The functional response of a generalist predator

Peer reviewedPublisher PD

On the basic computational structure of gene regulatory networks

Gene regulatory networks constitute the first layer of the cellular computation for cell adaptation and surveillance. In these webs, a set of causal relations is built up from thousands of interactions between transcription factors and their target genes. The large size of these webs and their entangled nature make difficult to achieve a global view of their internal organisation. Here, this problem has been addressed through a comparative study for {\em Escherichia coli}, {\em Bacillus subtilis} and {\em Saccharomyces cerevisiae} gene regulatory networks. We extract the minimal core of causal relations, uncovering the hierarchical and modular organisation from a novel dynamical/causal perspective. Our results reveal a marked top-down hierarchy containing several small dynamical modules for \textit{E. coli} and \textit{B. subtilis}. Conversely, the yeast network displays a single but large dynamical module in the middle of a bow-tie structure. We found that these dynamical modules capture the relevant wiring among both common and organism-specific biological functions such as transcription initiation, metabolic control, signal transduction, response to stress, sporulation and cell cycle. Functional and topological results suggest that two fundamentally different forms of logic organisation may have evolved in bacteria and yeast.Comment: This article is published at Molecular Biosystems, Please cite as: Carlos Rodriguez-Caso, Bernat Corominas-Murtra and Ricard V. Sole. Mol. BioSyst., 2009, 5 pp 1617--171

Reduced apoptotic levels in squamous but not basal cell carcinomas correlates with detection of cutaneous human papillomavirus

We have investigated the apoptotic levels and expression of the apoptotic inducer Bak in non-melanoma skin cancers. Squamous cell carcinomas of known human papillomavirus status from immunocompetent patients were analysed for the expression of the Bak protein, and the expression profile was compared both to the presence of apoptotic cells and the proliferation marker Ki-67. We demonstrate an inverse correlation between human papillomavirus positivity and Bak expression in squamous cell carcinomas, with concomitantly fewer apoptoic cells being detected in the human papillomavirus positive tumours. Bak expression was not observed in basal cell carcinomas irrespective of human papillomavirus status, suggesting that Bak only plays a role in signalling apoptosis in squamous, but not basal, cell cancers. No differences were observed in the proliferation rates between papillomavirus positive and negative squamous cell tumours. However, a significant decrease in the number of apoptotic cells was observed in human papillomavirus-positive squamous cell carcinomas which suggests that the virus may have significantly altered the relationship between proliferation and apoptosis in a proportion of these tumours

Towards a more-than-human approach to tree health

New ways of working and thinking in relation to tree health and plant biosecurity are required. The climate is changing and the number of pests and diseases is increasing. A review of the social science literature on plant health reveals that scholars are not quite sure what this ‘new thinking’ might entail. In this chapter, we begin the process of re-imagining tree health by starting with the trees and our research engagement with them. Trees are acknowledged in this chapter as never static, but rather fluid, shape-shifters, translated across time and space. Health and disease are revealed as relational, and a fixed approach to tree health management won’t work. In a world of rapid change, this way of working is not just relevant for trees

The Test Your Memory cognitive screening tool: sociodemographic and cardiometabolic risk correlates in a population-based study of older British men.

OBJECTIVE: This study aimed to examine the association of Test Your Memory (TYM)-defined cognitive impairment groups with known sociodemographic and cardiometabolic correlates of cognitive impairment in a population-based study of older adults. METHODS: Participants were members of the British Regional Heart Study, a cohort across 24 British towns initiated in 1978-1980. Data stemmed from 1570 British men examined in 2010-2012, aged 71-92 years. Sociodemographic and cardiometabolic factors were compared between participants defined as having TYM scores in the normal cognitive ageing, mild cognitive impairment (MCI) and severe cognitive impairment (SCI) groups, defined as ≥46 (45 if ≥80 years of age), ≥33 and <33, respectively. RESULTS: Among 1570 men, 636 (41%) were classified in the MCI and 133 (8%) in the SCI groups. Compared with participants in the normal cognitive ageing category, individuals with SCI were characterized primarily by lower socio-economic position (odds ratio (OR) = 6.15, 95% confidence interval (CI) 4.00-9.46), slower average walking speed (OR = 3.36, 95% CI 2.21-5.10), mobility problems (OR = 4.61, 95% CI 3.04-6.97), poorer self-reported overall health (OR = 2.63, 95% CI 1.79-3.87), obesity (OR = 2.59, 95% CI 1.72-3.91) and impaired lung function (OR = 2.25, 95% CI 1.47-3.45). A similar albeit slightly weaker pattern was observed for participants with MCI. CONCLUSION: Sociodemographic and lifestyle factors as well as adiposity measures, lung function and poor overall health are associated with cognitive impairments in late life. The correlates of cognitive abilities in the MCI and SCI groups, as defined by the TYM, resemble the risk profile for MCI and Alzheimer's disease outlined in current epidemiological models. © 2016 The Authors. International Journal of Geriatric Psychiatry Published by John Wiley & Sons, Ltd

Gas kinematics in powerful radio galaxies at z ∼2: Energy supply from star formation, AGN, and radio jets⋆

We compare the kinetic energy and momentum injection rates from intense star formation, bolometric AGN radiation, and radio jets with the kinetic energy and momentum observed in the warm ionized gas in 24 powerful radio galaxies at z~2. These galaxies are amongst our best candidates for being massive galaxies near the end of their active formation period, when intense star formation, quasar activity, and powerful radio jets all co-exist. All galaxies have VLT/SINFONI imaging spectroscopy of the rest-frame optical line emission, showing emission-line regions with large velocity offsets (up to 1500 km/s) and line widths (typically 800-1000 km/s) consistent with very turbulent, often outflowing gas. As part of the HeRGE sample, they also have FIR estimates of the star formation and quasar activity obtained with Herschel/PACS and SPIRE, which enables us to measure the relative energy and momentum release from each of the three main sources of feedback in massive, star-forming AGN host galaxies during their most rapid formation phase. We find that star formation falls short by factors 10-1000 of providing the energy and momentum necessary to power the observed gas kinematics. The obscured quasars in the nuclei of these galaxies provide enough energy and momentum in about half of the sample, however, only if these are transfered to the gas relatively efficiently. We compare with theoretical and observational constraints on the efficiency of the energy and momentum transfer from jet and AGN radiation, which advocates that the radio jet is the main driver of the gas kinematics.Comment: A&A accepted. Comments welcom

Impacts of climate change on plant diseases – opinions and trends

There has been a remarkable scientific output on the topic of how climate change is likely to affect plant diseases in the coming decades. This review addresses the need for review of this burgeoning literature by summarizing opinions of previous reviews and trends in recent studies on the impacts of climate change on plant health. Sudden Oak Death is used as an introductory case study: Californian forests could become even more susceptible to this emerging plant disease, if spring precipitations will be accompanied by warmer temperatures, although climate shifts may also affect the current synchronicity between host cambium activity and pathogen colonization rate. A summary of observed and predicted climate changes, as well as of direct effects of climate change on pathosystems, is provided. Prediction and management of climate change effects on plant health are complicated by indirect effects and the interactions with global change drivers. Uncertainty in models of plant disease development under climate change calls for a diversity of management strategies, from more participatory approaches to interdisciplinary science. Involvement of stakeholders and scientists from outside plant pathology shows the importance of trade-offs, for example in the land-sharing vs. sparing debate. Further research is needed on climate change and plant health in mountain, boreal, Mediterranean and tropical regions, with multiple climate change factors and scenarios (including our responses to it, e.g. the assisted migration of plants), in relation to endophytes, viruses and mycorrhiza, using long-term and large-scale datasets and considering various plant disease control methods

Functional genomics of the horn fly, Haematobia irritans (Linnaeus, 1758)

<p>Abstract</p> <p>Background</p> <p>The horn fly, <it>Haematobia irritans </it>(Linnaeus, 1758) (Diptera: Muscidae) is one of the most important ectoparasites of pastured cattle. Horn flies infestations reduce cattle weight gain and milk production. Additionally, horn flies are mechanical vectors of different pathogens that cause disease in cattle. The aim of this study was to conduct a functional genomics study in female horn flies using Expressed Sequence Tags (EST) analysis and RNA interference (RNAi).</p> <p>Results</p> <p>A cDNA library was made from whole abdominal tissues collected from partially fed adult female horn flies. High quality horn fly ESTs (2,160) were sequenced and assembled into 992 unigenes (178 contigs and 814 singlets) representing molecular functions such as serine proteases, cell metabolism, mitochondrial function, transcription and translation, transport, chromatin structure, vitellogenesis, cytoskeleton, DNA replication, cell response to stress and infection, cell proliferation and cell-cell interactions, intracellular trafficking and secretion, and development. Functional analyses were conducted using RNAi for the first time in horn flies. Gene knockdown by RNAi resulted in higher horn fly mortality (protease inhibitor functional group), reduced oviposition (vitellogenin, ferritin and vATPase groups) or both (immune response and 5'-NUC groups) when compared to controls. Silencing of ubiquitination ESTs did not affect horn fly mortality and ovisposition while gene knockdown in the ferritin and vATPse functional groups reduced mortality when compared to controls.</p> <p>Conclusions</p> <p>These results advanced the molecular characterization of this important ectoparasite and suggested candidate protective antigens for the development of vaccines for the control of horn fly infestations.</p

Laboratory toxicity studies demonstrate no adverse effects of Cry1Ab and Cry3Bb1 to larvae of Adalia bipunctata (Coleoptera: Coccinellidae): the importance of study design

Scientific studies are frequently used to support policy decisions related to transgenic crops. Schmidt et al., Arch Environ Contam Toxicol 56:221–228 (2009) recently reported that Cry1Ab and Cry3Bb were toxic to larvae of Adalia bipunctata in direct feeding studies. This study was quoted, among others, to justify the ban of Bt maize (MON 810) in Germany. The study has subsequently been criticized because of methodological shortcomings that make it questionable whether the observed effects were due to direct toxicity of the two Cry proteins. We therefore conducted tritrophic studies assessing whether an effect of the two proteins on A. bipunctata could be detected under more realistic routes of exposure. Spider mites that had fed on Bt maize (events MON810 and MON88017) were used as carriers to expose young A. bipunctata larvae to high doses of biologically active Cry1Ab and Cry3Bb1. Ingestion of the two Cry proteins by A. bipunctata did not affect larval mortality, weight, or development time. These results were confirmed in a subsequent experiment in which A. bipunctata were directly fed with a sucrose solution containing dissolved purified proteins at concentrations approximately 10 times higher than measured in Bt maize-fed spider mites. Hence, our study does not provide any evidence that larvae of A. bipunctata are sensitive to Cry1Ab and Cry3Bb1 or that Bt maize expressing these proteins would adversely affect this predator. The results suggest that the apparent harmful effects of Cry1Ab and Cry3Bb1 reported by Schmidt et al., Arch Environ Contam Toxicol 56:221–228 (2009) were artifacts of poor study design and procedures. It is thus important that decision-makers evaluate the quality of individual scientific studies and do not view all as equally rigorous and relevant