Why we should conserve ‘limiting factors’, at least sometimes!

Körner's recent paper provided an excellent initial discussion of the term ‘limitation’ in ecology. I accept most of his arguments but would argue that there are some circumstances in applied ecology where the concept of limitation can be useful; these are (1) where there is a deficiency of a factor that prevents growth, and (2) where there is a need to manage an ecosystem so that a limitation is enforced.     

‘It is an entrustment’: Broad consent for genomic research and biobanks in sub‐Saharan Africa

In recent years, there has been an increase in the establishment of biobanks for genetic and genomic studies around the globe. One example of this is the Human Heredity and Health in Africa Initiative (H3Africa), which has established biobanks in the sub‐region to facilitate future indigenous genomic studies. The concept of ‘broad consent’ has been proposed as a mechanism to enable potential research participants in biobanks to give permission for their samples to be used in future research studies. However, questions remain about the acceptability of this model of consent. Drawing on findings from empirical research about the role of trust in decision‐making, we argue that an account of entrustment may be an appropriate way of addressing current challenges of seeking consent for biobank research in Africa. We propose a set of key points to consider that can support the proposed entrustment framework.     

A critique of the principle of ‘respect for autonomy’, grounded in African thought

I give an account how the principle of ‘respect for autonomy’ dominates the field of bioethics, and how it came to triumph over its competitors, ‘respect for persons’ and ‘respect for free power of choice’. I argue that ‘respect for autonomy’ is unsatisfactory as a basic principle of bioethics because it is grounded in too individualistic a worldview, citing concerns of African theorists and other communitarians who claim that the principle fails to acknowledge the fundamental importance of understanding persons within the nexus of their communal relationships. I defend the claim that ‘respect for persons’ is a more appropriate principle, as it is able to acknowledge both individual decision making and the essential relationality of persons. I acknowledge that my preference for ‘respect for persons’ is problematic because of the important debate around the definition of ‘personhood’ in bioethics discourse. Relying on Thaddeus Metz's conception of moral status, I propose a relational definition of personhood that distinguishes between persons with agency and persons without agency, arguing that we have different moral obligations to these distinct categories of persons. I claim that this conception of personhood is better able to accommodate our moral intuitions than conventional approaches, and that it is able to do so without being speciesist or question‐begging.     

The Plasmodium parasite—a ‘new’ challenge for insect innate immunity

Though lacking adaptive immunity, insects possess a powerful innate immune system, a genome-encoded defence machinery used to confront infections. Studies in the fruit fly Drosophila melanogaster revealed a remarkable capacity of the innate immune system to differentiate between and subsequently respond to different bacteria and fungi. However, hematophagous compared to non-hematophagous insects encounter additional blood-borne infectious agents, such as parasites and viruses, during their lifetime. Anopheles mosquitoes become infected with the malaria parasite Plasmodium during feeding on infected human hosts and may then transmit the parasite to new hosts during subsequent bites. Whether Anopheles has developed mechanisms to confront these infections is the subject of this review. Initially, we review our current understanding of innate immune reactions and give an overview of the Anopheles immune system as revealed through comparative genomic analyses. Then, we examine and discuss the capacity of mosquitoes to recognize and respond to infections, especially to Plasmodium, and finally, we explore approaches to investigate and potentially utilize the vector immune competence to prevent pathogen transmission. Such approaches constitute a new challenge for insect immunity research, a challenge for global health.     

Medical Innovation in a Children's Hospital: ‘Diseases desperate grown by desperate appliance are relieved,or not at all’

A balance needs to be struck between facilitating compassionate access to innovative treatments for those in desperate need, and the duty to protect such vulnerable individuals from the harms of untested/unlicensed treatments. We introduced a principle‐based framework (2009) to evaluate such requests and describe its application in the context of recently evolved UK, US and European regulatory processes. 24 referrals (20 individual; four group) were received by our quaternary children's hospital Clinical Ethics Committee (CEC) over the 5‐year period (2011‐16). The CEC‐rapid response group evaluated individual cases within 48‐hours; the main referrers being haematology/oncology, immunology or transplant services (14). Most requests were for drug/vaccine/pre‐trial access (13) or biological/cellular therapies (8). The majority of individual requests were approved (19/20); neutral or negative opinions were given in 5, including 3 group requests. Recently evolved regulatory processes share common criteria and conditions to our framework including: demonstration of clinical need; sound scientific basis with lack of viable alternative; risks‐benefit/best interests evaluation; arrangements for fully informed consent; no compromise of arrangements to test treatment for licensing purposes; consideration of resource implications. There are differences between individual processes and with our framework, with respect to procedures, scope, application format, costs and obligation to make available all outcome data. Our experience has emphasized the need for an independent, principled, consistent, fair and transparent response to the increasing demand for innovative treatment on a compassionate basis. We believe that there is a need for harmonization of the recent proliferation of regulation and legislation in this area.     

Focus: Antimicrobial Resistance: Inhaled Bacteriophage Therapy for Multi-Drug Resistant Achromobacter

The rise of antimicrobial resistant (AMR) bacteria is a global public health threat. AMR Achromobacter bacteria pose a challenging clinical problem, particularly for those with cystic fibrosis (CF) who are predisposed to chronic bacterial lung infections. Lytic bacteriophages (phages) offer a potential alternative to treat AMR infections, with the possible benefit that phage selection for resistance in target bacteria might coincide with reduced pathogenicity. The result is a genetic “trade-off,” such as increased sensitivity to chemical antibiotics, and/or decreased virulence of surviving bacteria that are phage resistant. Here, we show that two newly discovered lytic phages against Achromobacter were associated with stabilization of respiratory status when deployed to treat a chronic pulmonary infection in a CF patient using inhaled (nebulized) phage therapy. The two phages demonstrate traits that could be generally useful in their development as therapeutics, especially the possibility that the phages can select for clinically useful trade-offs if bacteria evolve phage resistance following therapy. We discuss the limitations of the current study and suggest further work that should explore whether the phages could be generally useful in targeting pulmonary or other Achromobacter infections in CF patients.     

Improving the Quality of Host Country Ethical Oversight of International Research: The Use of a Collaborative ‘Pre‐Review’ Mechanism for a Study of Fexinidazole for Human African Trypanosomiasis

Developing countries face numerous barriers to conducting effective and efficient ethics reviews of international collaborative research. In addition to potentially overlooking important scientific and ethical considerations, inadequate or insufficiently trained ethics committees may insist on unwarranted changes to protocols that can impair a study's scientific or ethical validity. Moreover, poorly functioning review systems can impose substantial delays on the commencement of research, which needlessly undermine the development of new interventions for urgent medical needs. In response to these concerns, the Drugs for Neglected Diseases Initiative (DNDi), an independent nonprofit organization founded by a coalition of public sector and international organizations, developed a mechanism to facilitate more effective and efficient host country ethics review for a study of the use of fexinidazole for the treatment of late stage African Trypanosomiasis (HAT). The project involved the implementation of a novel ‘pre‐review’ process of ethical oversight, conducted by an ad hoc committee of ethics committee representatives from African and European countries, in collaboration with internationally recognized scientific experts. This article examines the process and outcomes of this collaborative process.     

CO1 phylogenies in diploblasts and the ‘Barcoding of Life’— are we sequencing a suboptimal partition?

Partitions of the cytochrome oxidase subunit 1 (CO1) gene, especially the 5′ end, are frequently recruited to infer lower level phylogenies in animals. In diploblasts, mitochondrial genes were found to evolve in a slower rate than their bilaterian counterparts. Therefore, diploblast CO1 gene trees repeatedly remained unresolved, which also raises doubts on the suitability of CO1 for DNA barcoding in these animals. The complete mitochondrial genome sequences from Anthozoa and recently from Porifera allow us to compare the resolution power of the 5′ partition, which has also been proposed as the standard marker for DNA barcoding, with a less frequently used partition further downstream. We report on the finding of significantly different substitution patterns of the downstream partition opposed to the 5′ partition. We discuss the consequences and potential in the light of diploblast phylogenetic reconstruction and DNA barcoding.     

‘Fukusensor:’ a genetically engineered plant for reporting DNA damage in response to gamma radiation

Transgenic plants can be designed to be ‘phytosensors’ for detection of environmental contaminants and pathogens. In this study, we describe the design and testing of a radiation phytosensor in the form of green fluorescence protein (GFP)‐transgenic Arabidopsis plant utilizing a DNA repair deficiency mutant background as a host. Mutant lines of Arabidopsis AtATM (At3g48190), which are hypersensitive to gamma irradiation, were used to generate stable GFP transgenic plants in which a gfp gene was under the control of a strong constitutive CaMV 35S promoter. Mutant and nonmutant genetic background transgenic plants were treated with 0, 1, 5, 10 and 100 Gy radiation doses, respectively, using a Co‐60 source. After 1 week, the GFP expression levels were drastically reduced in young leaves of mutant background plants (treated by 10 and 100 Gy), whereas there were scant visible differences in the fluorescence of the nonmutant background plants. These early results indicate that transgenic plants could serve in a relevant sensor system to report radiation dose and the biological effects to organisms in response to radionuclide contamination.     

‘Real time’ genetic manipulation: a new tool for ecological field studies

Field experiments with transgenic plants often reveal the functional significance of genetic traits that are important for the performance of the plants in their natural environments. Until now, only constitutive overexpression, ectopic expression and gene silencing methods have been used to analyze gene‐related phenotypes in natural habitats. These methods do not allow sufficient control over gene expression for the study of ecological interactions in real time, of genetic traits that play essential roles in development, or of dose‐dependent effects. We applied the sensitive dexamethasone (DEX)‐inducible pOp6/LhGR expression system to the ecological model plant Nicotiana attenuata and established a lanolin‐based DEX application method to facilitate ectopic gene expression and RNA interference‐mediated gene silencing in the field and under challenging conditions (e.g. high temperature, wind and UV radiation). Fully established field‐grown plants were used to silence phytoene desaturase and thereby cause photobleaching only in specific plant sectors, and to activate expression of the cytokinin (CK) biosynthesis gene isopentenyl transferase (ipt). We used ipt expression to analyze the role of CKs in both the glasshouse and the field to understand resistance to the native herbivore Tupiocoris notatus, which attacks plants at small spatial scales. By spatially restricting ipt expression and elevating CK levels in single leaves, damage by T. notatus increased, demonstrating the role of CKs in this plant–herbivore interaction at a small scale. As the arena of most ecological interactions is highly constrained in time and space, these tools will advance the genetic analysis of dynamic traits that matter for plant performance in nature.     

The ‘mother knows best’ principle: should soil insects be included in the preference–performance debate?

Abstract.  1. Few entomological studies include soil-dwelling insects in mainstream ecological theory, for example the preference–performance debate. The preference–performance hypothesis predicts that when insect herbivores have offspring with limited capacity to relocate in relation to a host plant, there is a strong selection pressure for the adult to oviposit on plants that will maximise offspring performance.
2. This paper discusses the proposition that insect herbivores that live above ground, but have soil-dwelling offspring, should be included in the preference–performance debate. Twelve relevant studies were reviewed to assess the potential for including soil insects in this framework, before presenting a preliminary case study using the clover root weevil ( Sitona lepidus ) and its host plant, white clover ( Trifolium repens ).
3. Maternal S. lepidus preferentially oviposited on T. repens plants that had rhizobial root nodules (which enhance offspring performance) rather than T. repens plants without nodules, despite plants having similar foliar nutritional quality. This suggests that adult behaviour above ground was influenced by below-ground host-plant quality.
4. A conceptual model is presented to describe how information about the suitability for offspring below ground could underpin oviposition behaviour of parental insects living above ground, via plant- and soil-mediated semiochemicals. These interactions between genetically related, but spatially separated, insect herbivores raise important evolutionary questions such as how induced plant responses above ground affect offspring living below ground and vice versa.     

Thromboxane synthase inhibition: Implications for prostagland endoperoxide metabolism II testing the ‘redirection hypothesis’ in an acute intravenous challenge model

In the preceding paper we described the characterisation of an acute intravenous challenge model for the evaluation of the effects of thromboxane synthase inhibition (TXSI) on eicosanoid metabolism (1). Herein we describe the biochemical pharmacology of two TXSI and aspirin in this model. Both TXSI caused significant inhibition of plasma TXB₂ without elevation of 6-oxo-PGF_1α levels. Similar results were obtained when combined levels of 6-oxo-PGF_1α,13,14 dihydro 6-oxo-PGF_1α, 13,14 dihydro 6,15-dioxo-PGF_1α and 6-oxo-PGE₁ were measured as an index of PGI₂ biosynthesis (PGI₂m). Thus no evidence of redirection of PGH₂ to PGI₂ was found. experiments performed in serum gave an apparent stimulation of immunoreactive 6-oxo-PGF_1α following TXSI but RPHPLC analysis of extracted serum showed that this stimulation was accounted for by increase in a product co-eluting with [³H]PGF_2α. The implications of these findings in relation to TXSI and receptor antagonists are discussed.     

‘House and garden’: larval galleries enhance resource availability for a sedentary caddisfly

1. Sedentary grazers can be numerous in fresh waters, despite the constraints on resource availability and the increased predation risk inherent in this lifestyle. The retreats of sedentary grazers have been assumed to provide protection to the resident (a ‘house’), but also may provide additional fertilised food for the grazer (i.e. a ‘garden’). If retreats function as a garden, then they should (i) contain a higher quality and/or quantity of food than the alternative food source. Furthermore, the proportion of retreat‐derived carbon and nitrogen assimilated by the resident should be (ii) related to overall resource availability (more when resources are limited) or (iii) perhaps also to larval density. Alternatively, if retreats provide a less risky food source, then (iv) assimilation of material from the retreat is likely to be greater under conditions in which the risk of emerging from the retreat is high. 2. We tested these four hypotheses for the common and widespread gallery‐building grazing caddisfly Tinodes waeneri. Resource availability, larval density and biomass, and exposure were measured for populations from six lakes of differing productivity in August, October and January. 3. Galleries always contained more algal food than the surrounding epilithon, suggesting that gardening is effective. Furthermore, gallery chlorophyll a content in August, and the disparity in food quality (assessed from the C : N ratio) between gallery and epilithon (quality higher in the former) in October were positively related to the proportion of larval biomass that was derived from the gallery. Larval density and wave exposure parameters were not related to larval assimilation of gallery material. 4. Galleries that are fertilised by the occupant provide more, and sometimes also better quality, food (in terms of the C : N ratio) than is otherwise available. Thus, the gallery plays a substantial role in larval nutrition, and this role is greater at key times of food shortage.     

A plea for ‘genealogical thinking’ in comparative biology – a rebuttal to the reply of Szucsich,Wirkner, and Pass to my article ‘Deconstructing Morphology’

Scholtz G. in press. A plea for ‘genealogical thinking’ in comparative biology – a rebuttal to the reply of Szucsich, Wirkner, and Pass to my article ‘Deconstructing Morphology’. —Acta Zoologica (Stockholm) 00 : 1–4. Szucsich et al. (in press) claim that – in contrast to my statement – morphological thinking has to be ‘cladistic.’ Based on this premise, they stress the difference between the relationships among states of characters versus those among structures assigned to the same character state as implemented in numerical cladistic reasoning. SEA claim that my approach to the homology concept only deals with the problem of the integration of various character states into the same character, whereas the necessary relationships among structures assigned to the same state are not covered. Based on this distinction, SEA also criticise the application of similarity in my definition of homology. Furthermore, they address the issue of evolutionarily independent units.     

The concept of superfetation: a critical review on a ‘myth’ in mammalian reproduction

Superfetation is understood as another conception during an already ongoing pregnancy. This implies the existence of young of different developmental stages within the female reproductive tract during certain periods of pregnancy. Nevertheless, a clear definition of the term as well as distinct criteria to identify the occurrence of superfetation in a species is missing. The variable anatomy of mammalian reproductive tracts seems to make the occurrence of superfetation more or less likely but impedes the simple evaluation of whether it is present or not. Additionally, adequate determination methods are missing or are difficult to apply at the right time. Superfetation or rather superfetation‐like pregnancies are reported for numerous species including humans, livestock and rodents. The usual criteria to assume a case of superfetation include the finding of discordantly developed young within the uterus during post mortem or parturition of young after a birth interval shorter than the assumed pregnancy length. Often the occurrence of superfetation is concluded because other explanations of reproductive artifacts are missing. Even severe reproductive pathologies are often confused with superfetation. True superfetation or superfetation as a reproductive strategy may exist in some mammals. In the American mink (Neovison (Mustela) vison) and the European badger (Meles meles) superfetation occurs in combination with embryonic diapause. In the European brown hare (Lepus europaeus), superfetation has long been assumed to exist but evidence is still controversial. Superfetation definitely occurs in certain species of poeciliid and zenarchopterid fish, some of which also exhibit viviparity and maternal care. In mammals, the evolution of such a reproductive mechanism poses many interesting evolutionary, endocrine, microbial and immunological questions that require further investigation. Here we review the scant and at times ancient literature on this poorly understood topic. The different manifestations of superfetation are defined and reliable criteria to detect superfetation are outlined. Also, the differentiation of superfetation into a reproductive strategy or as a disrupted, abnormal reproductive function is discussed. Due to the different discussed functional aspects of superfetation, it is appropriate to establish a more detailed scheme to classify the true natural superfetation cases into superfertilization, superconception and superfetation proper. To date, there is no mammal species known for which superfetation proper in terms of finding discordantly developed fetuses has been conclusively demonstrated to be not only a rare occurence but an evolved reproductive strategy.     

Scab resistance in ‘Geneva’ apple is conditioned by a resistance gene cluster with complex genetic control

Apple scab, caused by the fungal pathogen Venturia inaequalis, is one of the most severe diseases of apple worldwide. It is the most studied plant–pathogen interaction involving a woody species using modern genetic, genomic, proteomic and bioinformatic approaches in both species. Although ‘Geneva’ apple was recognized long ago as a potential source of resistance to scab, this resistance has not been characterized previously. Differential interactions between various monoconidial isolates of V. inaequalis and six segregating F1 and F2 populations indicate the presence of at least five loci governing the resistance in ‘Geneva’. The 17 chromosomes of apple were screened using genotyping‐by‐sequencing, as well as single marker mapping, to position loci controlling the V. inaequalis resistance on linkage group 4. Next, we fine mapped a 5‐cM region containing five loci conferring both dominant and recessive scab resistance to the distal end of the linkage group. This region corresponds to 2.2 Mbp (from 20.3 to 22.5 Mbp) on the physical map of ‘Golden Delicious’ containing nine candidate nucleotide‐binding site leucine‐rich repeat (NBS‐LRR) resistance genes. This study increases our understanding of the complex genetic basis of apple scab resistance conferred by ‘Geneva’, as well as the gene‐for‐gene (GfG) relationships between the effector genes in the pathogen and resistance genes in the host.     

Potential ‘costs of reproduction’ in a skink: Inter‐ and intrapopulational variation

Reproductive costs are important determinants of reproductive effort in squamate reptiles. Consequently, differences in costs of reproduction between populations of geographically or climatically widespread species are likely to result in different patterns of reproductive effort. In the present study, the effect of pregnancy on sprint speed was examined in a small viviparous skink, Niveoscincus ocellatus (Gray 1845), from two populations at the climatic extremes of its distribution. Decreased sprint speed has the potential to be an important cost of reproduction in this species, through a reduced ability to avoid predation and/or decreased foraging efficiency. Lizards inhabiting the colder site were larger than those from the warmer site and, contrary to predictions from life history theory, had a higher reproductive effort. In both populations, sprint speed was lower in pregnant lizards than in either the same individuals after birth or non‐pregnant control lizards. Within each population, sprint speed was unrelated to the level of reproductive effort of the female in terms of either absolute mass of the reproductive burden or the burden relative to her post‐partum body mass. However, within each population, the mass of the clutch that an individual female was carrying relative to snout–vent length was an important determinant of her sprint speed while pregnant. Thus, within each population, a relatively high reproductive burden may potentially increase costs of reproduction in this species. Despite this relationship and predictions from life history theory suggesting that annual reproductive effort will be lower in populations with a large body size and delayed maturity, it is suggested that a higher reproductive effort at the cold site is possible because they have a higher absolute sprint speed because of their larger size and a relatively higher abundance of cover at the cold site, and differences in predation pressure may alter selective pressures on reproductive investment.     

Tackling ‘ghost nets’: Local solutions to a global issue in northern Australia

Summary We describe the inception and development of the Carpentaria Ghost Nets Programme, located across the Gulf of Carpentaria, which spans north Queensland and the Northern Territory. The program has grown from a small grass‐roots idea addressing issues around marine debris to become an internationally acknowledged project headed by the Northern Gulf Resource Management Group. This program, involving more than 18 Indigenous communities and over 90 Indigenous rangers, has become a way of building bridges across cultures and communities for a shared, common interest in land and sea protection. By incorporating traditional values and approaches to managing an international issue at a local scale, we have worked with local communities to increase pride and ownership on country whilst providing transferrable job skills. Success of this program ultimately depends upon the continued active engagements of the Indigenous communities and ranger groups. The project aims to address the fundamental issue of tackling the ghost nets problem at its source through cross‐cultural interactions between rangers and fishermen, increasing public, political and economic awareness, and ultimately reducing the incidental and intentional loss of fishing nets that act as ghost nets and result in tremendous biological, cultural and economic impacts. By putting in place long term management measures to ensure monitoring efforts, we can track ghost net debris arrival and changes through time, providing information to policy and cultural changes at regional and international scales.     

Phylogenetic evidence for a single,ancestral origin of a ‘true’ worker caste in termites

Phylogenetic analysis based on sequence variation in mitochondrial large‐subunit rRNA and cytochrome oxidase II genes was used to investigate the evolutionary relationships among termite families. Maximum likelihood and parsimony analyses of a combined nucleotide data set yield a single well‐supported topology, which is: (((((Termitidae, Rhinotermitidae), Serritermitidae), Kalotermitidae), (Hodotermitidae, Termopsidae)), Mastotermitidae). Although some aspects of this topology are consistent with previous schemes, overall it differs from any published. Optimization of ‘true’ workers onto the tree suggests that this caste originated once, early in the history of the lineage and has been lost secondarily twice. This scenario differs from the more widely accepted notion that workers are derived and of polyphyletic origin and that extant pseudergates, or ‘false’ workers, are their developmentally unspecialized ancestor caste. Worker gains and losses covary directly in number and direction with shifts in ‘ecological life type’. A test for correlated evolution which takes phylogenetic structure into account indicates that this pattern is of biological significance and suggests that the variable occurrence of a worker caste in termites has ecological determinants, apparently linked to differences in feeding and nesting habits.     

What can we Learn from Patients’ Ethical Thinking about the right ‘not to know’ in Genomics? Lessons from Cancer Genetic Testing for Genetic Counselling

This article is based on a qualitative empirical project about a distinct kinship group who were among the first identified internationally as having a genetic susceptibility to cancer (Lynch Syndrome). 50 were invited to participate (42 were tested; eight declined genetic testing). 15, who had all accepted testing, were interviewed. They form a unique case study. This study aimed to explore interviewees’ experiences of genetic testing and how these influenced their family relationships. A key finding was that participants framed the decision to be tested as ‘common sense’; the idea of choice around the decision was negated and replaced by a moral imperative to be tested. Those who did not follow ‘common sense’ were judged to be imprudent. Family members who declined testing were discussed negatively by participants. The article addresses what is ethically problematic about how test decliners were discussed and whether these ethical concerns extend to others who are offered genetic testing. Discussions showed that genetic testing was viewed as both an autonomous choice and a responsibility. Yet the apparent conflict between the right to autonomy and the moral imperative of responsibility allowed participants to defend test decliners’ decisions by expressing a preference for or defending choice over responsibility. The ‘right not to know’ seemed an important moral construct to help ethically manage unpopular decisions made by close family who declined testing. In light of this research, the erosion of the ‘right not to know’ in the genomic age could have subtle yet profound consequences for family relationships.