How formalin affects the outcome of routine and special stains

The discovery of formaldehyde for preserving tissue structures produced a new dimension in microscopy. Preserving structure and morphology became important; therefore, identifying a proper fixing agent for particular structures, chemical entities, and tissues, also became important. The methods for demonstrating tissue structures evolved and were implemented with careful observation and documentation of the results and outcomes. Formalin was incorporated into many techniques, and provided helpful results in many cases and hindrances in others. The effects of formalin on the outcomes of routine and special staining techniques are reported here.     

Recent advances in stem cell therapy for neurodegenerative disease: Three dimensional tracing and its emerging use

Neurodegenerative disease is a brain disorder caused by the loss of structure and function of neurons that lowers the quality of human life. Apart from the limited potential for endogenous regeneration, stem cell-based therapies hold considerable promise for maintaining homeostatic tissue regeneration and enhancing plasticity. Despite many studies, there remains insufficient evidence for stem cell tracing and its correlation with endogenous neural cells in brain tissue with three-dimensional structures. Recent advancements in tissue optical clearing techniques have been developed to overcome the existing shortcomings of cross-sectional tissue analysis in thick and complex tissues. This review focuses on recent progress of stem cell treatments to improve neurodegenerative disease, and introduces tissue optical clearing techniques that can implement a three-dimensional image as a proof of concept. This review provides a more comprehensive understanding of stem cell tracing that will play an important role in evaluating therapeutic efficacy and cellular interrelationship for regeneration in neurodegenerative diseases.     

Quantitative Histochemistry: Histologic Sampling of Sections of Frozen-Dried Tissues

Microchemical techniques are available for analyses of many enzymes and other components of tissue for which stains are not available. This paper describes techniques of freeze drying and histological sampling of certain cell groups or structures free from surrounding stroma, fat and other types of cells. Quantitative data can be obtained for many enzymes in 0.5 to 5 μ samples of freeze-dried tissue. For example, glucoses-phosphate dehydrogenase activity was measured and compared in the breast alveoli of mice in estrus, diestrus, gestation and lactation.     

Quantitative Histochemistry: Histologic Sampling of Sections of Frozen-Dried Tissues

Microchemical techniques are available for analyses of many enzymes and other components of tissue for which stains are not available. This paper describes techniques of freeze drying and histological sampling of certain cell groups or structures free from surrounding stroma, fat and other types of cells. Quantitative data can be obtained for many enzymes in 0.5 to 5 μ samples of freeze-dried tissue. For example, glucoses-phosphate dehydrogenase activity was measured and compared in the breast alveoli of mice in estrus, diestrus, gestation and lactation.     

Cellular Automata Modeling of Pulmonary Inflammation

Better understanding of the acute/chronic inflammation in airways is very important in order to avoid lung injuries for patients undergoing mechanical ventilation for treatment of respiratory problems. Local lung inflammation is triggered by many mechanisms within the lung, including pathogens. In this study, a cellular automata based model (CA) for pulmonary inflammation that incorporates biophysical processes during inflammatory responses was developed. The developed CA results in three possible outcomes related to homeostasis (healing), persistent infection, and resolved infection with high inflammation (inflamed state). The results from the model are validated qualitatively against other existing computational models. A sensitivity analysis was conducted on the model parameters and the outcomes were assessed. Overall, the model results showed possible outcomes that have been seen in clinical practice and animal models. The present model can be extended to include inflammation resulting from damage tissue and eventually to model inflammation resulting from acute lung injury and multiple organ dysfunction syndromes in critical illness and injury.     

Schiff and pseudo-Schiff reagents: the reactions and reagents of Hugo Schiff,including a classification of various kinds of histochemical reagents used to detect aldehydes

During the 1860’s, Hugo Schiff studied many reactions between amines and aldehydes, some of which have been used in histochemistry, at times without credit to Schiff. Much controversy has surrounded the chemical structures and reaction mechanisms of the compounds involved, but modern analytical techniques have clarified the picture. I review these reactions here. I used molecular modeling software to investigate dyes that contain primary amines representing eight chemical families. All dyes were known to perform satisfactorily for detecting aldehydes in tissue sections. The models verified the correct chemical structures at various points in their reactions and also determined how decolorization occurred in those with “leuco” forms. Decolorization in the presence of sulfurous acid can occur by either adduction or reduction depending on the dye. The final condensation product with aldehyde was determined to be either a C-sulfonic acid adduct on the carbonyl carbon atom or an aminal at the same atom. Based on the various outcomes, I have placed the dyes and their reactions into five categories. Because Hugo Schiff studied the reactions between aldehydes and amines with and without various acids or alcohol, it is only proper to call each of them Schiff reactions that used various types of Schiff reagents.     

LIBP-Pred: web server for lipid binding proteins using structural network parameters; PDB mining of human cancer biomarkers and drug targets in parasites and bacteria

Lipid-Binding Proteins (LIBPs) or Fatty Acid-Binding Proteins (FABPs) play an important role in many diseases such as different types of cancer, kidney injury, atherosclerosis, diabetes, intestinal ischemia and parasitic infections. Thus, the computational methods that can predict LIBPs based on 3D structure parameters became a goal of major importance for drug-target discovery, vaccine design and biomarker selection. In addition, the Protein Data Bank (PDB) contains 3000+ protein 3D structures with unknown function. This list, as well as new experimental outcomes in proteomics research, is a very interesting source to discover relevant proteins, including LIBPs. However, to the best of our knowledge, there are no general models to predict new LIBPs based on 3D structures. We developed new Quantitative Structure-Activity Relationship (QSAR) models based on 3D electrostatic parameters of 1801 different proteins, including 801 LIBPs. We calculated these electrostatic parameters with the MARCH-INSIDE software and they correspond to the entire protein or to specific protein regions named core, inner, middle, and surface. We used these parameters as inputs to develop a simple Linear Discriminant Analysis (LDA) classifier to discriminate 3D structure of LIBPs from other proteins. We implemented this predictor in the web server named LIBP-Pred, freely available at , along with other important web servers of the Bio-AIMS portal. The users can carry out an automatic retrieval of protein structures from PDB or upload their custom protein structural models from their disk created with LOMETS server. We demonstrated the PDB mining option performing a predictive study of 2000+ proteins with unknown function. Interesting results regarding the discovery of new Cancer Biomarkers in humans or drug targets in parasites have been discussed here in this sense.     

An integrated approach using orthogonal analytical techniques to characterize heparan sulfate structure

Heparan sulfate (HS), a glycosaminoglycan present on the surface of cells, has been postulated to have important roles in driving both normal and pathological physiologies. The chemical structure and sulfation pattern (domain structure) of HS is believed to determine its biological function, to vary across tissue types, and to be modified in the context of disease. Characterization of HS requires isolation and purification of cell surface HS as a complex mixture. This process may introduce additional chemical modification of the native residues. In this study, we describe an approach towards thorough characterization of bovine kidney heparan sulfate (BKHS) that utilizes a variety of orthogonal analytical techniques (e.g. NMR, IP-RPHPLC, LC-MS). These techniques are applied to characterize this mixture at various levels including composition, fragment level, and overall chain properties. The combination of these techniques in many instances provides orthogonal views into the fine structure of HS, and in other instances provides overlapping / confirmatory information from different perspectives. Specifically, this approach enables quantitative determination of natural and modified saccharide residues in the HS chains, and identifies unusual structures. Analysis of partially digested HS chains allows for a better understanding of the domain structures within this mixture, and yields specific insights into the non-reducing end and reducing end structures of the chains. This approach outlines a useful framework that can be applied to elucidate HS structure and thereby provides means to advance understanding of its biological role and potential involvement in disease progression. In addition, the techniques described here can be applied to characterization of heparin from different sources.     

缺铁和矫治缺铁对梨树叶片结构的影响

通过对不同缺铁黄化程度的酥梨叶片进行解剖结构分析和矫治缺铁后叶片解剖结构的恢复情况的研究,结果表明,缺铁黄化使叶片厚度,叶肉厚度,栅栏组织厚度,栅栏组织／海绵组织的比值均明显下降;栅栏组织细胞排列疏松,细胞变短甚至断裂成块状,叶绿体数量明显减少甚至无,并出现解体细胞;栅栏组织与海绵组织界限模糊,海绵组织细胞排列变密;维管束的导管口径变小,维管束鞘和韧皮部的细胞番红染色加重。进行缺铁黄化矫治后,叶片结构恢复正常。这些结构的变化,可作为梨树缺铁诊断和矫治的指标。     

Small-scale batch crystallization of proteins revisited: an underutilized way to grow large protein crystals

Growth of high-quality crystals is a major obstacle in many structural investigations. In recent years, the techniques for screening crystals have improved dramatically, whereas the methods for obtaining large crystals have progressed more slowly. This is an important issue since, although many structures can be solved from small crystals with synchrotron radiation, it is far easier to solve and refine structures when strong data is recorded from large crystals. In an effort to improve the size of crystals, a strategy for a small-scale batch method has been developed that in many cases yields far larger crystals than attainable by vapor diffusion.     

Multiple sequence alignment: Algorithms and applications

Elucidation of interrelationships among sequence, structure, function, and evolution (FESS relationships) of a family of genes or gene products is a central theme of modern molecular biology. Multiple sequence alignment has been proven to be a powerful tool for many fields of studies such as phylogenetic reconstruction, illumination of functionally important regions, and prediction of higher order structures of proteins and RNAs. However, it is far too trivial to automatically construct a multiple alignment from a set of related sequences. A variety of methods for solving this computationally difficult problem are reviewed. Several important applications of multiple alignment for elucidation of the FESS relationships are also discussed.For a long period, progressive methods have been the only practical means to solve a multiple alignment problem of appreciable size. This situation is now changing with the development of new techniques including several classes of iterative methods. Today's progress in multiple sequence alignment methods has been made by the multidisciplinary endeavors of mathematicians, computer scientists, and biologists in various fields including biophysicists in particular. The ideas are also originated from various backgrounds, pure algorithmics, statistics, thermodynamics, and others. The outcomes are now enjoyed by researchers in many fields of biological sciences.In the near future, generalized multiple alignment may play a central role in studies of FESS relationships. The organized mixture of knowledge from multiple fields will ferment to develop fruitful results which would be hard to obtain within each area. I hope this review provides a useful information resource for future development of theory and practice in this rapidly expanding area of bioinformatics.     

A case study of Chinese bound feet: application of footprint analysis

Foot print patterns of the bound feet of a 90-year-old Chinese female were made to obtain insight into the ergonomic consequences of a Chinese custom that caused significant disabilities for many women throughout history. Pressure patterns were evaluated using the techniques applied to standard thumb print analsyis. A digital summary of the pressure patterns were compared to the patterns obtained from a normal subject. The outcomes indicated that the bound foot produced greater plantar tissue pressures than the non-bound foot. These observations help explain the discomfort, gait abnormalities, and disabilities exhibited by many older women with bound feet living in China today. Although foot-binding is no longer practiced, this study offers an ergonomic perspective on a custom practiced in China for centuries.     

Twenty years of numerical syntaxonomy

The development of numerical syntaxonomy during its first 20 yr is reviewed. The use of methods of numerical classification and ordination is the dominating feature of the development. National and local phytosociological data banks were established, large data sets handled and many important vegetation monographs were methodically based on multivariate data analysis. Particularly the development in Italy, the Netherlands, Czechoslovakia, and Sweden contributed to new theoretical elements of numerical syntaxonomy. Ordination became a common tool of searching for reticulate synsystematic relations between community types. The most popular ordination techniques have been Principal Components Analysis and Detrended Correspondence Analysis. Hierarchical agglomerative techniques of clustering still prevail in classification, although the divisive strategy of TWINSPAN has also become an effective tool for phytosociological clustering and table sorting. Extensive program packages, also for personal computers have now become standard equipment for many vegetation scientists.     

Opportunities for biomineralization research using multiscale computed X-ray tomography as exemplified by bone imaging

Biominerals typically have complex hierarchical structures traversing many length scales. This makes their structural characterization complicated, since it requires 3D techniques that can probe full specimens at down to nanometer-resolution, a combination that is difficult – if not impossible – to achieve simultaneously. One challenging example is bone, a mineralized tissue with a highly complex architecture that is replete with a network of cells. X-ray computed tomography techniques enable multiscale structural characterization through the combination of various equipment and emerge as promising tools for characterizing biominerals. Using bone as an example, we discuss how combining different X-ray imaging instruments allow characterizing bone structures from the nano- to the organ-scale. In particular, we compare and contrast human and rodent bone, emphasize the importance of the osteocyte lacuno-canalicular network in bone, and finally illustrate how combining synchrotron X-ray imaging with laboratory instrumentation for computed tomography is especially helpful for multiscale characterization of biominerals.     

Radiation-induced changes of fibroblasts in the squamous cell carcinoma of the head and neck

The regrowth of mesenchymal tissue (stroma) surrounding the malignant epithelium is an important step in tissue remodelling during and after irradiation. The radiation-induced fibroblastic changes were studied on tissue samples taken before, during and after the radical irradiation of the squamous cell carcinoma of the head and neck. Elongated fibroblasts with large amount of rough endoplasmic reticulum were seen around the tumor epithelium before radiation. The fibrosis increased during irradiation and at the same time the shape of the fibroblasts changed so that they became more triangular and nuclear structures became more prominent together with hyperchromasia. The amount of cell organelles declined although there was a large amount collagen present. Epithelial cells invaded through the basal lamina. In most samples the basal lamina could not be seen at all and the tumor cells were dispersed between stromal elements. On the other hand there were close contacts between epithelial and mesenchymal cells throughout the study in places where the basal lamina was broken, which might indicate epithelio-mesenchymal interaction. Also the connective tissue formed by fibroblasts and collagen might be part of the radiation induced healing and destruction of the tumor cells.     

Permeabilized cell and skinned fiber techniques in studies of mitochondrial function in vitro

In this chapter we describe in details the permeabilized cell and skinned fiber techniques and their applications for studies of mitochondrial function in vivo. The experience of more than 10 years of research in four countries is summarized. The use of saponin in very low concentration (50-100 g/ml) for permeabilisation of the sarcolemma leaves all intracellular structures, including mitochondria, completely intact. The intactness of mitochondrial function in these skinned muscle fibers is demonstrated in this work by multiple methods, such as NADH and flavoprotein fluorescence studies, fluorescence imaging, confocal immunofluorescence microscopy and respiratory analysis. Permeabilized cell and skinned fiber techniques have several very significant advantages for studies of mitochondrial function, in comparison with the traditional methods of use of isolated mitochondria: (1) very small tissue samples are required; (2) all cellular population of mitochondria can be investigated; (3) most important, however, is that mitochondria are studied in their natural surrounding. The results of research by using this method show the existence of several new phenomenon - tissue dependence of the mechanism of regulation of mitochondrial respiration, and activation of respiration by selective proteolysis. These phenomena are explained by interaction of mitochondria with other cellular structures in vivo. The details of experimental studies with use of these techniques and problems of kinetic analysis of the results are discussed. Examples of large-scale clinical application of these methods are given.     

Large Ice Crystals in the Nucleus of Rapidly Frozen Liver Cells

Evidence in the literature shows that ice crystals that form in the nucleus of many rapidly cooled cells appear much larger than the ice crystals that form in the surrounding cytoplasm. We investigated the phenomenon in our laboratory using the techniques of freeze substitution and low temperature scanning electron microscopy on liver tissue frozen by liquid nitrogen plunge freezing. This method is estimated to cool the tissue at 1000°C/min. The results from these techniques show that the ice crystal sizes were statistically significantly larger in the nucleus than in the cytoplasm. It is our belief that this finding is important to cryobiology considering its potential role in the process of freezing and the mechanisms of damage during freezing of cells and tissues.     

植物水分利用策略研究进展

水分是影响植物生长发育的重要因子之一。地球上大多数生态系统中的植物都会经历一个降水相对稀少的干旱季节,植物在不同的季节与不同的生态系统中究竟如何利用水分,利用哪些水分去获得生存,成为一个人们关注的问题。在过去的20年,稳定同位素技术在植物生态学中的应用得到了稳定长足的发展。因为陆地植物(少数排盐种类除外)在水分吸收过程中不发生同位素分馏,因此可以利用δD与δ18O数据进行水分获取方式的研究。对植物木质部水分以及其潜在水源的稳定同位素进行分析,并参考土壤水势、叶片水势、土壤含水量等数据,同时运用二元或三元混合模型,可以定量确定植物的水分利用来源。大量的研究表明,不同功能型、生长阶段、季节的植物以及不同物种往往具有不同的水分利用策略。     

Lectin binding sites of glycoproteins as revealed by lectin-gold-silver and lectin-peroxidase-diaminobenzidine methods

Summary For the precise histochemical detection of lectin binding sites of glycoproteins, the results obtained by lectin-gold-silver (LT-G-S) staining methods have been systematicaly compared with those revealed by alternative techniques of lectin-peroxidase-diaminobenzidine (LT-PO-DAB) reactions in a series of organs from different mammalian species.Ricinus communis agglutinin-I and concanavalin A were the lectins used in the present study. In the tissues subjected to the LT-G-S procedures, reactive tissue structures exhibited positive reactions of varying intensities of black. The results of control staining for the LT-G-S methods substantiated the view that the reaction products demonstrated the precise lectin binding sites of glycoproteins. The staining images obtained by the LT-PO-DAB techniques were not necessarily correlated precisely with those revealed by the LT-G-S procedures, and unavoidable background staining in pale brownish shades was noted in the majority of LT-G-S negative tissue structures. In view of these results, the LT-G-S staining methods employed in the present study are believed to be a reliable technique for the precise localization of saccharide residues of glycoproteins in light microscopy.