Here is the evidence,now what is the hypothesis? The complementary roles of inductive and hypothesis‐driven science in the post‐genomic era

It is considered in some quarters that hypothesis-driven methods are the only valuable, reliable or significant means of scientific advance. Data-driven or 'inductive' advances in scientific knowledge are then seen as marginal, irrelevant, insecure or wrong-headed, while the development of technology--which is not of itself 'hypothesis-led' (beyond the recognition that such tools might be of value)--must be seen as equally irrelevant to the hypothetico-deductive scientific agenda. We argue here that data- and technology-driven programmes are not alternatives to hypothesis-led studies in scientific knowledge discovery but are complementary and iterative partners with them. Many fields are data-rich but hypothesis-poor. Here, computational methods of data analysis, which may be automated, provide the means of generating novel hypotheses, especially in the post-genomic era.     

Are island‐like systems biologically similar to islands? A review of the evidence

Islands are geographically defined as land masses completely surrounded by water, and island systems have been used as models for many biogeographic, ecological, and evolutionary theories ever since Darwin's pioneering efforts. However, their biological definition is complex. Over the past few decades these theories have been applied to many study systems that only share some geographic features with island systems. These features include spatial fragmentation, limited area, spatial and temporal isolation from adjacent parts of the system, and low connectivity between different parts within the system, to mention just a few. These systems vary in their form, the matrix that surrounds them, the factors defining their borders, the extent of insularity they impose on the different taxa, and their geological similarity to different types of actual islands. Here, I seek to understand whether such island‐like systems (ILS) function biologically as true islands. In the first part, I describe the wide diversity of ILS suggested in the literature and the variation in the features that define their insularity. In the second part, I review the extent to which the main theories of island biology are applicable to these systems: species–area and species–isolation relationships, community composition, evolutionary radiations, and the extent of endemism and genetic diversity. In the third and final part, I suggest a new conceptual framework within which to classify and study the biology of ILS, as well as practical future research directions. I conclude that the term ‘biological island’ is a multi‐faceted concept, loosely related to its geographical definition. As ILS are often less isolated than true islands, and their biological patterns are only partly similar to those of true islands (and even this is true only for some ILS) the use of the term ‘island’ to describe any isolated habitat is therefore inappropriate.     

What is the function of neuronal AP‐3?

Neurotransmission requires the proper organization and rapid recycling of synaptic vesicles. Rapid retrieval has been suggested to occur either by kiss-and-stay or kiss-and-run mechanisms, whereas classical recycling is mediated by clathrin-dependent endocytosis. Molecular coats are key components in the selection of cargos, AP-2 (adaptor protein 2) playing a prominent role in synaptic vesicle endocytosis. Another coat protein, AP-3, has been implicated in synaptic vesicle biogenesis and in the generation of secretory and lysosomal-related organelles. In the present review, we will particularly focus on the recent data concerning the recycling of synaptic vesicles and the function of AP-3 and the v-SNARE (vesicular soluble N-ethylmaleimide-sensitive fusion protein-attachment protein receptor) TI-VAMP (tetanus neurotoxin-insensitive vesicle-associated membrane protein) in these processes. We propose that AP-3 plays an important regulatory role in neurons which contributes to the basal and stimulated exocytosis of synaptic vesicles.     

Have we underestimated the importance of humans in the biogeography of free‐living terrestrial microorganisms?

The role of humans in the global dispersal of free‐living terrestrial microorganisms has received surprisingly little attention in the literature, compared with the frequent discussions of human dispersal for aquatic microbes. Here I argue that this area needs more study, using examples from the ecology of testate amoebae to illustrate the nature of the problem. The techniques of molecular ecology now make these ideas open to investigation in a way that would have been difficult in the past, and, in the case of testate amoebae, palaeoecological approaches may also be valuable.     

What is the mechanism of ParA‐mediated DNA movement?

The stable maintenance of low‐copy‐number plasmids requires active partitioning, with the most common mechanism in prokaryotes involving the ATPase ParA. ParA proteins undergo intricate spatiotemporal relocations across the nucleoid, dynamics that function to position plasmids at equally spaced intervals. This spacing naturally guarantees equal partitioning of plasmids to each daughter cell. However, the fundamental mechanism linking ParA dynamics with regular plasmid positioning has proved difficult to dissect. In this issue of Molecular Microbiology, Vecchiarelli et al. report on a time‐delay mechanism that allows a slow cycling between the nucleoid‐bound and unbound forms of ParA. The authors also propose a mechanism for plasmid movement that does not rely on ParA polymerization.     

Who is the ocean? Preface to the future seas 2030 special issue

Reviews in Fish Biology and Fisheries -     

Antixenosis phloem‐based resistance to aphids: is it the rule?

1. The concept of plant defence syndrome states that plant species growing in similar biotic or abiotic constraints should have convergent defensive traits. This article is a first step to test the prediction of this concept, by conducting experiments on wild Solanum species (or accessions) that originated from the Andes. The nature and the tissue localisation of the resistance of five wild Solanum species known to be resistant against the aphids Myzus persicae and Macrosiphum euphorbiae were determined by olfactometry and electrical penetration graph experiments. 2. Volatile organic compounds may contribute to wild Solanum resistance, depending on Solanum accessions and aphid species. Volatiles of S. bukasovii and S. stoloniferum PI 275248 were not attractive to M. persicae, whereas S. bukasovii was repulsive to M. euphorbiae. In contrast, volatiles of S. stoloniferum PI 275248 were attractive for M. euphorbiae. 3. Some wild Solanum species presented a generalised resistance in all plant tissues, so as for S. bukasovii and S. stoloniferum PI 275248 against M. persicae. However, except for S. bukasovii which was susceptible to M. euphorbiae, all tested Solanum species presented a phloem‐based antixenosis resistance against the two aphid species. 4. A review of articles focused on the nature of resistance of wild Solanum species against aphids corroborated with our results, i.e. a phloem‐based antixenosis resistance against aphids is the rule concerning the system aphids–wild Solanum species.     

Correction to: Who is the ocean? Preface to the future seas 2030 special issue

Reviews in Fish Biology and Fisheries - A correction to this paper has been published: https://doi.org/10.1007/s11160-021-09657-9     

Proteomics: is it an approach to understand the progression of chronic lung disorders?

Tissue injury, mediated by pathologically elevated production and action of various serine- and matrix metalloproteinases (MMPs), is a hallmark of chronic inflammatory airway diseases (CIAD). CIAD includes such diseases as bronchial asthma, bronchiectasis, and chronic obstructive pulmonary disease. Tissue injury, as a consequence of chronic inflammation, can disturb the relevant repair mechanisms and also result in irreversible alteration of lung architecture. By use of proteomic methods, we analyzed proteinase cascades as an initiator of tissue destruction in CIAD. The present results revealed that elevated levels of MMP-8, -13, -14, and -2, mainly in active forms, can also be detected in CIAD BALFs. Enhanced levels of different active MMPs evidently reflect ongoing tissue-destructive inflammation and airway remodeling occurring in CIAD lung. An inverse correlation between BALF MMP-8 levels and activation degree and airflow obstruction in bronchial asthma tissue injury was shown for the first time. This strongly indicates that chronic peri-inflammatory tissue injury is a main cause of decline of lung functional capacity. Together, these data suggest that the serine and MMP proteinase network is an important feature in predicting clinical worsening of airway obstruction in CIAD. Activation of elevated MMPs seems to have a common profile for all studied CIAD, but different lung disorders react differently to ICS treatment.     

Who can open the flower? Assessment of the flower opening force of mammal‐pollinated Mucuna macrocarpa

Effective pollinators in Fabaceae species with papillionaceous flowers should have sufficient force to open the petals and expose the stamens and pistils from the keel petals. Here, we assessed the force that is required (operative force) to open the petals of the mammal‐pollinated Mucuna macrocarpa, in parallel with estimating the force of bee species. The operative force of M. macrocarpa was quantified by a digital force gauge and the force of three bee species that frequent these flowers was estimated from body mass. The operative force was 1.635 ± 0.146 (mean ± SD) newton (N). This force was far larger than that estimated for the largest bee in the study area. In addition, the operative force of M. macrocarpa was 16–409 times greater than that of bee‐pollinated plants. Our results demonstrate that the operative force of M. macrocarpa flowers is adapted to mammalian openers, preventing potential nectar robbers.     

Duodenal expression of the epithelial calcium transporter gene TRPV6: is there evidence for Vitamin D-dependence in humans?

Intestinal absorption of dietary calcium is regulated by 1,25-dihydroxycholecalciferol (1,25(OH)(2)D(3)) in humans and in experimental animals but interspecies differences in responsiveness to 1,25(OH)(2)D(3) are found, possibly due to differences in the promoters of genes for intestinal calcium transport proteins or of the Vitamin D receptor (VDR). The epithelial calcium transporter, known as ECAC2 or CAT1, the product of the TRPV6 gene expressed in proximal intestinal enterocytes, is the first step in calcium absorption and studies in mice have shown that its expression is Vitamin D-dependent. In contrast in man, we showed that duodenal TRPV6 mRNA expression was independent of blood 1,25(OH)(2)D(3), although in Caco-2 cells, 1,25(OH)(2)D(3)-dependent changes have been demonstrated. We sought to explain these findings. A consensus Vitamin D response element in the mouse gene is absent in the human gene. We re-analysed our duodenal expression data according to a CDX2-site polymorphism in the VDR promoter. Mean TRPV6 expression was the same, but there was evidence of different responsiveness to 1,25(OH)(2)D(3). In the GG genotype group, but not the AG, duodenal TRPV6 expression increased with 1,25(OH)(2)D(3). We postulate that lower levels of expression of VDR in the GG group produce greater sensitivity to 1,25(OH)(2)D(3).     

Who was the first? An experimental application of carnivore and hominid overlapping marks at the Pleistocene archaeological sites

There are many types of evidence that provide information about methods for obtaining animal nutrients. Several researchers suggest that the main element to be considered is the skeletal representation of the different species identified in the faunal assemblage. This element must be associated to the animals’ age at death and the localisation of processing marks of the carcasses (both those of anthropic origin and those produced by carnivores). Occasionally, these marks coincide on the same point of the bone, giving cause for overlapping marks. These marks can be considered an aid more to identify the anthropic manner for obtaining animal recourses. However, these cases are very unusual at archaeological sites, and it is not always easy to identify which of the two predators has obtained the prey first. Through the experimental process presented in this article, we have observed diagnostic elements on overlapping marks that show the action sequence of the predators (hominids and carnivores) on carcasses. These experimental criteria were applied to different archaeological sites of the Lower and Middle Pleistocene in the Iberian Peninsula: Bolomor Cave (Valencia, Spain) and level TD10-1 and TD6-2 of Gran Dolina (Atapuerca, Burgos). In these assemblages, we were able to distinguish hunting and scavenging events through overlapping marks, providing a new element to the general interpretation of these sites.     

Regulation of mating genes during arbuscular mycorrhizal isolate co-existence—where is the evidence?

A recent study published by Mateus et al. [1] claimed that 18 “mating-related” genes are differentially expressed in the model arbuscular mycorrhizal fungus (AMF) Rhizophagus irregularis when genetically distinct fungal strains co-colonize a host plant. To clarify the level of evidence for this interesting conclusion, we first aimed to validate the functional annotation of these 18 R. irregularis genes using orthology predictions. These analyses revealed that, although sequence relationship exists, only 2 of the claimed 18 R. irregularis mating genes are potential orthologues to validated fungal mating genes. We also investigated the RNA-seq data from Mateus et al. [1] using classical RNA-seq methods and statistics. This analysis found that the over-expression during strain co-existence was not significant at the typical cut-off of the R. irregularis strains DAOM197198 and B1 in plants. Overall, we do not find convincing evidence that the genes involved have functions in mating, or that they are reproducibly up or down regulated during co-existence in plants.Subject terms: Microbiology, Environmental sciences     

Molecular and quantitative trait variation across the native range of the invasive species Hypericum canariense: evidence for ancient patterns of colonization via pre‐adaptation?

To understand the success of invasive species, it is important to know whether colonization events are facilitated by adaptive evolution or are limited to sites where a species is pre-adapted to thrive. Studies of the ancient colonization patterns of an invader in its native range provide an opportunity to examine its natural history of adaptation and colonization. This study uses molecular (internal transcribed spacer sequence and amplified fragment length polymorphism) and common garden approaches to assess the ancient patterns of establishment and quantitative trait evolution in the invasive shrub Hypericum canariense. This species has an unusually small and discrete native range in the Canary Islands. Our data reveal two genetic varieties with divergent life histories and different colonization patterns across the islands. Although molecular divergence within each variety is large (pairwise FST from 0.18 to 0.32 between islands) and nearly as great as divergence between them, life-history traits show striking uniformity within varieties. The discrepancy between molecular and life-history trait divergence points to the action of stabilizing selection within varieties and the influence of pre-adaptation on patterns of colonization. The colonization history of H. canariense reflects how the relationship between selective environments in founding and source populations can dictate establishment by particular lineages and their subsequent evolutionary stasis or change.     

Developmental programming of reproduction and fertility: what is the evidence?

The concept of the foetal/developmental origins of adult disease has been around for ~20 years and from the original epidemiological studies in human populations much more evidence has accumulated from the many studies in animal models. The majority of these have focused upon the role of early dietary intake before conception, through gestation and/or lactation and subsequent interactions with the postnatal environment, e.g. dietary and physical activity exposures. Whilst a number of theoretical models have been proposed to place the experimental data into a biological context, the underlying phenomena remain the same; developmental deficits (of single (micro) nutrients) during critical or sensitive periods of tissue growth alter the developmental pathway to ultimately constrain later functional capacity when the individual is adult. Ageing, without exception, exacerbates any programmed sequelae. Thus, adult phenotypes that have been relatively easy to characterise (e.g. blood pressure, insulin sensitivity, body fat mass) have received most attention in the literature. To date, relatively few studies have considered the effect of differential early environmental exposures on reproductive function and fecundity in predominantly mono-ovular species such as the sheep, cow and human. The available evidence suggests that prenatal insults, undernutrition for example, have little effect on lifetime reproductive capacity despite subtle effects on the hypothalamic-pituitary-gonadal axis and gonadal progenitor cell complement. The postnatal environment is clearly important, however, since neonatal/adolescent growth acceleration (itself not independent from prenatal experience) has been shown to significantly influence fecundity in farm animals. The present paper will expand these interesting areas of investigation and review the available evidence regarding developmental programming of reproduction and fertility. However, it appears there is little strong evidence to indicate that offspring fertility and reproductive senescence in the human and in farm animal species are overtly affected by prenatal nutrient exposure. Nevertheless, it is clear that the developing gonad is sensitive to its immediate environment but more detailed investigation is required to specifically test the long-term consequences of nutritional perturbations during pregnancy on adult reproductive well-being.