Animals and environments: resisting schisms in comparative physiology and biochemistry

The articles in this volume are a product of the enthusiasm shown by delegates to meet in a remote corner of southern Africa and to discuss comparative physiology and biochemistry in their wider interpretation and future course. This collection reflects a small but long-standing commitment to fostering the engagement of biological research with African issues and colleagues. Comparative physiology and biochemistry are evolving, but in this we must guard against fractionation of effort and purpose. Increasingly available molecular methods are seductive in encouraging work on model species and in employing these species in place of more appropriate comparative models. Concomitantly, the comparative approach is reaching out beyond the individual organism and organism-organism interactions to establish underlying principles at ecosystem and landscape levels. The integration of molecular methods into comparative studies will require judicious selection and use of such skills if it is to be achieved without abandoning nonmodel species. The physiological and metabolic bases of ecosystem and evolutionary approaches must be underpinned by relevant data, requiring comparative researchers to accommodate colleagues contributing this specialist knowledge. These articles report distinct symposia, prefaced by a plenary paper. While each paper is itself a review of an entire symposium, they all exhibit a common theme, that comparative physiology and biochemistry are about interactions. It is our hope that the Comparative Physiology and Biology in Africa meetings will continue to facilitate special interactions between the people who make this happen.     

兰科植物系统学及亲缘关系研究进展

兰科植物是开花植物中最大的家族之一,现已受到全世界的重视。其种间或品种间的分类鉴定和亲缘关系的研究为育种工作提供了一个早期的、辅助的、选择性的指标。本文综述了近几年来兰科植物在比较形态学、细胞学、生物化学和分子生物学的研究进展。     

Die Paläobiochemie,ein neues Arbeitsgebiet der Evolutionsforschung

Attention is focussed on a novel tool to study evolutionary trends in organisms. Emphasis is placed on the comparative biochemistry of shell proteins. It is tentatively concluded that the organic matrix of molluscan shells is predominantly a mixture of “secreted” collagen and k-m-e-f type proteins, and to a lesser extent of mucopolysaccharides. Each species has its characteristic organic pattern. Thus, the heterogeneity of calcified tissues can be related to molluscan phylogeny and evolution.     

Identification of enterococci by ribotyping with horseradish-peroxidase-labelled 16S rDNA probes.

Enterococci are frequently associated with hospital-acquired infection. Identification of enterococci using conventional biochemical tests are often tedious to perform in a routine diagnostic laboratory and may give equivocal results. This study evaluates the usefulness of ribotyping by DNA hybridisation to identify 68 members of the bacterial genus Enterococcus characterised by a conventional test scheme. DNA probes (830 bp in size) were derived from the 16S rRNA gene of E. coli or E. faecalis by PCR, labelled with horseradish peroxidase and used in Southern blot hybridisations of enterococcal DNA digested with EcoRI. Unique ribotypes were obtained for 11 different species using 12 Enterococcus type strains. Ribotyping identified 44 E. faecalis isolates, 19 E. faecium isolates, two E. durans isolates and one E. avium isolate in concordance with results of the biochemistry tests. Two isolates that had ribotype patterns identical to the E. faecium type strain were unable to be definitively identified by biochemical tests. The results show that ribotyping is able to differentiate between E. faecium and E. faecalis and may be useful for identifying other enterococci in the hospital setting. In addition, ribotyping using DNA probes and enhanced chemiluminescence is a safe and more reproducible alternative to radiolabelling RNA in a clinical microbiology laboratory.     

Comparative approaches to understand metal bioaccumulation in aquatic animals

Over the past decades, comparative physiology and biochemistry approaches have played a significant role in understanding the complexity of metal bioaccumulation in aquatic animals. Such a comparative approach is now further aided by the biokinetic modeling approach which can be used to predict the rates and routes of metal bioaccumulation and assist in the interpretation of accumulated body metal concentrations in aquatic animals. In this review, we illustrate a few examples of using the combined comparative and biokinetic modeling approaches to further our understanding of metal accumulation in aquatic animals. We highlight recent studies on the different accumulation patterns of metals in different species of invertebrates and fish, and between various aquatic systems (freshwater and marine). Comparative metal biokinetics can explain the differences in metal bioaccumulation among bivalves, although it is still difficult to explain the evolutionary basis for the different accumulated metal body concentrations (e.g., why some species have high metal concentrations). Both physiological/biochemical responses and metal geochemistry are responsible for the differences in metal concentrations observed in different populations of aquatic species, or between freshwater and marine species. A comparative approach is especially important for metal biology research, due to the very complicated and potentially variable physiological handling of metals during their accumulation, sequestration, distribution and elimination in different aquatic species or between different aquatic systems.     

Clinical biochemistry in sheep: A selected review

As in other species, the first point in sheep clinical biochemistry is the correct selection of the appropriate tests and, consequently, the optimal management of the pre-analytical phase from the collection of the samples to their management and possible transport or storage before analysis. There are so many different breeds and breeding systems in sheep, as well as laboratory techniques, that no universally acceptable reference values and ranges can be provided. Each laboratory should determine its own reference values and ranges, according to recommended methods. The main uses of clinical biochemistry in sheep health management are in the diagnosis of liver, muscle and nutritional disorders, for which selected examples are discussed in this paper.     

Body Surface Area Prediction in Odorrana grahami

Body surface area（BSA）was regarded as a more readily quantifiable parameter relative to body mass in the normalization of comparative biochemistry and physiology.The BSA prediction has attracted unceasing research back more than a century on animals,especially on humans and rats.Few studies in this area for anurans were reported,and the equation for body surface area（S）and body mass（W）：S=9.9 W 0.56,which was concluded from toads of four species in 1969,was generally adopted to estimate the body surface areas for anurans until recent years.However,this equation was not applicable to Odorrana grahami.The relationship between body surface area and body mass for this species was established as：S=15.4 W 0.579.Our current results suggest estimation equations should be used cautiously across different species and body surface area predictions on more species need to be conducted.     

Comparative aspects of the accessory sex glands and seminal biochemistry of mammals

• 1.1. Despite large gaps in the literature of semen biochemistry, especially of wild species, recent studies of the carbohydrate biochemistry of marsupial semen allow an approach to the question of the origin and evolution of mammalian seminal plasma.
• 2.2. The marsupials are a very important part of an overall picture of seminal plasma evolution because they are the end product of an alternative line of mammalian evolution genetically separated from the eutherians for over 100 million years.
• 3.3. The present paper discusses the accessory sex glands and seminal sugars of mammals from a comparative point of view in the light of present knowledge of evolutionary relationships and suggests possible schemes of evolution of mammalian seminal plasma.

     

稻瘟病菌拮抗性大豆根瘤内生细菌的筛选及抑制效果

【目的】从河南大豆根瘤的内生细菌资源中筛选对稻瘟病菌有拮抗作用的菌株,初步探讨其抑菌效果,为进一步研究其抑菌机理提供菌种资源。【方法】以稻瘟病菌为供试病原菌,采用对峙法进行拮抗性菌株筛选,显微观察法研究受抑制病原菌菌丝变化,对筛选拮抗性菌株进行细胞形态学及生理生化特性试验、16S rRNA基因测序和系统发育分析及接种防效试验。【结果】经复筛有17株内生菌拮抗效果较明显,最高抑制率为62.16%;受抑制病原菌丝呈现弯曲打结、断裂、原生质浓缩等畸形状态。拮抗性筛选过程中内生菌快速生长形成生物薄膜,包埋菌丝并使其断裂。拮抗菌株分布在7属9种,稻瘟病拮抗性大豆根瘤内生菌呈现种属多样性。防效试验表明内生菌处理组稻苗发病率和病情指数均显著降低,防治效果最高达74.19%。【结论】大豆根瘤内生拮抗性菌株具有种属多样性,拮抗性菌株处理组稻苗发病率和病情指数均显著降低,防治效果显著,为进一步研究其抑菌机理提供菌种资源。     

Comparative biochemistry and physiology in Brazil: a critical appraisal

Brazil stood out as the country with the highest number of submissions to the editorial project dedicated to Latin America by the journal Comparative Biochemistry and Physiology. Therefore, we felt that it was important to critically discuss the state of comparative biochemistry and physiology in this country. Our study is based on data collected from the ISI Web-of-Science. We analyzed publication trends through time, availability of novel approaches and techniques, patterns of collaboration among different geographical regions, patterns of collaboration with researchers abroad, and relative efforts dedicated to the study of biochemical and physiological adaptation of native fauna representing different terrestrial Brazilian biomes. Overall, our data shows that comparative biochemistry and physiology is a lively and productive discipline, but that some biases limit the scope of the field in Brazil. Some important limitations are the very heterogeneous distribution of research nuclei throughout the country and the absence of some important approaches, such as remote sensing and the use of molecular biology techniques in a comparative or evolutionary context. We also noticed that international collaboration far surpasses interregional collaboration, and discuss the possible causes and consequences of this situation. Finally, we found that Brazilian comparative biochemistry and physiology is biome-biased, as the Amazonian fauna has received far more attention than the whole pool of fauna representing other terrestrial biomes. We discuss the possible causes of these biases, and propose some directions that may contribute to invigorate the field in the country.     

Functional degradation of myelin basic protein. The proteomic approach

Proteolytic degradation of autoantigens is of prime importance in current biochemistry and immunology. The fundamental issue is the functional role of peptides produced in the process of change of the hydrolysis specificity during the transition from the normal to a pathologic state. In some cases identification of specific peptide fragments can be a diagnostic and prognostic criterion of the pathology progress. The subject of this work is the comparative study of degradation peculiarities of one of the major neuroantigens, myelin basic protein, by proteases activated upon the development of a pathological demyelinating process, and by proteasomes of different origin. Comparison of the specificity of the tested biocatalysts in some cases demonstrated critical changes in the set of myelin basic protein fragments capable of being presented on the major histocompatibility complex class I upon neurodegeneration, which may promote the development of autoimmune pathological processes.     

Functional degradation of myelin basic protein. Proteomic approach

Proteolytic degradation of autoantigens is of prime importance in current biochemistry and immunology. The most fundamental issue in this field is the functional role of peptides produced when the specificity of hydrolysis changes during the shift from health to disease and from normal state to pathology. The identification of specific peptide fragments in many cases proposes the diagnostic and prognostic criterion in the pathology progression. The aim of this work is comparative study of the degradation peculiarities of one of the main neuroantigen, myelin basic protein by proteases, activated during progress of pathological demyelinating process, and by proteasome of different origin. The comparison of specificity of different studied biocatalysts gives reason to discuss the critical change in the set of myelin basic protein fragments capable to be presented by major histocompatibility complex class I during neurodegeneration, which can promote the progress of autoimmune pathological process.     

Diagnostic testing for Legionnaires’ disease

Legionnaires’ disease is commonly diagnosed clinically using a urinary antigen test. The urinary antigen test is highly accurate for L. pneumophila serogroup 1, however other diagnostic tests should also be utilized in conjunction with the urinary antigen as many other Legionella species and serogroups are pathogenic. Culturing of patient specimens remains the gold standard for diagnosis of Legionnaires’ disease. Selective media, BYCE with the addition of antibiotics, allows for a high sensitivity and specificity. Culturing can identify all species and serogroups of Legionella. A major benefit of culturing is that it provides the recovery of a patient isolate, which can be used to find an environmental match. Other diagnostic tests, including DFA and molecular tests such as PCR and LAMP, are useful tests to supplement culturing. Molecular tests provide much more rapid results in comparison to culture, however these tests should not be a primary diagnostic tool given their lower sensitivity and specificity in comparison to culturing. It is recommended that all laboratories develop the ability to culture patient specimens in-house with the selective media.     

An investigation of the statistical power of neutrality tests based on comparative and population genetic data

In this report, we investigate the statistical power of several tests of selective neutrality based on patterns of genetic diversity within and between species. The goal is to compare tests based solely on population genetic data with tests using comparative data or a combination of comparative and population genetic data. We show that in the presence of repeated selective sweeps on relatively neutral background, tests based on the d(N)/d(S) ratios in comparative data almost always have more power to detect selection than tests based on population genetic data, even if the overall level of divergence is low. Tests based solely on the distribution of allele frequencies or the site frequency spectrum, such as the Ewens-Watterson test or Tajima's D, have less power in detecting both positive and negative selection because of the transient nature of positive selection and the weak signal left by negative selection. The Hudson-Kreitman-Aguadé test is the most powerful test for detecting positive selection among the population genetic tests investigated, whereas McDonald-Kreitman test typically has more power to detect negative selection. We discuss our findings in the light of the discordant results obtained in several recently published genomic scans.     

Comparative methods for examining adaptation depend on evolutionary models

Comparisons among taxa provide a powerful means for helping to understand why primate species differ from each other in morphology, behaviour and life history. Comparative tests can also mislead when not applied correctly, and correct application means taking into account the phylogenetic relationships among the species being compared. Adaptation is defined as a comparative concept. The reasons for phenotypic similarity among closely related taxa are summarized. Different models of evolutionary change dictate different methods for reconstructing ancestral character states and for performing comparative analyses on categorical and continuously varying character. All comparative methods rely either implicitly of explicitly on some model of how evolution proceeds. The choice of a particular method of analysis is, therefore, an implicit choice of a model of evolution.     

Comparative biochemistry and physiology in Latin America over the last decade (1997-2006)

We investigate the distribution of Latin American comparative biochemistry and physiology across subject areas and systematic groups. Our study focuses on papers published over the last decade (1997-2006) in four leading topical journals. Brazil dominates the production of papers, followed by Argentina, Mexico and Chile, which together account for 91% of the production in numbers. These countries differ in a number of variables that we discuss in the text. Questions regarding the physiology of wild animals are particularly common, but comparative approaches to study practical issues are also well represented throughout the continent. The most frequent topics in the latter context include the action of snake venoms, the physiology of pathogens and their hosts, and the physiology of domestic or cultured species. The subjects of metabolism, thermoregulation and digestive physiology constitute 40% of the contributions in the database. Regarding systematic groups, most attention has been devoted to vertebrates, mostly anuran amphibians. Other highlighted groups are octodontid rodents, phocid mammals and characid fish. Among invertebrates, malacostracan decapods are by far the best studied group. Many taxa of wild animals are represented by just one or a few studies, thus limited information is available about a large number of Latin American species.     

Evaluation of an immunomagnetic separation method to capture <Emphasis Type="Italic">Candida</Emphasis> yeasts cells in blood

Background  

Candida species have become the fourth most-frequent cause of nosocomial bloodstream infections in immunocompromised patients. Therefore, rapid identification of pathogenic fungi to species level has been considered critical for treatment. Conventional diagnostic procedures such as blood culture or biochemical tests are lacking both sensitivity and species specificity, so development of rapid diagnostic is essential.     

Abrus kaokoensis (Leguminosae-Papilionoideae-Abreae), a new species from Namibia

Abrus kaokoensis Swanepoel & H.Kolberg, a woody subshrub, is described as a new species. It is only known from the vicinity of the Kunene River and the Baynes Mountains in the Kaokoveld Centre of Endemism, Namibia. Its range is likely to extend into the botanically poorly explored adjacent mountainous parts of southwestern Angola. Illustrations of the species and a distribution map are provided. Probably most closely related to A. schimperi Baker, diagnostic characters of the new species include a suffrutescent habit and terminal elongated racemes with flowers clustered on appressed cushion-like reduced branchlets. A comparative table with diagnostic morphological characters to distinguish between the new species and A. schimperi is provided.     

Hemoglobins and hemocyanins: comparative aspects of structure and function.

Comparative studies of protein structure and function can be quite interesting by themselves, and even more interesting when interpreted with respect to an animal's physiology. In the case of fish hemoglobins, some success in the latter has been achieved but there are still many unsolved problems. It appears that comparative physiology and biochemistry have entered an era where results from comparative studies can shed a great deal of light on biochemical mechanisms in general. The trout hemoglobin system is an example. Distinctive hemoglobins in this system are presently being used as high resolution probes of the ligand-binding mechanism. Characterization of the multiple, structurally distinct subunits of the 60S Limulus hemocyanin molecule may similarly aid in understanding its function. Our studies suggest the possibility of using Limulus hemocyanin and other hemocyanins as structural homologs and analogs of more complex macromolecular arrays. The rapid development of molecular structural data from X-ray crystallographers combined with the vast data of comparative physiology and biochemistry makes this one of the most exciting areas in present day science.