Mistletoes are semiparasite plants containing pharmaceutical proteins with applications in cancer treatment. Previous research has demonstrated that somaclonal variation can lead to the biosynthesis of novel proteins from mistletoe callus cultures. The protein content of Viscum album subsp. abietis tissues and biotechnologically propagated calluses, was analyzed to identify proteins with putative anticancer properties. In addition, evolutionary relations among linked species to Viscum were studied. Calluses were propagated from stem explants. The protein extracts mass spectra were processed with Proteome Discoverer and a search was performed using as reference the Uniprot V. album reviewed database. A phylogenetic tree was reconstructed using the LG amino acid substitution model by homologous sequences for Beta galactoside-specific lectin 2. The homology modeling of the Beta-galactoside-specific lectin 2 was carried out using Modeller software. Considerable differences were observed by comparing the protein content of the calluses and the maternal tissues. Four mistletoe lectins, six viscotoxins and the chitin binding lectin-cbML were identified within the species tissues. An in silico phylogenetic and structural study provides insights to the role of these lectins and the mechanism of semiparasite survival and evolution, towards a novel anticancer and immune system modulation pipeline. Callogenesis exhibited protein biosynthesis alterations and novel protein isoforms expression. Phyllogenetic analysis revealed evolutionary relations primarily within the Viscum genus and other species containing 2-ribosome inactivating proteins. The homology modeling of the mistletoe lectin 2 revealed possible structure related anticancer properties. In conclusion, mistletoe calluses were shown to possess a unique protein biosynthetic profile compared to donor plant tissues.
Rhamnogalacturonan lyases (RGLs; EC 4.2.2.23) degrade the rhamnogalacturonan I (RG‐I) backbone of pectins present in the plant cell wall. These enzymes belong to polysaccharide lyase family 4, members of which are mainly from plants and plant pathogens. RGLs are investigated, as a rule, as pathogen ‘weapons’ for plant cell wall degradation and subsequent infection. Despite the presence of genes annotated as RGLs in plant genomes and the presence of substrates for enzyme activity in plant cells, evidence supporting the involvement of this enzyme in certain processes is limited. The differential expression of some RGL genes in flax (Linum usitatissimum L.) tissues, revealed in our previous work, prompted us to carry out a total revision (phylogenetic analysis, analysis of expression and protein structure modeling) of all the sequences of flax predicted as coding for RGLs. Comparison of the expressions of LusRGL in various tissues of flax stem revealed that LusRGLs belong to distinct phylogenetic clades, which correspond to two co‐expression groups. One of these groups comprised LusRGL6‐A and LusRGL6‐B genes and was specifically upregulated in flax fibers during deposition of the tertiary cell wall, which has complex RG‐I as a key noncellulosic component. The results of homology modeling and docking demonstrated that the topology of the LusRGL6‐A catalytic site allowed binding to the RG‐I ligand. These findings lead us to suggest the presence of RGL activity in planta and the involvement of special isoforms of RGLs in the modification of RG‐I of the tertiary cell wall in plant fibers. 相似文献
The computer modeling was applied for investigation of the processes of laser-induced tissue damage. The melanin granule models
for the processes of laser-induced thermal damage and the results of computer modeling of the optical, thermophysical, and
thermochemical processes during selective laser interaction with melanoprotein granules (melanosomes) in retinal pigment epithelium
are presented in this paper. Physical-mathematical model and system of equations are formulated which describe thermal interaction
processes for “short” laser pulses of duration tp<10−6 s and for “ long’ pulses of duration tp10−6 s. Results of numerical simulation of the processes give the space–time distributions of temperature and degrees of thermodenaturation
of the protein molecules inside and around melanosomes and in the volume of irradiated tissues. Energy absorption, heat transfer
and thermochemical (thermodenaturation, coagulation) processes occurring during the interaction of laser pulses with pigmented
spherical and spheroidal granules in heterogeneous tissues are theoretically investigated. The possibility for selective interaction
of short laser pulses with pigmented granules is discussed which results in the formation of denaturation microregions inside
and near the pigmented granules (granular thermodenaturation) without origination of a continuous macroscopic thermodenaturation
lesion in tissue. Analytical model of heating of single spherical and spheroidal granule under laser pulse is presented. Simple
equations for time dependencies of particle temperature are obtained. The presented results are of essential interest for
laser applications in and can be used for investigation of laser interaction with pigmented tissues in different fields of
laser medicine. 相似文献
A comprehensive understanding of the structure and properties of gramineous lignocelluloses is needed to facilitate their uses in biorefinery. In this study, lignocelluloses from fractionated internode tissues of two taxonomically close species, Erianthus arundinaceus and sugarcane (Saccharum spp.), were characterized. Our analyses determined that syringyl (S) lignins were predominant over guaiacyl (G) or p-hydroxyphenyl (H) lignins in sugarcane tissues; on the other hand, S lignin levels were similar to those of G lignin in Erianthus tissues. In addition, tricin units were detected in sugarcane tissues, but not in Erianthus tissues. Distributions of lignin inter-monomeric linkage types were also different in Erianthus and sugarcane tissues. Alkaline treatment removed lignins from sugarcane tissues more efficiently than Erianthus tissues, resulting in a higher enzymatic digestibility of sugarcane tissues compared with Erianthus tissues. Our data indicate that Erianthus biomass displayed resistance to alkaline delignification and enzymatic digestion. 相似文献
In the log cultivation of Shiitake (Lentinula edodes), early colonization of this fungus is extremely retarded in living wood tissues, in particular in inner bark tissues. To estimate the viability of inner bark tissues of Quercus serrata, a substrate for log cultivation of Shiitake, we employed a colorimetric assay utilizing a tetrazolium salt (2,3,5-triphenyltetrazolium chloride, TTC) and investigated the relationships between degree of decrease in viability and increase in growth of L. edodes in the tissues. When the mixtures of different proportions of living and dead tissues were assayed, formazan production was proportional to the percentage of living tissues. When logs dried for various time periods were inoculated with L. edodes, the fungus grew more extensively in tissues with reduced formazan production. These results indicate that the TTC assay is a useful method for estimation of viability and thus can be used to decide the proper timing for inoculation of L. edodes.Contribution no. 372 from the Tottori Mycological Institute 相似文献
Optical properties of tissues are required for theoretical modeling of Laser Ablation in tumor therapy. The light scattering characteristic of tissues is described by the anisotropy coefficient, g. The relationship between the angular distribution of scattered light and g is given by the Henyey‐Greenstein (HG) phase function. This work describes the estimation of anisotropy coefficients of ex vivo swine pancreas, liver and muscle at 1064 nm. The intensities of scattered light at fixed angles were measured under repeatability conditions. Experimental data were fitted with a two‐term HG, estimating the anisotropy coefficients for the forward (e.g., 0.956 for pancreas, 0.964 for liver and 0.968 for muscle) and the backward (e.g., –0.481 for pancreas, –0.414 for liver and –0.372 for muscle) scattering.
Experimental set up employed to estimate the anisotropy coefficient of biological tissues. The image on the left depicts the holder used to house tissue, laser fiber and photodetector; on the left an example of scattered light beam is shown, as well as the effect due to Snell's law. 相似文献
Central to modern Histochemistry and Cell Biology stands the need for visualization of cellular and molecular processes. In the past several years, a variety of techniques
has been achieved bridging traditional light microscopy, fluorescence microscopy and electron microscopy with powerful software-based
post-processing and computer modeling. Researchers now have various tools available to investigate problems of interest from
bird’s- up to worm’s-eye of view, focusing on tissues, cells, proteins or finally single molecules. Applications of new approaches
in combination with well-established traditional techniques of mRNA, DNA or protein analysis have led to enlightening and
prudent studies which have paved the way toward a better understanding of not only physiological but also pathological processes
in the field of cell biology. This review is intended to summarize articles standing for the progress made in “histo-biochemical”
techniques and their manifold applications. 相似文献
Abstract Research into human metabolism is expanding rapidly due to the emergence of metabolism as a key factor in common diseases. Mathematical modeling of human cellular metabolism has traditionally been performed via kinetic approaches whose applicability for large-scale systems is limited by lack of kinetic constants data. An alternative computational approach bypassing this hurdle called constraint-based modeling (CBM) serves to analyze the function of large-scale metabolic networks by solely relying on simple physical-chemical constraints. However, while extensive research has been performed on constraint-based modeling of microbial metabolism, large-scale modeling of human metabolism is still in its infancy. Utilizing constraint-based modeling to model human cellular metabolism is significantly more complicated than modeling microbial metabolism as in multi-cellular organisms the metabolic behavior varies across cell-types and tissues. It is further complicated due to lack of data on cell type- and tissue-specific metabolite uptake from the surrounding microenvironments and tissue-specific metabolic objective functions. To overcome these problems, several studies suggested CBM methods that integrate metabolic networks with gene expression data that is easily measurable under various conditions. This specific objective functions are expected to improve the prediction accuracy of the presented methods. Such objective functions may be derived based on computational learning that would give optimal correspondence between predicted and measured metabolic phenotypes (Burgard, 2003). The CBM methods presented here open the way for future computational investigations of metabolic disorders given the relevant expression data. A first attempt to visualize and interpret changes in gene expression data measured following gastric bypass surgery via a genome-scale metabolic network was done by Duarte et al (Duarte, 2007). Another potential application would be the prediction of diagnostic biomarkers for metabolic diseases that could be identified via biofluid metabolomics (Kell, 2007). Towards this goal, we have recently developed a CBM method for predicting metabolic biomarkers for in-born errors of metabolism by searching for changes in metabolite uptake and secretion rate due to genetic alterations (Shlomi, 2009). Incorporating cell type- and tissue-specific gene expression data within this framework can potentially improve the identification of diagnostic biomarkers. Overall, the methods presented here lay the foundation for studying normal and abnormal human cellular metabolism in tissue-specific manner based on commonly measured gene expression data. 相似文献
Rieske protein gene in the Pacific oyster Crassostrea gigas was obtained by in silico cloning for the first time, and its expression profiles and subcellular localization were determined,
respectively. The full-length cDNA of Cgisp is 985 bp in length and contains a 5′- and 3′-untranslated regions of 35 and 161 bp, respectively, with an open reading frame
of 786 bp encoding a protein of 262 amino acids. The predicted molecular weight of 30 kDa of Cgisp protein was verified by prokaryotic expression. Conserved Rieske [2Fe–2S] cluster binding sites and highly matched-pair tertiary
structure with 3CWB_E (Gallus gallus) were revealed by homologous analysis and molecular modeling. Eleven putative SNP sites and two conserved hexapeptide sequences,
box I (THLGC) and II (PCHGS), were detected by multiple alignments. Real-time PCR analysis showed that Cgisp is expressed in a wide range of tissues, with adductor muscle exhibiting the top expression level, suggesting its biological
function of energy transduction. The GFP tagging Cgisp indicated a mitochondrial localization, further confirming its physiological
function. 相似文献
Much of the experimental work in soft tissue mechanics has been focused on fitting approximate relations for specific tissue
types from aggregate data on multiple samples of the tissue. Such relations are needed for modeling applications and have
reasonable predictability - especially given the natural variance in specimens. There is, however, much theoretical and experimental
work to be done in determining constitutive behaviors for particular specimens and tissues. In so doing, it may be possible
to exploit the natural variation in tissue ultrastructure - so to relate ultrastructure composition to tissue behavior. Thus,
this study focuses on an experimental method for determining constitutive behaviors and illustrates the method with analysis
of a porcine pulmonary artery strip. The method characterizes the elastic part of the response (implicitly in terms of stretch)
and the inelastic part in terms of short term stretch history (i.e., stretch-rate) Ht2, longer term stretch history Ht1, and time since the start of testing T. 相似文献
One of the major challenges facing fishery scientists and managers today is determining how fish populations are influenced
by habitat conditions. Many approaches have been explored to address this challenge, all of which involve modeling at one
level or another. In this paper, we explore a process-oriented model approach whereby the critical population processes of
birth and death rates are explicitly linked to habitat conditions. Application of this approach to five species of Great Lakes
fishes including: walleye (Sander vitreus), lake trout (Salvelinus namaycush), smallmouth bass (Micropterus dolomieu), yellow perch (Perca flavescens), and rainbow trout (Onchorynchus mykiss), yielded a number of insights into the modeling process. One of the foremost insights is that processes determining movement
and transport of fish are critical components of such models since these processes largely determine the habitats fish occupy.
Because of the importance of fish location, an individual-based model appears to be a nearly inescapable modeling requirement.
There is, however, a paucity of field-based data directly relating birth, death, and movement rates to habitat conditions
experienced by individual fish. There is also a paucity of habitat information at a fine temporal and spatial scale for many
important habitat variables. Finally, the general occurrence of strong ontogenetic changes in the response of different life
stages to habitat conditions emphasizes the need for a modeling approach that considers all life stages in an integrated fashion. 相似文献
We describe a database of protein structure alignments as well as methods and tools that use this database to improve comparative protein modeling. The current version of the database contains 105 alignments of similar proteins or protein segments. The database comprises 416 entries, 78,495 residues, 1,233 equivalent entry pairs, and 230,396 pairs of equivalent alignment positions. At present, the main application of the database is to improve comparative modeling by satisfaction of spatial restraints implemented in the program MODELLER (?ali A, Blundell TL, 1993, J Mol Biol 234:779–815). To illustrate the usefulness of the database, the restraints on the conformation of a disulfide bridge provided by an equivalent disulfide bridge in a related structure are derived from the alignments; the prediction success of the disulfide dihedral angle classes is increased to approximately 80%, compared to approximately 55% for modeling that relies on the stereochemistry of disulfide bridges alone. The second example of the use of the database is the derivation of the probability density function for comparative modeling of the cis/trans isomerism of the proline residues; the prediction success is increased from 0% to 82.9% for cis-proline and from 93.3% to 96.2% for trans-proline. The database is available via electronic mail. 相似文献
New crystalline structures have been observed in argon ion‐milled conodont elements from a diverse suite of Ordovician taxa (‘Cordylodus robustus’, Drepanoistodus suberectus, Panderodus gracilis, Plectodina? sp., Aphelognathus sp., Periodon aculeatus), using transmission electron microscopy (TEM). Electron diffraction patterns of albid tissue reveal that the component crystals are extraordinarily large, in the order of hundred(s) of microns. These large albid crystals show typical cancellate porosity, although a distinctly lamellar structure has also been observed within a large albid crystal positioned between hyaline lamellar and cancellate albid tissues. There is a distinct absence of ‘interlamellar space’ within all hyaline tissues examined, which are characterized by a polycrystalline matrix of micron‐scale elongate crystals that are both strongly aligned and tightly bound within a broader lamellar structure. Optical opacity, caused by light scattering within large (≥ 0.5 µm) pores, is also a feature of both albid and polycrystalline lamellar crown tissues. Accordingly, conodont hard tissues are differentiated by crystal size and shape, as well as inter‐ and intracrystalline porosity. These new observations highlight the structural complexities of conodont histologies and the need for more comprehensive investigations particularly of transitional crown tissues, which are not well defined by terms typically used in the literature. Their histological structures are interpreted to be a product of in vivo crystallization and thus provide new insights into the relative porosity, permeability, and inherent integrity of the tissues as well as their growth relationships. Accordingly, these data not only have implications for earlier histological and palaeobiological interpretations of conodont hard tissues but are also fundamental in determining their chemical integrity, which is crucial for characterizing palaeoseawater composition and palaeoenvironmental change. The potential for conodont apatite to retain primary chemical information depends on crystal size and permeability, so the large albid crystal domains are consistent with parallel geochemical studies that suggest that cancellate albid crown is more resistant to diagenetic modification. 相似文献
Xenotransplantation shows great promise for providing a virtually limitless supply of cells, tissues, and organs for a variety
of therapeutical procedures. However, the potential of porcine endogenous retrovirus (PERV) as a human-tropic pathogen, particularly
as a public health risk, is a major concern for xenotransplantation. This study focus on the detection of copy number in various
tissues and organs in Banna Minipig Inbreed (BMI) from 2006 to 2007 in West China Hospital, Sichuan University. Real-time
quantitative polymerase chain reaction (SYBR Green I) was performed in this study. The results showed that the pol gene had the most copy number in tissues compared with gag, envA, and envB. Our experiment will offer a rapid and accurate method for the detection of the copy number in various tissues and was especially
suitable for the selection of tissues or organs in future clinical xenotransplantation. 相似文献
Neural tube defects (NTDs) are a spectrum of severe congenital malformations of fusion failure of the neural tube during early embryogenesis. Evidence on aberrant DNA methylation in NTD development remains scarce, especially when exposure to environmental pollutant is taken into consideration. DNA methylation profiling was quantified using the Infinium HumanMethylation450 array in neural tissues from 10 NTD cases and 8 non-malformed controls (stage 1). Subsequent validation was performed using a Sequenom MassARRAY system in neural tissues from 20 NTD cases and 20 non-malformed controls (stage 2). Correlation analysis of differentially methylated CpG sites in fetal neural tissues and polycyclic aromatic hydrocarbons concentrations in fetal neural tissues and maternal serum was conducted. Differentially methylated CpG sites of neural tissues were further validated in fetal mice with NTDs induced by benzo(a)pyrene given to pregnant mice. Differentially hypermethylated CpG sites in neural tissues from 17 genes and 6 pathways were identified in stage 1. Subsequently, differentially hypermethylated CpG sites in neural tissues from 6 genes (BDKRB2, CTNNA1, CYFIP2, MMP7, MYH2, and TIAM2) were confirmed in stage 2. Correlation analysis showed that methylated CpG sites in CTNNA1 and MYH2 from NTD cases were positively correlated to polycyclic aromatic hydrocarbon level in fetal neural tissues and maternal serum. The correlation was confirmed in NTD-affected fetal mice that were exposed to benzo(a)pyrene in utero. In conclusion, hypermethylation of the CTNNA1 and MYH2 genes in tight junction pathway is associated with the risk for NTDs, and the DNA methylation aberration may be caused by exposure to benzo(a)pyrene. 相似文献
Research on plankton ecology in the oceans has traditionally been conducted via two scientific approaches: in situ (in the field) and in vitro (in the laboratory). There is, however, a third approach: exploring plankton dynamics in silico, or using computer models as tools to study marine ecosystems. Models have been used for this purpose for over 60 years, and the innovations and implementations of historical studies provide a context for how future model applications can continue to advance our understanding. To that end, this paper presents a chronology of the in silico approach to plankton dynamics, beginning with modeling pioneers who worked in the days before computers. During the first 30 years of automated computation, plankton modeling focused on formulations for biological processes and investigations of community structure. The changing technological context and conceptual paradigms of the late-1970s and 1980s resulted in simulations becoming more widespread research tools for biological oceanographers. This period saw rising use of models as hypothesis-testing tools, and means of exploring the effects of circulation on spatial distributions of organisms. Continued computer advances and increased availability of data in the 1990s allowed old approaches to be applied to old and new problems, and led to developments of new approaches. Much of the modeling in the new millennium so far has incorporated these sophistications, and many cutting-edge applications have come from a new generation of plankton scientists who were trained by modeling gurus of previous eras. The future directions for modeling plankton dynamics are rooted in the historical studies. 相似文献
Verticillium dahliae is a devastating pathogenic fungus that causes severe vascular wilts in more than 400 dicotyledonous plants. The conidiation of V. dahliae in plant vascular tissues is the key strategy for its adaptation to the nutrient-poor environment and is required for its pathogenicity. However, it remains unclear about the regulatory mechanism of conidium production of V. dahliae in vascular tissues. Here, we found that VdAsp1, encoding an inositol polyphosphate kinase, is indispensable for the pathogenicity of V. dahliae. Loss of VdAsp1 function does not affect the invasion of the host, but it impairs the colonization and proliferation in vascular tissues. The ΔVdAsp1 mutant shows defective initiation of conidiophore formation and reduced expression of genes associated with the central developmental pathway. By live-cell imaging, we observed that some of ΔVdAsp1 mutant hyphae are swollen, and microtubule arrangements at the apical region of these hyphae are disorganized. These results indicate that VdAsp1 regulates the transition from vegetative growth to asexual reproduction by modulating microtubule dynamic organization, which is essential for V. dahliae to colonize and proliferate in vascular tissues. These findings provided a potential new direction in the control of vascular wilt pathogen by targeting conidium production in vascular tissues. 相似文献