A gene’s eye view of Darwinian populations

Biologists and philosophers differ on whether selection should be analyzed at the level of the gene or of the individual. In Peter Godfrey-Smith’s book, Darwinian Populations and Natural Selection, he argues that individuals can be good members of Darwinian populations, whereas genes rarely can. I take issue with parts of this view, and suggest that Godfrey-Smith’s scheme for thinking about Darwinian populations is also applicable to populations of genes.     

The gene’s-eye view,major transitions and the formal darwinism project

I argue that Grafen’s formal darwinism project could profitably incorporate a gene’s-eye view, as informed by the major transitions framework. In this, instead of the individual being assumed to maximise its inclusive fitness, genes are assumed to maximise their inclusive fitness. Maximisation of fitness at the individual level is not a straightforward concept because the major transitions framework shows that there are several kinds of biological individual. In addition, individuals have a definable fitness, exhibit individual-level adaptations and arise in a major transition, only to the extent that the inclusive-fitness interests of genes within them coincide. Therefore, as others have suggested, the fundamental level at which fitness is maximised is the gene level. Previous reconciliations of the concepts of gene-level fitness and individual-level fitness implicitly recognise this point. Adaptations always maximise the fitness of their causative genes, but may be simple or complex. Simple adaptations may be controlled by single genes and be maladaptive at higher levels, whereas complex adaptations are controlled by multiple genes and rely on those genes having coinciding fitness interests at a higher level, for a given trait.     

Haldane’s view of natural selection

Among many things, J. B. S. Haldane is known for demonstrating how the principle of natural selection can be used to build a mathematical, and in particular quantitative, theory of evolution. However, to the end, he remained open to the idea of other evolutionary mechanisms. In his late writings, he repeatedly drew attention to situations in which natural selection did not operate, was hemmed in by constraints, or worked in a surprising manner. In this respect Haldane stands out among the architects of the Modern Synthesis.     

Wild Bird’s-eye View of Influenza Virus A(H1N1) Phylogenetic Evolution

Wild bird fecal samples collected and characterized by the USDA as part of a national surveillance effort were sequenced to study the genetic relatedness of avian, swine, and human H1 and N1 subtypes. Our results find that the 2009 H1N1 human outbreak is closely related to swine virus, but falls into different clades in the H1 and N1 trees. Further, there is evidence of multiple viral genetic exchanges between birds and swine. Ongoing research across host species contributes to an understanding of the circulation of influenza viruses.     

Hundred and sixty years of Australian lady bird beetle Crypotolaemus montrouzieri Mulsant – a global view

ABSTRACT

The Australian lady bird beetle Cryotolaemus montrouzieri Mulsant was first discovered in 1853 in Queensland and New South Wales of Eastern Australia and New Caledonia. It has provided very good control of the sucking insect pests, particularly soft scales and mealybugs at different locations in more than 60 countries since its introduction in 1892 from Australia to California. Besides, C. montrouzieri is also known to feed on whiteflies, aphids, hard scales, dactylopiids, eriococcids, margorodids, psyllids, etc. Cryptolaemus montrouzieri takes 30 days to complete life cycle at 30°C. Pupae of C. montrouzieri are stored for about 20 days without having any adverse effect on the fecundity of the resulting adults. Potato sprouts or ripe pumpkins have been used as laboratory hosts for multiplication of mealybugs and C. montrouzieri. Cryptolaemus montrouzieri provided very good control of mealybugs and soft scales in the absence of ants. It plays a great role in the suppression of soft scales belonging to the genus Pulvinaria and the mealybugs Planococcus citri, Ferrisia virgata, Maconellicoccus hirsutus, Nipaecoccus viridis, Pseudococcus jackbeardsleyi, Coccidihystrix insolita, Pseudococcus comstocki, Pseudococcus obscures, Pseudococcus aurilanatus, etc. Botanicals, biopesticide mineral oils, insecticidal soaps, conventional insecticides dichlorvos and chlorpyriphos and the new molecules spirotetramat, imidacloprid, abamectin, fluvalinate, profenophos, ethnfenprox, flufenoxuron, spinosad and bufrofezin appear to be safer to the adults and grubs of C. montrouzieri. Therefore, these chemicals are to be integrated cautiously in the management of mealybugs and soft scales.     

Genetics,development and composition of the insect head – A beetle’s view

Many questions regarding evolution and ontogeny of the insect head remain open. Likewise, the genetic basis of insect head development is poorly understood. Recently, the investigation of gene expression data and the analysis of patterning gene function have revived interest in insect head development. Here, we argue that the red flour beetle Tribolium castaneum is a well suited model organism to spearhead research with respect to the genetic control of insect head development. We review recent molecular data and discuss its bearing on early development and morphogenesis of the head. We present a novel hypothesis on the ontogenetic origin of insect head sutures and review recent insights into the question on the origin of the labrum. Further, we argue that the study of developmental genes may identify the elusive anterior non-segmental region and present some evidence in favor of its existence. With respect to the question of evolution of patterning we show that the head Anlagen of the fruit fly Drosophila melanogaster and Tribolium differ considerably and we review profound differences of their genetic regulation. Finally, we discuss which insect model species might help us to answer the open questions concerning the genetic regulation of head development and its evolution.     

Effects of salinity on the immune response of an ‘osmotic generalist’ bird

Salt stress can suppress the immune function of fish and other aquatic animals, but such an effect has not yet been examined in air-breathing vertebrates that frequently cope with waters (and prey) of contrasting salinities. We investigated the effects of seawater salinity on the strength and cost of mounting an immune response in the dunlin Calidris alpina, a long-distance migratory shorebird that shifts seasonally from freshwater environments during the breeding season to marine environments during migration and the winter period. Phytohaemagglutinin (PHA)-induced skin swelling, basal metabolic rate (BMR), body mass, fat stores, and plasma ions were measured in dunlins acclimated to either freshwater or seawater (salinity: 0.3 and 35.0 ‰, respectively). Seawater-acclimated dunlins mounted a PHA-induced swelling response that was up to 56 % weaker than those held under freshwater conditions, despite ad libitum access to food. Freshwater-acclimated dunlins significantly increased their relative BMR 48 h after PHA injection, whereas seawater-acclimated dunlins did not. However, this differential immune and metabolic response between freshwater- and seawater-acclimated dunlins was not associated with significant changes in body mass, fat stores or plasma ions. Our results indicate that the strength of the immune response of this small-sized migratory shorebird was negatively influenced by the salinity of marine habitats. Further, these findings suggest that the reduced immune response observed under saline conditions might not be caused by an energy or nutrient limitation, and raise questions about the role of osmoregulatory hormones in the modulation of the immune system.     

A remarkable new ‘gruiform’ bird from the Middle Eocene of Messel (Hessen, Germany)

Salmila robusta n. gen., n. sp. (Aves: ‘Gruiformes’) is described from the Middle Eocene of Messel (Hessen, Germany). The new species is assumed to have had a predominantly terrestrial habit. It shares derived features of the carpometacarpus with the recent Psophiidae and some taxa of the Cariamae. In several features, however, it distinctly differs from other ‘gruiform’ birds (e. g. in the larger proximal end of the humerus and in the shape of the margo caudalis of the sternum). AlthoughSalmila robusta has been tentatively assigned to the Cariamae in this study, its exact systematic position deserves further investigations. The rather short tarsometatarsus of the new species resembles that of the ‘Messel-phorusrhacid’Aenigmavis sapea Peters 1987.     

Siderophore uptake in bacteria and the battle for iron with the host; a bird’s eye view

Siderophores are biosynthetically produced and secreted by many bacteria, yeasts, fungi and plants, to scavenge for ferric iron (Fe³⁺). They are selective iron-chelators that have an extremely high affinity for binding this trivalent metal ion. The ferric ion is poorly soluble but it is the form of iron that is predominantly found in oxygenated environments. Siderophore uptake in bacteria has been extensively studied and over the last decade, detailed structural information for many of the proteins that are involved in their transport has become available. Specifically, numerous crystal structures for outer membrane siderophore transporters, as well as for soluble periplasmic siderophore-binding proteins, have been reported. Moreover, unique siderophore-binding proteins have recently been serendipitously discovered in humans, and the structures of some of their siderophore-complexes have been characterized. The binding pockets for different ferric-siderophores in these proteins have been described in great molecular detail. In addition to highlighting this structural information, in this review paper we will also briefly discuss the relevant chemical properties of iron, and provide a perspective on our current understanding of the human and bacterial iron uptake pathways. Potential clinical uses of siderophores will also be discussed. The emerging overall picture is that iron metabolism plays an extremely important role during bacterial infections. Because levels of free ferric iron in biological systems are always extremely low, there is serious competition for iron and for ferric-siderophores between pathogenic bacteria and the human or animal host.     

SUMO1 promotes Aβ production via the modulation of autophagy

Autophagy is one of the main mechanisms in the pathophysiology of neurodegenerative disease. The accumulation of autophagic vacuoles (AVs) in affected neurons is responsible for amyloid-β (Aβ) production. Previously, we reported that SUMO1 (small ubiquitin-like modifier 1) increases Aβ levels. In this study, we explored the mechanisms underlying this. We investigated whether AV formation is necessary for Aβ production by SUMO1. Overexpression of SUMO1 increased autophagic activation, inducing the formation of LC3-II-positive AVs in neuroglioma H4 cells. Consistently, autophagic activation was decreased by the depletion of SUMO1 with small hairpin RNA (shRNA) in H4 cells. The SUMO1-mediated increase in Aβ was reduced by the autophagy inhibitors (3-methyladenine or wortmannin) or genetic inhibitors (siRNA targeting ATG5, ATG7, ATG12, or HIF1A), respectively. Accumulation of SUMO1, ATG12, and LC3 was seen in amyloid precursor protein transgenic mice. Our results suggest that SUMO1 accelerates the accumulation of AVs and promotes Aβ production, which is a key mechanism for understanding the AV-mediated pathophysiology of Alzheimer disease.     

Exploring differences in stakeholders’ perceptions of illegal bird trapping in Cyprus

Background

Cyprus is recognised as a hotspot for illegal bird trapping in the Mediterranean basin. A consumer demand for the Eurasian blackcap (Sylvia atricapilla) is driving the use of non-selective trapping methods, resulting in the indiscriminate killing of millions of migratory birds. Efforts to tackle the issue have so far been characterised mostly by a top-down approach, focusing on legislation and enforcement. However, trapping levels are not decreasing and conflict between stakeholder groups is intensifying.

Methods

To understand why efforts to stop illegal bird trapping have not been effective, we used semi-structured interviews to interview 18 local bird trappers and nine representatives from the pertinent environmental non-governmental organisations (NGOs) and the governmental agencies responsible for enforcing the legislation.

Results

We found distinct differences between the views of the local trapping community and the environmental NGOs, particularly on why trapping is occurring and its impact on the avifauna. This disparity has contributed to misrepresentations of both sides and a high degree of conflict, which is potentially proving counterproductive to conservation interventions. In addition, it appears that trappers are a heterogeneous group, likely driven by various motivations besides profit.

Conclusion

We argue that stakeholders interested in reducing illegal bird trapping need to develop anti-poaching strategies that aim at minimising the disparity in the views, and subsequently the conflict, acknowledging also that trappers are not a homogenous group, as often treated.

     

The prospects for biogas—A European point of view

In many parts of the world, alternative energy sources are already needed or will be needed to augment fossil fuel supplies. ‘Biogas’, methanol, ethanol and hydrogen are all potentially useful in this respect, as they can be obtained (biologically or thermochemically) from renewable resources like biomass (trees, crops, etc.) and organic wastes (sewage, domestic refuse, animal manure). Some aspects of biofuel research and development in Member States of the European Community are highlighted, and estimates of the contributions that these fuels might make to current and future energy demands are reviewed. Some of the potential uses of biogases and liquid biofuels in a gas industry context are described. In the author's opinion, production of biogases and other biofuels will ultimately play a significant but relatively small rôle in conserving supplies of natural gas and other fossil fuels, and in alleviating or preventing environmental pollution.     

SUMO1 promotes Aβ production via the modulation of autophagy

Autophagy is one of the main mechanisms in the pathophysiology of neurodegenerative disease. The accumulation of autophagic vacuoles (AVs) in affected neurons is responsible for amyloid-β (Aβ) production. Previously, we reported that SUMO1 (small ubiquitin-like modifier 1) increases Aβ levels. In this study, we explored the mechanisms underlying this. We investigated whether AV formation is necessary for Aβ production by SUMO1. Overexpression of SUMO1 increased autophagic activation, inducing the formation of LC3-II-positive AVs in neuroglioma H4 cells. Consistently, autophagic activation was decreased by the depletion of SUMO1 with small hairpin RNA (shRNA) in H4 cells. The SUMO1-mediated increase in Aβ was reduced by the autophagy inhibitors (3-methyladenine or wortmannin) or genetic inhibitors (siRNA targeting ATG5, ATG7, ATG12, or HIF1A), respectively. Accumulation of SUMO1, ATG12, and LC3 was seen in amyloid precursor protein transgenic mice. Our results suggest that SUMO1 accelerates the accumulation of AVs and promotes Aβ production, which is a key mechanism for understanding the AV-mediated pathophysiology of Alzheimer disease.     

A periodic table for ecology? A chemist's view of plant functional types

Abstract. A functional type approach, in which the complexity found in nature is reduced by grouping organisms that are functionally similar into a single classification, is being promoted in global change research. This paper examines a proposed analogy between this functional type approach in global change ecology and the periodic table of the elements in chemistry. When applied to a ‘bottom-up’ approach for defining functional types in ecology, in which large numbers of organisms are classified into smaller groups based on similarity of certain functions, the analogy fails. Ecological functions are not simple attributes of a biological entity, as electronic structure is for a chemical element, but are themselves complex chemical and physical systems that often interact strongly with the environment. The analogy to the periodic table may be of some use as an organizing tool in a ‘top-down’ approach in which a modelling context is used to define the number of ‘elements’ and their properties. This will be elaborated for plant functional types. Each PFT is assigned characteristics that allow its response to the driving forces of change, e.g. temperature, precipitation, soil nutrients, disturbance, to be predicted. ‘Rules of combination’ determine how the mix of PFTs in a particular ecosystem changes to form different ecosystems, which would correspond in the analogy to chemical compounds. However, these requirements present significant challenges to the usefulness of the analogy, even as an organizing tool in the ‘top-down’ approach.     

Patients’ view of the differences in topical creams for radiation dermatitis prevention. A pilot study of cosmetic properties

AimTo investigate the feasibility of including patients’ reports on the cosmetic properties of topical formulations for acute radiation dermatitis (ARD).BackgroundNo topical agent tested for acute radiation dermatitis (ARD) has proven to be better than any other, all achieving similar objective outcomes. No clear guidelines have therefore been established in clinics. Because the vehicle for such creams has shown to be an important factor in patient adherence to treatments in other dermatological diseases, patients’ opinions are evaluated.Material and methodsSeventy breast cancer patients referred for postoperative radiotherapy after conservative surgery were enrolled. Patients were assigned to use one of the 7 topical agents that are most-commonly used in the prevention of ARD. Patients’ reports were assessed using continuous visual analogue scales (VAS), objective signs and symptoms produced by ARD, and were rated using the RTOG and RISRAS scales.ResultsThe creams tested differed in their cosmetic properties significantly (p = 0.044). The performance of the agent, their absorption and any residue left over were also significantly different (p = 0.022, 0.014 and 0.02, respectively).ConclusionsTopical agents for preventive ARD are reported by patients to show different cosmetic properties. Cosmetic properties are important when choosing topical agents for ARD prevention. Recommending those with better cosmetic profiles would improve patient adherence to treatments.     

Non-canonical autophagy: an exception or an underestimated form of autophagy?

Macroautophagy (hereafter called autophagy) is a dynamic and evolutionarily conserved process used to sequester and degrade cytoplasm and entire organelles in a sequestering vesicle with a double membrane, known as the autophagosome, which ultimately fuses with a lysosome to degrade its autophagic cargo. Recently, we have unraveled two distinct forms of autophagy in cancer cells, which we term canonical and non-canonical autophagy. In contrast to classical or canonical autophagy, non-canonical autophagy is a process that does not require the entire set of autophagy-related (Atg) proteins in particular Beclin 1, to form the autophagosome. Non-canonical autophagy is therefore not blocked by the knockdown of Beclin 1 or of its binding partner hVps34. Moreover overexpression of Bcl-2, which is known to block canonical starvation-induced autophagy by binding to Beclin 1, is unable to reverse the non-canonical autophagy triggered by the polyphenol resveratrol in the breast cancer MCF-7 cell line. In MCF-7 cells, at least, non-canonical autophagy is involved in the caspase-independent cell death induced by resveratrol.