Comparative genomics of vertebrate Fox cluster loci

BACKGROUND: Vertebrate genomes contain numerous duplicate genes, many of which are organised into paralagous regions indicating duplication of linked groups of genes. Comparison of genomic organisation in different lineages can often allow the evolutionary history of such regions to be traced. A classic example of this is the Hox genes, where the presence of a single continuous Hox cluster in amphioxus and four vertebrate clusters has allowed the genomic evolution of this region to be established. Fox transcription factors of the C, F, L1 and Q1 classes are also organised in clusters in both amphioxus and humans. However in contrast to the Hox genes, only two clusters of paralogous Fox genes have so far been identified in the Human genome and the organisation in other vertebrates is unknown. RESULTS: To uncover the evolutionary history of the Fox clusters, we report on the comparative genomics of these loci. We demonstrate two further paralogous regions in the Human genome, and identify orthologous regions in mammalian, chicken, frog and teleost genomes, timing the duplications to before the separation of the actinopterygian and sarcopterygian lineages. An additional Fox class, FoxS, was also found to reside in this duplicated genomic region. CONCLUSION: Comparison of loci identifies the pattern of gene duplication, loss and cluster break up through multiple lineages, and suggests FoxS1 is a likely remnant of Fox cluster duplication

Comparative genomics of Lbx loci reveals conservation of identical Lbx ohnologs in bony vertebrates.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: Lbx/ladybird genes originated as part of the metazoan cluster of Nk homeobox genes. In all animals investigated so far, both the protostome genes and the vertebrate Lbx1 genes were found to play crucial roles in neural and muscle development. Recently however, additional Lbx genes with divergent expression patterns were discovered in amniotes. Early in the evolution of vertebrates, two rounds of whole genome duplication are thought to have occurred, during which 4 Lbx genes were generated. Which of these genes were maintained in extant vertebrates, and how these genes and their functions evolved, is not known. RESULTS: Here we searched vertebrate genomes for Lbx genes and discovered novel members of this gene family. We also identified signature genes linked to particular Lbx loci and traced the remnants of 4 Lbx paralogons (two of which retain Lbx genes) in amniotes. In teleosts, that have undergone an additional genome duplication, 8 Lbx paralogons (three of which retain Lbx genes) were found. Phylogenetic analyses of Lbx and Lbx-associated genes show that in extant, bony vertebrates only Lbx1- and Lbx2-type genes are maintained. Of these, some Lbx2 sequences evolved faster and were probably subject to neofunctionalisation, while Lbx1 genes may have retained more features of the ancestral Lbx gene. Genes at Lbx1 and former Lbx4 loci are more closely related, as are genes at Lbx2 and former Lbx3 loci. This suggests that during the second vertebrate genome duplication, Lbx1/4 and Lbx2/3 paralogons were generated from the duplicated Lbx loci created during the first duplication event. CONCLUSION: Our study establishes for the first time the evolutionary history of Lbx genes in bony vertebrates, including the order of gene duplication events, gene loss and phylogenetic relationships. Moreover, we identified genetic hallmarks for each of the Lbx paralogons that can be used to trace Lbx genes as other vertebrate genomes become available. Significantly, we show that bony vertebrates only retained copies of Lbx1 and Lbx2 genes, with some Lbx2 genes being highly divergent. Thus, we have established a base on which the evolution of Lbx gene function in vertebrate development can be evaluated

Pollination by hoverflies in the Anthropocene

Pollinator declines, changes in land use and climate-induced shifts in phenology have the potential to seriously affect ecosystem function and food security by disrupting pollination services provided by insects. Much of the current research focuses on bees, or groups other insects together as ‘non-bee pollinators’, obscuring the relative contribution of this diverse group of organisms. Prominent among the ‘non-bee pollinators’ are the hoverflies, known to visit at least 72% of global food crops, which we estimate to be worth around US$300 billion per year, together with over 70% of animal pollinated wildflowers. In addition, hoverflies provide ecosystem functions not seen in bees, such as crop protection from pests, recycling of organic matter and long-distance pollen transfer. Migratory species, in particular, can be hugely abundant and unlike many insect pollinators, do not yet appear to be in serious decline. In this review, we contrast the roles of hoverflies and bees as pollinators, discuss the need for research and monitoring of different pollinator responses to anthropogenic change and examine emerging research into large populations of migratory hoverflies, the threats they face and how they might be used to improve sustainable agriculture

A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila.

Insects determine their body segments in two different ways. Short-germband insects, such as the flour beetle Tribolium castaneum, use a molecular clock to establish segments sequentially. In contrast, long-germband insects, such as the vinegar fly Drosophila melanogaster, determine all segments simultaneously through a hierarchical cascade of gene regulation. Gap genes constitute the first layer of the Drosophila segmentation gene hierarchy, downstream of maternal gradients such as that of Caudal (Cad). We use data-driven mathematical modelling and phase space analysis to show that shifting gap domains in the posterior half of the Drosophila embryo are an emergent property of a robust damped oscillator mechanism, suggesting that the regulatory dynamics underlying long- and short-germband segmentation are much more similar than previously thought. In Tribolium, Cad has been proposed to modulate the frequency of the segmentation oscillator. Surprisingly, our simulations and experiments show that the shift rate of posterior gap domains is independent of maternal Cad levels in Drosophila. Our results suggest a novel evolutionary scenario for the short- to long-germband transition and help explain why this transition occurred convergently multiple times during the radiation of the holometabolan insects.MINECO BFU2009-10184/BFU2012-33775/SEV-2012-0208 European Commission FP7/KBBE-2011/5/289434 La Caixa Savings Bank (PhD fellowship to BV) KLI Klosterneuburg (PhD Writing-up & Postdoctoral Fellowships to BV) Wissenschaftskolleg zu Berlin (Wiko) (Fellowships to JJ and AC

Adaptive strategies of high-flying migratory hoverflies in response to wind currents: Flight behaviour of migrant hoverflies

Large migrating insects, flying at high altitude, often exhibit complex behaviour. They frequently elect to fly on winds with directions quite different from the prevailing direction, and they show a degree of common orientation, both of which facilitate transport in seasonally beneficial directions. Much less is known about the migration behaviour of smaller (10-70 mg) insects. To address this issue, we used radar to examine the high-altitude flight of hoverflies (Diptera: Syrphidae), a group of day-active, medium-sized insects commonly migrating over the UK. We found that autumn migrants, which must move south, did indeed show migration timings and orientation responses that would take them in this direction, despite the unfavourability of the prevailing winds. Evidently, these hoverfly migrants must have a compass (probably a time-compensated solar mechanism), and a means of sensing the wind direction (which may be determined with sufficient accuracy at ground level, before take-off). By contrast, hoverflies arriving in the UK in spring showed weaker orientation tendencies, and did not correct for wind drift away from their seasonally adaptive direction (northwards). However, the spring migrants necessarily come from the south (on warm southerly winds), so we surmise that complex orientation behaviour may not be so crucial for the spring movements

Mechanisms and consequences of partial migration in insects

Partial migration, where a proportion of a population migrates, while other individuals remain resident, is widespread across most migratory lineages. However, the mechanisms driving individual differences in migratory tendency are still relatively poorly understood in most taxa, but may be influenced by morphological, physiological, and behavioral traits, controlled by phenotypic plasticity and the underlying genetic complex. Insects differ from vertebrates in that partial migration is often associated with pronounced morphological differences between migratory and resident phenotypes, such as wing presence or length. In contrast, the mechanisms influencing migratory tendency in wing-monomorphic insects is less clear. Insects are the most abundant and diverse group of terrestrial migrants, with trillions of animals moving across the globe annually, and understanding the drivers and extent of partial migration across populations will have considerable implications for ecosystem services, such as the management of pests and the conservation of threatened or beneficial species. Here, we present an overview of our current but incomplete knowledge of partial migration in insects. We discuss the factors that lead to the maintenance of partial migration within populations, and the conditions that may influence individual decision making, particularly in the context of individual fitness and reproductive tradeoffs. Finally, we highlight current gaps in knowledge and areas of future research that should prove fruitful in understanding the ecological and evolutionary drivers, and consequences of partial migration in insects

Adaptive strategies of high-flying migratory hoverflies in response to wind currents

Large migrating insects, flying at high altitude, often exhibit complex behaviour. They frequently elect to fly on winds with directions quite different from the prevailing direction, and they show a degree of common orientation, both of which facilitate transport in seasonally beneficial directions. Much less is known about the migration behaviour of smaller (10–70 mg) insects. To address this issue, we used radar to examine the high-altitude flight of hoverflies (Diptera: Syrphidae), a group of day-active, medium-sized insects commonly migrating over the UK. We found that autumn migrants, which must move south, did indeed show migration timings and orientation responses that would take them in this direction, despite the unfavourability of the prevailing winds. Evidently, these hoverfly migrants must have a compass (probably a time-compensated solar mechanism), and a means of sensing the wind direction (which may be determined with sufficient accuracy at ground level, before take-off). By contrast, hoverflies arriving in the UK in spring showed weaker orientation tendencies, and did not correct for wind drift away from their seasonally adaptive direction (northwards). However, the spring migrants necessarily come from the south (on warm southerly winds), so we surmise that complex orientation behaviour may not be so crucial for the spring movements

The TGF-β/Smad Repressor TG-Interacting Factor 1 (TGIF1) Plays a Role in Radiation-Induced Intestinal Injury Independently of a Smad Signaling Pathway

Despite advances in radiation delivery protocols, exposure of normal tissues during the course of radiation therapy remains a limiting factor of cancer treatment. If the canonical TGF-β/Smad pathway has been extensively studied and implicated in the development of radiation damage in various organs, the precise modalities of its activation following radiation exposure remain elusive. In the present study, we hypothesized that TGF-β1 signaling and target genes expression may depend on radiation-induced modifications in Smad transcriptional co-repressors/inhibitors expressions (TGIF1, SnoN, Ski and Smad7). In endothelial cells (HUVECs) and in a model of experimental radiation enteropathy in mice, radiation exposure increases expression of TGF-β/Smad pathway and of its target gene PAI-1, together with the overexpression of Smad co-repressor TGIF1. In mice, TGIF1 deficiency is not associated with changes in the expression of radiation-induced TGF-β pathway-related transcripts following localized small intestinal irradiation. In HUVECs, TGIF1 overexpression or silencing has no influence either on the radiation-induced Smad activation or the Smad3-dependent PAI-1 overexpression. However, TGIF1 genetic deficiency sensitizes mice to radiation-induced intestinal damage after total body or localized small intestinal radiation exposure, demonstrating that TGIF1 plays a role in radiation-induced intestinal injury. In conclusion, the TGF-β/Smad co-repressor TGIF1 plays a role in radiation-induced normal tissue damage by a Smad-independent mechanism

An analysis of sickness absence in chronically ill patients receiving Complementary and Alternative Medicine: A longterm prospective intermittent study

BACKGROUND: The popularity of complementary and alternative medicine (CAM) has led to a growing amount of research in this area. All the same little is known about the effects of these special treatments in every-day practice of primary care, delivered by general practitioners within the health insurance system. From 1994 to 2000 more than 20 German Company health insurances initiated the first model project on CAM according to the German social law. Aim of this contribution is to investigate the effectiveness of multi-modal CAM on chronic diseases within primary health care. METHODS: A long-term prospective intermittent study was conducted including 44 CAM practitioners and 1221 self-selected chronically ill patients (64% women) of whom 441 were employed. Main outcome measure is sick-leave, controlled for secular trends and regression-to-the mean and self-perceived health status. RESULTS: Sick-leave per year of 441 patients at work increased from 22 (SD ± 45.2) to 31 (± 61.0) days within three years prior to intervention, and decreased to 24 (± 55.6) in the second year of treatment, sustaining at this level in the following two years. Detailed statistical analysis show that this development exceeds secular trends and the regression-toward-the-mean effect. Sick-leave reduction was corroborated by data on self-reported improvement of patients' health status. CONCLUSION: Results of this longterm observational study show a reduction of sick leave in chronically ill patients after a complex multimodal CAM intervention. However, as this is an uncontrolled observational study efficacy of any specific CAM treatment can not be proven. The results might indicate an general effectiveness of CAM in primary care, worthwhile further investigations. Future studies should identify the most suitable patients for CAM practices, the most appropriate and safe treatments, provide information on the magnitude of the effects to facilitate subsequent definitive randomised controlled studies that will help to position complementary and alternative medicine in health care