Against the naming of fungi

The use of molecular bar-coding and consensus on nomenclatural practices has encouraged optimism about the future of fungal taxonomy and systematics. There are, however, profound deficiencies in our understanding of fungal diversity and broader problems with the taxonomic enterprise that deserve greater attention. For 250 years mycologists have tried to reconcile fungal diversity with the Linnean fantasy of a divine order throughout nature that included unambiguous species. This effort has failed and today's taxonomy rests on an unstable philosophical foundation. Rather than persisting with the present endeavour, it may be more fruitful to abandon the notion of fungal species pending further basic research. In the meantime, mycologists should consider tagging collections with digital codes and assigning these operational taxonomic units to higher taxonomic ranks whose objective reality is corroborated by strong phylogenetic evidence.     

WHAT ARE THE CHROMIDIA OF POLYPHAGUS EUGLENAE?

Zoospores, prosporangia, and asexual sporangia were studied with electron microscopy to determine the ultrastructural identification of “chromidia,” granular masses surrounding nuclei that classical mycologists believed to be extruded chromatin used for lipid synthesis. In the zoospore the nucleus was enclosed by an aggregation of ribosomes. In other developmental stages the behavior of microbodies was identical to that described for “chromidia.” A microbody network with interspersed ER surrounded nuclei in young prosporangia. As the prosporangium matured, lipid globules became associated with the microbodies. When the single, large nucleus migrated into the elongate asexual sporangium, microbodies still surrounded the nucleus; but after the nucleus divided and a multinucleate sporangium formed, microbodies were scattered throughout the cytoplasm. When incubated in the diaminobenzidine medium for the cytochemical detection of catalase, reaction product was found in these microbodylike structures, confirming that “chromidia” described in prosporangia and asexual sporangia by classical mycologists are really microbodies. Rather than giving rise to lipid, these microbodies are probably involved in the metabolism of the lipid globules with which they are associated. The “chromidia” in zoospores are not extruded chromatin as suggested earlier, but correspond in their location around the nucleus to an aggregation of ribosomes.     

Structure of complex viruses and virus-infected cells by electron cryo tomography

In microbiology, and in particular in virus research, electron microscopy (EM) is an important tool, offering a broad approach for investigating viral structure throughout their intracellular and extracellular life cycles. Currently, molecular tools and rapid developments in advanced light microscopy dominate the field and supply an enormous amount of information concerning virus biology. In recent years, numerous fascinating high-resolution EM structures obtained by single-particle electron cryo microscopy (cryo-EM) were revealed for viral particles that possess icosahedral symmetry. However, no comprehensive three-dimensional analysis of complex viruses or viruses within cells has yet been achieved using EM. Recent developments in electron cryo-tomography render this a proficient tool for the analysis of complex viruses and viruses within cells in greater detail.     

三维电子显微镜方法进展

从生物样品（细胞或大分子）的电镜图象重组其三维结构的方法近年取得了重大进展,这是冷冻电镜样品制备、电镜设备、图象处理和分析方法等几方面进步的综合结果。三维电镜方法的进步和完善,使细胞和学家得以了解在复杂的细胞过程中各种相关细胞器之间的空间关系,而使分子生物学家不仅可以研究那些能够形成二维结晶的样品,并为分析具有重要生物功能但不能形成二维结晶的大分子或分子聚休物的结构提供了一种强大的手段。     

Malassezia Baillon, emerging clinical yeasts

The human and animal pathogenic yeast genus Malassezia has received considerable attention in recent years from dermatologists, other clinicians, veterinarians and mycologists. Some points highlighted in this review include recent advances in the technological developments related to detection, identification, and classification of Malassezia species. The clinical association of Malassezia species with a number of mammalian dermatological diseases including dandruff, seborrhoeic dermatitis, pityriasis versicolor, psoriasis, folliculitis and otitis is also discussed.     

Genomics of the filamentous fungi - moving from the shadow of the bakers yeast

Fungi have now well and truly entered the genomic age. We currently know the complete DNA sequence for 18 fungal species and many more fungal genome sequencing projects are in progress. Whilst yeasts dominated the early genomic years, recently there has been a dramatic increase in filamentous fungal genome projects. The implications of this wealth of genetic information for mycologists worldwide is immense. In this review we summarise the background to fungal genome projects with an emphasis on the filamentous fungi. We discuss efforts to determine gene function and to compare genomes from different species. Since this is such a fast-moving field, useful web sites are listed that will enable the reader to keep up to date with developments.     

Bridging fluorescence microscopy and electron microscopy

Development of new fluorescent probes and fluorescence microscopes has led to new ways to study cell biology. With the emergence of specialized microscopy units at most universities and research centers, the use of these techniques is well within reach for a broad research community. A major breakthrough in fluorescence microscopy in biology is the ability to follow specific targets on or in living cells, revealing dynamic localization and/or function of target molecules. One of the inherent limitations of fluorescence microscopy is the resolution. Several efforts are undertaken to overcome this limit. The traditional and most well-known way to achieve higher resolution imaging is by electron microscopy. Moreover, electron microscopy reveals organelles, membranes, macromolecules, and thus aids in the understanding of cellular complexity and localization of molecules of interest in relation to other structures. With the new probe development, a solid bridge between fluorescence microscopy and electron microscopy is being built, even leading to correlative imaging. This connection provides several benefits, both scientifically as well as practically. Here, I summarize recent developments in bridging microscopy.     

虫生真菌研究与应用的发展与机遇 ——2012年虫生真菌专刊序言

我国从事虫生真菌基础及应用研究的人员众多,各方面均取得了重要的研究成果。2012年“虫生真菌专刊”收集了国内关于虫生真菌资源、基因克隆及活性成分代谢等方面的最新研究进展。进一步的基础研究,应加强致病基因功能和真菌-昆虫分子相互作用等研究,以提高真菌杀虫剂或药用虫生真菌的应用效率。     

Depositing electron microscopy maps

A meeting was held at the European Bioinformatics Institute (EBI) in Hinxton, United Kingdom to discuss recent progress in the development of EMD, a database for maps determined by electron microscopy that is now integrated with MSD, the macromolecular structure database at EBI. This meeting of representatives of many of the major image processing groups in electron microscopy also discussed possible software developments that would ease the documentation and deposition of such datasets. The meeting concluded with a strong endorsement of map deposition in electron microscopy and its linkage with the family of archival databases in biomedical research.     

中国银耳研究之历史回顾

银耳是一种经济价值很高的食用菌,又是我国医学中一种久负盛名的药用真菌.我国的银耳研究凝聚着几代菌物学家和科技人员的心血和汗水,在银耳纯菌种的分离培养、生活史、生态系、遗传育种、分子生物学及人工栽培等研究方面,经过艰苦的努力和富于创意的探究,终于取得了诸多颇有分量的科研成果,推动了生产力的大发展,创造了显著的社会效益和经济效益.回顾中国银耳的研究历程,我国的菌物学科研工作者,特别是菌物学的前辈们,在缺资金、缺设备的艰苦条件下,始终坚持科研与生产实际紧密结合,取得了一个又一个辉煌的成果.是我们学习的楷模,将激励着我们在科学发展的道路上锐意进取,开拓创新!     

The ups and downs of beam damage,contrast and noise in biological electron microscopy

A personal account of the early problems associated with contrast in images obtained by electron microscopy from biological specimens is presented, together with the effects of electron beam damage. The author's experiences with different types of electron microscope as well as problems of contrast enhancement is described. A short account is given of the physical effects occuring during specimen preparation and their relation to structural preservation when attempting to achieve atomic resolution. Recent developments in biological electron microscopy are also discussed with a view to future trends.     

The evolutionary ecology of myco-heterotrophy

Nonphotosynthetic mycorrhizal plants have long attracted the curiosity of botanists and mycologists, and they have been a target for unabated controversy and speculation. In fact, these puzzling plants dominated the very beginnings of the field of mycorrhizal biology. However, only recently has the mycorrhizal biology of this diverse group of plants begun to be systematically unravelled, largely following a landmark Tansley review a decade ago and crucial developments in the field of molecular ecology. Here I explore our knowledge of these evolutionarily and ecologically diverse plant-fungal symbioses, highlighting areas where there has been significant progress. The focus is on what is arguably the best understood example, the monotropoid mycorrhizal symbiosis, and the overarching goal is to lay out the questions that remain to be answered about the biology of myco-heterotrophy and epiparasitism.     

Seeing is believing: the impact of electron microscopy on autophagy research

Autophagy was first discovered by transmission electron microscopy more than 50 years ago. For decades, electron microscopy was the only way to reliably detect autophagic compartments in cells because no specific protein markers were known. In the 1970s, however, the introduction of biochemical methods enabled quantitative studies of autophagic-lysosomal degradation, and in the 1980s specific biochemical assays for autophagic sequestration became available. Since the identification of autophagy-related genes in the 1990s, combined fluorescence microscopy, biochemical and genetic methods have taken the leading role in autophagy research. However, electron microscopy is still needed to confirm and verify results obtained by other methods, and also to produce novel knowledge that would not be achievable by any other experimental approach. Confocal microscopy, with its ever-improving resolution, is probably the best-suited morphological approach to investigate the dynamic aspects of autophagy. However, for analyzing the ultrastructural details of the many novel organelles and mechanisms involved in specific subtypes of autophagy, the electron microscope is still indispensable. This review will summarize the impact that electron microscopy has had on autophagy research since the discovery of this self-degradation process in the mid-1950s. Astonishingly, some of the "novel" concepts and principles of autophagy, presented in the recent studies, were already proposed several decades ago by the pioneering, accurate and passionate work of virtuoso electron microscopists.     

Seeing is believing: The impact of electron microscopy on autophagy research

Autophagy was first discovered by transmission electron microscopy more than 50 years ago. For decades, electron microscopy was the only way to reliably detect autophagic compartments in cells because no specific protein markers were known. In the 1970s, however, the introduction of biochemical methods enabled quantitative studies of autophagic-lysosomal degradation, and in the 1980s specific biochemical assays for autophagic sequestration became available. Since the identification of autophagy-related genes in the 1990s, combined fluorescence microscopy, biochemical and genetic methods have taken the leading role in autophagy research. However, electron microscopy is still needed to confirm and verify results obtained by other methods, and also to produce novel knowledge that would not be achievable by any other experimental approach. Confocal microscopy, with its ever-improving resolution, is probably the best-suited morphological approach to investigate the dynamic aspects of autophagy. However, for analyzing the ultrastructural details of the many novel organelles and mechanisms involved in specific subtypes of autophagy, the electron microscope is still indispensable. This review will summarize the impact that electron microscopy has had on autophagy research since the discovery of this self-degradation process in the mid-1950s. Astonishingly, some of the “novel” concepts and principles of autophagy, presented in the recent studies, were already proposed several decades ago by the pioneering, accurate and passionate work of virtuoso electron microscopists.     

Electron microscopy—The U.K. involvement

The development of the electron microscope in the advanced form we know today is the result of a loosely organized but effective world-wide scientific and technological collaboration, that readily transcends national and cultural barriers. The birth of the subject was undoubtedly in Berlin but the United Kingdom has played a prominent part, sometimes in an accidental way, at critical periods in this development both at the scientific and manufacturing level. In 1927, for example, G.P. Thompson established experimentally the wave nature of the electron and its scattering and diffraction by thin foils. This followed his invention of the electron diffraction camera at a time when De Broglie's postulates on the wave of nature of the electron were not enjoying much support, even in his native France. C.W. Oatley in Cambridge University was successful in introducing the first commercial scanning electron microscope (SEM) where several commercial firms had previously failed. D. Gabor invented electron holography in a moment of boredom while watching a tennis match. The U.K. has also played a key role in fostering international collaboration by means of conferences and exchange visits between electron microscopists. The present paper concentrates on some of the critical developments that took place in the U.K. in the commercial development of transmission electron microscopy, in scanning electron microscopy and more recently in high resolution electron microscopy. These developments are placed as far as possible in a world-wide context.     

XMIPP: a new generation of an open-source image processing package for electron microscopy

X-windows based microscopy image processing package (Xmipp) is a specialized suit of image processing programs, primarily aimed at obtaining the 3D reconstruction of biological specimens from large sets of projection images acquired by transmission electron microscopy. This public-domain software package was introduced to the electron microscopy field eight years ago, and since then it has changed drastically. New methodologies for the analysis of single-particle projection images have been added to classification, contrast transfer function correction, angular assignment, 3D reconstruction, reconstruction of crystals, etc. In addition, the package has been extended with functionalities for 2D crystal and electron tomography data. Furthermore, its current implementation in C++, with a highly modular design of well-documented data structures and functions, offers a convenient environment for the development of novel algorithms. In this paper, we present a general overview of a new generation of Xmipp that has been re-engineered to maximize flexibility and modularity, potentially facilitating its integration in future standardization efforts in the field. Moreover, by focusing on those developments that distinguish Xmipp from other packages available, we illustrate its added value to the electron microscopy community.     

Fungal research in ASEAN countries

A preliminary survey on the mycological activities and areas of research in ASEAN countries was conducted. This survey was carried out through a literature search and correspondence with some ASEAN mycologists. The results of the survey showed that there is a high level and standard of mycological research in various ASEAN countries. These include research on fungal flora and taxonomy, physiology and development, biochemistry, molecular biology, genetics, fungal-plant interactions, bioconversion, biodeterioration, and edible mushrooms. Compilation and publication of works of ASEAN mycologists is important for the promotion of contacts and collaborative research. This short paper is a preliminary step towards this objective.     

Scanning electron microscopy in gastric adenocarcinoma and intestinal metaplasia

In recent years scanning electron microscopy has been used in gastric biopsy studies, contributing to better recognition of intestinal metaplasia and carcinoma, as a complement to light and transmission electron microscopy. During the second half of 1983, 53 cases of gastric carcinoma were diagnosed at the Department of Pathology of Hospital Mexico, of which six were studied ultrastructurally. A pattern similar to that of intestinal epithelium was found in cases of intestinal metaplasia. Well differentiated adenocarcinomas showed marked tumor cell proliferation with irregular "projections". In poorly differentiated carcinomas, changes were limited to areas where tumor cells invaded the epithelial surface. In summary, scanning electron microscopy is of great help in research and diagnosis of pathologic changes occurring in mucosal surfaces.     

鸡马立克氏病毒抗性相关基因研究进展

马立克氏病（MD）对养禽业危害极大,可导致鸡群的免疫抑制,引起继发感染和免疫失败。然而,不同品系鸡对马立克氏病毒（MDV）抗性差异较大,呈现出较高的遗传相关性。近年来,随着MDV抗性研究的不断深入,与MDV抗性相关基因的研究已成为研究热点,本文就其研究进展作一综述。     

Hard X-ray micro(spectro)scopy: a powerful tool for the geomicrobiologists

During the past few decades, the use of electron microscopy approaches – many developed by Terry Beveridge – to probe the physiology of microorganisms has become a mainstay in fields including microbiology, human health, and geomicrobiology. Recent developments of third-generation synchrotron X-ray sources and X-ray-based microscopy approaches for studying microbial systems have proved their utility as complements to the very powerful approaches regularly employed by electron microscopists. In addition, in recent geomicrobiological studies, researchers have begun to take advantage of the strengths of each technique by using the superior spatial resolution of the electron microscope (relative to the X-ray microscope) and the superior elemental sensitivity of the X-ray microscope (relative to the electron microscope), along with the ability of the X-ray microscope to spatially probe the chemical speciation of elements. The benefits of integrating these two nanoprobes for investigating the same microenvironments within a geomicrobial system are far superior to those of independent studies separately employing each probe.