The circular definition of populations and its implications for biological sampling

Application of population-based theoretical models to the study of real world populations requires the relationship between the real and theoretical populations to be defined. Otherwise, it is not possible to take a representative field sample or census of a population. I demonstrate that the concept of a biological population is based on a circular definition and is logically untenable. A population is composed of a number of individuals whose membership of the population is determined by their relationship to the rest of the population. This has serious implications for common practice in a range of ecological and evolutionary disciplines.     

Frozen fungi: cryogenic storage is an effective method to store Fusarium cultures for the long‐term

Microbial culture collections provide a vast amount of genotypic and phenotypic information which are invaluable resources for future advancements in research. For most microbial strains, cryopreservation in the vapour phase above liquid nitrogen provides the most stable and long‐term storage method. However, in the case of fungal microbes, not all are suited for cryogenic storage and few studies have addressed the effectiveness of storage in the vapour phase above liquid nitrogen on a diverse collection of Fusarium species. In this work, a collection of 374 Fusarium strains from the Fungal Genetics Stock Center, including 24 unique species, were duplicated and sent to the National Laboratory for Genetic Resource Preservation for storage in the vapour phase above liquid nitrogen. After 5 years of storage the entire collection was tested for viability and phenotypic stability by using plating, cellular staining assays, assessing the number of viable cells and measuring the rate of growth of each isolate. Additionally, the rate of growth for ～10% of the isolates were compared with the same isolates which had been stored at ?80°C at the Fungal Genetics Stock Center over the same timeframe to determine if cryopreservation in liquid nitrogen vapour provided a comparable method of storage. All National Laboratory for Genetic Resources Preservation isolates grew after being stored at ?165°C for 5 years. In general, the isolates that were stored at ?165°C grew at a faster rate than the isolates stored at ?80°C for the same period. Of the isolates stored at ?165°C, most had greater than 80% cell viability, however, those isolates that had less than 50% cell viability generally also had fewer conidia germinate. These isolates may be at a greater risk for storage over longer times. In conclusion, storage at ?165°C liquid nitrogen provided reliable preservation of a diverse collection of Fusarium spp. over 5 years, and culture viability data indicates that they will remain viable during additional storage for longer periods.     

Decoding the drivers of deep-time wetland biodiversity: insights from an early Permian tropical lake ecosystem

Wetlands are important to continental evolution, providing both arenas and refugia for emerging and declining biotas. This significance and the high preservation potential make the resulting fossiliferous deposits essential for our understanding of past and future biodiversity. We reconstruct the trophic structure and age of the early Permian Manebach Lake ecosystem, Germany, a thriving wetland at a time when the tropical biosphere faced profound upheaval in the peaking Late Palaeozoic Icehouse. Nine excavations, high-resolution spatiotemporal documentation of fossils and strata, and U–Pb radioisotopic dating of tuffs allow us to distinguish autogenic and allogenic factors shaping the limnic biocoenosis. The Manebach Lake was an exorheic, oxygen-stratified, perennial water body on the 10¹–10² km² scale, integrated into the catchment draining much of the European Variscides. Lake formation paralleled an Asselian regional wet climatic interval and benefited from rising base level due to post-Variscan half-graben tectonics. Stromatolite-forming cyanobacteria, bivalves, several crustaceans, amblypterids and xenacanthid sharks formed a differentiated biocoenosis in the lake. Fossil stomach remains and teeth prove the rare presence of acanthodians, branchiosaurs and large amphibians. The results indicate woody-debris-bearing lake littorals devoid of semi-aquatic and aquatic plants as places suitable for stromatolites to grow, underpin the model of declining freshwater-shark diversity in most Permian Variscan basins, demonstrate fish/amphibian ratios in limnic assemblages to measure lake perenniality and reveal taphonomic biases in lake taphocoenoses. Our outcomes call for more knowledge about the diversity, ecology and fossilization pathways of past limnic biotas, particularly microorganisms and actinopterygian fishes, to reconstruct deep-time continental ecosystems.     

Short‐term temperature change may impact freshwater carbon flux: a microbial perspective

Small freshwater bodies are abundant and economically and ecologically important on a global scale. Within these, protozoa play an important role in structuring planktonic food webs and sequestering CO₂. We hypothesized that short‐term (～20 days) fluctuations, of 2–10 °C, will significantly alter carbon flux associated with predator–prey interactions within the microbial planktonic food web. We examined the model ciliate, Urotricha farcta, which is abundant and common; it was fed the autotrophic flagellate Cryptomonas sp., which is also common. Laboratory experiments were conducted over relevant ranges: 8–24 °C; 0–2 × 10⁵ prey mL^?1. Mechanistic‐phenomenological multiple regressions were developed and fit to the data to obtain relationships for (1) growth rate and volume changes of the flagellate vs. temperature and (2) growth rates, grazing, and cell volume change of the ciliate vs. temperature and prey concentration. Responses revealed interaction between temperature and prey levels on all ciliate parameters, indicating it is inappropriate to apply simple temperature corrections (e.g. Q₁₀) to such functions. The potential impact of such temperature changes on carbon flux was illustrated using a simple ciliate–flagellate predator–prey model, with and without the top grazer, Daphnia, added. The model indicated that predator–prey pulses occurred over 20 days, with the ciliate controlling the prey population. For ciliates and prey, carbon production peaked at 20 °C and rapidly decreased above and below this maximum; differences between minimum and maximum were approximately fourfold, for both prey and ciliate, with low levels at 25–30 °C and 10–15 °C. Including literature data to parameterize, the influence of the grazer Daphnia did not alter the prediction that the ciliate may control short‐term flagellate pulses and temperature will influence these in a nonintuitive fashion.     

中国北方常见芫菁分子物种界定(鞘翅目: 芫菁科)

【目的】应用线粒体COI和核CAD基因片段探讨自动条形码间隔探索(automatic barcode gapdiscovery, ABGD)、广义混合Yule溯祖模型(generalized mixed Yule coalescent, GMYC)、贝叶斯泊松树进程(Bayesian Poisson tree processes, bPTP)和贝叶斯系统发育和系统地理分析(Bayesianphylogenetics and phylogeography, BPP) 4种分析方法在芫菁科(Meloidae)昆虫分子物种界定中的适用性。【方法】分别基于COI, CAD和COI+CAD串联序列数据集,应用ABGD, GMYC, bPTP和BPP 4种方法对中国北方芫菁科常见的6属(沟芫菁属Hycleus、斑芫菁属Mylabris、豆芫菁属Epicauta、绿芫菁属Lytta、星芫菁属Megatrachelus和短翅芫菁属Meloe)18个形态种进行分子物种界定,并与形态学鉴定结果进行比较。【结果】利用COI+CAD串联序列数据集所得物种界定结果与形态鉴定结果一致;COI数据集使用ABGD和GMYC方法的界定结果与形态鉴定结果一致,而bPTP划分的物种数较形态鉴定结果多;基于CAD序列在3种单基因物种界定方法的结果中,除GMYC与形态划分一致外,其余均显示部分结果与形态划分不同。【结论】在芫菁科分子物种界定中,多基因联合序列、多种界定方法分析所得结果优于单一基因片段和界定方法的分析结果。本研究的结果为芫菁科昆虫的分子物种界定和整合分类提供了数据支持和参考。     

The embryonic epicardium: an essential element of cardiac development

The epicardium has recently been identified as an active and essential element of cardiac development. Recent reports have unveiled a variety of functions performed by the embryonic epicardium, as well as the cellular and molecular mechanisms regulating them. However, despite its developmental importance, a number of unsolved issues related to embryonic epicardial biology persist. In this review, we will summarize our current knowledge about (i) the ontogeny and evolution of the epicardium, including a discussion on the evolutionary origins of the proepicardium (the epicardial primordium), (ii) the nature of epicardial–myocardial interactions during development, known to be essential for myocardial growth and maturation, and (iii) the contribution of epicardially derived cells to the vascular and connective tissue of the heart. We will finish with a note on the relationships existing between the primordia of the viscera and their coelomic epithelial lining. We would like to suggest that at least a part of the properties of the embryonic epicardium are shared by many other coelomic cell types, such that the role of epicardium in cardiac development is a particular example of a more general mechanism for the contribution of coelomic and coelomic-derived cells to the morphogenesis of organs such as the liver, kidneys, gonads or spleen.     

The voltage-dependent anion channel: an essential player in apoptosis

The increase of outer mitochondrial membrane permeability is a central event in apoptotic cell death, since it releases several apoptogenic factors such as cytochrome c into the cytoplasm that activate the downstream destructive processes. The voltage-dependent anion channel (VDAC or mitochondrial porin) plays an essential role in the increase of mitochondrial membrane permeability, and it is regulated by the Bcl-2 family of proteins via direct interaction. Anti-apoptotic Bcl-2 family members close the VDAC, whereas some (but not all) pro-apoptotic members interact with the VDAC to generate a protein-conducting channel through which cytochrome c can pass. Although the VDAC is directly involved in the apoptotic increase of mitochondrial membrane permeability and is known to be a component of the permeability transition pore complex, its role in the regulation of outer membrane permeability can be separated from the occurrence of permeability transition events, such as mitochondrial swelling followed by rupture of the outer mitochondrial membrane. The VDAC not only interacts with Bcl-2 family members, but also with other proteins, and probably acts as a convergence point for a variety of life-or-death signals.     

Redefining community: towards an ecological republicanism

This paper makes some suggestions for a concept of community which arguably satisfies the most important criteria for both human communities, as defined in the social sciences and humanities, and natural communities, as defined in ecology and biology. Beginning with the former, I arrive at two such criteria: (1) a material and social connection among members, and (2) some kind and degree of awareness of other members. These are then supplemented with a third drawn from civic republicanism, with its focus on citizenship and the common good: communities (3) enable and require certain practices for their maintainence. Turning to ecological definitions of community, I find the dominant (reductionist) one seriously deficient as compared with a more holist and ecosystemic approach. However, I invoke a nonreductive holism to defend the idea of community, and go on to argue that each of the three above-mentioned criteria can be fruitfully extended to include both social and ecological communities in a nonreductionist way – that is, in a way that neither reduces ecosystemic properties to individual organisms nor the reverse. This culminates in a discussion of what I call ecological republicanism, which I suggest could have powerfully positive effects on the contemporary crisis of undue human impact on the natural world.     

Understanding plant defence responses against herbivore attacks: an essential first step towards the development of sustainable resistance against pests

Plant-herbivore relationships are complex interactions encompassing elaborate networks of molecules, signals and strategies used to overcome defences developed by each other. Herbivores use multiple feeding strategies to obtain nutrients from host plants. In turn, plants respond by triggering defence mechanisms to inhibit, block or modify the metabolism of the pest. As part of these defences, herbivore-challenged plants emit volatiles to attract natural enemies and warn neighbouring plants of the imminent threat. In response, herbivores develop a variety of strategies to suppress plant-induced protection. Our understanding of the plant-herbivore interphase is limited, although recent molecular approaches have revealed the participation of a battery of genes, proteins and volatile metabolites in attack-defence processes. This review describes the intricate and dynamic defence systems governing plant-herbivore interactions by examining the diverse strategies plants employ to deny phytophagous arthropods the ability to breach newly developed mechanisms of plant resistance. A cornerstone of this understanding is the use of transgenic tools to unravel the complex networks that control these interactions.     

Circulating endothelial cells, microparticles and progenitors: key players towards the definition of vascular competence

The balance between lesion and regeneration of the endothelium is critical for the maintenance of vessel integrity. Exposure to cardiovascular risk factors (CRF) alters the regulatory functions of the endothelium that progresses from a quiescent state to activation, apoptosis and death. In the last 10 years, identification of circulating endothelial cells (CEC) and endothelial-derived microparticles (EMP) in the circulation has raised considerable interest as non-invasive markers of vascular dysfunction. Indeed, these endothelial-derived biomarkers were associated with most of the CRFs, were indicative of a poor clinical outcome in atherothrombotic disorders and correlated with established parameters of endothelial dysfunction. CEC and EMP also behave as potential pathogenic vectors able to accelerate endothelial dysfunction and promote disease progression. The endothelial response to injury has been enlarged by the discovery of a powerful physiological repair process based on the recruitment of circulating endothelial progenitor cells (EPC) from the bone marrow. Recent studies indicate that reduction of EPC number and function by CRF plays a critical role in the progression of cardiovascular diseases. This EPC-mediated repair to injury response can be integrated into a clinical endothelial phenotype defining the 'vascular competence' of each individual. In the future, provided that standardization of available methodologies could be achieved, multimarker strategies combining CEC, EMP and EPC levels as integrative markers of 'vascular competence' may offer new perspectives to assess vascular risk and to monitor treatment efficacy.     

Microbial Metabolism as an Evolutionary Response: The Cybernetic Approach to Modeling

ABSTRACT:?

The growth and metabolic capabilities of microorganisms depend on their interactions with the culture medium. Many media contain two or more key substrates, and an organism may have different preferences for the components. Microorganisms adjust their preferences according to the prevailing conditions so as to favor their own survival. Cybernetic modeling describes this evolutionary strategy by defining a goal that an organism tries to attain optimally at all times. The goal is often, but not always, maximization of growth, and it may require the cells to manipulate their metabolic processes in response to changing environmental conditions.

The cybernetic approach overcomes some of the limitations of metabolic control analysis (MCA), but it does not substitute MCA. Here we review the development of the cybernetic modeling of microbial metabolism, how it may be combined with MCA, and what improvements are needed to make it a viable technique for industrial fermentation processes.

IMTECH communication no.001/2001     

The Genome Sequence DataBase: towards an integrated functional genomics resource.

During 1998 the primary focus of the Genome Sequence DataBase (GSDB; http://www.ncgr.org/gsdb ) located at the National Center for Genome Resources (NCGR) has been to improve data quality, improve data collections, and provide new methods and tools to access and analyze data. Data quality has been improved by extensive curation of certain data fields necessary for maintaining data collections and for using certain tools. Data quality has also been increased by improvements to the suite of programs that import data from the International Nucleotide Sequence Database Collaboration (IC). The Sequence Tag Alignment and Consensus Knowledgebase (STACK), a database of human expressed gene sequences developed by the South African National Bioinformatics Institute (SANBI), became available within the last year, allowing public access to this valuable resource of expressed sequences. Data access was improved by the addition of the Sequence Viewer, a platform-independent graphical viewer for GSDB sequence data. This tool has also been integrated with other searching and data retrieval tools. A BLAST homology search service was also made available, allowing researchers to search all of the data, including the unique data, that are available from GSDB. These improvements are designed to make GSDB more accessible to users, extend the rich searching capability already present in GSDB, and to facilitate the transition to an integrated system containing many different types of biological data.     

High and ultra‐high definition of infrared spectral histopathology gives an insight into chemical environment of lung metastases in breast cancer

Using high definition (HD) and ultra‐high definition (UHD) of Fourier‐transform infrared (FTIR) spectroscopic imaging, we characterized spectrally pulmonary metastases in a murine model of breast cancer comparing them with histopathological results (Hematoxylin and eosin [H&E] staining). This comparison showed excellent agreement between the methods in case of localization of metastases with size below 1 mm and revealed that label‐free HD and UHD IR spectral histopathology distinguish the type of neoplastic cells. We primary focused on differentiation between metastatic foci in the pleural cavity from cancer cells present in lung parenchyma and inflamed cells present in extracellular matrix of lungs due to growing of advanced metastases. In addition, a combination of unsupervised clustering and IR imaging indicated the high sensitivity of FTIR spectroscopy to identify chemical features of small macrometastases located under the pleural cavity and during epithelial‐mesenchymal transition. FTIR‐based spectral histopathology was proved to detect not only phases of breast cancer metastasis to lungs but also to differentiate various origins of metastases seeded from breast cancer.      

Seeking functional homogeneity: A framework for definition and classification of fish assemblage types to support assessment tools on temperate reefs

Due to their important role in the ecosystem and high economic value, there is a need to assess the effect of anthropogenic impacts on marine fish assemblages. However, this can only be achieved if variations due to natural causes are known. Moreover, while most assessment tools rely on functional traits, bottom-up habitat classification frameworks tend to use species composition. The present study proposes an innovative framework to define fish assemblage types through metric pairwise constrained k-means (MPCK-means) clustering of sites based on functional guild categories and univariate metrics, an approach that takes into account within-site variability due to the sampling method and natural causes. This was followed by a label-based ensemble clustering approach, which finds patterns that minimise information loss when integrating clustering results from individual metrics. In order to test the method, fish assemblages on 14 nearshore rocky reefs along the Portuguese coast were sampled. The final typology configuration achieved through ensemble clustering consisted of three assemblage types and maintained an average normalised mutual information of 0.605 with the individual clustering results. Nested PERMANOVA found differences among types and the most variable metrics in the face of natural variation were identified. Ultimately, a k-nearest neighbours classifier is proposed to label new sites, based only on environmental variables that are unlikely to be directly affected by the presence of anthropogenic impacts. Optimal performance for the classification model was achieved with inverse distance-weighted voting of the 4 nearest neighbours with an average classification accuracy of 96.08%.     

Successional phases and species replacements in freshwater rock pools: towards a biological definition of ephemeral systems

1. In temporary aquatic habitats, time is probably the dominant environmental factor affecting community composition, mainly by setting constraints on colonization success and the replacement of taxa over time. The mechanism and effect of a decreasing inundation period on community development, mostly in terms of truncation, are still poorly documented. The permanent and ephemeral components of temporary communities are expected to be differently influenced by the degree of persistence of the habitat. 2. To study the effect of time on invertebrate community assembly and dynamics in a short duration type of temporary aquatic habitat, we monitored 16 ephemeral rock pools which persisted from less than a week to about 1 month at two rock pool sites in semi‐arid south‐eastern Botswana. Data were collected every 2 days during a full inundation cycle. 3. All communities were initially assembled by permanent residents recolonizing the habitat from egg banks and were later joined by actively dispersing ephemeral taxa. Species replacements only occurred in two pools. Concurrent with a decrease in the densities of Branchipodopsis wolfi, population sizes of Leberis sp. and Culicidae (Aedes sp. and Anopheles sp.) increased in these pools. Although it was possible to distinguish two successive phases at one rock pool site, community assembly was generally a gradual process determined by dispersal strategies of the inhabitants. Additional rains after initial filling triggered dispersal by ephemeral taxa, mainly Micronecta youngiana and Hydroglyphus infirmus, and positively influenced colonization success. 4. Decreasing persistence shortens community development down to a critical point below which lack of time eliminates the possibility of species replacement. Based on these findings, we define ephemeral waters as aquatic habitats lacking species replacements. Other temporary water types have a relatively longer persistence, permitting successional replacement of species.     

The maize two-dimensional gel protein database: towards an integrated genome analysis program

This paper describes the first maize database of proteins separated by two-dimensional electrophoresis. Fifty-six coleoptile proteins and 18 leaf proteins from two maize lines were partially microsequenced. Thirty-six proteins (49%) displayed high similarity with database proteins. Nine of these proteins, representing five different functions, had never been described in maize. No conclusive function could be found for 45 polypeptides (61% of the microsequenced proteins). In addition, an alternative identification method, based on amino acid analysis, allowed candidates to be proposed for 17 proteins out of 44 additional proteins analyzed in the coleoptiles. These results are stored in a database which also includes, when available, genetic information about the chromosomal location of structural genes and regulatory factors of proteins. This database is being used in the context of a project on the genetic mapping of the expressed genome in maize.     

Response probability and response time: a straight line, the Tagging/Retagging interpretation of short term memory, an operational definition of meaningfulness and short term memory time decay and search time

The functional relationship between correct response probability and response time is investigated in data sets from Rubin, Hinton and Wenzel, J Exp Psychol Learn Mem Cogn 25:1161–1176, 1999 and Anderson, J Exp Psychol [Hum Learn] 7:326–343, 1981. The two measures are linearly related through stimulus presentation lags from 0 to 594 s in the former experiment and for repeated learning of words in the latter. The Tagging/Retagging interpretation of short term memory is introduced to explain this linear relationship. At stimulus presentation the words are tagged. This tagging level drops slowly with time. When a probe word is reintroduced the tagging level has to increase for the word to be properly identified leading to a delay in response time. The tagging time is related to the meaningfulness of the words used—the more meaningful the word the longer the tagging time. After stimulus presentation the tagging level drops in a logarithmic fashion to 50% after 10 s and to 20% after 240 s. The incorrect recall and recognition times saturate in the Rubin et al. data set (they are not linear for large time lags), suggesting a limited time to search the short term memory structure: the search time for recall of unusual words is 1.7 s. For recognition of nonsense words the corresponding time is about 0.4 s, similar to the 0.243 s found in Cavanagh (1972).