct 2-Dimensional Pattern Finder (D2D) is composed of an iterative reordering step of the rows and columns in the matrix using a new similarity measure, and a flexible scanning-and-growing step to identify the biclusters. Experiments on a large variety of simulation data show that the method works consistently well under different conditions, whereas the existing methods compared may work well under some certain conditions but fail under some other conditions. The impact of noise levels, overlapping degrees between clusters and different setting of parameters were also investigated, which indicated that the D2D method is robust against these factors. The proposed D2D method can efficiently discover many different types of biclusters given that they have distinctive features from the background. The computer program is available upon request.