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1.
Allium sativum germplasm collected from different parts of India was subjected to critical analysis of 14 easily noticeable morphological traits. Variability encountered in quantitative as well as qualitative, bulb and plant traits was documented. While analysing this variability, an attempt was made to highlight the genotype-environment interaction, its impact on the expression of morphological traits in this apomict and evaluate the different collections for intraspecific phylogeny.  相似文献   

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Luz Boyero 《Hydrobiologia》2003,499(1-3):161-168
The effect of substrate heterogeneity on the structure of stream macroinvertebrate assemblages (total abundance, taxon richness, and evenness) is still not clear, but this could be due to the lack of standard methods for quantifying substrate heterogeneity. An accurate quantification of substrate heterogeneity was obtained from photographs of sampled areas (each 225 cm2), which were used to create maps that were subsequently digitized and analyzed using image analysis software. These maps allowed the calculation of multiple metrics quantifying two aspects of substrate heterogeneity: composition and spatial configuration of substrate patches. The diversity of substrate types (calculated as the Shannon diversity index), and the heterogeneity of patch compactness (calculated as the coefficient of variation of the relationship between patch dimensions) were the metrics explaining more biotic variance at the sample scale, but at higher scales there were no relationships between assemblage structure and substrate heterogeneity. Most variation in substrate heterogeneity occurred at the sample scale, while some metrics varied significantly at riffle or segment scales; these patterns of variation match those of macroinvertebrate assemblages, which had been previously studied. The importance of quantifying substrate heterogeneity and considering the spatial scales of its study are discussed.  相似文献   

4.
The presence of amyloid fibrils is a hallmark of more than 50 human disorders, including neurodegenerative diseases and systemic amyloidoses. A key unresolved challenge in understanding the involvement of amyloid in disease is to explain the relationship between individual structural polymorphs of amyloid fibrils, in potentially mixed populations, and the specific pathologies with which they are associated. Although cryo-electron microscopy (cryo-EM) and solid-state nuclear magnetic resonance (ssNMR) spectroscopy methods have been successfully employed in recent years to determine the structures of amyloid fibrils with high resolution detail, they rely on ensemble averaging of fibril structures in the entire sample or significant subpopulations. Here, we report a method for structural identification of individual fibril structures imaged by atomic force microscopy (AFM) by integration of high-resolution maps of amyloid fibrils determined by cryo-EM in comparative AFM image analysis. This approach was demonstrated using the hitherto structurally unresolved amyloid fibrils formed in vitro from a fragment of tau (297–391), termed ‘dGAE’. Our approach established unequivocally that dGAE amyloid fibrils bear no structural relationship to heparin-induced tau fibrils formed in vitro. Furthermore, our comparative analysis resulted in the prediction that dGAE fibrils are structurally closely related to the paired helical filaments (PHFs) isolated from Alzheimer’s disease (AD) brain tissue characterised by cryo-EM. These results show the utility of individual particle structural analysis using AFM, provide a workflow of how cryo-EM data can be incorporated into AFM image analysis and facilitate an integrated structural analysis of amyloid polymorphism.  相似文献   

5.
Ultramicroscopy is a powerful tool to reveal detailed three-dimensional structures of large microscopical objects. Using high magnification, we observed that formalin induces fluorescence more in extra-cellular space and stains cellular structures negatively, rendering cells as dark objects in front of a bright background. Here, we show this effect on a three-dimensional image stack of a hippocampus sample, focusing on the CA1 region. This method, called FIF-Ultramicroscopy, allows for the three-dimensional observation of cellular structures in various tissue types without complicated staining techniques.  相似文献   

6.
ObjectivesThe species Palarus latifrons (bee pirates) has been recorded in Saudi Arabia as an invasive species. This pest can destroy honey bee colonies under certain conditions. The origin of this species in Africa and it has a good ability to adapt to desert conditions. Studies on this species are very few but its current distribution in the Arabian deserts is mainly in the Arabian Gulf countries. This study presents maps for the possible expansion of this species to invade other desert areas in the Arabian countries’ under current and near-future conditions (2030).MethodsThis pest is a solitary insect with high activity during summer. It is hypothesized that summer conditions and especially temperature are the limiting factor for its distribution in the deserts. The analysis depended on generating maps based on temperatures during summer and based on two bioclimatic factors. Maxent and the geographical information system (GIS) were used to perform the analysis.Results and conclusionsAll maps showed the high ability of this pest to spread in the Gulf countries. In North Africa: south Egypt and Libya, and some parts of Algeria showed suitability for Palarus. The invasion of this pest towards North Africa can happen mostly due to trading activities with Gulf countries especially materials containing soil. Continues monitoring for the activity of Palarus in the risk areas is highly advised.  相似文献   

7.

Background

Chaos Game Representation (CGR) is an iterated function that bijectively maps discrete sequences into a continuous domain. As a result, discrete sequences can be object of statistical and topological analyses otherwise reserved to numerical systems. Characteristically, CGR coordinates of substrings sharing an L-long suffix will be located within 2 -L distance of each other. In the two decades since its original proposal, CGR has been generalized beyond its original focus on genomic sequences and has been successfully applied to a wide range of problems in bioinformatics. This report explores the possibility that it can be further extended to approach algorithms that rely on discrete, graph-based representations.

Results

The exploratory analysis described here consisted of selecting foundational string problems and refactoring them using CGR-based algorithms. We found that CGR can take the role of suffix trees and emulate sophisticated string algorithms, efficiently solving exact and approximate string matching problems such as finding all palindromes and tandem repeats, and matching with mismatches. The common feature of these problems is that they use longest common extension (LCE) queries as subtasks of their procedures, which we show to have a constant time solution with CGR. Additionally, we show that CGR can be used as a rolling hash function within the Rabin-Karp algorithm.

Conclusions

The analysis of biological sequences relies on algorithmic foundations facing mounting challenges, both logistic (performance) and analytical (lack of unifying mathematical framework). CGR is found to provide the latter and to promise the former: graph-based data structures for sequence analysis operations are entailed by numerical-based data structures produced by CGR maps, providing a unifying analytical framework for a diversity of pattern matching problems.  相似文献   

8.

Background

Prediction of protein structures from their sequences is still one of the open grand challenges of computational biology. Some approaches to protein structure prediction, especially ab initio ones, rely to some extent on the prediction of residue contact maps. Residue contact map predictions have been assessed at the CASP competition for several years now. Although it has been shown that exact contact maps generally yield correct three-dimensional structures, this is true only at a relatively low resolution (3–4 Å from the native structure). Another known weakness of contact maps is that they are generally predicted ab initio, that is not exploiting information about potential homologues of known structure.

Results

We introduce a new class of distance restraints for protein structures: multi-class distance maps. We show that C α trace reconstructions based on 4-class native maps are significantly better than those from residue contact maps. We then build two predictors of 4-class maps based on recursive neural networks: one ab initio, or relying on the sequence and on evolutionary information; one template-based, or in which homology information to known structures is provided as a further input. We show that virtually any level of sequence similarity to structural templates (down to less than 10%) yields more accurate 4-class maps than the ab initio predictor. We show that template-based predictions by recursive neural networks are consistently better than the best template and than a number of combinations of the best available templates. We also extract binary residue contact maps at an 8 Å threshold (as per CASP assessment) from the 4-class predictors and show that the template-based version is also more accurate than the best template and consistently better than the ab initio one, down to very low levels of sequence identity to structural templates. Furthermore, we test both ab-initio and template-based 8 Å predictions on the CASP7 targets using a pre-CASP7 PDB, and find that both predictors are state-of-the-art, with the template-based one far outperforming the best CASP7 systems if templates with sequence identity to the query of 10% or better are available. Although this is not the main focus of this paper we also report on reconstructions of C α traces based on both ab initio and template-based 4-class map predictions, showing that the latter are generally more accurate even when homology is dubious.

Conclusion

Accurate predictions of multi-class maps may provide valuable constraints for improved ab initio and template-based prediction of protein structures, naturally incorporate multiple templates, and yield state-of-the-art binary maps. Predictions of protein structures and 8 Å contact maps based on the multi-class distance map predictors described in this paper are freely available to academic users at the url http://distill.ucd.ie/.  相似文献   

9.
Although tree ferns are an important component of temperate and tropical forests, very little is known about their ecology. Their peculiar biology (e.g., dispersal by spores and two-phase life cycle) makes it difficult to extrapolate current knowledge on the ecology of other tree species to tree ferns. In this paper, we studied the effects of negative density dependence (NDD) and environmental heterogeneity on populations of two abundant tree fern species, Cyathea caracasana and Alsophila engelii, and how these effects change across a successional gradient. Species patterns harbor information on processes such as competition that can be easily revealed using point pattern analysis techniques. However, its detection may be difficult due to the confounded effects of habitat heterogeneity. Here, we mapped three forest plots along a successional gradient in the montane forests of Southern Ecuador. We employed homogeneous and inhomogeneous K and pair correlation functions to quantify the change in the spatial pattern of different size classes and a case–control design to study associations between juvenile and adult tree ferns. Using spatial estimates of the biomass of four functional tree types (short- and long-lived pioneer, shade- and partial shade-tolerant) as covariates, we fitted heterogeneous Poisson models to the point pattern of juvenile and adult tree ferns and explored the existence of habitat dependencies on these patterns. Our study revealed NDD effects for C. caracasana and strong environmental filtering underlying the pattern of A. engelii. We found that adult and juvenile populations of both species responded differently to habitat heterogeneity and in most cases this heterogeneity was associated with the spatial distribution of biomass of the four functional tree types. These findings show the effectiveness of factoring out environmental heterogeneity to avoid confounding factors when studying NDD and demonstrate the usefulness of covariate maps derived from mapped communities.  相似文献   

10.
In pH?5.5 2-(N-morpholino)-ethanosulfonic acid buffer solution containing 0.0125?M NaCl at 80?°C, the single-stranded substrate DNA hybrid with enzyme DNA to form double-stranded DNA (dDNA). The substrate chain of dDNA could be cracked catalytically by UO 2 2+ to produce a short single-stranded DNA (ssDNA) that adsorbed on the nanogold (NG) surface to form stable NGssDNA conjugate, and the unadsorbed NG take place aggregation to produce the NG aggregations in blue color. Both NG and NGssDNA exhibited strong catalytic activity on the gold particle reaction between HAuCl4 and ascorbic acid that can be monitored by resonance scattering (RS) spectral technique at 620?nm. However, the catalytic effect of NG aggregation was very weak and it cannot be separated from the cracked reaction solution. When the UO 2 2+ concentration increased, the ssDNA increased, the NGssDNA increased, the formed gold particles increased, and the RS intensity at 620?nm increased. The increased RS intensity ??I 620?nm was linear to UO 2 2+ concentration in the range of 3.35?C23.45?pM, with a regression equation of ??I 620?nm?=?27.6C?+?29.1, and detection limit of 0.1?pM. This new RS assay was applied to analysis of UO 2 2+ in water sample with satisfactory results.  相似文献   

11.
Sedimentation velocity analytical ultracentrifugation combines relatively high hydrodynamic resolution of macromolecular species with the ability to study macromolecular interactions, which has great potential for studying dynamically assembled multiprotein complexes. Complicated sedimentation boundary shapes appear in multicomponent mixtures when the timescale of the chemical reaction is short relative to the timescale of sedimentation. Although the Lamm partial differential equation rigorously predicts the evolution of concentration profiles for given reaction schemes and parameter sets, this approach is often not directly applicable to data analysis due to experimental and sample imperfections, and/or due to unknown reaction pathways. Recently, we have introduced the effective particle theory, which explains quantitatively and in a simple physical picture the sedimentation boundary patterns arising in the sedimentation of rapidly interacting systems. However, it does not address the diffusional spread of the reaction boundary from the cosedimentation of interacting macromolecules, which also has been of long-standing interest in the theory of sedimentation velocity analytical ultracentrifugation. Here, effective particle theory is exploited to approximate the concentration gradients during the sedimentation process, and to predict the overall, gradient-average diffusion coefficient of the reaction boundary. The analysis of the heterogeneity of the sedimentation and diffusion coefficients across the reaction boundary shows that both are relatively uniform. These results support the application of diffusion-deconvoluting sedimentation coefficient distributions c(s) to the analysis of rapidly interacting systems, and provide a framework for the quantitative interpretation of the diffusional broadening and the apparent molar mass values of the effective sedimenting particle in dynamically associating systems.  相似文献   

12.
The flexible manufacturing system (FMS) considered in this paper is composed of two CNC machines working in series—a punching machine and a bending machine connected through rollers acting as a buffer system of finite capacity. The main difference between the present problem and the standard two-machine flow shop problem with finite intermediate capacity is precisely the buffer system, which in our problem consists of two stacks of parts supported by rollers: the first stack contains the output of the punching machine, while the second stack contains the input for the bending machine. When the second stack is empty, the first stack may be moved over. Furthermore, the capacity of each stack depends on the particular part type being processed. The FMS can manufacture a wide range of parts of different types. Processing times on the two machines are usually different so that an unbalance results in their total workload. Furthermore, whenever there is a change of the part type in production, the machines must be properly reset—that is, some tools need to be changed or repositioned. A second important difference between the present problem and the usual two-machine flow shop problem is the objective. Given a list ofp part types to be produced in known quantities, the problem considered here is how to sequence or alternate the production of the required part types so as to achieve various hierarchical targets: minimize the makespan (the total time needed to complete production) and, for instance, compress the idle periods of the machine with less workload into a few long enough intervals that could be utilized for maintenance or other reasons. Although Johnson's rule is optimal in some particular cases, the problem addressed in the paper isNP-hard in general: heuristic procedures are therefore provided.  相似文献   

13.
The atomic coordinates derived from cryo-electron microscopy (cryo-EM) maps can be inaccurate when the voxel scaling factors are not properly calibrated. Here, we describe a method for correcting relative voxel scaling factors between pairs of cryo-EM maps for the same or similar structures that are expanded or contracted relative to each other. We find that the correction of scaling factors reduces the amplitude differences of Fourier-inverted structure factors from voxel-rescaled maps by up to 20–30%, as shown by two cryo-EM maps of the SARS-CoV-2 spike protein measured at pH 4.0 and pH 8.0. This allows for the calculation of the difference map after properly scaling, revealing differences between the two structures for individual amino acid residues. Unexpectedly, the analysis uncovers two previously overlooked differences of amino acid residues in structures and their local structural changes. Furthermore, we demonstrate the method as applied to two cryo-EM maps of monomeric apo-photosystem II from the cyanobacteria Synechocystis sp. PCC 6803 and Thermosynechococcus elongatus. The resulting difference maps reveal many changes in the peripheral transmembrane PsbX subunit between the two species.  相似文献   

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15.
Ultrastructure of the Z-organ and associated apophyses in Xiphinema coxi coxi was studied by transmission electron microscopy to determine their structural origin and relationship with other parts of the genital tract. The Z-organ of X. coxi coxi is oval-shaped, ca. 30 µm long and 16 µm wide. It is clearly distinguished from the other parts of the female genital tract by its thick muscular outer wall, epithelium-lined lumen, and 4-5 centrally located apophyses. Each apophysis is continuous with the epithelial lining of the Z-organ, suggesting that it originated from epithelium. The apophyses appear as thickened and densely folded masses forming numerous interlaced pores and (or) chambers containing mucous-like materials and electron-dense crystals. These apophyses are characteristic of a typical Z-organ; no globular structures characteristics of the pseudo-Z-organ were observed. The thickness of the muscular layer of the oviduct and uterus varied with position. The overall Z-organ ultrastructure of this study, including body wall and internal apophyses, was comparable to the typical Z-organ of X. ifacolum. This suggests that X. coxi coxi should be classified as a Xiphinema species that contains the typical Z-organ.  相似文献   

16.
Mitochondria are cellular organelles with multifaceted tasks and thus composed of different sub-compartments. The inner mitochondrial membrane especially has a complex nano-architecture with cristae protruding into the matrix. Related to their function, the localization of mitochondrial membrane proteins is more or less restricted to specific sub-compartments. In contrast, it can be assumed that membrane proteins per se diffuse unimpeded through continuous membranes. Fluorescence recovery after photobleaching is a versatile technology used in mobility analyses to determine the mobile fraction of proteins, but it cannot provide data on subpopulations or on confined diffusion behavior. Fluorescence correlation spectroscopy is used to analyze single molecule diffusion, but no trajectory maps are obtained. Single particle tracking (SPT) technologies in live cells, such as tracking and localization microscopy (TALM), do provide nanotopic localization and mobility maps of mitochondrial proteins in situ. Molecules can be localized with a precision of between 10 and 20 nm, and single trajectories can be recorded and analyzed; this is sufficient to reveal significant differences in the spatio-temporal behavior of diverse mitochondrial proteins. Here, we compare diffusion coefficients obtained by these different technologies and discuss trajectory maps of diverse mitochondrial membrane proteins obtained by SPT/TALM. We show that membrane proteins in the outer membrane generally display unhindered diffusion, while the mobility of inner membrane proteins is restricted by the inner membrane architecture, resulting in significantly lower diffusion coefficients. Moreover, tracking analysis could discern proteins in the inner boundary membrane from proteins preferentially diffusing in cristae membranes, two sub-compartments of the inner mitochondrial membrane. Thus, by evaluating trajectory maps it is possible to assign proteins to different sub-compartments of the same membrane.  相似文献   

17.
Sabal uresana was the palm most often discussed in published historic accounts from Sonora, Mexico, and the only palm mentioned from the earliest written documents to the present. An inventory of topographic maps identified 337 palm place names, thus reinforcing the cultural significance of palms in this region. Participant observation and formal interviews were used to learn how wild-harvested palms are utilized in present-day Sonora.Sabal uresana is the most economically important palm. Its leaves are employed for weaving, the major use of palms in this region, and for thatching and broom-making. Palm logs are used for construction and the fruits are eaten in certain parts of the state. The use of palms in Sonora is changing. Weaving and thatching could probably be maintained as viable crafts and sources of income with appropriate resource management and marketing.  相似文献   

18.
Human pluripotent stem (hPS) cells are a potential source of cells for medical therapy and an ideal system to study fate decisions in early development. However, hPS cells cultured in vitro exhibit a high degree of heterogeneity, presenting an obstacle to clinical translation. hPS cells grow in spatially patterned colony structures, necessitating quantitative single-cell image analysis. We offer a tool for analyzing the spatial population context of hPS cells that integrates automated fluorescent microscopy with an analysis pipeline. It enables high-throughput detection of colonies at low resolution, with single-cellular and sub-cellular analysis at high resolutions, generating seamless in situ maps of single-cellular data organized by colony. We demonstrate the tool''s utility by analyzing inter- and intra-colony heterogeneity of hPS cell cycle regulation and pluripotency marker expression. We measured the heterogeneity within individual colonies by analyzing cell cycle as a function of distance. Cells loosely associated with the outside of the colony are more likely to be in G1, reflecting a less pluripotent state, while cells within the first pluripotent layer are more likely to be in G2, possibly reflecting a G2/M block. Our multi-scale analysis tool groups colony regions into density classes, and cells belonging to those classes have distinct distributions of pluripotency markers and respond differently to DNA damage induction. Lastly, we demonstrate that our pipeline can robustly handle high-content, high-resolution single molecular mRNA FISH data by using novel image processing techniques. Overall, the imaging informatics pipeline presented offers a novel approach to the analysis of hPS cells that includes not only single cell features but also colony wide, and more generally, multi-scale spatial configuration.  相似文献   

19.
BackgroundBiosynthesis of Te nanoparticles may occur in higher plants exposed to Te, as reported on microorganisms. However, unambiguous observations of the biogenic nanoparticles (BgNPs) of Te in plants are lacking. Hence, in this study, we investigated the formation of insoluble BgNPs of Te in garlic (Allium sativum) as a model plant.MethodWe performed elemental analysis based on inductively coupled plasma-mass spectrometry (ICP-MS) technique, and obtained Te concentration and distribution in various parts of garlic. In addition, insoluble Te particles were detected by fast time-resolved ICP-MS. Direct observation of the insoluble Te particle was also conducted by scanning electron microscope (SEM) and transmission electron microscope (TEM).ResultsA part of the roots and clove from Te-exposed garlic showed black coloration. Te concentrations in the black-colored parts were significantly increased compared with the non-colored parts. Transient signals of Te unique to nanoparticles were detected from the insoluble fractions of the black-colored parts. Finally, rod-shaped biogenic Te nanoparticles consisting of highly crystalline elemental Te was observed by SEM and TEM.ConclusionOur data provide new insights to the metabolic pathway of Te in higher plants for the formation of insoluble biogenic nanoparticles, which is extremely important for the detoxification of Te.  相似文献   

20.
Genetic heterogeneity could reduce the power of linkage analysis to detect risk loci for complex traits such as alcohol dependence (AD). Previously, we performed a genomewide linkage analysis for AD in African-Americans (AAs) (Biol Psychiatry 65:111–115, 2009). The power of that linkage analysis could have been reduced by the presence of genetic heterogeneity owing to differences in admixture among AA families. We hypothesized that by examining a study sample whose genetic ancestry was more homogeneous, we could increase the power to detect linkage. To test this hypothesis, we performed ordered subset linkage analysis in 384 AA families using admixture proportion as a covariate to identify a more homogeneous subset of families and determine whether there is increased evidence for linkage with AD. Statistically significant increases in lod scores in subsets relative to the overall sample were identified on chromosomes 4 (P = 0.0001), 12 (P = 0.021), 15 (P = 0.026) and 22 (P = 0.0069). In a subset of 44 families with African ancestry proportions ranging from 0.858 to 0.996, we observed a genomewide significant linkage at 180 cM on chromosome 4 (lod = 4.24, pointwise P < 0.00001, empirical genomewide P = 0.008). A promising candidate gene located there, GLRA3, which encodes a subunit of the glycine neurotransmitter receptor. Our results demonstrate that admixture proportion can be used as a covariate to reduce genetic heterogeneity and enhance the detection of linkage for AD in an admixed population such as AAs. This approach could be applied to any linkage analysis for complex traits conducted in an admixed population.  相似文献   

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