What is geometric information and how do animals use it?

Unlike investigations of animals’ use of spatial cues such as landmarks, studies of sensitivity to the geometry of surfaces in an enclosure have proceeded mostly as an attempt to explain a laboratory finding with few direct tests of how animals use such a cue in nature. In this brief review, I discuss the current debate over whether global or local information from the enclosure drives the typical rotational error pattern in such studies. A consideration of the form and function of geometric cues in natural settings suggests that the natural boundaries for which arena walls are considered analogous might better be thought as landmarks. With a clearer picture of what geometric information is and how it might be used in nature, the generality of findings from laboratory studies of geometry enclosure can be better assessed.     

How much do army ants eat? On the prey intake of a neotropical top-predator

New World army ants (Ecitoninae) are nomadic group-predators that are widely thought to have a substantial impact on their prey. Nevertheless, quantitative data on prey intake by army ants is scarce and mostly limited to chance encounters. Here, I quantify the prey intake of the army ant Eciton hamatum at the contrasting scales of raid, colony (sum of simultaneous raids), and population. Like most army ants, E. hamatum conducts narrow ‘column raids’ and has a specialized diet of ant prey. I show that individual raids often had periods of no prey intake, and raid intake rates, calculated in g/min, differed significantly among colonies. Moreover, neither mean nor peak raid intake rates were correlated with colony size. Similarly, colony intake rates differed significantly among colonies, and mean colony intake rates were not correlated with colony size. However, mean colony intake rates were significantly higher than mean raid intake rates, and peak colony intake rate was correlated with colony size. Having multiple raids thus improves colony-level intake rates, and larger colonies can harvest more prey per unit time. Mean colony intake rate across colonies was 0.067 g/min dry weight and mean daily colony intake was calculated at 38.2 g. This intake is comparable to that of Eciton burchellii, which has a more generalized diet and conducts spectacular ‘swarm raids’ that are seen as having a greater impact on prey than column raids. Population size on Barro Colorado Island, Panama, was estimated to be 57 colonies, which extrapolates to a daily population intake of nearly 2 kg of prey dry weight, or 120 g/km². Broadly, these findings demonstrate that column raiding army ants experience considerable variation in prey intake for individual raids, but can still achieve notable impact at the larger scales of colony and population. Furthermore, they challenge the idea that swarm-raiding species necessarily have greater intake and thus impact on prey. Instead, I suggest that conducting multiple column raids may be a strategy that allows for comparable intake from a more specialized diet.     

The evolution of noncoding DNA: how much junk, how much func?

Comparative sequence analysis on a genomic scale has opened the door for the systematic analysis of cis-acting regulatory DNA. It is now possible to begin to answer basic questions such as, how much meaningful noncoding sequence is in the genome? How strong is natural selection on functional noncoding sequences in different species? Two recent articles have capitalized on the comparative genomic approach in an attempt to answer these questions with surprising results.     

The costs of using unauthenticated, over-passaged cell lines: how much more data do we need?

Increasing data demonstrate that cellular cross-contamination, misidentified cell lines, and the use of cultures at high-passage levels contribute to the generation of erroneous and misleading results as well as wasted research funds. Contamination of cell lines by other lines has been recognized and documented back to the 1950s. Based on submissions to major cell repositories in the last decade, it is estimated that between 18% and 36% of cell lines may be contaminated or misidentified. More recently, problems surrounding practices of over-subculturing cells are being identified. As a result of selective pressures and genetic drift, cell lines, when kept in culture too long, exhibit reduced or altered key functions and often no longer represent reliable models of their original source material. A review of papers showing significant experimental variances between low- and high-passage cell culture numbers, as well as contaminated lines, makes a strong case for using verified, tested cell lines at low- or defined passage numbers. In the absence of cell culture guidelines, mandates from the National Institutes of Health (NIH) and other funding agencies or journal requirements, it becomes the responsibility of the scientific community to perform due diligence to ensure the integrity of cell cultures used in research.     

Collagen-induced arthritis and related animal models: how much of their pathogenesis is auto-immune, how much is auto-inflammatory?

In this review, we discuss our studies on the pathogenesis of collagen-induced arthritis (CIA) and related mouse models for rheumatoid arthritis. Of note, these models invariably rely on the use of complete Freund's adjuvant (CFA). Our analysis has focused on explaining the dichotomous - either protective or disease-promoting - role of endogenous IFN-γ. Induction of a myelopoietic burst by CFA was identified as an important and underestimated factor in mediating the role of IFN-γ and other cytokines (IL-6, IL-17, GCP-2, RANK-L). Myelopoiesis provides an excess in precursors for joint-infiltrating neutrophils and osteoclasts. We postulate that classical CIA is primarily an auto-inflammatory disease, in part because of a strong innate immune response to the adjuvant. Superimposed on this, collagen-specific auto-immunity reinforces inflammatory reactivity in joints.     

The biology of desmin filaments: how do mutations affect their structure, assembly, and organisation?

Desmin, the major intermediate filament (IF) protein of muscle, is evolutionarily highly conserved from shark to man. Recently, an increasing number of mutations of the desmin gene has been described to be associated with human diseases such as certain skeletal and cardiac myopathies. These diseases are histologically characterised by intracellular aggregates containing desmin and various associated proteins. Although there is progress regarding our knowledge on the cellular function of desmin within the cytoskeleton, the impact of each distinct mutation is currently not understood at all. In order to get insight into how such mutations affect filament assembly and their integration into the cytoskeleton we need to establish IF structure at atomic detail. Recent progress in determining the dimer structure of the desmin-related IF-protein vimentin allows us to assess how such mutations may affect desmin filament architecture.     

Ecological and evolutionary consequences of size‐selective harvesting: how much do we know?

Size-selective harvesting, where the large individuals of a particular species are preferentially taken, is common in both marine and terrestrial habitats. Preferential removal of larger individuals of a species has been shown to have a negative effect on its demography, life history and ecology, and empirical studies are increasingly documenting such impacts. But determining whether the observed changes represent evolutionary response or phenotypic plasticity remains a challenge. In addition, the problem is not recognized in most management plans for fish and marine invertebrates that still mandate a minimum size restriction. We use examples from both aquatic and terrestrial habitats to illustrate some of the biological consequences of size-selective harvesting and discuss possible future directions of research as well as changes in management policy needed to mitigate its negative biological impacts.     

Obtaining data from randomised controlled trials: how much do we need for reliable and informative meta-analyses?

Many randomised controlled trials compare treatments that will produce only moderate differences in outcome, but these differences can be clinically important. However, they are difficult to assess reliably and require a large amount of randomised evidence. This can be achieved through large prospective randomised trials which will accrue future patients, the meta-analysis of results from randomised trials involving patients from the past, or--ideally--both. The techniques require that all possible biases are minimised, and in meta-analyses this can best be achieved by ensuring that all of the randomised evidence--both trials and participants in those trials--is included. The meta-analysis of individual patient data has been described as the gold standard for this approach. It will remove many of the problems associated with relying solely on published data and some of the problems arising from a reliance on aggregate data, and will also add to the analyses that can be performed. Such projects, however, require considerable time and effort.     

Towards a framework for the evolutionary genomics of Kinetoplastids: what kind of data and how much?

The current status of kinetoplastids phylogeny and evolution is discussed in view of the recent progresses on genomics. Some ideas on a potential framework for the evolutionary genomics of kinetoplastids are presented.     

A case of non-scaling in mammalian physiology? Body size, digestive capacity, food intake, and ingesta passage in mammalian herbivores

As gut capacity is assumed to scale linearly to body mass (BM), and dry matter intake (DMI) to metabolic body weight (BM(0.75)), it has been proposed that ingesta mean retention time (MRT) should scale to BM(0.25) in herbivorous mammals. We test these assumptions with the most comprehensive literature data collations (n=74 species for gut capacity, n=93 species for DMI and MRT) to date. For MRT, only data from studies was used during which DMI was also recorded. Gut capacity scaled to BM(1.06). In spite of large differences in feeding regimes, absolute DMI (kg/d) scaled to BM(0.76) across all species tested. Regardless of this allometry inherent in the dataset, there was only a very low allometric scaling of MRT with BM(0.14) across all species. If species were divided according to the morphophysiological design of their digestive tract, there was non-significant scaling of MRT with BM(0.04) in colon fermenters, BM(0.08) in non-ruminant foregut fermenters, BM(0.06) in browsing and BM(0.04) in grazing ruminants. In contrast, MRT significantly scaled to BM(0.24) (CI 0.16-0.33) in the caecum fermenters. The results suggest that below a certain body size, long MRTs cannot be achieved even though coprophagy is performed; this supports the assumption of a potential body size limitation for herbivory on the lower end of the body size range. However, above a 500 g-threshold, there is no indication of a substantial general increase of MRT with BM. We therefore consider ingesta retention in mammalian herbivores an example of a biological, time-dependent variable that can, on an interspecific level, be dissociated from a supposed obligatory allometric scaling by the morphophysiological design of the digestive tract. We propose that very large body size does not automatically imply a digestive advantage, because long MRTs do not seem to be a characteristic of very large species only. A comparison of the relative DMI (g/kg(0.75)) with MRT indicates that, on an interspecific level, higher intakes are correlated to shorter MRTs in caecum, colon and non-ruminant foregut fermenters; in contrast, no significant correlation between relative DMI and MRT is evident in ruminants.     

Litter decomposition of woody species in shrublands of NW Patagonia: how much do functional groups and microsite conditions influence decomposition?

The study examined the effects of leaf traits, soil microsite, and microclimate characteristics on litter decomposition of the dominant species in two functional groups (FG), deciduous and evergreen, in shrublands in NW Patagonia, Argentina. Leaf traits considered were nutrient concentration (C, N, P, C/N, and N/P) and physical characteristics (area, strength, specific leaf area, and dry matter content). Soil microsite characteristics measured were pH, C, N, P, C/N and water retention capacity, while soil microclimate characteristics recorded were soil and air, temperature and moisture, and solar radiation. Five evergreen and five deciduous woody shrub species were selected. During 1 year, litter and microsite properties were measured below canopy: (i) senescent leaf chemical and physical properties, and the quantity as well as field decomposition of litter and (ii) soil chemistry, and soil and air physical properties. The factors controlling litter decomposition were different for each FG. In deciduous species, C/N ratio had a negative effect on decomposition. In evergreen species, decomposition was affected negatively by leaf carbon and dry matter content. Litter decomposition depended exclusively on the inherent senescent leaves traits. The common decomposition pattern between species of both FG could be attributed to similar leaf traits and the correlation between variables that control decomposition in both groups. Plant nutrient inputs associated with the litter decomposition process did not explain the soil nutrient content. These results suggest that other organic matter sources (roots, branches, and fruits) are more important than leaves on soil fertility.     

The case for increasing the statistical power of eddy covariance ecosystem studies: why,where and how?

Eddy covariance (EC) continues to provide invaluable insights into the dynamics of Earth's surface processes. However, despite its many strengths, spatial replication of EC at the ecosystem scale is rare. High equipment costs are likely to be partially responsible. This contributes to the low sampling, and even lower replication, of ecoregions in Africa, Oceania (excluding Australia) and South America. The level of replication matters as it directly affects statistical power. While the ergodicity of turbulence and temporal replication allow an EC tower to provide statistically robust flux estimates for its footprint, these principles do not extend to larger ecosystem scales. Despite the challenge of spatially replicating EC, it is clearly of interest to be able to use EC to provide statistically robust flux estimates for larger areas. We ask: How much spatial replication of EC is required for statistical confidence in our flux estimates of an ecosystem? We provide the reader with tools to estimate the number of EC towers needed to achieve a given statistical power. We show that for a typical ecosystem, around four EC towers are needed to have 95% statistical confidence that the annual flux of an ecosystem is nonzero. Furthermore, if the true flux is small relative to instrument noise and spatial variability, the number of towers needed can rise dramatically. We discuss approaches for improving statistical power and describe one solution: an inexpensive EC system that could help by making spatial replication more affordable. However, we note that diverting limited resources from other key measurements in order to allow spatial replication may not be optimal, and a balance needs to be struck. While individual EC towers are well suited to providing fluxes from the flux footprint, we emphasize that spatial replication is essential for statistically robust fluxes if a wider ecosystem is being studied.     

Comparative genomics of archaea: how much have we learned in six years,and what's next?

Archaea comprise one of the three distinct domains of life (with bacteria and eukaryotes). With 16 complete archaeal genomes sequenced to date, comparative genomics has revealed a conserved core of 313 genes that are represented in all sequenced archaeal genomes, plus a variable 'shell' that is prone to lineage-specific gene loss and horizontal gene exchange. The majority of archaeal genes have not been experimentally characterized, but novel functional pathways have been predicted.     

What is Causal Specificity About,and What is it Good for in Philosophy of Biology?

Acta Biotheoretica - The concept of causal specificity is drawing considerable attention from philosophers of biology. It became the rationale for rejecting (and occasionally, accepting) a thesis...     

The molecular biology of recombination in Mycobacteria: what do we know and how can we use it?

Recombination is a ubiquitous genetic process which results in the exchange of DNA between two substrates. Homologous recombination occurs between DNA species with identical sequence whereas illegitimate recombination can occur between DNA with very little or no homology. Site-specific recombination is often used by temperate phages to stably integrate into bacterial chromosomes. Characterisation of the mechanisms of recombination in mycobacteria has mainly focussed on RecA-dependent homologous recombination and phage-directed site-specific recombination. In contrast the high frequency of illegitimate recombination in slow-growing mycobacteria has not been explained. The role of DNA repair in dormancy and infection have not yet been fully established, but early work suggests that RecA-mediated pathways are not required for virulence. All three recombination mechanisms have been utilised in developing genetic techniques for the analysis of the biology and pathogenesis of mycobacteria. A recently developed method for studying essential genes will generate further insights into the biology of these important organisms.