Are microorganisms everywhere they can be?

Baas-Becking is famously attributed with the conjecture that ‘everything is everywhere, but the environment selects’. Although this aphorism is largely challenged by microbial biogeographical data, even weak versions of the claim leave unanswered the question about whether all environments that could theoretically support life contain life. In the last decade, the discovery of thermally sterilized habitable environments disconnected from inhabited regions, and habitats within organisms such as the sterile, but habitable human fetal gut, suggest the existence of a diversity of macroscopic habitable environments apparently devoid of actively metabolizing or reproducing life. Less clear is the status of such environments at the micron scale, for example, between colonies of organisms within rock interstices or on and within other substrates. I discuss recent evidence for these types of environments. These environments have practical uses in: (i) being negative controls for understanding the role of microbial processes in geochemical cycles and geological processes, (ii) yielding insights into the extent to which the biosphere extends into all spaces it theoretically can, (iii) suggesting caution in interpreting the results of life detection instrumentation, and (iv) being useful for establishing the conditions for the origin of life and its prevalence on other planetary bodies.     

Can root electrical capacitance be used to predict root mass in soil?

Background

Electrical capacitance, measured between an electrode inserted at the base of a plant and an electrode in the rooting substrate, is often linearly correlated with root mass. Electrical capacitance has often been used as an assay for root mass, and is conventionally interpreted using an electrical model in which roots behave as cylindrical capacitors wired in parallel. Recent experiments in hydroponics show that this interpretation is incorrect and a new model has been proposed. Here, the new model is tested in solid substrates.

Methods

The capacitances of compost and soil were determined as a function of water content, and the capacitances of cereal plants growing in sand or potting compost in the glasshouse, or in the field, were measured under contrasting irrigation regimes.

Key Results

Capacitances of compost and soil increased with increasing water content. At water contents approaching field capacity, compost and soil had capacitances at least an order of magnitude greater than those of plant tissues. For plants growing in solid substrates, wetting the substrate locally around the stem base was both necessary and sufficient to record maximum capacitance, which was correlated with stem cross-sectional area: capacitance of excised stem tissue equalled that of the plant in wet soil. Capacitance measured between two electrodes could be modelled as an electrical circuit in which component capacitors (plant tissue or rooting substrate) are wired in series.

Conclusions

The results were consistent with the new physical interpretation of plant capacitance. Substrate capacitance and plant capacitance combine according to standard physical laws. For plants growing in wet substrate, the capacitance measured is largely determined by the tissue between the surface of the substrate and the electrode attached to the plant. Whilst the measured capacitance can, in some circumstances, be correlated with root mass, it is not a direct assay of root mass.     

Can Wolbachia be used to control malaria?

Malaria is a mosquito-borne infectious disease caused by Plasmodium parasites transmitted by the infectious bite of Anopheles mosquitoes. Vector control of malaria has predominantly focused on targeting the adult mosquito through insecticides and bed nets. However, current vector control methods are often not sustainable for long periods so alternative methods are needed. A novel biocontrol approach for mosquito-borne diseases has recently been proposed, it uses maternally inherited endosymbiotic Wolbachia bacteria transinfected into mosquitoes in order to interfere with pathogen transmission. Transinfected Wolbachia strains in Aedes aegypti mosquitoes, the primary vector of dengue fever, directly inhibit pathogen replication, including Plasmodium gallinaceum, and also affect mosquito reproduction to allow Wolbachia to spread through mosquito populations. In addition, transient Wolbachia infections in Anopheles gambiae significantly reduce Plasmodium levels. Here we review the prospects of using a Wolbachia-based approach to reduce human malaria transmission through transinfection of Anopheles mosquitoes.     

How can soil monitoring networks be used to improve predictions of organic carbon pool dynamics and CO2 fluxes in agricultural soils?

As regional and continental carbon balances of terrestrial ecosystems become available, it becomes clear that the soils are the largest source of uncertainty. Repeated inventories of soil organic carbon (SOC) organized in soil monitoring networks (SMN) are being implemented in a number of countries. This paper reviews the concepts and design of SMNs in ten countries, and discusses the contribution of such networks to reducing the uncertainty of soil carbon balances. Some SMNs are designed to estimate country-specific land use or management effects on SOC stocks, while others collect soil carbon and ancillary data to provide a nationally consistent assessment of soil carbon condition across the major land-use/soil type combinations. The former use a single sampling campaign of paired sites, while for the latter both systematic (usually grid based) and stratified repeated sampling campaigns (5?C10 years interval) are used with densities of one site per 10?C1,040 km². For paired sites, multiple samples at each site are taken in order to allow statistical analysis, while for the single sites, composite samples are taken. In both cases, fixed depth increments together with samples for bulk density and stone content are recommended. Samples should be archived to allow for re-measurement purposes using updated techniques. Information on land management, and where possible, land use history should be systematically recorded for each site. A case study of the agricultural frontier in Brazil is presented in which land use effect factors are calculated in order to quantify the CO₂ fluxes from national land use/management conversion matrices. Process-based SOC models can be run for the individual points of the SMN, provided detailed land management records are available. These studies are still rare, as most SMNs have been implemented recently or are in progress. Examples from the USA and Belgium show that uncertainties in SOC change range from 1.6?C6.5 Mg C ha^?1 for the prediction of SOC stock changes on individual sites to 11.72 Mg C ha^?1 or 34% of the median SOC change for soil/land use/climate units. For national SOC monitoring, stratified sampling sites appears to be the most straightforward attribution of SOC values to units with similar soil/land use/climate conditions (i.e. a spatially implicit upscaling approach).     

Can ultrasound be used to stimulate nerve tissue?

Background  

The stimulation of nerve or cortical tissue by magnetic induction is a relatively new tool for the non-invasive study of the brain and nervous system. Transcranial magnetic stimulation (TMS), for example, has been used for the functional mapping of the motor cortex and may have potential for treating a variety of brain disorders.     

Step on it: can footprints from tracking tunnels be used to identify lizard species?

There are few effective or efficient established methods for monitoring cryptic herpetofauna. Footprint tracking tunnels are routinely used to index small mammal populations, but also have potential for monitoring herpetofauna. We evaluated the utility of tracking tunnels for identification of New Zealand lizards using captive- and wild-sourced animals (four skink and eight gecko species). All skink prints that we obtained were indistinct or obscure, but we obtained relatively clear, measurable prints for all gecko species. We found that identification to species level was possible for the two gecko species for which we had a large sample—Naultinus gemmeus and Woodworthia ‘Otago large’—using linear discriminant analysis (the best model correctly assigned 96.1% of individuals). Our findings suggest that footprints from tracking tunnels may be used to distinguish between species of geckos. Additional research is needed to assess the ability to further discriminate intra- and inter-genera lizard footprints from tracking tunnels, and the utility of the technique for surveying and monitoring lizard populations.     

UV-induced changes in the skin: can they be repaired?

The damaging effects of UVB light have been described previously and include a number of changes to multiple cell types. At previous meetings of this society, we have shown that Langerhans' cells are the most susceptible to UVB induced damage which can be shown as ultrastructural changes in dendrites, nucleus and cytoplasm by transmission electron microscopy. We have also shown that their patterns of migration from skin to regional lymph node and their ability to present antigens to autologous T cells have been profoundly altered by UVB irradiation. The aim of this work was to establish if it was possible to reverse any of the damage done to Langerhans' cells by UVB exposure by topical application of a DNA repair enzyme such as T4N5 endonuclease. These experiments were undertaken in a sheep model that allowed collection of cells as they migrate from the skin. This allowed for a direct examination of the migration characteristics and ultrastructural features of all Langerhans' cells before, during, and for 2 weeks after exposure to a single dose of UVB. Results obtained from this project indicate that treatment by topical application of DNA repair enzyme immediately after UVB irradiation may restore a number of normal immune parameters associated with the structure and function of migrating Langerhans' cells. It appears that there is a dose related correction of the increased tempo of cell migration and some improvements in the number of ultrastructurally damaged Langerhans' cells have also been associated with application of higher doses of DNA repair enzyme. These preliminary findings indicate that some potential therapeutic benefits are associated with the use of such agents in reversing the immunological damage caused by exposure to erythemal doses of UVB light.     

UV-induced changes in the skin: can they be repaired?

Abstract

The damaging effects of UVB light have been described previously and include a number of changes to multiple cell types. At previous meetings of this society, we have shown that Langerhans' cells are the most susceptible to UVB induced damage which can be shown as ultrastructural changes in dendrites, nucleus and cytoplasm by transmission electron microscopy. We have also shown that their patterns of migration from skin to regional lymph node and their ability to present antigens to autologous T cells have been profoundly altered by UVB irradiation.

The aim of this work was to establish if it was possible to reverse any of the damage done to Langerhans' cells by UVB exposure by topical application of a DNA repair enzyme such as T4N5 endonuclease. These experiments were undertaken in a sheep model that allowed collection of cells as they migrate from the skin. This allowed for a direct examination of the migration characteristics and ultrastructural features of all Langerhans' cells before, during, and for 2 weeks after exposure to a single dose of UVB.

Results obtained from this project indicate that treatment by topical application of DNA repair enzyme immediately after UVB irradiation may restore a number of normal immune parameters associated with the structure and function of migrating Langerhans' cells. It appears that there is a dose related correction of the increased tempo of cell migration and some improvements in the number of ultrastructurally damaged Langerhans' cells have also been associated with application of higher doses of DNA repair enzyme. These preliminary findings indicate that some potential therapeutic benefits are associated with the use of such agents in reversing the immunological damage caused by exposure to erythemal doses of UVB light.     

What criteria should be used to select biodiversity indicators?

The conservation of biodiversity is a major goal in nature conservation, but measuring the total biodiversity of a site or a region is not possible; thus there is a great demand for indicators to represent biodiversity. To be able to make use of indicators, criteria must first be established for their selection, and the degree to which the indicators meet the criteria must be tested. However, the purposes for which indicators are applied—and thus sometimes the criteria themselves—differ between ecological science and environmental policy. As transparency in choosing and testing suitable biodiversity indicators will optimize the results of an indicator, this article first aims to determine if there are common approaches in selecting biodiversity indicators in ecology and environmental policy. Second, we asked which criteria biodiversity indicators were scientifically tested against to determine their suitability. To answer these questions, we analyzed papers on biodiversity indicators referenced in the Web of Science. Our results demonstrate different patterns for selecting biodiversity indicators in the different fields of application. In ecology, the quality of indicators is mainly determined by a close relationship between indicator and indicandum (i.e., indicated phenomenon), while the relevance of an indicator for a given issue, e.g., reserve selection or an assessment of a certain impact, is of paramount importance for conservation policy. Surprisingly, few biodiversity indicators are empirically tested to determine if they meet the criteria by which they were purportedly chosen. We argue that this is due to the different conceptualizations of biodiversity indicators in science and environmental policy. Since the suitability of biodiversity indicators remains untested in many cases, our findings suggest room to make better use of indicators in ecology and environmental policy. As the results of ecological research are put to use to solve environmental problems, the selection of indicators for ecological research should correspond to a large extent with those used in environmental policy. Further, to assess the suitability of a biodiversity indicator, it should be tested against all of the criteria relevant for its selection.     

Can sugarcoated fingerprints be used to identify lurking viruses?

Comparative proteomics is increasingly used to detect biomarkers and therapeutic targets that differ between healthy and diseased populations; however, differences in posttranslational modifications have received less attention. In this issue, Yang et al. (Proteomics 2016, 16, 1872–1880) present data indicating that a glycoproteomics approach can detect N‐glycosylated membrane protein differences between non‐HIV‐infected and latently infected human CD4⁺ T‐cell lines, identifying 172 proteins differentially expressed by these cells. Latently infected CD4⁺ T cells are thought to represent the major barrier to eventual HIV cure, but do not express detectable levels of viral protein and have not been shown to express biomarkers that can distinguish them from the vastly more abundant uninfected CD4⁺ T‐cell population. The findings of Yang et al. suggest that glycoproteomic analyses may have untapped potential to identify novel biomarkers and therapeutic targets in cell populations not readily distinguishable be standard proteomic analyses.     

Can ecological theory be used to improve water quality?

The role of ecology in environmental management has been more to warn of the dangers of pollution than to propose technical solutions for environmental problems, this being mostly left to chemists and engineers. Only limited aspects of the broad and diverse theory of ecology have been applied in the present bottom-up-control approach to water management (nutrient reduction). Another aspect of ecological theory which has recently become applicable is the top-down-control approach known as biomanipulation (promoting efficient herbivores). Both approaches are likely to be reinforced in the future by further application of ecological theory to water management. Of the multiple possibilities of applying ecological theory to environmental problems, one is the use of our knowledge on chemical communication in aquatic habitats, the phenomena by which prey detect the presence of their predators. I postulate that the phytoplankton standing crop might be reduced by chemical regulation of the physiology and life cycles of algae and cyanobacteria, as well as by chemical regulation of the behaviour and life histories of planktonic herbivores and their predators. At present planktivorous fish seem to be the most logical target for such chemical manipulation. A desirable effect, i.e. a reduction in algal standing crop, could be achieved by scaring fish from the lake pelagial thus releasing predation pressure on the offshore herbivorous zooplankton.     

Can ribozymes be used to regulate procaryote gene expression?

The in vivo activity of ribozymes designed against mRNA coding for E. coli beta-galactosidase was tested both in intramolecular and in intermolecular conditions. When recombinant M13 phage DNA carrying on the same molecule the information for both the ribozyme and the target was transfected into bacterial cells, ribozyme activity was observed. Conversely, a ribozyme coded by a recombinant M13 vector, but targeted against an mRNA transcribed from the F episome including the remaining part of the beta-galactosidase gene, was inefficient.     

Can treadmill walking be used to assess propulsion generation?

Instrumented treadmills offer significant advantages for analysis of human locomotion, including recording consecutive steady-state gait cycles, precisely controlling walking speed, and avoiding force plate targeting. However, some studies of hemiparetic walking on a treadmill have suggested that the moving treadmill belt may fundamentally alter propulsion mechanics. Any differences in propulsion mechanics during treadmill walking would be problematic since recent studies assessing propulsion have provided fundamental insight into hemiparetic walking. The purpose of this study was to test the hypothesis that there would be no difference in the generation of anterior/posterior (A/P) propulsion by performing a carefully controlled comparison of the A/P ground reaction forces (GRFs) and impulses in healthy adults during treadmill and overground walking. Gait data were collected from eight subjects walking overground and on a treadmill with speed and cadence controlled. Peak negative and positive horizontal GRFs in early and late stance, respectively, were reduced by less than 5% of body weight (p<0.05) during treadmill walking compared to overground walking. The magnitude of the braking impulse was similarly lower (p<0.05) during treadmill walking, but no significant difference was found between propulsion impulses. While there were some subtle differences in A/P GRFs between overground and treadmill walking, these results suggest there is no fundamental difference in propulsion mechanics. We conclude that treadmill walking can be used to investigate propulsion generation in healthy and by implication clinical populations.     

How long before a change in soil organic carbon can be detected?

When planning sampling in an experiment where soil organic carbon (SOC) content is expected to change, it is necessary to know how many samples will need to be taken to demonstrate a change in SOC and after how long this change will be detectable. Much has been published on the number of samples required to demonstrate the minimum detectable difference in SOC, but less on how long it takes for this change to be detectable. In this paper, a model of SOC dynamics is used to estimate the minimum time taken for a change in total SOC content to become measurable under different carbon inputs, land uses and soil types. For free air carbon dioxide enrichment (FACE), and other experiments in which SOC is expected to increase, relationships between the percentage change in C inputs and the time taken to measure a change in SOC are presented, for two levels of sampling intensity corresponding to the maximum that is practically possible in most experiments (～100 samples) and that used regularly in field experiments (10–20 samples). In FACE experiments, where C inputs increase by a maximum of about 20–25%, SOC change could be detected with 90% confidence after about 6–10 years if a sampling regime allowing 3% change in background SOC level (probably requiring a very large number of samples) were used, but could not be detected at all if a sampling regime were used that allowed only a 15% change in background SOC to be detected. If increases in C inputs are much below 15%, it might not be possible to detect a change in soil C without an enormous number of samples. Relationships between the change in C inputs and the time taken to measure a change in SOC are robust over a range of soil types and land uses. The results demonstrate how models of SOC dynamics can be used to complement statistical power analyses for planning when, and how intensively, to sample soils during experiments. An advantage of the modelling approach demonstrated here is that estimates of the minimum time taken for a change in soil carbon to become detectable can be made, even before any detailed soil samples are taken, simply from estimates of the likely increase in carbon inputs to the soil (via expected changes in net primary production).     

Abstractions can be causes — A response to professor hogan

In Can Abstractions be Causes, David Johnson defends the view that abstractions can have causal force. He offers as his own example of natural kinds ecological niches, arguing that the causal force of these niches in nature is akin to the force of Aristotelian final causes. He concludes that, rooted as it is in seventeenth century mechanism, the currently-accepted model of causality which recognises only efficient causes is inadequate to the needs of contemporary science. In Natural Kinds and Ecological Niches — Response to Johnson's Paper, Melinda Hogan offers a critique of Johnson's paper which, by begging the question in favor of the very sort of causality Johnson seeks to supplement, misses the epistemological implications of his idea. In this paper I will attempt to clarify and defend Johnson's position, pointing out some of its implications for the epistemology of science in general.