A computational image analysis glossary for biologists

Recent advances in biological imaging have resulted in an explosion in the quality and quantity of images obtained in a digital format. Developmental biologists are increasingly acquiring beautiful and complex images, thus creating vast image datasets. In the past, patterns in image data have been detected by the human eye. Larger datasets, however, necessitate high-throughput objective analysis tools to computationally extract quantitative information from the images. These tools have been developed in collaborations between biologists, computer scientists, mathematicians and physicists. In this Primer we present a glossary of image analysis terms to aid biologists and briefly discuss the importance of robust image analysis in developmental studies.     

Optimizing potentiometric ionophore and electrode design for environmental on-site control of antibiotic drugs: application to sulfamethoxazole

Potentiometric sensors are typically unable to carry out on-site monitoring of environmental drug contaminants because of their high limits of detection (LODs). Designing a novel ligand material for the target analyte and managing the composition of the internal reference solution have been the strategies employed here to produce for the first time a potentiometric-based direct reading method for an environmental drug contaminant. This concept has been applied to sulfamethoxazole (SMX), one of the many antibiotics used in aquaculture practices that may occur in environmental waters. The novel ligand has been produced by imprinting SMX on the surface of graphitic carbon nanostructures (CN)<500 nm. The imprinted carbon nanostructures (ICN) were dispersed in plasticizer and entrapped in a PVC matrix that included (or not) a small amount of a lipophilic additive. The membrane composition was optimized on solid-contact electrodes, allowing near-Nernstian responses down to 5.2 μg/mL and detecting 1.6 μg/mL. The membranes offered good selectivity against most of the ionic compounds in environmental water. The best membrane cocktail was applied on the smaller end of a 1000 μL micropipette tip made of polypropylene. The tip was then filled with inner reference solution containing SMX and chlorate (as interfering compound). The corresponding concentrations were studied for 1 × 10(-5) to 1 × 10(-10) and 1 × 10(-3) to 1 × 10(-8)mol/L. The best condition allowed the detection of 5.92 ng/L (or 2.3 × 10(-8)mol/L) SMX for a sub-Nernstian slope of -40.3 mV/decade from 5.0 × 10(-8) to 2.4 × 10(-5)mol/L. The described sensors were found promising devices for field applications. The good selectivity of the sensory materials together with a carefully selected composition for the inner reference solution allowed LODs near the nanomolar range. Both solid-contact and "pipette tip"-based sensors were successfully applied to the analysis of aquaculture waters.     

Design, synthesis and biological evaluation of potent NAD+-dependent DNA ligase inhibitors as potential antibacterial agents. Part 2: 4-amino-pyrido[2,3-d]pyrimidin-5(8H)-ones

A series of 4-amino-pyrido[2,3-d]pyrimidin-5(8H)-ones were designed and synthesized as a novel class of inhibitors of NAD(+)-dependent DNA ligase that possess potency against Gram-positive bacteria.     

Complex interactions between spatial pattern of resident species and invasiveness of newly arriving species affect invasibility

Understanding the factors that affect establishment success of new species in established communities requires the study of both the ability of new species to establish and community resistance. Spatial pattern of species within a community can affect plant performance by changing the outcome of inter-specific competition, and consequently community invasibility. We studied the effects of spatial pattern of resident plant communities on fitness of genotypes from the native and introduced ranges of two worldwide invasive species, Centaurea stoebe and Senecio inaequidens, during their establishment stage. We experimentally established artificial plant mixtures with 4 or 8 resident species in intra-specifically aggregated or random spatial patterns, and added seedlings of genotypes from the native and introduced ranges of the two target species. Early growth of both S. inaequidens and C. stoebe was higher in aggregated than randomly assembled mixtures. However, a species-specific interaction between invasiveness and invasibility highlighted more complex patterns. Genotypes from native and introduced ranges of S. inaequidens showed the same responses to spatial pattern. By contrast, genotypes from the introduced range of C. stoebe did not respond to spatial pattern whereas native ones did. Based on phenotypic plasticity, we argue that the two target species adopted different strategies to deal with the spatial pattern of the resident plant community. We show that effects of spatial pattern of the resident community on the fitness of establishing species may depend on the diversity of the recipient community. Our results highlight the need to consider the interaction between invasiveness and invasibility in order to increase our understanding of invasion success.     

Thirty‐five years of spatial autocorrelation analysis in population genetics: an essay in honour of Robert Sokal (1926–2012)

We could not start this review, literally from the beginning, without expressing our sadness over the passing of Professor Robert R. Sokal. We are sure, nevertheless, that the importance of his scientific achievements will ensure he is long remembered. In this modest tribute to Professor Sokal, we highlight his contributions to the field of population genetics and spatial statistical methods. Specifically, we discuss how two papers, co‐authored with Professor N. L. Oden and published in the pages of the Biological Journal of the Linnean Society in 1978, revolutionized the field of analytical population genetics. In these papers, Sokal and Oden created an elegant framework for inferring evolutionary processes (e.g. isolation‐by‐distance, demic diffusion, selection gradients, genetic drift) from the spatial autocorrelation analysis of genetic variation patterns. We also highlight the pivotal importance of Sokal's work to the development of emerging fields (e.g. landscape and conservation genetics). We hope this virtual issue containing the papers that Professor Sokal published in BJLS, and later, related papers by other researchers, will help to remember his work and maintain his legacy of spatial analysis in genetics, ecology, and evolutionary biology. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ??, ??–??.     

Können Tiere zählen?

The “magical” number four We know already since more than 140 years that humans have the inborn ability to recognize only up to four objects correctly if counting is strictly inhibited. Many vertebrates and the honeybee workers can remember up to four objects albeit they are unable to count. This inborn numerical competence common to humans and animals raises interesting questions concerning the purpose and the evolution of this ability. The “magical” number four is obviously a neurological, historical and mythological enigma.     

Non-classic androgen actions in Sertoli cell membrane in whole seminiferous tubules: effects of nandrolone decanoate and catechin

Studies show a mechanism of action of testosterone, nandrolone and catechin as agonists of the membrane androgen receptor. The aim of this work is to investigate the non-classical effect of androgens and catechin in Sertoli cells from immature rats. The membrane potential of Sertoli cells in whole seminiferous tubules was recorded using a standard single microelectrode technique. It was performed a topical application of testosterone (1 μM), nandrolone (0.1, 0.5 and 1 μM) and the flavonoid catechin (0.1, 0.5 and 1 μM) alone and also after infusion with flutamide (1 μM), diazoxide (100 μM) or U73122 (1 μM). The immature testes were incubated for 5 min in KRb with (45)Ca(2+), with or without nandrolone (1 μM). The results were given as mean±SEM. The data were analyzed using ANOVA for repeated measures with Bonferroni post-test. Testosterone produces a depolarization in the membrane potential at 120 s after application. Catechin (1 μM) and nandrolone (1 μM) have shown a similar response to testosterone: depolarization at 120 s after the application. The same response of catechin and nandrolone was observed at different doses. The effects of testosterone, catechin and nandrolone were not affected after perfusion with flutamide. Perfusion with diazoxide and U73122 nullified the effect of nandrolone (1 μM) and catechin (1 μM). Nandrolone and testosterone increased (45)Ca(2+) uptake with or without flutamide within 5min. These results indicate that nandrolone and catechin act through a receptor on the plasmatic membrane, as well as testosterone, showing a non-classical pathway in Sertoli cells from immature rat testes.     

A universal scaling law determines time reversibility and steady state of substitutions under selection

Monomorphic loci evolve through a series of substitutions on a fitness landscape. Understanding how mutation, selection, and genetic drift drive this process, and uncovering the structure of the fitness landscape from genomic data are two major goals of evolutionary theory. Population genetics models of the substitution process have traditionally focused on the weak-selection regime, which is accurately described by diffusion theory. Predictions in this regime can be considered universal in the sense that many population models exhibit equivalent behavior in the diffusion limit. However, a growing number of experimental studies suggest that strong selection plays a key role in some systems, and thus there is a need to understand universal properties of models without a priori assumptions about selection strength. Here we study time reversibility in a general substitution model of a monomorphic haploid population. We show that for any time-reversible population model, such as the Moran process, substitution rates obey an exact scaling law. For several other irreversible models, such as the simple Wright-Fisher process and its extensions, the scaling law is accurate up to selection strengths that are well outside the diffusion regime. Time reversibility gives rise to a power-law expression for the steady-state distribution of populations on an arbitrary fitness landscape. The steady-state behavior is dominated by weak selection and is thus adequately described by the diffusion approximation, which guarantees universality of the steady-state formula and its applicability to the problem of reconstructing fitness landscapes from DNA or protein sequence data.     

The search for life on Earth and other planets

As the NASA rover Curiosity approaches Mars on its quest to look for signs of past or present life there and sophisticated instruments like the space telescopes Kepler and CoRoT keep discovering additional, more Earth-like planets orbiting distant stars, science faces the question of how to spot life on other planets. Even here on Earth biotopes remain to be discovered and explored.