What is antibiotic resistance and how can we measure it?

Antibiotic resistance is being found with increasing frequency in both pathogenic and commensal bacteria of humans and animals. Quantifying resistance within and between bacterial and host populations presents scientists with complex challenges in terms of laboratory methodologies and sampling design. Here, we discuss, from an epidemiological perspective, how antibiotic resistance can be defined and measured and the limitations of current approaches.     

What is speciation and how should we study it?

To understand speciation, we first need to know what species are. Yet debates over species concepts have seemed endless, with little obvious relevance to the study of speciation. Recently, there has been progress in resolving these debates, favoring a lineage-based, evolutionary species concept. This progress calls for reconsideration of the study of speciation. Traditional speciation research based on the biological species concept has led to great advances in understanding how nonallopatric speciation occurs and how species diverge and remain separate from each other. However, this research has neglected the question of how new species arise in the first place for the most common geographic mode (allopatric). A new and very different research program is needed to understand the ecological and evolutionary processes that split an ancestral species into new allopatric lineages. This research program will connect speciation to many other fundamental questions in evolutionary biology, ecology, biogeography, and conservation biology.     

What to do, or how to do it?

In this issue of Neuron, Ajemian et al. present a computational model of the activity of neurons in primary motor cortex (M1) during isometric movements in different postures. By modeling the output of M1 neurons in terms of their influence on muscles, they find each M1 neuron maps its output into a particular pattern of muscle actions.     

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.     

Measuring bone mass in children: can we really do it?

Bone densitometry is used to assess skeletal health in clinical and research settings, with the goal of achieving reproducible measurements of bone mass that help to identify individuals predisposed to fracture. The search is now on for better methods of capturing additional factors that contribute to bone strength, including bone size, geometry, microarchitecture, and turnover rates. This has proved particularly challenging in growing children, whose bones continually change in size, shape, and mass. Dual energy X-ray absorptiometry is the preferred method for measuring bone mass in children, but the technique has several limitations, and interpreting the findings can be problematic. Peripheral quantitative computed tomography is a promising method for assessing bone mass and other indices correlating with bone strength, but a lack of precision and paediatric norms currently restricts its clinical utility. Although bone mineral density is predictive of future fracture risk in adults, the evidence in children is less conclusive, and a diagnosis of osteoporosis in a child should not be made on densitometric findings alone. Developing a clearer understanding of how measures of bone mass and strength correlate with bone fracture in children will help target preventive strategies for those in greatest need.     

Antioxidant activity: what do we measure?

Inhibition of oxidation of 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) by free radicals generated by decomposition of 2,2'-azobis(2-amidopropane) (ABAP) by antioxidants and biological material was studied. A correlation was found between the ability of various substances to delay the onset of ABTS oxidation and their rapid reduction of the ABTS+* cation radical, and between the ability to reduce the maximal rate of ABTS oxidation and slow reduction of ABTS+*. The length of the lag period of ABTS oxidation was found to be independent of ABTS concentration. Similar decrease of peroxynitrite-induced ABTS+* formation by antioxidants was observed when the antioxidants were added before and after peroxynitrite. All these findings indicate that the main effect of antioxidants in this system is reduction of ABTS+* and not prevention of its formation. Reduction of oxidation products rather than inhibition of their formation may be the predominant mode of action of antioxidants in various assays of antioxidant activity.     

Fish and fisheries in hot water: What is happening and how do we adapt?

Rapid climate changes are currently driving substantial reorganizations of marine ecosystems around the world. A key question is how these changes will alter the provision of ecosystem services from the ocean, particularly from fisheries. To answer this question, we need to understand not only the ecological dynamics of marine systems, but also human adaptation and feedbacks between humans and the rest of the natural world. In this review, we outline what we have learned from research primarily in continental shelf ecosystems and fishing communities of North America. Key findings are that marine animals are highly sensitive to warming and are responding quickly to changes in water temperature, and that such changes are often happening faster than similar processes on land. Changes in species distributions and productivity are having substantial impacts on fisheries, including through changing catch compositions and longer distances traveled for fishing trips. Conflicts over access to fisheries have also emerged as species distributions are no longer aligned with regulations or catch allocations. These changes in the coupled natural-human system have reduced the value of ecosystem services from some fisheries and risk doing so even more in the future. Going forward, substantial opportunities for more effective fisheries management and operations, marine conservation, and marine spatial planning are likely possible through greater consideration of climate information over time-scales from years to decades.     

Harmonisation of Measurement Procedures: how do we get it done?

Clinical laboratory measurement results must be comparable among different measurement procedures, different locations and different times in order to be used appropriately for identifying and managing disease conditions. Harmonisation in the broad sense is the overall process of achieving comparability of results among clinical laboratory measurement procedures that measure the same measurand. The term standardisation is used when comparable results among measurement procedures are based on calibration traceability to SI using a reference measurement procedure of the highest available order. When there is no higher order reference measurement procedure available, and it is unlikely that one can be developed, the term harmonisation refers to any process for achieving comparable results among measurement procedures for an individual measurand.This review explains calibration traceability and focuses on the principles of harmonisation for those measurands for which a reference measurement procedure does not exist. We discuss the value of harmonisation, the importance of commutable reference materials, the barriers to harmonisation that exist today, and conclude with a discussion of a current global effort to improve the state of harmonisation.     

Quantitation of NAD+: Why do we need to measure it?

Background

Nicotinamide adenine dinucleotide (NAD⁺) is an essential pyridine nucleotide that is currently investigated as an important target to extend lifespan and health span. Age-related NAD+ depletion due to the accumulation of oxidative stress is associated with reduced energy production, impaired DNA repair and genomic instability.

Mechanosensitive channels: what can they do and how do they do it?

While mechanobiological processes employ diverse mechanisms, at their heart are force-induced perturbations in the structure and dynamics of molecules capable of triggering subsequent events. Among the best characterized force-sensing systems are bacterial mechanosensitive channels. These channels reflect an intimate coupling of protein conformation with the mechanics of the surrounding membrane; the membrane serves as an adaptable sensor that responds to an input of applied force and converts it into an output signal, interpreted for the cell by mechanosensitive channels. The cell can exploit this information in a number of ways: ensuring cellular viability in the presence of osmotic stress and perhaps also serving as a signal transducer for membrane tension or other functions. This review focuses on the bacterial mechanosensitive channels of large (MscL) and small (MscS) conductance and their eukaryotic homologs, with an emphasis on the outstanding issues surrounding the function and mechanism of this fascinating class of molecules.     

The impact of the summer 2003 heat wave in Iberia: how should we measure it?

We present a new approach to improve the reliability of quantifying the impact of a heat wave on mortality rates. We show, for the recent European summer 2003 heat wave, that the use of absolute maximum temperature values, or number of days above a given threshold, can be misleading. Here, we have assessed the impact of the heat wave on Iberian mortality by applying a four step procedure: (1) calculating, for each observatory, the local maximum temperature (T _max) distributions, (2) calculating the corresponding 95th percentile values (T _threshold), (3) locally defining extremely hot days (EHD) as those days on which the local threshold of the 95th percentile of the series is exceeded, and (4) calculating the total degrees-days (DD) of exceedance, by calculating the difference T _max−T _threshold and summing these values for all days above T _threshold. We show that the relationship between summer mortality rates and the DD index is non-linear and can be described by a logarithmic function, with a correlation coefficient of 0.78, which explains 60.6% of the mortality variance (F value of 24.64, significant at P<0.0001). Using maximum temperatures, no significant relationship is found with mortality, whereas the EHD frequency shows a significant association with mortality, albeit weaker than that obtained with DD.     

What do the indices of reproductive skew measure?

Several indices of reproductive skew that quantify the degree of unequal partitioning of reproductive output among individuals have been proposed without consensus on their merits and defects. We believe that the major reason for the disagreement is the lack of discussion on what the population parameter of skew (population skew or true skew) should measure. In our view, the skew index should be an unbiased estimate of a population skew, and the estimated skew needs to satisfy the following two conditions. First, if the group size is equal and the distribution of potential of reproductive output (pi), which is scaled by the proportion of the individual's to the total group reproductive output, is also fixed, skew remains constant even when the total number of offspring in the group changes. Second, if the group size is different, skew should have intuitive biological meaning. Our analyses revealed that, among various indices so far proposed, only the skews estimated by Kokko and Lindstr?m's lambda and Morisita's I(delta) satisfy the first condition. However, the two indices estimate different population parameters, thus implying different biological meanings. Morisita's I(delta) is a linear function of CV(2) (squared coefficient of variation) of pi, and lambda is a positive function of [Formula: see text] when offspring number follows a multinomial distribution. In the special cases where a group consists of discrete classes of breeders and nonbreeders, lambda behaves roughly inversely parallel to the absolute number of breeders, while I(delta) moves almost parallel to the proportion of nonbreeders. Furthermore, lambda is sensitive to the total proportion of reproductive output possessed by the dominants but is relatively less sensitive to the number of subordinates. We discussed the possible situations where either of the two indices will be useful.     

What do we measure by a luminol-dependent chemiluminescence of phagocytes?

The review presents a survey of published findings concerning the mechanism of luminol-dependent chemiluminescence in biological systems. The potential of various oxygen species (superoxide anion, hydrogen peroxide, hydroxyl radical) to react with luminol is discussed. The ability of commonly used enzymes (superoxide dismutase, catalase), inhibitors, and oxygen radical scavengers to discriminate between individual oxygen species is assessed together with the potential of a variety of substances encountered in biological systems to interfere in luminol-dependent chemiluminescence reactions. It is concluded that luminol-dependent chemiluminescence gives at present very little ability to discriminate between individual oxygen or radical species. Furthermore, luminol-dependent chemiluminescence used in biological systems is extremely prone to many interferences, which are very difficult to control.     

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.