Three decades of listeriology through the prism of technological advances

Decades of breakthroughs resulting from cross feeding of microbiological research and technological innovation have promoted Listeria monocytogenes to the rank of model microorganism to study host–pathogen interactions. The extraordinary capacity of this bacterium to interfere with a vast array of host cellular processes uncovered new concepts in microbiology, cell biology and infection biology. Here, we review technological advances that revealed how bacteria and host interact in space and time at the molecular, cellular, tissue and whole body scales, ultimately revolutionising our understanding of Listeria pathogenesis. With the current bloom of multidisciplinary integrative approaches, Listeria entered a new microbiology era.     

Introduction: microbiology and immunology: lessons learned from Salmonella.

Salmonella enterica, a Gram-negative bacterium, causes significant morbidity and mortality worldwide, and is an excellent model to study bacterial pathogenesis and cellular immune responses. With the development of powerful new technologies, there has been a fusion of research on immunology, molecular biology and cellular microbiology of S. enterica infections. This multidisciplinary research will enhance our understanding of the basic mechanisms of bacterial infections and immunity; it also provides new approaches towards therapeutic and control measures.     

Acute lymphoblastic leukemia and developmental biology

The latest scientific findings in the field of cancer research are redefining our understanding of the molecular and cellular basis of the disease, moving the emphasis toward the study of the mechanisms underlying the alteration of the normal processes of cellular differentiation. The concepts best exemplifying this new vision are those of cancer stem cells and tumoral reprogramming. The study of the biology of acute lymphoblastic leukemias (ALLs) has provided seminal experimental evidence supporting these new points of view. Furthermore, in the case of B cells, it has been shown that all the stages of their normal development show a tremendous degree of plasticity, allowing them to be reprogrammed to other cellular types, either normal or leukemic. Here we revise the most recent discoveries in the fields of B-cell developmental plasticity and B-ALL research and discuss their interrelationships and their implications for our understanding of the biology of the disease.     

Locating macromolecules and determining structures inside bacterial cells using electron cryotomography

Electron cryotomography (cryo-ET) is an imaging technique uniquely suited to the study of bacterial ultrastructure and cell biology. Recent years have seen a surge in structural and cell biology research on bacteria using cryo-ET. This research has driven major technical developments in the field, with applications emerging to address a wide range of biological questions. In this review, we explore the diversity of cryo-ET approaches used for structural and cellular microbiology, with a focus on in situ localization and structure determination of macromolecules. The first section describes strategies employed to locate target macromolecules within large cellular volumes. Next, we explore methods to study thick specimens by sample thinning. Finally, we review examples of macromolecular structure determination in a cellular context using cryo-ET. The examples outlined serve as powerful demonstrations of how the cellular location, structure, and function of any bacterial macromolecule of interest can be investigated using cryo-ET.     

Acute lymphoblastic leukemia and developmental biology: A crucial interrelationship

The latest scientific findings in the field of cancer research are redefining our understanding of the molecular and cellular basis of the disease, moving the emphasis toward the study of the mechanisms underlying the alteration of the normal processes of cellular differentiation. The concepts best exemplifying this new vision are those of cancer stem cells and tumoral reprogramming. The study of the biology of acute lymphoblastic leukemias (ALLs) has provided seminal experimental evidence supporting these new points of view. Furthermore, in the case of B cells, it has been shown that all the stages of their normal development show a tremendous degree of plasticity, allowing them to be reprogrammed to other cellular types, either normal or leukemic. Here we revise the most recent discoveries in the fields of B-cell developmental plasticity and B-ALL research and discuss their interrelationships and their implications for our understanding of the biology of the disease.Key words: leukemia, hematopoietic development, leukemic stem cells, lymphopoiesis, developmental plasticity, B cells, stem cells, cancer, B-ALL     

现代分子生物学技术在基础医学微生物学专业研究生培养中的作用

研究生教育是我国高等教育的重要组成部分,是国家创新发展的重要力量,现代分子生物学技术已广泛应用到各类医学研究生专业学科,并且成为了医学研究的基本技能,基础医学微生物学专业研究生是为微生物领域的科学研究提供高级后备人才,学习和掌握现代分子生物学技术势在必行。本文将对现代分子生物学技术在基础医学微生物学专业研究生教育中的应用及其意义,获得的实践效果进行阐述,为培养微生物学研究生的科研思路、学习基本的研究手段,从事生命科学研究提供一定的基础。     

以前沿进展启迪创新思维——“微生物生物学”课程特色专题讲座

"微生物生物学"课程作为理科基地学生的必修课程,对学生夯实专业基础理论知识、开拓科研视野具有积极而重要的作用。如何平衡基础与前沿、理论与实践、教学与科研之间的关系,对课程的内容、形式等都提出了更高的要求。为了丰富和增加学生对微生物学的理解和认识,为生物学理科基地学生明确研究方向提供信息。微生物生物学课程每学期安排8学时专题讲座,其内容不仅与本系教师的科研工作紧密相关,而且还邀请各领域校外专家,讲座内容丰富,涵盖了课程大纲中的主要内容。为学生们深刻明确学习目的、激发科研兴趣、启迪创新性思维搭建了一个平台。通过面对面的交流互动,同学们不仅可获得更多课外知识,了解当今微生物学领域的研究热点,还可从讲座专家那里获得更多切实的科研体会。     

Learning cell biology as a team: a project-based approach to upper-division cell biology

To help students develop successful strategies for learning how to learn and communicate complex information in cell biology, we developed a quarter-long cell biology class based on team projects. Each team researches a particular human disease and presents information about the cellular structure or process affected by the disease, the cellular and molecular biology of the disease, and recent research focused on understanding the cellular mechanisms of the disease process. To support effective teamwork and to help students develop collaboration skills useful for their future careers, we provide training in working in small groups. A final poster presentation, held in a public forum, summarizes what students have learned throughout the quarter. Although student satisfaction with the course is similar to that of standard lecture-based classes, a project-based class offers unique benefits to both the student and the instructor.     

The actin comet guides the way: How Listeria actin subversion has impacted cell biology,infection biology and structural biology

The discovery of the role of ActA to polymerise actin at one pole of Listeria monocytogenes represents a key event in the field of cellular microbiology. It uncovered much more than the molecular principle behind actin‐based motility of Listeria within the cytosol of infected cells, and it changed the way how actin dynamics could be studied and eventually understood. The ActA discovery took place at a time when cell biology, biochemistry and microbiology came together in a very fruitful fashion. Here, we provide an overview of the science that took place around this event. Then, we outline the wide array of research fields that have been impacted by this finding. This ranges from structural and biophysical investigations on actin and its dynamics, the role of actin polymerisation during infection with different pathogens, to actin‐dynamics during various pathologies. Like a comet in the sky, Pascale Cossart's work on ActA has inspired and will inspire generations of (life) scientists.     

Evolutionary cell biology: functional insight from “endless forms most beautiful”

In animal and fungal model organisms, the complexities of cell biology have been analyzed in exquisite detail and much is known about how these organisms function at the cellular level. However, the model organisms cell biologists generally use include only a tiny fraction of the true diversity of eukaryotic cellular forms. The divergent cellular processes observed in these more distant lineages are still largely unknown in the general scientific community. Despite the relative obscurity of these organisms, comparative studies of them across eukaryotic diversity have had profound implications for our understanding of fundamental cell biology in all species and have revealed the evolution and origins of previously observed cellular processes. In this Perspective, we will discuss the complexity of cell biology found across the eukaryotic tree, and three specific examples of where studies of divergent cell biology have altered our understanding of key functional aspects of mitochondria, plastids, and membrane trafficking.The field of cell biology has made tremendous strides in understanding eukaryotic cells, especially animals and yeast. Concurrently, evolutionary biology has opened up a window to the origins of our species and the genes that define us. Though these fields have intersected conceptually for decades, a recent movement is explicitly uniting these two fields into the discipline of evolutionary cell biology with great success (Brodsky et al., 2012 ; Lynch et al., 2014 ) and, we argue here, potentially an even greater future. One drive behind this movement is to harness the comparative approach of evolutionary biology and apply it to questions of cellular origins and cellular function. This approach has yielded beautiful insight into animal cellular function from mitotic spindle dynamics (Helmke and Heald, 2014 ) to glycosylation machinery (Varki, 2006 ). However, expanding the scope of investigation to organisms beyond fungi and animals to span eukaryotic diversity has allowed for discoveries that force us to adjust some fundamental ideas of how eukaryotic organelles work, and why.     

Zooming in on the cell biology of disease

Today’s cell biology could be considered a fusion of disciplines that blends advanced genetics, molecular biology, biochemistry, and engineering to answer fundamental as well as medically relevant scientific questions. Accordingly, our understanding of diseases is greatly aided by an existing vast knowledge base of fundamental cell biology. Gunter Blobel captured this concept when he said, “the tremendous acquisition of basic knowledge will allow a much more rational treatment of cancer, viral infection, degenerative disease and mental disease.” In other words, without cell biology can we truly understand, prevent, or effectively treat a disease?

R. M. Perera     

New insights into Whipple’s disease and Tropheryma whipplei infections

Whipple’s disease is a rare multi-systemic disease associated with the ubiquitous environmental bacterium Tropheryma whipplei. Over the last 10 years, since the isolation of the bacterium, recent advances in medical microbiology, epidemiology and cellular biology have provided major insights into the understanding of the pathophysiology of T. whipplei infections that may result in Whipple’s disease.     

Sequenced dermatophyte strains: growth rate, conidiation, drug susceptibilities, and virulence in an invertebrate model

Although dermatophytes are the most common cause of fungal infections in the world, their basic biology is not well understood. The recent sequencing and annotation of the genomes of five representative dermatophyte species allows for the creation of hypotheses as to how they cause disease and have adapted to their distinct environments. An understanding of the microbiology of these strains will be essential for testing these hypotheses. This study is the first to generally characterize these five sequenced strains of dermatophytes for their microbiological aspects. We measured the growth rate on solid medium and found differences between species, with Microsporum gypseum CBS118893 having the fastest growth and Trichophyton rubrum CBS118892 the slowest. We also compared different media for conidia production and found that the highest numbers of conidia were produced when dermatophytes were grown on MAT agar. We determined the Minimum Inhibitory Concentration (MIC) of nine antifungal agents and confirmed susceptibility to antifungals commonly used as selectable markers. Finally, we tested virulence in the Galleria mellonella (wax moth) larvae model but found the results variable. These results increase our understanding of the microbiology and molecular biology of these dermatophyte strains and will be of use in advancing hypothesis-driven research about dermatophytes.     

Cell biology in model systems as the key to understanding corals

Corals provide the foundation of important tropical reef ecosystems but are in global decline for multiple reasons, including climate change. Coral health depends on a fragile partnership with intracellular dinoflagellate symbionts. We argue here that progress in understanding coral biology requires intensive study of the cellular processes underlying this symbiosis. Such study will inform us on how the coral symbiosis will be affected by climate change, mechanisms driving coral bleaching and disease, and the coevolution of this symbiosis in the context of other host-microbe interactions. Drawing lessons from the broader history of molecular and cell biology and the study of other host-microbe interactions, we argue that a model-systems approach is essential for making effective progress in understanding coral cell biology.     

培育基础医学微生物学专业研究生人文素养和科学素养方式

微生物学是基础医学和生物学的重要基础学科,微生物学专业培养的研究生是微生物领域科学研究和教学的高级后备人才,随着基础医学的发展,对微生物学专业研究人员的人文素养和科学素养要求越来越高,本专业研究生全面发展培育方式的改革,已成为高等医学教育改革的重要课题。本研究针对基础医学微生物专业研究生培养的现状,根据基础医学微生物学专业研究生的特点,着重探讨其人文素养和科学素养培育方式的改革,为培养具有优良的科研能力、科学素养、健全人格的人才提供一定的思路。     

Focusing light on infection in four dimensions

The fusion of cell biology with microbiology has bred a new discipline, cellular microbiology, in which the primary aim is to understand host-pathogen interactions at a tissue, cellular and molecular level. In this context, we require techniques allowing us to probe infection in situ and extrapolate quantitative information on its spatiotemporal dynamics. To these ends, fluorescent light-based imaging techniques offer a powerful tool, and the state-of-the-art is defined by paradigms using so-called multidimensional (multi-D) imaging microscopy. Multi-D imaging aims to visualize and quantify biological events through time and space and, more specifically, refers to combinations of: three (3D, volume), four (4D, time) and five (5D, multiwavelength)-dimensional recordings. Successful multi-D imaging depends upon understanding the available technologies and their limitations. This is especially true in the field of microbiology where visualization of infectious/pathogenic activities inside living host systems presents particular technical challenges. Thus, as multi-D imaging rapidly becomes a common bench tool to the cellular microbiologist, this review provides the new user with some of the necessary technical insight required to get the best from these methods.     

Systems microscopy: An emerging strategy for the life sciences

Dynamic cellular processes occurring in time and space are fundamental to all physiology and disease. To understand complex and dynamic cellular processes therefore demands the capacity to record and integrate quantitative multiparametric data from the four spatiotemporal dimensions within which living cells self-organize, and to subsequently use these data for the mathematical modeling of cellular systems. To this end, a raft of complementary developments in automated fluorescence microscopy, cell microarray platforms, quantitative image analysis and data mining, combined with multivariate statistics and computational modeling, now coalesce to produce a new research strategy, “systems microscopy”, which facilitates systems biology analyses of living cells. Systems microscopy provides the crucial capacities to simultaneously extract and interrogate multiparametric quantitative data at resolution levels ranging from the molecular to the cellular, thereby elucidating a more comprehensive and richly integrated understanding of complex and dynamic cellular systems. The unique capacities of systems microscopy suggest that it will become a vital cornerstone of systems biology, and here we describe the current status and future prospects of this emerging field, as well as outlining some of the key challenges that remain to be overcome.     

A trip in the “New Microbiology” with the bacterial pathogen Listeria monocytogenes

Listeria monocytogenes is a food-borne pathogen causing an opportunistic disease called listeriosis. This bacterium invades and replicates in most cell types, due to its multiple strategies to exploit host molecular mechanisms. Research aiming at unravelling Listeria invasion and intracellular lifestyle has led to a number of key discoveries in infection biology, cell biology and also microbiology. In this review, we report on our most recent advances in understanding the intimate crosstalk between the bacterium and its host, resulting from in-depth studies performed over the past five years. We specifically highlight new concepts in RNA-based regulation in bacteria and discuss important findings in cell biology, including a new role for clathrin and an atypical mitochondrial fragmentation mechanism. We also illustrate the notion that bacterial infection regulates host gene expression at the chromatin level, contributing to an emerging field called patho-epigenetics. This review corresponds to the lecture given by one of us (P.C.) on the occasion of the 2014 FEBS|EMBO Woman in Science Award.     

Molecular biology and gene transfer in atherosclerosis in the stenting era

Atherosclerosis is the major cause of death in the developed world. Understanding the pathogenesis of atherosclerosis has been a major challenge to cardiovascular research over the past several decades. During this period a number of advances in various scientific disciplines has increased our understanding of this disease. These include improved understanding of the structural and functional components of normal vessel wall and more recently the use of cell biology and molecular biology techniques to elucidate the pathogenesis of atherosclerosis. None of these advances has been more dramatic nor has potentially more far reaching consequences as the application of molecular biology and gene technology to the practice of cardiovascular medicine. These developments have already opened new and exciting areas of vascular research and may in the future provide for earlier identification of genetic predisposition to atherosclerosis, strategic planning of preventive therapy and more tailored pharmacologic approaches for established disease.     

Controlling the maturation of pathogen-containing vacuoles: a matter of life and death

Once considered to be contained, infectious diseases of bacterial origin are now making a comeback. A lack of innovative therapies and the appearance of drug-resistant pathogens are becoming increasingly serious problems. A better understanding of pathogen-host interactions at the cellular and molecular levels is necessary to define new targets in our fight against microorganisms. In the past few years, the merging of cell biology and microbiology has started to yield critical and often surprising new information on the interactions that occur between various pathogens and their mammalian host cells. Here we focus on the intracellular routing of vacuoles containing microorganisms, as well as on the bacterial effectors and their host-cell targets that control vacuole maturation. We also describe new approaches for isolating microorganism-containing vacuoles and analysing their molecular composition, which will help researchers to define the molecules and mechanisms governing vacuole biogenesis.