植物荧光原位杂交技术的发展及其在植物基因组分析中的应用

荧光原位杂交(FISH)是在染色体、间期核和DNA纤维上定位特定DNA序列的一种有效而精确的分子细胞遗传学方法。20年来,植物荧光原位杂交技术发展迅速:以增加检测的靶位数为目的,发展了双色FISH、多色FISH和多探针FISH鸡尾酒技术;为增加很小染色体目标的检测灵敏度,发展了BAC-FISH和酪胺信号放大FISH(TSA-FISH)等技术;以提高相邻杂交信号的空间分辨力为主要目的,发展了高分辨的粗线期染色体FISH、间期核FISH、DNA纤维FISH和超伸展的流式分拣植物染色体FISH技术。在植物基因组分析中,FISH技术发挥了不可替代的重要作用,它可用于:物理定位DNA序列,并为染色体的识别提供有效的标记;对相同DNA序列进行比较物理定位,探讨植物基因组的进化;构建植物基因组的物理图谱;揭示特定染色体区域的DNA分子组织;分析间期核中染色质的组织和细胞周期中染色体的动态变化;鉴定植物转基因。     

Conservation of neurogenic genes and mechanisms.

Reports from the past year have demonstrated that neural basic helix-loop-helix genes and LIM homeobox genes contribute to neuronal subtype specification in vertebrates and invertebrates, that Notch signaling specifies cell fates in the developing vertebrate inner ear, and that the organization of the central nervous system into three columns is shared by vertebrates and invertebrates. These findings pave the way for future work that will help to establish the extent to which these similarities represent evolutionary conservation.     

Die for the community: an overview of programmed cell death in bacteria

Programmed cell death is a process known to have a crucial role in many aspects of eukaryotes physiology and is clearly essential to their life. As a consequence, the underlying molecular mechanisms have been extensively studied in eukaryotes and we now know that different signalling pathways leading to functionally and morphologically different forms of death exist in these organisms. Similarly, mono-cellular organism can activate signalling pathways leading to death of a number of cells within a colony. The reason why a single-cell organism would activate a program leading to its death is apparently counterintuitive and probably for this reason cell death in prokaryotes has received a lot less attention in the past years. However, as summarized in this review there are many reasons leading to prokaryotic cell death, for the benefit of the colony. Indeed, single-celled organism can greatly benefit from multicellular organization. Within this forms of organization, regulation of death becomes an important issue, contributing to important processes such as: stress response, development, genetic transformation, and biofilm formation.     

Hierarchical phylogenetics as a quantitative analytical framework for evolutionary developmental biology

Phylogenetics has inherent utility in evolutionary developmental biology (EDB) as it is an established methodology for estimating evolutionary relationships and for making comparisons between levels of biological organization. However, explicit phylogenetic methods generally have been limited to two levels of organization in EDB-the species and the gene. We demonstrate that phylogenetic methods can be applied broadly to other organizational levels, such as morphological structures or cell types, to identify evolutionary patterns. We present examples at and between different hierarchical levels of organization to address questions central to EDB. We argue that this application of "hierarchical phylogenetics" can be a unifying analytical approach to the field of EDB.     

Mechano-regulated cell–cell signaling in the context of cardiovascular tissue engineering

Cardiovascular tissue engineering (CVTE) aims to create living tissues, with the ability to grow and remodel, as replacements for diseased blood vessels and heart valves. Despite promising results, the (long-term) functionality of these engineered tissues still needs improvement to reach broad clinical application. The functionality of native tissues is ensured by their specific mechanical properties directly arising from tissue organization. We therefore hypothesize that establishing a native-like tissue organization is vital to overcome the limitations of current CVTE approaches. To achieve this aim, a better understanding of the growth and remodeling (G&R) mechanisms of cardiovascular tissues is necessary. Cells are the main mediators of tissue G&R, and their behavior is strongly influenced by both mechanical stimuli and cell–cell signaling. An increasing number of signaling pathways has also been identified as mechanosensitive. As such, they may have a key underlying role in regulating the G&R of tissues in response to mechanical stimuli. A more detailed understanding of mechano-regulated cell–cell signaling may thus be crucial to advance CVTE, as it could inspire new methods to control tissue G&R and improve the organization and functionality of engineered tissues, thereby accelerating clinical translation. In this review, we discuss the organization and biomechanics of native cardiovascular tissues; recent CVTE studies emphasizing the obtained engineered tissue organization; and the interplay between mechanical stimuli, cell behavior, and cell–cell signaling. In addition, we review past contributions of computational models in understanding and predicting mechano-regulated tissue G&R and cell–cell signaling to highlight their potential role in future CVTE strategies.

     

Molecular basis of cell integrity and morphogenesis in Saccharomyces cerevisiae.

In fungi and many other organisms, a thick outer cell wall is responsible for determining the shape of the cell and for maintaining its integrity. The budding yeast Saccharomyces cerevisiae has been a useful model organism for the study of cell wall synthesis, and over the past few decades, many aspects of the composition, structure, and enzymology of the cell wall have been elucidated. The cell wall of budding yeasts is a complex and dynamic structure; its arrangement alters as the cell grows, and its composition changes in response to different environmental conditions and at different times during the yeast life cycle. In the past few years, we have witnessed a profilic genetic and molecular characterization of some key aspects of cell wall polymer synthesis and hydrolysis in the budding yeast. Furthermore, this organism has been the target of numerous recent studies on the topic of morphogenesis, which have had an enormous impact on our understanding of the intracellular events that participate in directed cell wall synthesis. A number of components that direct polarized secretion, including those involved in assembly and organization of the actin cytoskeleton, secretory pathways, and a series of novel signal transduction systems and regulatory components have been identified. Analysis of these different components has suggested pathways by which polarized secretion is directed and controlled. Our aim is to offer an overall view of the current understanding of cell wall dynamics and of the complex network that controls polarized growth at particular stages of the budding yeast cell cycle and life cycle.     

Coordinating cytoskeletal tracks to polarize cellular movements

For many years after the discovery of actin filaments and microtubules, it was widely assumed that their polymerization, organization, and functions were largely distinct. However, in recent years it has become increasingly apparent that coordinated interactions between microtubules and filamentous actin are involved in many polarized processes, including cell shape, mitotic spindle orientation, motility, growth cone guidance, and wound healing. In the past few years, significant strides have been made in unraveling the intricacies that govern these intertwined cytoskeletal rearrangements.     

Aspects of the three-dimensional intracellular organization of mesocarp cells as revealed by scanning electron microscopy

Summary The osmium-ligand binding technique and scanning electron microscopy have been applied to the study of the three-dimensional organization of mesocarp cells of a mature avocado fruit. Using this approach the mitochondria of the cells appear as elongated, branching structures and the endoplasmic reticulum consists of a complex of tubular strands, vesiculated strands and lamellar sheets. Associations of the endoplasmic reticulum with other organelles are also apparent. It is suggested that this approach provides a valuable means to assess the structural transitions in cell organization that occur during development or with functional changes.     

Meet the neighbours: tools to dissect nuclear structure and function

The eukaryotic cell nucleus displays a high degree of spatial organization, with discrete functional subcompartments that provide microenvironments where specialized processes take place. Concordantly, the genome also adopts defined conformations that, in part, enable specific genomic regions to interface with these functional centers. Yet the roles of many subcompartments and the genomic regions that contact them have not been explored fully. More fundamentally, it is not entirely clear how genome organization impacts function, and vice versa. The past decade has witnessed the development of a new breed of methods that are capable of assessing the spatial organization of the genome. These stand to further our understanding of the relationship between genome structure and function, and potentially assign function to various nuclear subcompartments. Here, we review the principal techniques used for analyzing genomic interactions, the functional insights they have afforded and discuss the outlook for future advances in nuclear structure and function dynamics.     

The foot formation stimulating peptide pedibin is also involved in patterning of the head in hydra

Avian neural crest cells migrate on precise pathways to their target areas where they form a wide variety of cellular derivatives, including neurons, glia, pigment cells and skeletal components. In one portion of their pathway, trunk neural crest cells navigate in the somitic mesoderm in a segmental fashion, invading the rostral, while avoiding the caudal, half-sclerotome. This pattern of cell migration, imposed by the somitic mesoderm, contributes to the metameric organization of the peripheral nervous system, including the sensory and sympathetic ganglia. At hindbrain levels, neural crest cells also travel from the neural tube in a segmental manner via three migratory streams of cells that lie adjacent to even-numbered rhombomeres. In this case, the adjacent mesoderm does not possess an obvious segmental organization, compared to the somitic mesoderm at trunk levels. Thus, the mechanisms by which the embryo controls segmentally-organized cell migrations have been a fascinating topic over the past several years. Here, I discuss findings from classical and recent studies that have delineated several of the tissue, cellular and molecular elements that contribute to the segmental organization of neural crest migration, primarily in the avian embryo. One common theme is that neural crest cells are prohibited from entering particular territories in the embryo due to the expression of inhibitory factors. However, permissive, migration-promoting factors may also play a key role in coordinating neural crest migration.     

The Ran GTPase: theme and variations

The small GTPase Ran has roles in multiple cellular processes, including nuclear transport, mitotic spindle assembly, the regulation of cell cycle progression and nuclear assembly. The past year has seen a remarkable unification of these different roles with respect to the effectors and mechanisms through which they function. Our emergent understanding of Ran suggests that it plays a central role in spatial and temporal organization of the vertebrate cell.     

Electric Field-Induced Transmembrane Potential Depends on Cell Density and Organizatio

Electrochemotherapy is a novel technique to enhance the delivery of chemotherapeutic drugs into tumor cells. In this procedure, electric pulses are delivered to cancerous cells, which induce membrane permeabilization, to facilitate the passage of cytotoxic drugs through the cell membrane. This study examines how electric fields interact with and polarize a system of cells. Specifically, we consider how cell density and organization impact on induced cell transmembrane potential due to an external electric field. First, in an infinite volume of spherical cells, we examined how cell packing density impacts on induced transmembrane potential. With high cell density, we found that maximum induced transmembrane potential is suppressed and that the transmembrane potential distribution is altered. Second, we considered how orientation of cell sheets and strands, relative to the applied field, affects induced transmembrane potential. Cells that are parallel to the field direction suppress induced transmembrane potential, and those that lie perpendicular to the applied field potentiate its effect. Generally, we found that both cell density and cell organization are very important in determining the induced transmembrane potential resulting from an applied electric field.     

Advances in fluorescent tracking of nucleic acids in living cells

Nucleic acids are typically detected in morphologically preserved fixed cells and tissues using in situ hybridization techniques. This review discusses a variety of established and more challenging fluorescence-based methods for the detection and tracking of DNA or RNA sequences in living cells. Over the past few years, various fluorescent in vivo labeling methods have been developed, and dedicated microscope and image analysis tools have been designed. These advances in technologies indicate that live-cell imaging of nucleic acids is likely to become a standard research tool for understanding genome organization and gene expression regulation in the near future. Recent live-cell imaging studies have already provided important insights into the dynamic behaviors of chromatin and RNAs in the cell.     

Signaling role of Cdc42 in regulating mammalian physiology

Cdc42 is a member of the Rho GTPase family of intracellular molecular switches regulating multiple signaling pathways involved in actomyosin organization and cell proliferation. Knowledge of its signaling function in mammalian cells came mostly from studies using the dominant-negative or constitutively active mutant overexpression approach in the past 2 decades. Such an approach imposes a number of experimental limitations related to specificity, dosage, and/or clonal variability. Recent studies by conditional gene targeting of cdc42 in mice have revealed its tissue- and cell type-specific role and provide definitive information of the physiological signaling functions of Cdc42 in vivo.     

An update on some structural aspects of the mighty miniwall

Peptidoglycan (PG), the mighty miniwall, is the main structural component of practically all bacterial cell envelopes and has been the subject of a wealth of research over the past 60 years, if only because its biosynthesis is the target of many antibiotics that have successfully been used in the treatment of bacterial infections. This review is mainly focused on the most recent achievements in research on the modification of PG glycan strands, which contribute to the resistance of bacteria to the host immune response to infection and to their own lytic enzymes, and on studies on the spatial organization of the macromolecule.     

Planar Cell Polarity: Keeping Hairs Straight Is Not So Simple

The fur on a cat''s back, the scales on a fish, or the bristles on a fly are all beautifully organized, with a high degree of polarization in their surface organization. Great progress has been made in understanding how individual cell polarity is established, but our understanding of how cells coordinate their polarity in forming coherent tissues is still fragmentary. The organization of cells in the plane of the epithelium is known as planar cell polarity (PCP), and studies in the past decade have delineated a genetic pathway for the control of PCP. This review will first briefly review data from the Drosophila field, where PCP was first identified and genetically characterized, and then explore how vertebrate tissues become polarized during development.     

Intermediate filaments: versatile building blocks of cell structure

Cytoskeletal intermediate filaments (IF) are organized into a dynamic nanofibrillar complex that extends throughout mammalian cells. This organization is ideally suited to their roles as response elements in the subcellular transduction of mechanical perturbations initiated at cell surfaces. IF also provide a scaffold for other types of signal transduction that together with molecular motors ferries signaling molecules from the cell periphery to the nucleus. Recent insights into their assembly highlight the importance of co-translation of their precursors, the hierarchical organization of their subunits in the formation of unit-length filaments (ULF) and the linkage of ULF into mature apolar IF. Analyses by atomic force microscopy reveal that mature IF are flexible and can be stretched to over 300% of their length without breaking, suggesting that intrafilament subunits can slide past one another when exposed to mechanical stress and strain. IF also play a role in the organization of organelles by modulating their motility and providing anchorage sites within the cytoplasm.     

The Nucleus Introduced

Now is an opportune moment to address the confluence of cell biological form and function that is the nucleus. Its arrival is especially timely because the recognition that the nucleus is extremely dynamic has now been solidly established as a paradigm shift over the past two decades, and also because we now see on the horizon numerous ways in which organization itself, including gene location and possibly self-organizing bodies, underlies nuclear functions.

“We have entered the cell, the Mansion of our birth, and started the inventory of our acquired wealth.”—Albert Claude

When I first read that morsel from Albert Claude’s 1974 Nobel Prize lecture it seemed Solomonic wisdom, as it indeed was. Though he was referring to cell biology en toto, the study of the nucleus was then at a tipping point and new advances were just at hand. Since then, the nucleus field has literally nucleated and we are now at a position to both admire the recent past and register excitement about the present and where the nucleus field may be headed.