Focused ion beam (FIB) combined with high resolution scanning electron microscopy: A promising tool for 3D analysis of chromosome architecture

Focused ion beam (FIB) milling in combination with field emission scanning electron microscopy (FESEM) was applied to investigations of metaphase barley chromosomes, providing new insight into the chromatin packaging in the chromosome interior and 3D distribution of histone variants in the centromeric region. Whole mount chromosomes were sectioned with FIB with thicknesses in the range of 7–20 nm, resulting in up to 2000 sections, which allow high resolution three-dimensional reconstruction. For the first time, it could be shown that the chromosome interior is characterized by a network of interconnected cavities, with openings to the chromosome surface. In combination with immunogold labeling, the centromere-correlated distribution of histone variants (phosphorylated histone H3, CENH3) could be investigated with FIB in three dimensions. Limitations of classical SEM analysis of whole mount chromosomes with back-scattered electrons requiring higher accelerating voltages, e.g. faint and blurred interior signals, could be overcome with FIB milling: from within the chromosome even very small labels in the range of 10 nm could be precisely visualized. This allowed direct quantification of marker molecules in a three-dimensional context. Distribution of DNA in the chromosome interior could be directly analyzed after staining with a DNA-specific platinorganic compound Platinum Blue. Higher resolution visualization of DNA distribution could be performed by preparation of FIB lamellae with the in situ lift-out technique followed by investigation in dark field with a scanning transmission electron detector (STEM) at 30 kV.     

Modeling circadian clocks: Roles,advantages, and limitations

Circadian rhythms are endogenous oscillations characterized by a period of about 24h. They constitute the biological rhythms with the longest period known to be generated at the molecular level. The abundance of genetic information and the complexity of the molecular circuitry make circadian clocks a system of choice for theoretical studies. Many mathematical models have been proposed to understand the molecular regulatory mechanisms that underly these circadian oscillations and to account for their dynamic properties (temperature compensation, entrainment by light dark cycles, phase shifts by light pulses, rhythm splitting, robustness to molecular noise, intercellular synchronization). The roles and advantages of modeling are discussed and illustrated using a variety of selected examples. This survey will lead to the proposal of an integrated view of the circadian system in which various aspects (interlocked feedback loops, inter-cellular coupling, and stochasticity) should be considered together to understand the design and the dynamics of circadian clocks. Some limitations of these models are commented and challenges for the future identified.     

Romanowsky staining in cytopathology: history,advantages and limitations

Abstract

If the entire discipline of diagnostic cytopathology could be distilled into a single theme, it would be the Papanicolaou stain. Yet it was the Romanowsky stain upon which the discipline of cytopathology was founded. Both stains are used today in the cytopathology laboratory, each for a different and complementary purpose. We trace the history of cytopathological stains and discuss the advantages and limitations of Romanowsky-type stains for cytological evaluation. We also provide suggestions for the advantageous use of Romanowsky-type stains in cytopathology.     

Transgenic mouse models of hormonal mammary carcinogenesis: advantages and limitations

Mouse models of breast cancer, especially transgenic and knockout mice, have been established as valuable tools in shedding light on factors involved in preneoplastic changes, tumor development and malignant progression. The majority of mouse transgenic models develop estrogen receptor (ER) negative tumors. This is seen as a drawback because the majority of human breast cancers present an ER positive phenotype. On the other hand, several transgenic mouse models have been developed that produce ER positive mammary tumors. These include mice over-expressing aromatase, ERα, PELP-1 and AIB-1. In this review, we will discuss the value of these models as physiologically relevant in vivo systems to understand breast cancer as well as some of the pitfalls involving these models. In all, we argue that the use of transgenic models has improved our understanding of the molecular aspects and biology of breast cancer.     

Evaluation of the CFP-substrate-YFP system for protease studies: advantages and limitations

A protease can be defined as an enzyme capable of hydrolyzing peptide bonds. Thus, characterization of a protease involves identification of target peptide sequences, measurement of activities toward these sequences, and determination of kinetic parameters. Biological protease substrates based on fluorescent protein pairs, which allow for use of fluorescence resonance energy transfer (FRET), have been recently developed for in vivo protease activity detection and represent a very interesting alternative to chemical substrates for in vitro protease characterization. Here, we analyze a FRET system consisting of cyan and yellow fluorescent proteins (CFP and YFP, respectively), which are fused by a peptide linker serving as protease substrate. Conditions for CFP-YFP fusion protein production in Escherichia coli and purification of proteins were optimized. FRET between CFP and YFP was found to be optimum at a pH between 5.5 and 10.0, at low concentrations of salt and a temperature superior to 25 degrees C. For efficient FRET to occur, the peptide linker between CFP and YFP can measure up to 25 amino acids. The CFP-substrate-YFP system demonstrated a high degree of resistance to nonspecific proteolysis, making it suitable for enzyme kinetic analysis. As with chemical substrates, substrate specificity of CFP-substrate-YFP proteins was tested towards different proteases and kcat/Km values were calculated.     

Some advantages and limitations of mitosis as a phylogenetic criterion

The advantages and disadvantages of mitosis as a phylogenetic character are discussed. Mitosis is suggested to be a good character on the grounds that it is universally applicable and that it reflects features of the basic organism since it is unlikely to have arisen through multiple endosymbiotic events. Since mitosis is an absolutely essential feature of the cell cycle it is subject to a great deal of evolutionary pressure and one would not expect a priori that relatively inefficient mitotic apparatuses would persist. It is suggested that supposedly primitive mitotic apparatuses are not inefficient and that the evidence that they are functionally different from those of higher organisms is largely negative electron microscopic evidence. This type of evidence is not very satisfactory since it can result from poor preservation and consequently it should be continually retested. Another weakness of mitosis as a phylogenetic criterion (shared with other essentially morphological criteria) is that there is no easy way to relate structural change with genetic change. Thus, while mitosis is a useful phylogenetic character, its usefulness is limited.     

Tuber aestivum Vittad. mycelium quantified: advantages and limitations of a qPCR approach

A quantitative real-time PCR (qPCR) marker Ta0 with hydrolysis probe (“TaqMan”), targeted to the internal transcribed spacer region of the ribosomal DNA, has been developed for quantification of summer truffle (Tuber aestivum) mycelium. Gene copy concentrations determined by the qPCR were calibrated against pure culture mycelium of T. aestivum, enabling quantification of the mycelium in soil and in host roots from the fields. Significant concentrations of the fungus were observed not only in the finest roots with ectomycorrhizae but also in other root types, indicating that the fungus is an important component of the microbial film at the root surface. The concentration of T. aestivum in soil is relatively high compared to other ectomycorrhizal fungi. To evaluate the reliability of the measurement of the soil mycelium density using qPCR, the steady basal extracellular concentration of the stabilized T. aestivum DNA should be known and taken into account. Therefore, we addressed the stability of the qPCR signal in soil subjected to different treatments. After the field soil was sieved, regardless of whether it was dried/rewetted or not, the T. aestivum DNA was quickly decomposed. It took just about 4 days to reach a steady concentration. This represents a conserved pool of T. aestivum DNA and determines detection limit of the qPCR quantification in our case. When the soil was autoclaved and recolonized by saprotrophic microorganisms, this conserved DNA pool was eliminated and the soil became free of T. aestivum DNA.     

植物三维染色质构型研究进展

染色质在细胞核内的缠绕、折叠及其在细胞核内的空间排布是真核生物染色质构型的主要特征。在经典DNA探针荧光原位杂交显微观察的基础上,基于新一代测序技术的Hi-C及ChIA-PET染色质构型捕获技术已经被广泛应用于动物及植物细胞核染色质构型的研究中,并以新的角度定义了包括:染色体(质)域(chromosome territory)、A/B染色质区室(compartment A/B)、拓扑偶联结构域(topological associated domains,TADs)、染色质环(chromatin loops)等在内的多个更为精细的染色质构型。利用以上两种主流技术,越来越多的植物物种染色质构型特征被鉴定、分析和比较。本文系统分析和总结了近年来以植物细胞为模型的细胞核染色构型领域取得的重要成果,包括各级染色质构型特征的组成、建立机制和主要影响因素等。在此基础上,分析了目前研究植物染色质构型技术的瓶颈和突破性的技术进展,并对后续研究主要关注的问题和研究内容进行了展望,以期为相关领域的研究提供更多的理论参考和依据。     

DNA-protein interactions and bacterial chromosome architecture

Bacteria, like eukaryotic organisms, must compact the DNA molecule comprising their genome and form a functional chromosome. Yet, bacteria do it differently. A number of factors contribute to genome compaction and organization in bacteria, including entropic effects, supercoiling and DNA-protein interactions. A gamut of new experimental techniques have allowed new advances in the investigation of these factors, and spurred much interest in the dynamic response of the chromosome to environmental cues, segregation, and architecture, during both exponential and stationary phases. We review these recent developments with emphasis on the multifaceted roles that DNA-protein interactions play.     

FIB/SEM tomography with TEM-like resolution for 3D imaging of high-pressure frozen cells

Focused ion beam/scanning electron microscopy (FIB/SEM) tomography is a novel powerful approach for three-dimensional (3D) imaging of biological samples. Thereby, a sample is repeatedly milled with the focused ion beam (FIB) and each newly produced block face is imaged with the scanning electron microscope (SEM). This process can be repeated ad libitum in arbitrarily small increments allowing 3D analysis of relatively large volumes such as eukaryotic cells. High-pressure freezing and freeze substitution, on the other hand, are the gold standards for electron microscopic preparation of whole cells. In this work, we combined these methods and substantially improved resolution by using the secondary electron signal for image formation. With this imaging mode, contrast is formed in a very small, well-defined area close to the newly produced surface. By using this approach, small features, so far only visible in transmission electron microscope (TEM) (e.g., the two leaflets of the membrane bi-layer, clathrin coats and cytoskeletal elements), can be resolved directly in the FIB/SEM in the 3D context of whole cells.     

Computer simulation modelling and visualization of 3D architecture of biological tissues

Recent technical improvements, such as 3D microscopy imaging, have shown the necessity of studying 3D biological tissue architecture during carcinogenesis. In the present paper a computer simulation model is developed allowing the visualization of the microscopic biological tissue architecture during the development of metaplastic and dysplastic lesions.The static part of the model allows the simulation of the normal, metaplastic and dysplastic architecture of an external epithelium. This model is associated to a knowledge base which contains only data on the nasal epithelium. The latter has been well studied by numerous authors and its lesional states are well known. An inference engine allows the initialization of the static model parameters. A statistical comparison between simulated epithelia and real epithelia is achieved by adjusting the parameter values during the simulation.The dynamic part of the model allows the simulation of a growth process on a 3D representation based on the static model. The main hypothesis is that nasal epithelium is submitted to a continuous transformation from normal to cancer through metaplasia and dysplasia. The evolution of each cell (represented by its nucleus) depends on its local environment and also on its heritage from its mother-cell.Simulation of tissue renewal of the nasal pseudostratified epithelium has been achieved. The evolution from normal to hyperplasia has been simulated. After modification of the cell cycle modelling, the simulation of the development of metaplastic foci has been obtained.     

The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture: 3D structured illumination microscopy of defined chromosomal structures visualized by 3D (immuno)-FISH opens new perspectives for studies of nuclear architecture

Three-dimensional structured illumination microscopy (3D-SIM) has opened up new possibilities to study nuclear architecture at the ultrastructural level down to the ~100 nm range. We present first results and assess the potential using 3D-SIM in combination with 3D fluorescence in situ hybridization (3D-FISH) for the topographical analysis of defined nuclear targets. Our study also deals with the concern that artifacts produced by FISH may counteract the gain in resolution. We address the topography of DAPI-stained DNA in nuclei before and after 3D-FISH, nuclear pores and the lamina, chromosome territories, chromatin domains, and individual gene loci. We also look at the replication patterns of chromocenters and the topographical relationship of Xist-RNA within the inactive X-territory. These examples demonstrate that an appropriately adapted 3D-FISH/3D-SIM approach preserves key characteristics of the nuclear ultrastructure and that the gain in information obtained by 3D-SIM yields new insights into the functional nuclear organization.     

Titin organisation and the 3D architecture of the vertebrate-striated muscle I-band

The giant muscle protein titin (connectin) is known to serve as a cytoskeletal element in muscle sarcomeres. It elastically restrains lengthening sarcomeres, it aids the integrity and central positioning of the A-band in the sarcomere and it may act as a template upon which some sarcomeric components are laid down during myogenesis. A puzzle has been how titin molecules, arranged systematically within the hexagonal A-band lattice of myosin filaments, can redistribute through the I-band to their anchoring sites in the tetragonal Z-band lattice. Recent work by Liversage and colleagues has suggested that there are six titin molecules per half myosin filament. Since there are two actin filaments per half myosin filament in a half sarcomere, this means that there are three titin molecules interacting with each Z-band unit cell containing one actin filament in the same sarcomere and one of opposite polarity from the next sarcomere. Liversage et al. suggested that the three titins might be distributed with two on an actin filament of one polarity and one on the filament of opposite polarity. Here, we build on this suggestion and discuss the transition of titin from the A-band to the Z-band. We show that there are good structural and mechanical reasons why titin might be organised as Liversage et al., suggested and we discuss the possible relationships between A-band arrangements in successive sarcomeres along a myofibril.     

Unusual chromosome architecture and behaviour at an HSR

Amplification of sequences within mammalian chromosomes is often accompanied by the formation of homogeneously staining regions (HSRs). The arrangement of DNA sequences within such amplicons has been investigated, but little is known about the chromosome structure or behaviour of these unusual regions. We have analysed the metaphase chromosome structure of the dihydrofolate reductase (DHFR) amplicon of CHOC400 cells. The chromatin in this region contains hyperacetylated nucleosomes yet, at the same time, appears to be densely packed like heterochromatin. The region does not bind heterochromatin proteins. We show that the dense packing of the region is restricted to DNA located close to the chromosome core/scaffold. In contrast, levels of the chromosome scaffold protein topoisomerase II at HSRs are the same as those found at other euchromatic locations. Metaphase chromosome condensation of the HSR is shown to be sensitive to topoisomerase II inhibitors, and sister chromatids often appear to remain attached within the HSRs at metaphase. We suggest that these features underlie anaphase bridging and the aberrant interphase structure of the HSR. The DHFR amplicon is widely used as a model system to study mammalian DNA replication. We conclude that the higher-order chromosome structure of this amplicon is unusual and suggest that caution needs to be exercised in extrapolating data from HSRs to normal chromosomal loci. Received: 19 October 1999; in revised form: 13 December 1999 / Accepted: 27 December 1999     

Micro CT and Micro MR imaging of 3D architecture of animal skeleton

Quantitative assessment of three-dimensional (3D) trabecular structural characteristics may improve our ability to understand the pathophysiology of osteoporosis, to test the efficacy of pharmaceutical intervention, and to estimate bone biomechanical properties. Considerable progress has been made in advanced imaging techniques for noninvasive and/or nondestructive assessment of 3D trabecular structure and connectivity. Micro computed tomography (microCT) has been used to measure 3D trabecular bone structure in rats, both in vivo and in vitro. It can directly quantify 3D trabecular bone structure such as trabecular volume, trabecular thickness, number, separation, structure model index, degree of anisotropy, and connectivity, in a model-independent manner. We have used microCT to study ovariectomy (OVX) induced osteopenia in rats and its treatment with agents such as estrogen, and sodium fluoride. We have demonstrated that 3D microCT can quantify mouse trabecular and cortical bone structure with an isotropic resolution of 9 microm(3). It is also useful for studying osteoporosis in mice and in phenotypes of transgenic mice or gene knockout mice. MicroCT can be used to quantify osteogenesis in mouse Ilizarov leg lengthening procedures, to quantify osteoconduction in a rat cranial defect model, and to quantify cortical bone porosity. Recently, microCT using high intensity and tight collimation synchrotron radiation to achieve spatial resolution of 1-2 microm has provided the capability to assess additional features such as resorption cavities. Unlike microCT, micro magnetic resonance imaging (IMRI) is nonionizing. Recently, the ability of microMRI to assess osteoporosis in animal models has been explored. Using a small, high-efficiency coil in a high-field imager, microMRI can give resolutions sufficient to discriminate individual trabeculae. We have shown that, with appropriate settings, it is possible to image trabecular bone in rats in vivo and in vitro. In our study of OVX rats, analysis of microMR images can demonstrate differences in rat trabecular bone that are not detected by DXA measurements. In a rabbit OA model, with the OA induced by meniscectomy or anterior cruciate ligament transection, MRI shows decreased cartilage thickness, subchondral osteosclerosis and osteophytes, while radiographs can only show subchondral osteosclerosis and osteophytes could not be found. Advanced imaging methods are able to measure 3D trabecular structure and connectivity in arbitrary orientations in a highly automated, objective, non-user-specific manner, allowing greater numbers of samples for unbiased comparisons between controls and the disordered or treated. They can be utilized on a large sample leading to fewer sampling errors. They are non-destructive allowing multiple tests such as biomechanical testing and chemical analysis on the same sample; and non-invasive permitting longitudinal studies and reducing the number of animals needed.