A (selective) history of Australian involvement in cytokine biology

This review focuses on contributions to cytokine biology made by Australians in Australia. It is clearly biased by my own experiences and selective recollections especially related to the colony-stimulating factors in which Australian involvement has been pre-eminent from discovery to clinical use. Nevertheless Australian scientists have also made profound contributions to other areas of cytokine and growth factor biology (including interferons, inflammatory cytokines, chemokines and epidermal, insulin-like and vascular endothelial growth factors) that are briefly described in this review as well as other chapters in this volume.     

Brain peptides: The dangers of constricted nomenclatures

Peptides being discovered in the brain and elsewhere in the body continue to be named for the function by which they were first described. This approach is reasonable, but involves the risk that scientists may feel restricted to examine only the action described by the nomenclature, as was initially done with pituitary and hypothalamic hormones as well as opiate and gut peptides.     

Improving usability and accessibility of cheminformatics tools for chemists through cyberinfrastructure and education

Some of the latest trends in cheminformatics, computation, and the world wide web are reviewed with predictions of how these are likely to impact the field of cheminformatics in the next five years. The vision and some of the work of the Chemical Informatics and Cyberinfrastructure Collaboratory at Indiana University are described, which we base around the core concepts of e-Science and cyberinfrastructure that have proven successful in other fields. Our chemical informatics cyberinfrastructure is realized by building a flexible, generic infrastructure for cheminformatics tools and databases, exporting "best of breed" methods as easily-accessible web APIs for cheminformaticians, scientists, and researchers in other disciplines, and hosting a unique chemical informatics education program aimed at scientists and cheminformatics practitioners in academia and industry.     

我国东海赤潮原甲藻应属哪种？

阐述并讨论了中国东海长江口外经常发生的原甲藻赤潮原因种的种类认知问题．论述了自从Stein提出具齿原甲藻(Prorocendrum dentatum Stein)新种后迄今中外专家报告该种的描述及分布,并对比了具齿原甲藻与长江口的原甲藻的异同．研究证实我国东海的原甲藻与具齿原甲藻有较大的差别,主要表现在体积大小、藻体末端形态以及藻体前端突起的大小和形态等方面．本文汇集了国内外对具齿原甲藻与我国原甲藻的研究成果,对比认为。我国长江口外经常发生赤潮的原甲藻为东海原甲藻(Prorocendrum donghaiense Lu)．文中还讨论了由陆斗定发表的东海原甲藻需要补充修正的观点．在过去的数年中,我国东海长江口海域频繁爆发大面积的原甲藻赤潮,但对于赤潮原因种原甲藻(Prorocentrum)的定种问题存在两种不同的观点,一种观点认为本种是具齿原甲藻,另一种观点认为是东海原甲藻．为了阐明此种原甲藻的命名问题,于2002年11月在深圳召开了题为“我国东海赤潮原因种原甲藻分类学国际研讨会”．认为是P．dentatum的依据是长期以来国际上通常把类似我国东海的原甲藻定为P．dentatum,其根据是它的前端有突起等．而持不同观点的专家认为我国东海的这种原甲藻在细胞长度上与Stein描述的原P．dentatum差异很大,并且除少数样品末端尖伸外,大多数细胞末端是钝圆的．专家们还认为在日本、韩国等亚洲海域分布的被报告为P．dentatum的原甲藻与我国东海的此种原甲藻为同一种．综观各种观点,作者认为东海本种原甲藻应为东海原甲藻.     

The dynamics of Brazilian protozoology over the past century

Brazilian scientists have been contributing to the protozoology field for more than 100 years with important discoveries of new species such asTrypanosoma cruzi and Leishmania spp. In this work, we used a Brazilian thesis database (Coordination for the Improvement of Higher Education Personnel) covering the period from 1987-2011 to identify researchers who contributed substantially to protozoology. We selected 248 advisors by filtering to obtain researchers who supervised at least 10 theses. Based on a computational analysis of the thesis databases, we found students who were supervised by these scientists. A computational procedure was developed to determine the advisors’ scientific ancestors using the Lattes Platform. These analyses provided a list of 1,997 researchers who were inspected through Lattes CV examination and allowed the identification of the pioneers of Brazilian protozoology. Moreover, we investigated the areas in which researchers who earned PhDs in protozoology are now working. We found that 68.4% of them are still in protozoology, while 16.7% have migrated to other fields. We observed that support for protozoology by national or international agencies is clearly correlated with the increase of scientists in the field. Finally, we described the academic genealogy of Brazilian protozoology by formalising the “forest” of Brazilian scientists involved in the study of protozoa and their vectors over the past century.     

Observations on the history of non-insect invertebrate pathology from the perspective of a participant

This paper discusses diseases of commercially important non-insect invertebrates from both a historical and a personal perspective. Early studies of curious scientists such as Metchnikoff using invertebrate systems led to important discoveries with much wider impact. As commercial culture of oysters, shrimp, and other invertebrates grew, so did studies of their diseases. Here, the impact of pioneering scientists and important new techniques on our understanding of these diseases is described.     

Glycoscience aids in biomarker discovery

The glycome consists of all glycans (or carbohydrates) within a biological system, and modulates a wide range of important biological activities, from protein folding to cellular communications. The mining of the glycome for disease markers represents a new paradigm for biomarker discovery; however, this effort is severely complicated by the vast complexity and structural diversity of glycans. This review summarizes recent developments in analytical technology and methodology as applied to the fields of glycomics and glycoproteomics. Mass spectrometric strategies for glycan compositional profiling are described, as are potential refinements which allow structure-specific profiling. Analytical methods that can discern protein glycosylation at a specific site of modification are also discussed in detail. Biomarker discovery applications are shown at each level of analysis, highlighting the key role that glycoscience can play in helping scientists understand disease biology.     

Digital reviews in molecular biology: approaches to structured digital publication

MOTIVATION: It is widely appreciated that it is no longer possible for biomedical research scientists to keep up with as much of what is published in their field as they ought. One solution to this problem is to increase the efficiency of information use by moving away from the classical browsing model for scientific information dissemination towards an information on demand model which would allow researchers to access information quickly and efficiently only as they need it. The most common approach to this goal has been to use information retrieval technology to improve access to text databases of biomedical information. We are interested in exploring an alternative; encoding this information for storage in structured databases for efficient retrieval. RESULTS: Two small databases described here are test beds for development of structured digital publication software; the Tumor Gene Database, containing information about genes which are the sites for cancer-causing mutations, and the Mammary Transgene Database, containing information about expression of transgenes in agriculturally important animals. Both have been successfully searched by users and edited by curators via the World Wide Web.     

From paper chromatography to drug discovery: Zaffaroni.

A paper chromatography assay for adrenocortical steroids, published just as cortisone's therapeutic value in arthritis was announced, had far-reaching consequences. Its use by Upjohn scientists led to the first synthesis of cortisone. Interest in the assay also led the author to an association with Syntex S.A. in Mexico, which he was instrumental in transforming from a small chemical company into the large pharmaceutical firm, Syntex Corporation, having its base of operations in the United States. The major events of this history are described, showing how steroid product development helped establish Syntex and later played a role in the founding of ALZA Corporation.     

Citizen Science as a New Tool in Dog Cognition Research

Family dogs and dog owners offer a potentially powerful way to conduct citizen science to answer questions about animal behavior that are difficult to answer with more conventional approaches. Here we evaluate the quality of the first data on dog cognition collected by citizen scientists using the Dognition.com website. We conducted analyses to understand if data generated by over 500 citizen scientists replicates internally and in comparison to previously published findings. Half of participants participated for free while the other half paid for access. The website provided each participant a temperament questionnaire and instructions on how to conduct a series of ten cognitive tests. Participation required internet access, a dog and some common household items. Participants could record their responses on any PC, tablet or smartphone from anywhere in the world and data were retained on servers. Results from citizen scientists and their dogs replicated a number of previously described phenomena from conventional lab-based research. There was little evidence that citizen scientists manipulated their results. To illustrate the potential uses of relatively large samples of citizen science data, we then used factor analysis to examine individual differences across the cognitive tasks. The data were best explained by multiple factors in support of the hypothesis that nonhumans, including dogs, can evolve multiple cognitive domains that vary independently. This analysis suggests that in the future, citizen scientists will generate useful datasets that test hypotheses and answer questions as a complement to conventional laboratory techniques used to study dog psychology.     

Can biological control benefit from genetically‐modified crops? Tritrophic interactions on insect‐resistant transgenic plants

Abstract. The use of recombinant DNA technology to develop genetically‐modified crops is considered as a major breakthrough for agriculture by many scientists. However, some scientists, and an even larger proportion of the general public, are sceptical about the advantages and are even more concerned about the potential risk of this new technology. To evaluate this novel technology, cost‐benefit analyses are needed in which the real risks are measured and judged against the benefits. A tiered risk assessment scheme is described herein. This allows comparisons to be made with other insect‐control technologies (e.g. insecticides) and risks to be determined, rather than only hazards being identified. Recombinant DNA technology could allow plants to be designed that are well suited for use alongside biological control programmes. Unfortunately, plant breeders have continued to attempt to breed for total resistance, and biocontrol specialists have ignored the role of the plant in ensuring successful foraging behaviour by insect natural enemies. Although some scientists have highlighted the need to consider both the bottom‐up (plant defence) and top‐down (biocontrol) control of insect pests, there have been few serious attempts to combine these approaches. As more is understood about the proximate and ultimate causes of direct and indirect defences, the potential exists for engineering plants that combine both strategies. This new possibility for controlling insect pests, which will combine both ‘nature’s' own defences with man's ingenuity, may stack the odds in our favour in the continual struggle against insect pests.     

Cancer cell biology: a student-centered instructional module exploring the use of multimedia to enrich interactive,constructivist learning of science

Multimedia has the potential of providing bioscience education novel learning environments and pedagogy applications to foster student interest, involve students in the research process, advance critical thinking/problem-solving skills, and develop conceptual understanding of biological topics. Cancer Cell Biology, an interactive, multimedia, problem-based module, focuses on how mutations in protooncogenes and tumor suppressor genes can lead to uncontrolled cell proliferation by engaging students as research scientists/physicians with the task of diagnosing the molecular basis of tumor growth for a group of patients. The process of constructing the module, which was guided by scientist and student feedback/responses, is described. The completed module and insights gained from its development are presented as a potential "multimedia pedagogy" for the development of other multimedia science learning environments.     

On the Trail of Atmospheric Mutagens and Carcinogens: A Combined Chemical/Microbiological Approach

Major ecological problems of our polluted troposphere includeairborne toxic chemicals, acid rain and photochemical smog,all three of which are now recognized as being closely relatedchemical phenomena. We also recognize that inorder to developcost-effective strategies for their control, which protect publichealth and the environment, there must be close scientific interactionsbetween chemists and biological scientists. For example, ofrapidly emerging importance is the development of risk assessmentevaluations for specific aspects of each of these problem areas.In preparing such assessments, chemists must define the "exposure,"and biological scientists the "effects." In this paper, I discuss an example of how such close interactionsproved indispensible in our search for atmospheric mutagensand carcinogens. Thus, an integrated chemical/ microbiologicalprocedure for the isolation and identificationof particulatechemical mutagens in respirable diesel soot and ambient particlesis described. Emphasis is placed on our use of the short-term,Ames Salmonella typhimurium bacterial mutagenicity test as arapid, and relatively inexpensive, means of following the biologicalactivities of these environmental mutagens through the chemicalsteps of their separation, isolation and identification fromhighly complex environmental samples. Possible mechanisms offormation of these particulate mutagens are discussed. Theyinclude the reactions of polycyclic aromatic hydrocarbons presenton the surfaces of combustion-generated particles with gaseousco-pollutants such as nitrogen dioxide plus nitric acid, andozone. In discussing this research on a societally "relevant" problem,we illustrate the importance of "Science as a Way of Knowing."We further suggest that this integrated approach to scientificproblem solving by chemical and biological scientists mightserve as an example of a discussion topic on human ecology forundergraduate courses in the natural sciences.     

A further food-washing tradition in Japanese macaques (Macaca fuscata)

A case of food-washing tradition is reported in a captive group of Japanese macaques. Two techniques are employed, with one or both hands being used to wash food under water flowing from watering spouts. Processes of diffusion of the behaviour in the group follow the patterns previously described by Japanese scientists observing this species. It is suggested that development of such a behaviour could be related to particular environmental conditions.     

How is Scientific Credibility Affected by Communicating Uncertainty? The Case of Endocrine Disrupter Effects on Male Fertility

Using the case of endocrine disrupter effects on male fertility, we explored how communicating uncertainty influences the credibility of the information that laypeople receive from scientists and how laypeople form judgments about the relationship between uncertainty and credibility. We found that laypeople assess the credibility of scientific information—whether or not it is accompanied by uncertainty—by referencing their “science model” and using non-scientific references (i.e., situations encountered in one's daily life, information received from other sources, one's own observations of the world, and one's education or professional experience). Scientific credibility is a mixture of (sometimes contradictory) considerations along these different axes. Previous studies have found that some scientists assume that communicating uncertainty will lower public credibility of science. Our results contradict this assumption for situations in which academic scientists communicate uncertainty, which is perceived as additional knowledge bringing a new perspective on certain information. People expect scientists to provide practical solutions and feel disillusionment when scientists lack straight answers. However, they accepted uncertainty as an intrinsic characteristic of science and a consequence of the limits to human beings’ capacity to understand the world. Further, the low credibility of industry scientists is further reinforced when they communicate uncertainty.     

Modeling of biological and medical systems: a systemic strategy.

A strategy in the frame of General System Theory is proposed for the study of biological systems for medical purposes. Its definition and use requires in each experiment the collaboration between physician and system scientists and hence the definition of a common language, by which the real system under study is described. The strategy is based on three intermingled steps: first an ingenuous model is proposed, gathering all the medical knowledge about the studied system, organized within an informal frame derived from the state space approach. Next, a functional model is derived, enlightening the organization of the relations in the medical model. Finally, this organization is formalized by the most suitable algebraic tools, which are thereafter translated into APL programs. This last version is used for simulation, which is exploited not only as a tool to describe and make provisions on the dynamics of the models, but also to deepen and improve the knowledge about the observed system.     

菌物DNA条形码技术原理与操作

DNA条形码技术是通过对1个较短目的基因的DNA序列进行分析从而进行物种鉴定的方法,它通过对1个或多个相关基因进行大范围的扫描,进而鉴定未知物种或者发现新种。当传统的分类学受到阻碍时,这种技术可以发挥其优势。相对于其他生物,菌物的生活史独特而复杂,这就使得对其进行的形态学鉴定要受到菌物自身生长发育时期的限制。国内外科学家对寻找适合于大多数菌物的标准DNA条码进行过探索,但还没有找到满足全部特征的基因片段。文中对DNA条形码技术的概念、原理依据、操作步骤和优缺点方面进行了介绍,并对DNA条形码技术在我国菌物研究方面的应用前景进行了展望。     

The bacteriorhodopsin model membrane system as a prototype molecular computing element

The quest for more sophisticated integrated circuits to overcome the limitation of currently available silicon integrated circuits has led to the proposal of using biological molecules as computational elements by computer scientists and engineers. While the theoretical aspect of this possibility has been pursued by computer scientists, the research and development of experimental prototypes have not been pursued with an equal intensity. In this survey, we make an attempt to examine model membrane systems that incorporate the protein pigment bacteriorhodopsin which is found in Halobacterium halobium. This system was chosen for several reasons. The pigment/membrane system is sufficiently simple and stable for rigorous quantitative study, yet at the same time sufficiently complex in molecular structure to permit alteration of this structure in an attempt to manipulate the photosignal. Several methods of forming the pigment/membrane assembly are described and the potential application to biochip design is discussed. Experimental data using these membranes and measured by a tunable voltage clamp method are presented along with a theoretical analysis based on the Gouy-Chapman diffuse double layer theory to illustrate the usefulness of this approach. It is shown that detailed layouts of the pigment/membrane assembly as well as external loading conditions can modify the time course of the photosignal in a predictable manner. Some problems that may arise in the actual implementation and manufacturing, as well as the use of existing technology in protein chemistry, immunology, and recombinant DNA technology are discussed.     

Evolving Scientific Epistemologies and the Artifacts of Empirical Philosophy of Science: A Reply Concerning Mesosomes

In a 1993 paper, I argued that empirical treatments of the epistemologyused by scientists in experimental work are too abstract in practice tocounter relativist efforts to explain the outcome of scientificcontroversies by reference to sociological forces. This was because, atthe rarefied level at which the methodology of scientists is treated byphilosophers, multiple mutually inconsistent instantiations of theprinciples described by philosophers are employed by contestingscientists. These multiple construals change within a scientificcommunity over short time frames, and these different versions ofscientific methodology can determine the outcome of a controversy. Iillustrated with a comparatively detailed analysis of the methodologyused by biologists debating the existence of an entity called thebacterial mesosome between the mid-1950s and the mid-1970s. This 1993piece has drawn several critiques in the philosophical literature. Inthis present piece I respond to these critiques and argue that they failto address the core argument of the original paper, and I reflectfurther on the methodologies of philosophers of science pursuingempirical or `naturalistic' epistemology.