Living on the edge: parasite taxonomy in Australia

The way in which the huge Australian parasite fauna is described (discovery and naming) is the subject of this address. The approach to the task has never been well-organised so that a few groups of parasites are now relatively well-known because of the efforts of small groups of workers who have made sustained efforts in these groups, but equally some host-parasite systems have been almost completely ignored in that no worker has ever given them sustained attention. A high proportion of Australian parasites have been described by international workers. The sustaining of interest in a group of parasites over a long period is the key to real progress being made. The nature of the organisation of Australian science presently means that few positions are available for parasite taxonomists and funding for taxonomic research is scarce. Thus, parasite taxonomy (like the taxonomy of many groups of Australian plants and animals) can only be considered to be in crisis.     

Blood,sweat and plaster casts: Reviewing the history,composition, and scientific value of the Raymond A. Dart Collection of African Life and Death Masks

This paper addresses the history, composition and scientific value of one of the most comprehensive facemask collections in Africa, the Raymond A. Dart Collection of African Life and Death Masks. Housed within the School of Anatomical Sciences at the University of the Witwatersrand (South Africa), it comprises 1110 masks (397 life, 487 death, 226 unknown). Life masks represent populations throughout Africa; death masks predominately southern Africa. Males preponderate by 75%. Recorded ages are error prone, but suggest most life masks are those of <35 year-olds, death masks of 36+ year-olds. A total of 241 masks have associated skeletons, 209 presenting a complete skull.Life masks date between 1927 and c.1980s, death masks 1933 and 1963. This historical collection presents uncanny associations with outmoded typological and evolutionary theories. Once perceived an essential scientific resource, performed craniofacial superimpositions identify the nose as the only stable feature maintained, with the remaining face best preserved in young individuals with minimal body fat. The facemask collection is most viable for teaching and research within the history of science, specifically physical anthropology, and presents some value to craniofacial identification. Future research will have to be conducted with appropriate ethical considerations to science and medicine.     

Implicit-explicit methods for reaction-diffusion problems in pattern formation

Reaction-diffusion mechanisms have been used to explain pattern formation in developmental biology and in experimental chemical systems. To approximate the corresponding spatially discretized models, an explicit scheme can be used for the reaction term and an implicit scheme for the diffusion term. Such implicit-explicit (IMEX) schemes have been widely used, especially in conjunction with spectral methods in fluid flow problems.In this work, we analyze the performance of several of the best known linear multistep IMEX schemes for reaction-diffusion problems in pattern formation. For the linearized two chemical system, the growth properties exhibited by IMEX schemes are examined. Schemes which accurately represent the growth of the linearized problem for large time steps are identified. Numerical experiments show that first order accurate schemes, as well as schemes which produce only a weak decay of high frequency spatial error may yield plausible results which are nonetheless qualitatively incorrect. For such schemes, computations using refinements in the time step are likely to produce essentially the same (erroneous) results. Higher order schemes which produce a strong decay of high frequency errors are proposed instead.Our findings are demonstrated on several examples.The work of the author was partially supported by an NSERC Postgraduate Scholarship     

两种给药途径对联合抗生素建立伪无菌大鼠模型比较

利用联合抗生素通过饮水和灌胃2种给药途径干预大鼠,评估是否可建立伪无菌大鼠模型。

将15只SD大鼠随机分为正常组（Nor组）,饮水组（Dri组）和灌胃组（Ig组）,每组5只。饮水组：用超纯水配制成浓度为0.5 g/L万古霉素、1.0 g/L氨苄西林、1.0 g/L新霉素和1.0 g/L甲硝唑的混悬液,自由饮水。灌胃组：用生理盐水配制成浓度为200 mg/mL万古霉素,400 mg/mL氨苄西林,400 mg/mL新霉素和400 mg/mL甲硝唑的混悬液,0.5 mL/kg体积灌胃。建模14 d。收集空肠、盲肠和结肠的肠道内容物分别进行菌群培养,并对混合的肠道内容物样本进行测序。

与正常组相比,在有氧和厌氧培养条件下,饮水组和灌胃组肠道内容物在培养基上的菌落数量显著减少。饮水组和灌胃组肠道菌群丰富度和多样性均明显降低,肠道菌群的物种数量显著减少。饮水组大鼠肠道菌群主要以埃希-志贺菌属为主,灌胃组以克雷伯菌属为主。

通过饮水和灌胃给予大鼠联合抗生素,均清除了其大部分的肠道菌群,可以达到建立伪无菌大鼠模型的要求。

     

Explanation and prediction in vegetation science

A definition of vegetation science is given, spanning 6 levels of integration and stressing the interrelations among them. The problems of realism are discussed. The selection of levels is related to the adequate correspondence between conceptualization and research aims. Pattern and process are introduced as the central concepts of vegetation science. The perception of reality is dependent on the spatial and temporal scale chosen. The concept of noise is discussed in relation to stochasticity and randomness of events. Traces of essentialism are found both in classification of communities and habitat ecology. Classification is important, particularly the coexistence of alternative classification approaches. Organicism as a basis of vegetation research is rejected because the organismic view is inadequate on higher integration levels. The concept of function is redefined in a non-teleologic way.Present vegetation ecological research is inductivistic. One possible alternative to inductivism is falsificationism. The major domain of this approach is hypothesis testing, which will become more important. Progress can only be reached by a maximum degree of communication among scientific individuals.Predictive ecology is partly based on historic explanation, partly on complementary approaches. Characters of vegetation worthwhile to be predicted are listed and the necessary requirements for vegetation science to become predictive are discussed. A major requirement is the development of succession and life-history theory. A further elaboration of the individualistic concept will be a main task of vegetation science in the near future.     

The proximate/ultimate distinction in the multiple careers of Ernst Mayr

Ernst Mayr's distinction between “ultimate” and “proximate” causes is justly considered a major contribution to philosophy of biology. But how did Mayr come to this “philosophical” distinction, and what role did it play in his earlier “scientific” work? I address these issues by dividing Mayr's work into three careers or phases: 1) Mayr the naturalist/researcher, 2) Mayr the representative of and spokesman for evolutionary biology and systematics, and more recently 3) Mayr the historian and philosopher of biology. If we want to understand the role of the proximate/ultimate distinction in Mayr's more recent career as a philosopher and historian, then it helps to consider hisearlier use of the distinction, in the course of his research, and in his promotion of the professions of evolutionary biology and systematics. I believe that this approach would also shed light on some other important “philosophical” positions that Mayr has defended, including the distinction between “essentialism: and “population thinking.”     

Development trends in taxonomy,with special reference to fungi

Taxonomy is a traditional subject, but it still receives attention and has become a topic of much discussion in recent years. Many of these discussions have raised concerns about the future of taxonomy, especially with regard to the workforce responsible for the discovery of new species in the context of declining biodiversity. Previous discussions were based on the taxonomic data of plants and animals, but the status of fungal taxonomy has not been mentioned. Fungi have one of the highest levels of biodiversity among all living organisms, second only to insects. The discussion of the future of taxonomy without the inclusion of fungal data is incomplete. Here, we present the results of analyses based on all new fungal taxa published since 1753. Fungal taxonomy is an ever‐growing area of study with increasing numbers of new taxa being described and growing numbers of fungal taxonomists. Compared with plants and most animal groups, there has been a much sharper increase in the rate at which new fungal taxa are being described. Furthermore, the number of taxonomists studying fungi has increased at a faster speed than those studying plants or animals. This indicates that fungal taxonomy is a prosperous subject and a dynamic area for scientific studies, and that it deserves much more attention and support. The study of fungal taxonomy will deepen our understanding of the biodiversity of our planet.     

Pollenanalytical research in the Grisons (Switzerland)

In the first part, an overview of the history of palynological researeh in Switzerland and particularly in the Grisons is given, with a map showing all investigated areas in the Grisons. The second part deals with the significance of the pollenanalytical research in the Grisons, namely, the history of vegetation during the Late and Post Glacial, climatic fluctuations and applications in geomorphology, archaeology and forestry research. Finally, some results concerning the history of vegetation during the Late and Post Glacial are discussed.I would like to thank my colleague H. Holzhauser for his help with the drawing of the figures.     

Variation and taxonomy ofFritillaria graeca (Liliaceae) in Greece

The geographic variation inFritillaria graeca, an endemic of Greece, is explored, using multivariate techniques. Eleven morphological features were measured in each of 630 individual plants from 38 localities throughout the range of the species.Scheffe's a posteriori test revealed an almost continuous geographic variation and did not identify groups clearly. Discriminant analysis of the groups derived from an F significance test ofMahalanobis distance resulted in five major groups on the first two discriminant axes representing the subspeciesgraeca, ionica, guicciardii, thessala and its var.othria. A diagnostic key to theF. graeca subspecies is provided.This paper is a part of a doctoral dissertation dealing withFritillaria in Greece, to be submitted to the department of Biology of the Aristotelian University of Thessaloniki.     

On the holocene history of vegetation in SE Bulgaria (Lake Arkutino,Ropotamo region)

Palynological studies and investigations on macrofossil remains have been carried out on two profiles of the Holocene sediments of Lake Arkutino situated near to the Black Sea coast of SE Bulgaria. Lake Arkutino is a freshwater lake with shallow water. The lake is separated from the Black Sea by a dune barrier. Sedimentation started at about 6100 B.P. No marine or brackish influence could be traced in the sediments although the lake level is around sea level. The history of vegetation does not display major fluctuations except for the lake vegetation itself and for the swamp forests (Longos forests) surrounding the lake. Forests on normal mineral soils were mainly occupied by deciduous oaks throughout the last 6100 years. Deciduous oaks are represented in the pollen diagrams by the Quercus robur type and the Quercus cerris type. Until about 5800 B.P., one of the two pollen diagrams indicates that forests still contained more Pinus and Corylus than afterwards. After 5800 B.P., Fagus and a hundred years later together with Carpinus betulus became more important in addition with submediterranean elements as Carpinus orientalis, Fraxinus ornus and Phillyrea. After 5200 B.P., Carpinus betulus became somewhat less important. Indicators for human influence are rare. The archaeological record speaks for a small population in the area under study since the 12th century B.C. Swamp forests of the so-called Longos forests type started to develop at about 3000 B.P. The macrofossil record offers possibilities to trace hydrological changes by tracing the history of hydrophyte and reed plant comminties. From about 5100 to at least 4000 B.P., the record for Lemnetea and Potametea communities is poor and the processes of terrestrialization was interrupted. It can be assumed that the highest Black Sea transgression which is dated to 5700–4000 B.P. and which showed a sea level 3–4 m higher than today heavily influenced Lake Arkutino. That may have resulted in a higher lake level and in some water supply from the nearby river Ropotamo which would explain certain changes in the sediments and in the composition of hydrophyte communities.     

2008-2017年度微生物资源分类方向申请与资助情况

本文简要统计分析了2008至2017年度国家自然科学基金微生物学科在资源、分类和系统发育方向的项目申请、受理和资助情况。针对本方向项目资助与管理过程中的突出问题,对未来工作提出若干建议。     

SCOP数据库蛋白质折叠类型的自动分类分析

蛋白质折叠规律研究是生命科学领域重要的前沿课题之一,蛋白质折叠类型分类是折叠规律研究的基础。本研究以SCOP数据库的蛋白质折叠类型分类为基础、以Astral SCOPe 2.05数据库中相似性小于40%的α、β、α+β及α/β类所属的折叠类型为研究对象,完成了989种蛋白质折叠类型的模板构建并形成模板数据库;基于折叠类型设计模板建立了蛋白质折叠类型分类方法,实现了SCOP数据库蛋白质折叠类型的自动化分类。家族模板自洽性检验与独立性检验所得的敏感性、特异性以及MCC的平均值分别为:95.00%、99.99%、0.94与90.00%、99.97%、0.92,折叠类型模板自洽性检验与独立性检验所得的敏感性、特异性以及MCC的平均值分别为:93.71%、99.97%、0.91与86.00%、99.93%、0.87。结果表明:模板设计合理,可有效用于对已知结构的蛋白质进行分类。     

中国菌物分类学和多样性研究的历史与现状概况

我国菌物分类学研究始于20世纪初,经过百余年的不断探索和发展,取得了丰硕的成果,并逐渐走进世界前列。本研究通过对世界菌物名称信息库Fungal Names进行数据统计,对发现自中国的菌物新物种和中国学者发表菌物新分类单元等数据开展分析,从中揭示中国菌物分类学的历史和发展趋势。过去,一共有2 214位中国学者参与发表了15 626个菌物新分类单元,包括 3个新纲、27个新目及亚目、117个新科及亚科、769个新属及亚属、11 100个新种、322个新种下单元和3 288个新组合。在全球已知的菌物物种中,自中国发现的新物种有10 233种,隶属于 3界13门44纲174目572科2 379属,占全球已知物种多样性的6.84%,居世界第二位。地理分布上,我国西南地区(云南、四川、贵州、西藏)和低纬度的热带、亚热带地区(中国台湾、广东)发现的新物种最多。根据每年发现的新分类单元数量趋势和命名作者的构成,可将中国菌物分类学的发展历史分为五个阶段：外人在华采菌及研究(1750s-1929)、中国菌物分类学起步(1930-1949)、新中国菌物分类学早期发展(1950-1977)、全国性菌物标本采集与研究(1978-2010)、走进世界前列(2011至今)。本研究对每个发展时期的分类学概况和重要历史事件进行了总结和回顾,通过上述综述性研究,有助于系统地了解中国菌物分类学不同阶段的发展趋势和研究概况,为学科当下和未来的发展提供参考。