Two-dimensional protein profiles of palisade parenchyma and of spongy parenchyma of Vicia faba leaf

Specific probes such as targeted-enzyme assays have failed to reveal qualitative differences between the metabolism of spongy parenchyma and that of palisade parenchyma cells. To determine whether the results from these definite assays support a general conclusion concerning the overall biochemical similarity of these cells, two-dimensional protein profiles have been constructed for these two types of cells. Protein extracts were prepared from freeze-dried homogeneous tissue samples or from isolated protoplasts of Vicia faba L. cv. Longpod leaves. Proteins separated by micro two-dimensional gel electrophoresis were stained with silver. The relative apparent abundance (based on visual judgment of the area and intensity of staining) was estimated for each spot. Pairwise comparison of nominally 125 stained proteins of each of approximately 75 gel pairs did not reveal a consistent qualitative difference between the profiles. Recognizing that polypeptides escaped detection in our investigation through loss, failure to stain sufficiently, or incomplete resolution, we qualify our conclusion that spongy parenchyma and palisade are similar in their overall protein complement.     

Al-hyperaccumulator Vochysiaceae from the Brazilian Cerrado store aluminum in their chloroplasts without apparent damage

We investigated the pattern of aluminum (Al) accumulation in leaf tissues of native hyperaccumulator Vochysiaceae species Qualea grandiflora,Callisthene major, and Vochysia pyramidalis, from the Brazilian Cerrado. Non-accumulator Sclerolobium paniculatum was used as a control species. We expected a strong compartmentalization of Al in non-active leaf cell compartments such as cell walls and vacuoles in Al-accumulating species and the absence of Al in critical metabolic sites such as the chloroplasts. Plant leaves were harvested in the field and cut in small segments for histological analysis; hematoxylin dye was used for Al localization in tissues. Results of soil analysis of the three sites and the concentration of Al in leaves indicated that there is no direct relationship between Al availability in soils and Al hyperaccumulation among the Vochysiaceae species evaluated. The cross-sections of leaf tissues showed hematoxylin color in the palisade and spongy parenchyma cells (chloroplast) of Q. grandiflora and C. major. The vascular system of Q. grandiflora was not colored, but some cells from the xylem region of C. major were stained. In contrast, the adaxial and abaxial epidermal cells of V. pyramidalis were colored by hematoxylin, as were some cells from the vascular bundle, but color formation was not observed in the cells of palisade parenchyma. Al was not detected in leaves of S. paniculatum. We concluded that, although hyperaccumulation of Al is a common trait in the Vochysiaceae family, the processes of storage and detoxification in leaf tissues differ among the species. Two of the three hyperaccumulator species use chloroplasts as a sink for Al, with no apparent signs of toxicity. Therefore, the physiological role of Al in plant tissues remains to be elucidated.     

Compartmentation in Vicia faba Leaves: II. Kinetics of C-Sucrose Redistribution among Individual Tissues following Pulse Labeling

Leaflets of Vicia faba L. were pulse labeled with ¹⁴CO₂ and the kinetics of ¹⁴C-sucrose redistribution among individual tissues was followed. Sucrose specific activity in the whole leaf peaked about 15 minutes after labeling and declined with a half-time of about 80 minutes. In one experiment, leaflet discs taken at various times during the ¹²CO₂ chase were quick frozen, freeze-substituted, and embedded in plastic. The tissue was sectioned paradermally and sections of palisade parenchyma, of spongy parenchyma, and of spongy parenchyma that contained veins were collected. Water extracts from these sections were assayed for sucrose specific activity. Sucrose specific activity in the palisade parenchyma was higher than that of the spongy parenchyma and reached a maximum in both tissues 9 to 15 minutes after labeling. Sucrose specific activity initially declined rapidly in the palisade parenchyma followed by a period during which little or no loss occurred. Sucrose specific activity in sections containing veins peaked at 15 minutes with a maximum value substantially higher than either mesophyll tissue, indicating that recently synthesized sucrose was preferentially exported from the mesophyll. Decline of activity in these sections containing veins continued for the remainder of the experiment. Sucrose specific activity in lower epidermal peels peaked several minutes after that of the whole leaflet and remained lower. Sucrose specific activity in upper epidermal peels was variable (probably due to contamination), but the limited data suggest that the sucrose specific activity there reached somewhat higher values than those of the lower epidermis. The experiments indicate that each leaf tissue contains a kinetically identifiable sucrose pool (which we refer to as “histological compartmentation”), and that further compartmentation may occur at the intracellular level. A simulation of leaf sucrose compartmentation is presented.     

Leaf anatomical variation in Alchornea triplinervia (Spreng) Mull. Arg. (Euphorbiaceae) under distinct light and soil water regimes

Alchornea triplinervia (Spreng.) Müll. Arg. (Euphorbiaceae) is a tree which occurs in a broad range of habitats in Brazil. In the State of Rio de Janeiro, it occurs from montane forests to swamplands at sea level. A quantitative approach was used to examine the role of light and soil water regime on the variations found in anatomical traits of the palisade and spongy parenchyma, outer epidermal cell wall of the abaxial and adaxial surfaces, the percentage of sclerenchymatous area in relation to the total midrib area and the ratio of palisade to spongy parenchyma for five distinct ecological populations: M—late secondary montane forest (shaded, unflooded); M2—early secondary montane forest (semi-exposed, unflooded); SI—primary swamp forest (semi-exposed, flooded); S2—secondary swamp forest (exposed, flooded); and D—deforestation area (exposed, unflooded). Tukey tests were carried out for multiple comparisons, while one-way factor variance analysis was used to test for differences among ecological populations. A principal component analysis was used to order the populations as well as to find the higher variance component. These populations developed different response levels to the environmental factors studied, namely light and soil water regime. Light accounted for the variations found in palisade and spongy parenchyma while the combination of light and soil water determined the variations found regarding the outer epidermal cell wall of the abaxial surface, the percentage of sclerenchymatous area in relation to the total midrib area and the compaction of the spongy parenchyma. The separation of S1/M2 and S2/D populations into two groups was due to similar light regimes, which suggested that light was affecting the leaf anatomical variation of A. triplinervia more than the interaction of light and soil water regime.     

Compartmentation in Vicia faba Leaves: I. Kinetics of C in the Tissues following Pulse Labeling

Leaflets of Vicia faba were pulse-labeled with ¹⁴CO₂ to follow the subsequent movement of photosynthate between leaf tissues. Samples were taken during a ¹²CO₂ chase, quick frozen, freeze-substituted, and embedded in methacrylate. Paradermal sections provided tissue samples consisting only of upper epidermis, palisade parenchyma, spongy parenchyma and veins, spongy parenchyma, or lower epidermis. Most CO₂ fixation occurred in the palisade parenchyma, but its ¹⁴C content declined rapidly after labeling. Concomitant with the decline of activity in the palisade parenchyma, there was an increase in activity in the spongy parenchyma and upper epidermis and a slow increase in the lower epidermis. Activity in the palisade parenchyma and spongy parenchyma eventually reached similar levels and remained constant. Tissue samples containing veins were consistently the most radioactive, and activity in those samples showed a decline. Very little change occurred in the insoluble fraction from any tissue. The results support previous assumptions regarding the pathway of assimilate transport to the veins, and demonstrate the rapidity of such transport. Sucrose is apparently the principal mobile compound.     

石蒜属12 种植物叶片比较解剖学研究

 对石蒜属( Lycoris Herb. ) 12 种植物叶片的比较解剖学研究表明: (1) 石蒜属植物叶片横切面的端部、中部及基部的轮廓基本呈浅“W”或“V”字型, 有些种的表皮细胞上具有明显的尖刺状乳突; ( 2)石蒜属植物均为异面叶, 叶肉组织有一定的栅栏组织和海绵组织分化, 但二者的厚度、叶肉中所占比例及栅栏组织的细胞层数在种间有一定的差异; (3) 海绵组织发达、具有大而明显的薄壁细胞或细胞裂溶后形成空腔(分泌腔或气腔); (4) 叶片中维管束数目大多为奇数, 叶脉维管束鞘由薄壁细胞组成; (5) 石蒜属植物横切面上叶缘的形状分为圆弧形和楔形两种类型。石蒜属植物叶的解剖结构具有许多相似特征; 同时又具有一定的种间差异, 可为石蒜属植物的种间关系和开发利用提供有价值的信息。     

LEAF ANATOMY OF TISSUE-CULTURED LIQUIDAMBAR STYRACIFLUA (HAMAMELIDACEAE) DURING ACCLIMATIZATION

Structural changes accompanying the acclimation process were observed in leaves of sweetgum, Liquidambar styraciflua, using light and transmission electron microscopy (TEM). Comparisons were made of leaves obtained from tissue culture, plantlets acclimated after transfer from the in vitro environment to soil, and field grown trees. Leaves of cultured plantlets lacked a differentiated palisade parenchyma and had spongy parenchyma interspersed with large air spaces. Field grown leaves showed distinct palisade and spongy tissues and a high cell density. New leaves from acclimated plantlets showed an elongation of the upper mesophyll with fewer intercellular spaces than cultured plants. Cells from leaves from in vitro plantlets had large vacuoles, limited cytoplasmic content and flattened chloroplast with an irregularly arranged internal membrane system. Acclimated and field leaf cells had a greater cytoplasmic content than cultured leaves, with the former having more dominate vacuoles. Chloroplasts had evident grana. Acclimated and field leaves had a well developed cuticle unlike leaves from culture.     

Applying machine learning based on multiscale classifiers to detect remote phenology patterns in Cerrado savanna trees

Plant phenology is one of the most reliable indicators of species responses to global climate change, motivating the development of new technologies for phenological monitoring. Digital cameras or near remote systems have been efficiently applied as multi-channel imaging sensors, where leaf color information is extracted from the RGB (Red, Green, and Blue) color channels, and the changes in green levels are used to infer leafing patterns of plant species. In this scenario, texture information is a great ally for image analysis that has been little used in phenology studies. We monitored leaf-changing patterns of Cerrado savanna vegetation by taking daily digital images. We extract RGB channels from the digital images and correlate them with phenological changes. Additionally, we benefit from the inclusion of textural metrics for quantifying spatial heterogeneity. Our first goals are: (1) to test if color change information is able to characterize the phenological pattern of a group of species; (2) to test if the temporal variation in image texture is useful to distinguish plant species; and (3) to test if individuals from the same species may be automatically identified using digital images. In this paper, we present a machine learning approach based on multiscale classifiers to detect phenological patterns in the digital images. Our results indicate that: (1) extreme hours (morning and afternoon) are the best for identifying plant species; (2) different plant species present a different behavior with respect to the color change information; and (3) texture variation along temporal images is promising information for capturing phenological patterns. Based on those results, we suggest that individuals from the same species and functional group might be identified using digital images, and introduce a new tool to help phenology experts in the identification of new individuals from the same species in the image and their location on the ground.     

How to measure diagnosis-associated information in virtual slides

The distribution of diagnosis-associated information in histological slides is often spatial dependent. A reliable selection of the slide areas containing the most significant information to deriving the associated diagnosis is a major task in virtual microscopy. Three different algorithms can be used to select the appropriate fields of view: 1) Object dependent segmentation combined with graph theory; 2) time series associated texture analysis; and 3) geometrical statistics based upon geometrical primitives. These methods can be applied by sliding technique (i.e., field of view selection with fixed frames), and by cluster analysis. The implementation of these methods requires a standardization of images in terms of vignette correction and gray value distribution as well as determination of appropriate magnification (method 1 only). A principle component analysis of the color space can significantly reduce the necessary computation time. Method 3 is based upon gray value dependent segmentation followed by graph theory application using the construction of (associated) minimum spanning tree and Voronoi's neighbourhood condition. The three methods have been applied on large sets of histological images comprising different organs (colon, lung, pleura, stomach, thyroid) and different magnifications, The trials resulted in a reproducible and correct selection of fields of view in all three methods. The different algorithms can be combined to a basic technique of field of view selection, and a general theory of "image information" can be derived. The advantages and constraints of the applied methods will be discussed.     

Automatic tumor-stroma separation in fluorescence TMAs enables the quantitative high-throughput analysis of multiple cancer biomarkers

The upcoming quantification and automation in biomarker based histological tumor evaluation will require computational methods capable of automatically identifying tumor areas and differentiating them from the stroma. As no single generally applicable tumor biomarker is available, pathology routinely uses morphological criteria as a spatial reference system. We here present and evaluate a method capable of performing the classification in immunofluorescence histological slides solely using a DAPI background stain. Due to the restriction to a single color channel this is inherently challenging. We formed cell graphs based on the topological distribution of the tissue cell nuclei and extracted the corresponding graph features. By using topological, morphological and intensity based features we could systematically quantify and compare the discrimination capability individual features contribute to the overall algorithm. We here show that when classifying fluorescence tissue slides in the DAPI channel, morphological and intensity based features clearly outpace topological ones which have been used exclusively in related previous approaches. We assembled the 15 best features to train a support vector machine based on Keratin stained tumor areas. On a test set of TMAs with 210 cores of triple negative breast cancers our classifier was able to distinguish between tumor and stroma tissue with a total overall accuracy of 88%. Our method yields first results on the discrimination capability of features groups which is essential for an automated tumor diagnostics. Also, it provides an objective spatial reference system for the multiplex analysis of biomarkers in fluorescence immunohistochemistry.     

Uterine Synchronization Analysis During Pregnancy and Labor Using Graph Theory,Classification Based on Neural Network and Deep Learning

1) ObjectivesPreterm birth caused by preterm labor is one of the major health problems in the world. In this article, we present a new framework for dealing with this problem through the processing of electrohysterographic signals (EHG) that are recorded during labor and pregnancy. The objective in this research is to improve the classification between labor and pregnancy contractions by using a new approach that focuses on the connectivity analysis based on graph parameters, representative of uterine synchronization, and comparing neural network and machine learning methods in order to classify between labor and pregnancy.2) Material and methodsafter denoising of the 16 EHG signals recorded from pregnant women abdomen, we applied different connectivity methods to obtain connectivity matrices; then by using the graph theory, we extracted some graph parameters from the connectivity matrices; finally, we tested different neural network and machine learning methods on the features obtained from both graph and connectivity methods in order to classify between labor and pregnancy.3) ResultsThe best results were obtained by using the logistic regression method. We also evidence the power of graph parameters extracted from the connectivity matrices to improve the classification results.4) ConclusionThe use of graph analysis associated with machine learning methods can be a powerful tool to improve labor and pregnancy classification based on the analysis of EHG signals.     

Protein side-chain packing problem: a maximum edge-weight clique algorithmic approach

"Protein Side-chain Packing" has an ever-increasing application in the field of bio-informatics, dating from the early methods of homology modeling to protein design and to the protein docking. However, this problem is computationally known to be NP-hard. In this regard, we have developed a novel approach to solve this problem using the notion of a maximum edge-weight clique. Our approach is based on efficient reduction of protein side-chain packing problem to a graph and then solving the reduced graph to find the maximum clique by applying an efficient clique finding algorithm developed by our co-authors. Since our approach is based on deterministic algorithms in contrast to the various existing algorithms based on heuristic approaches, our algorithm guarantees of finding an optimal solution. We have tested this approach to predict the side-chain conformations of a set of proteins and have compared the results with other existing methods. We have found that our results are favorably comparable or better than the results produced by the existing methods. As our test set contains a protein of 494 residues, we have obtained considerable improvement in terms of size of the proteins and in terms of the efficiency and the accuracy of prediction.     

龙苍沟国家森林公园7种花楸属植物的叶解剖特征及其环境适应性

采用石蜡切片法对四川省龙苍沟国家森林公园内7种花楸属（Sorbus）植物的叶解剖特征进行研究,探究其结构特征与生境的相关性。结果显示：7种植物的叶片均为典型的背腹叶;叶片厚度介于108.16~208.21 μm,种间差异极显著（P<0.01）;上表皮厚度均大于下表皮厚度,且复叶物种的下表皮细胞均有乳突;栅栏组织由1~2层细胞构成,仅多对西康花楸（S. prattii var. aestivalis）的栅海比（栅栏组织与海绵组织的厚度比）为1.93,其余6种植物的栅海比均小于1;中脉维管束均呈心型,为典型的外韧型维管束,种间中脉突起度存在极显著差异（P<0.01）。各解剖结构中,上、下表皮可塑性最大,在生境中具有较强的潜在适应能力;中脉可塑性最小,整体结构较为稳定。栅栏组织、海绵组织和中脉组织是7种植物中种间差异最大的解剖结构。叶解剖结构与生境因子的相关性分析表明,栅栏组织厚度、栅海比和紧密度与年降水量、最暖季降水和海拔正相关（P<0.05）,与季节性温差负相关（P<0.05）;中脉直径和突起度与季节性温差呈正相关（P<0.01）,与年降水量、最暖季降水和海拔正相关负相关（P<0.05）。叶解剖结构性状的适应性变化,体现了7种花楸属植物在龙苍沟国家森林公园的生存策略。     

Feature extraction for the analysis of colon status from the endoscopic images

Background

Extracting features from the colonoscopic images is essential for getting the features, which characterizes the properties of the colon. The features are employed in the computer-assisted diagnosis of colonoscopic images to assist the physician in detecting the colon status.

Methods

Endoscopic images contain rich texture and color information. Novel schemes are developed to extract new texture features from the texture spectra in the chromatic and achromatic domains, and color features for a selected region of interest from each color component histogram of the colonoscopic images. These features are reduced in size using Principal Component Analysis (PCA) and are evaluated using Backpropagation Neural Network (BPNN).

Results

Features extracted from endoscopic images were tested to classify the colon status as either normal or abnormal. The classification results obtained show the features' capability for classifying the colon's status. The average classification accuracy, which is using hybrid of the texture and color features with PCA (τ = 1%), is 97.72%. It is higher than the average classification accuracy using only texture (96.96%, τ = 1%) or color (90.52%, τ = 1%) features.

Conclusion

In conclusion, novel methods for extracting new texture- and color-based features from the colonoscopic images to classify the colon status have been proposed. A new approach using PCA in conjunction with BPNN for evaluating the features has also been proposed. The preliminary test results support the feasibility of the proposed method.

     

Structural Adaptation of the Leaf Mesophyll to Shading

Structural characteristics of the mesophyll were studied in five boreal grass species experiencing a wide range of light and water supply conditions. Quantitative indices of the palisade and spongy mesophyll tissues (cell and chloroplast sizes, the number of chloroplasts per cell, the total cell and chloroplast surface area per unit leaf surface area) were determined in leaves of each of the species. The cell surface area and the cell volume in spongy mesophyll were determined with a novel method based on stereological analysis of cell projections. An important role of spongy parenchyma in the photosynthetic apparatus was demonstrated. In leaves of the species studied, the spongy parenchyma constituted about 50% of the total volume and 40% of the total surface area of mesophyll cells. The proportion of the palisade to spongy mesophyll tissues varied with plant species and growth conditions. In a xerophyte Genista tinctoria, the total cell volume, cell abundance, and the total surface area of cells and chloroplasts were 30–40% larger in the palisade than in the spongy mesophyll. In contrast, in a shade-loving species Veronica chamaedris, the spongy mesophyll was 1.5–2 times more developed than the palisade mesophyll. In mesophyte species grown under high light conditions, the cell abundance and the total cell surface area were 10–20% greater in the palisade mesophyll than in the spongy parenchyma. In shaded habitats, these indices were similar in the palisade and spongy mesophyll or were 10–20% lower in the palisade mesophyll. In mesophytes, CO₂ conductance of the spongy mesophyll accounted for about 50% of the total mesophyll conductance, as calculated from the structural characteristics, with the mesophyll CO₂ conductance increasing with leaf shading.     

STUDIES ON THE LEAF OF POPULUS DELTOIDES (SALICACEAE): ULTRASTRUCTURE,PLASMODESMATAL FREQUENCY,AND SOLUTE CONCENTRATIONS

The minor veins and contiguous tissues of mature leaves of Populus deltoides Bartr. ex Marsh. were examined with the electron microscope to determine the ultrastructural characteristics of the component cells and to determine the structure, distribution, and frequency of plasmodesmata between the various cell types. In addition, plasmolytic studies were carried out to determine the solute concentrations of the various cell types of the minor veins and contiguous tissues. The cells comprising the mesophyll and bundle sheath contain all the components typical of photosynthetic cells. Paraveinal mesophyll cells and bundle-sheath cells have fewer microbodies and smaller chloroplasts than do palisade parenchyma cells. Vascular parenchyma and companion cells tend to intergrade with one another structurally but can be distinguished from one another by their characteristic plastids. The mature, enucleate sieve-tube member is lined by a parietal layer of cytoplasm consisting of plasmalemma, endoplasmic reticulum, mitochondria, plastids, and P-protein. Plasmodesmata occur along all possible routes from the palisade parenchyma cells to the sieve tubes of the minor veins, and their frequency increases with increasing proximity to the sieve-tube members. Plasmolytic studies revealed that the paraveinal mesophyll cells had a higher C₅₀ (estimated mannitol concentration plasmolyzing, on the average, 50% of a given cell type) than any other cell type of the leaf. Concentration gradients existed along the palisade cell/bundle-sheath cell/companion cell (or vascular parenchyma cell) route as well as along the paraveinal mesophyll cell/bundle-sheath cell/companion cell (or vascular parenchyma cell) route. Considering the frequency of plasmodesmata along these routes, it is conceivable that photosynthate diffuses from palisade cells to the companion cells along concentration gradients. Within the minor veins, the C₅₀ was higher for sieve-tube members than for either companion cells or vascular parenchyma cells, indicating that loading of the sieve tubes is an active, energy-dependent process.     

Shortest path analysis using partial correlations for classifying gene functions from gene expression data

MOTIVATION: Gaussian graphical models (GGMs) are a popular tool for representing gene association structures. We propose using estimated partial correlations from these models to attach lengths to the edges of the GGM, where the length of an edge is inversely related to the partial correlation between the gene pair. Graphical lasso is used to fit the GGMs and obtain partial correlations. The shortest paths between pairs of genes are found. Where terminal genes have the same biological function intermediate genes on the path are classified as having the same function. We validate the method using genes of known function using the Rosetta Compendium of yeast (Saccharomyces Cerevisiae) gene expression profiles. We also compare our results with those obtained using a graph constructed using correlations. RESULTS: Using a partial correlation graph, we are able to classify approximately twice as many genes to the same level of accuracy as when using a correlation graph. More importantly when both methods are tuned to classify a similar number of genes, the partial correlation approach can increase the accuracy of the classifications.