Convergence and parallelism reconsidered: what have we learned about the genetics of adaptation?

Biologists often distinguish 'convergent' from 'parallel' evolution. This distinction usually assumes that when a given phenotype evolves, the underlying genetic mechanisms are different in distantly related species (convergent) but similar in closely related species (parallel). However, several examples show that the same phenotype might evolve among populations within a species by changes in different genes. Conversely, similar phenotypes might evolve in distantly related species by changes in the same gene. We thus argue that the distinction between 'convergent' and 'parallel' evolution is a false dichotomy, at best representing ends of a continuum. We can simplify our vocabulary; all instances of the independent evolution of a given phenotype can be described with a single term - convergent.     

Human welfare and its connection to nature: What have we learned from crop pollination studies?

Human welfare depends on the function of natural systems. This idea is paradigmatic to ecologists and has been the theme of a growing branch of applied ecology. I examine the narrative of human dependence on nature by considering the literature on crop pollination by animals and its importance for food production. Making the connections between human welfare and natural systems is seen as a way to better motivate society to make better decisions, but the debate around crop pollination has been surprisingly contentious. There have been confusing messages, disagreements on the facts, an unfortunate focus on dire projections for the future and a lesser focus on solutions. Most of these problems arise not from poor science but instead from poor communication of complex ideas and differences in perspective, such as the deep disciplinary gap between agricultural scientists and ecologists. By understanding these problems, we can improve the way we do our science and communicate our ideas. I argue that ecologists should continue to communicate the principle that human welfare depends on the function of natural systems and discuss how we can do so in a way that is more genuinely connected to society's needs, such as growing food. If we succeed, we will be changing an intellectually interesting conversation into a dialogue that influences how society interacts with nature.     

What have we learned about the kallikrein-kinin and renin-angiotensin systems in neurological disorders?

The kallikrein-kinin system(KKS) is an intricate endogenous pathway involved in several physiological and pathological cascades in the brain. Due to the pathological effects of kinins in blood vessels and tissues, their formation and degradation are tightly controlled. Their components have been related to several central nervous system diseases such as stroke, Alzheimer's disease, Parkinson's disease, multiple sclerosis, epilepsy and others. Bradykinin and its receptors(B1R and B2R) may have a role in the pathophysiology of certain central nervous system diseases. It has been suggested that kinin B1R is up-regulated in pathological conditions and has a neurodegenerative pattern, while kinin B2R is constitutive and can act as a neuroprotective factor in many neurological conditions. The renin angiotensin system(RAS) is an important blood pressure regulator and controls both sodium and water intake. AngⅡ is a potent vasoconstrictor molecule and angiotensin converting enzyme is the major enzyme responsible for its release. AngⅡ acts mainly on the AT1 receptor, with involvement in several systemic and neurological disorders. Brain RAS has been associated with physiological pathways, but is also associated with brain disorders. This review describes topics relating to the involvement of both systems in several forms of brain dysfunction and indicates components of the KKS and RAS that have been used as targets in several pharmacological approaches.     

How should we normalize electromyograms obtained from healthy participants? What we have learned from over 25 years of research

Electromyograms (EMGs) need to be normalized if comparisons are sought between trials when electrodes are reapplied, as well as between different muscles and individuals. The methods used to normalize EMGs recorded from healthy individuals have been appraised for more than a quarter of a century. Eight methods were identified and reviewed based on criteria relating to their ability to facilitate the comparison of EMGs. Such criteria included the magnitude and pattern of the normalized EMG, reliability, and inter-individual variability. If the aim is to reduce inter-individual variability, then the peak or mean EMG from the task under investigation should be used as the normalization reference value. However, the ability of such normalization methods to facilitate comparisons of EMGs is questionable. EMGs from MVCs can be as reliable as those from submaximal contractions, and do not appear to be affected by contraction mode or joint kinematics, particularly for the elbow flexors. Thus, the EMG from an isometric MVC is endorsed as a normalization reference value. Alternatively the EMG from a dynamic MVC can be used, although it is recognized that neither method is guaranteed to be able to reveal how active a muscle is in relation to its maximal activation capacity.     

What have we learned from 15 years of free-air CO2 enrichment (FACE)? A meta-analytic review of the responses of photosynthesis, canopy properties and plant production to rising CO2

Free-air CO(2) enrichment (FACE) experiments allow study of the effects of elevated [CO(2)] on plants and ecosystems grown under natural conditions without enclosure. Data from 120 primary, peer-reviewed articles describing physiology and production in the 12 large-scale FACE experiments (475-600 ppm) were collected and summarized using meta-analytic techniques. The results confirm some results from previous chamber experiments: light-saturated carbon uptake, diurnal C assimilation, growth and above-ground production increased, while specific leaf area and stomatal conductance decreased in elevated [CO(2)]. There were differences in FACE. Trees were more responsive than herbaceous species to elevated [CO(2)]. Grain crop yields increased far less than anticipated from prior enclosure studies. The broad direction of change in photosynthesis and production in elevated [CO(2)] may be similar in FACE and enclosure studies, but there are major quantitative differences: trees were more responsive than other functional types; C(4) species showed little response; and the reduction in plant nitrogen was small and largely accounted for by decreased Rubisco. The results from this review may provide the most plausible estimates of how plants in their native environments and field-grown crops will respond to rising atmospheric [CO(2)]; but even with FACE there are limitations, which are also discussed.     

Split‐root systems applied to the study of the legume‐rhizobial symbiosis: What have we learned?

Split‐root system (SRS) approaches allow the differential treatment of separate and independent root systems, while sharing a common aerial part. As such, SRS is a useful tool for the discrimination of systemic (shoot origin) versus local (root/nodule origin) regulation mechanisms. This type of approach is particularly useful when studying the complex regulatory mechanisms governing the symbiosis established between legumes and Rhizobium bacteria. The current work provides an overview of the main insights gained from the application of SRS approaches to understand how nodule number (nodulation autoregulation) and nitrogen fixation are controlled both under non‐stressful conditions and in response to a variety of stresses. Nodule number appears to be mainly controlled at the systemic level through a signal which is produced by nodule/root tissue, translocated to the shoot, and transmitted back to the root system, involving shoot Leu‐rich repeat receptor‐like kinases. In contrast, both local and systemic mechanisms have been shown to operate for the regulation of nitrogenase activity in nodules. Under drought and heavy metal stress, the regulation is mostly local, whereas the application of exogenous nitrogen seems to exert a regulation of nitrogen fixation both at the local and systemic levels.     

Proteomic analysis of red blood cells and the potential for the clinic: what have we learned so far?

Introduction: Red blood cells (RBC) are the most abundant host cells in the human body. Mature erythrocytes are devoid of nuclei and organelles and have always been regarded as circulating ‘bags of hemoglobin’. The advent of proteomics has challenged this assumption, revealing unanticipated complexity and novel roles for RBCs not just in gas transport, but also in systemic metabolic homeostasis in health and disease.

Areas covered: In this review we will summarize the main advancements in the field of discovery mode and redox/quantitative proteomics with respect to RBC biology. We thus focus on translational/clinical applications, such as transfusion medicine, hematology (e.g. hemoglobinopathies) and personalized medicine. Synergy of omics technologies – especially proteomics and metabolomics – are highlighted as a hallmark of clinical metabolomics applications for the foreseeable future.

Expert commentary: The introduction of advanced proteomics technologies, especially quantitative and redox proteomics, and the integration of proteomics data with omics information gathered through orthogonal technologies (especially metabolomics) promise to revolutionize many biomedical areas, from hematology and transfusion medicine to personalized medicine and clinical biochemistry.     

MHC studies in nonmodel vertebrates: what have we learned about natural selection in 15 years?

Elucidating how natural selection promotes local adaptation in interaction with migration, genetic drift and mutation is a central aim of evolutionary biology. While several conceptual and practical limitations are still restraining our ability to study these processes at the DNA level, genes of the major histocompatibility complex (MHC) offer several assets that make them unique candidates for this purpose. Yet, it is unclear what general conclusions can be drawn after 15 years of empirical research that documented MHC diversity in the wild. The general objective of this review is to complement earlier literature syntheses on this topic by focusing on MHC studies other than humans and mice. This review first revealed a strong taxonomic bias, whereby many more studies of MHC diversity in natural populations have dealt with mammals than all other vertebrate classes combined. Secondly, it confirmed that positive selection has a determinant role in shaping patterns of nucleotide diversity in MHC genes in all vertebrates studied. Yet, future tests of positive selection would greatly benefit from making better use of the increasing number of models potentially offering more statistical rigour and higher resolution in detecting the effect and form of selection. Thirdly, studies that compared patterns of MHC diversity within and among natural populations with neutral expectations have reported higher population differentiation at MHC than expected either under neutrality or simple models of balancing selection. Fourthly, several studies showed that MHC-dependent mate preference and kin recognition may provide selective factors maintaining polymorphism in wild outbred populations. However, they also showed that such reproductive mechanisms are complex and context-based. Fifthly, several studies provided evidence that MHC may significantly influence fitness, either by affecting reproductive success or progeny survival to pathogens infections. Overall, the evidence is compelling that the MHC currently represents the best system available in vertebrates to investigate how natural selection can promote local adaptation at the gene level despite the counteracting actions of migration and genetic drift. We conclude this review by proposing several directions where future research is needed.     

What have we learned from the dead? A compilation of three years of cooperation between entomologists and crime scene investigators in Southern Brazil

With homicide rates higher than the world average, Brazil stands out as one of the most violent countries worldwide. Time of death estimation based solely on body changes can be biased or inaccurate; forensic entomology can play a determinant role in such cases. Accurate knowledge of necrophilous fauna is essential to validate experimental data and allows for the application of entomological evidence in forensic investigations, which benefits scientists, investigators, and society in general. Entomological evidence from Curitiba and 22 nearby cities were collected by crime scene investigators from the Scientific Police of Paraná. The corpses were found in diverse environments and specimens from each species were collected from all life stages. We present data from 25 cases from 2011 to 2014, including associated species, new records, and comparisons between existing experimental data and data from species collected in the cases presented. We identified 23 total species, of which eight species of Coleoptera and two species of Diptera have not previously been recorded on corpses. In all cases, Calliphoridae (76%) and Silphidae (48%) were the most numerous families collected. Working together with the scientific police gave us insight into which species lacked detailed records and enabled us to collaboratively focus on resolving deficits in our knowledge of necrophagous insects.     

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.     

Maracas for Macaca? Evaluation of three potential enrichment objects in two species of zoo‐housed macaques

One group each of Barbary macaques and stump‐tailed macaques, both zoo‐housed, received hard replica fruits in three experimental conditions: as empty (“unresponsive”) objects, as maracas that rattled when manipulated (“simple responsive”), and as objects from which food items could be extracted (“foraging devices”). Both groups manipulated the replica fruits most when they functioned as foraging devices, and responsiveness tended to decrease within sessions in all conditions. Thus, objects that increased the animals' sense of control in addition to providing food rewards appeared particularly suitable as enrichment devices, although novelty and indirect behavioral effects point to the need for thorough evaluation of enrichment interventions. Zoo Biol 19:181–191, 2000. © 2000 Wiley‐Liss, Inc.     

Will photosynthesis of maize (Zea mays) in the US Corn Belt increase in future [CO2] rich atmospheres? An analysis of diurnal courses of CO2 uptake under free‐air concentration enrichment (FACE)

The C₄ grass Zea mays (maize or corn) is the third most important food crop globally in terms of production and demand is predicted to increase 45% from 1997 to 2020. However, the effects of rising [CO₂] upon C₄ plants, and Z. mays specifically, are not sufficiently understood to allow accurate predictions of future crop production. A rainfed, field experiment utilizing free‐air concentration enrichment (FACE) technology in the primary area of global corn production (US Corn Belt) was undertaken to determine the effects of elevated [CO₂] on corn. FACE technology allows experimental treatments to be imposed upon a complete soil–plant–atmosphere continuum with none of the effects of experimental enclosures on plant microclimate. Crop performance was compared at ambient [CO₂] (354 μ mol mol^?1) and the elevated [CO₂] (549 μmol mol^?1) predicted for 2050. Previous laboratory studies suggest that under favorable growing conditions C₄ photosynthesis is not typically enhanced by elevated [CO₂]. However, stomatal conductance and transpiration are decreased, which can indirectly increase photosynthesis in dry climates. Given the deep soils and relatively high rainfall of the US Corn Belt, it was predicted that photosynthesis would not be enhanced by elevated [CO₂]. The diurnal course of gas exchange of upper canopy leaves was measured in situ across the growing season of 2002. Contrary to the prediction, growth at elevated [CO₂] significantly increased leaf photosynthetic CO₂ uptake rate (A) by up to 41%, and 10% on average. Greater A was associated with greater intercellular [CO₂], lower stomatal conductance and lower transpiration. Summer rainfall during 2002 was very close to the 50‐year average for this site, indicating that the year was not atypical or a drought year. The results call for a reassessment of the established view that C₄ photosynthesis is insensitive to elevated [CO₂] under favorable growing conditions and that the production potential of corn in the US Corn Belt will not be affected by the global rise in [CO₂].     

The value of juvenile animal studies “What have we learned from preclinical juvenile toxicity studies? II”

Recent changes in the regulations from the FDA and EMA have shifted the focus of juvenile toxicity studies more to the safe use of all pharmaceuticals and the absence of label or safety information for the pediatric population. Unlike other regulatory guidance, the need or design of these animal studies is not specified. Ideally these should be decided “case‐by‐case” based on the patient population, pharmacology, existing toxicological and clinical data, dosing regimen, and developing system impact. Following the publishing of a small intercompany survey (Bailey and Mariën, 2009), a more extensive survey was commissioned by the ILSI/HESI DART Technical Committee to clarify what has been learned for the safety assessment for pediatrics. Contributions from 24 companies totaling 241 studies (84% rat and 14% dog) were received. In 12 of 82 programs (15%) were the existing adult preclinical or clinical data considered a sufficient safety prediction for pediatric trials. Clinical/preclinical correlates were observed in 17.2% (rat) and 42.9% (dog) of the studies and a lack of predictability from the pharmacology or the adult toxicity data was seen in 25% of rat and 14.3% of dog studies. Many of the studies were large, lengthy, complex, included parameters that mirrored the adult studies and yielded no new or useful information. We should avoid conducting complex or inappropriate studies and Contract Research Organisations and regulatory agencies have a role in encouraging more targeted designs. Only with appropriate designs can we adequately identify safety or pharmacokinetic issues, suggest clinical endpoints, and contribute to the product label. Birth Defects Res (Part B) 92:273–291, 2011. © 2011 Wiley‐Liss, Inc.     

Models for truth‐telling in physician‐patient encounters: What can we learn from Yoruba concept of Ooto?

Empirical studies have now established that many patients make clinical decisions based on models other than Anglo American model of truth‐telling and patient autonomy. Some scholars also add that current medical ethics frameworks and recent proposals for enhancing communication in health professional‐patient relationship have not adequately accommodated these models. In certain clinical contexts where health professional and patients are motivated by significant cultural and religious values, these current frameworks cannot prevent communication breakdown, which can, in turn, jeopardize patient care, cause undue distress to a patient in certain clinical contexts or negatively impact his/her relationship with the community. These empirical studies have now recommended that additional frameworks developed around other models of truth‐telling; and which take very seriously significant value‐differences which sometimes exist between health professional and patients, as well as patient's cultural/religious values or relational capacities, must be developed. This paper contributes towards the development of one. Specifically, this study proposes a framework for truth‐telling developed around African model of truth‐telling by drawing insights from the communitarian concept of oot?? amongst the Yoruba people of south west Nigeria. I am optimistic that if this model is incorporated into current medical ethics codes and curricula, it will significantly enhance health professional‐patient communication.     

Can fast‐growing plantation trees escape biochemical down‐regulation of photosynthesis when grown throughout their complete production cycle in the open air under elevated carbon dioxide?

Poplar trees sustain close to the predicted increase in leaf photosynthesis when grown under long-term elevated CO2 concentration ([CO2]). To investigate the mechanisms underlying this response, carbohydrate accumulation and protein expression were determined over four seasons of growth. No increase in the levels of soluble carbohydrates was observed in the young expanding or mature sun leaves of the three poplar genotypes during this period. However, substantial increases in starch levels were observed in the mature leaves of all three poplar genotypes grown in elevated [CO2]. Despite the very high starch levels, no changes in the expression of photosynthetic Calvin cycle proteins, or in the starch biosynthetic enzyme ADP-glucose pyrophosphorylase (AGPase), were observed. This suggested that no long-term photosynthetic acclimation to CO2 occurred in these plants. Our data indicate that poplar trees are able to 'escape' from long-term, acclimatory down-regulation of photosynthesis through a high capacity for starch synthesis and carbon export. These findings show that these poplar genotypes are well suited to the elevated [CO2] conditions forecast for the middle of this century and may be particularly suited for planting for the long-term carbon sequestration into wood.