VESPA: Very large-scale Evolutionary and Selective Pressure Analyses

Background: Large-scale molecular evolutionary analyses of protein coding sequences requires a number of preparatory inter-related steps from finding gene families, to generating alignments and phylogenetic trees and assessing selective pressure variation. Each phase of these analyses can represent significant challenges, particularly when working with entire proteomes (all protein coding sequences in a genome) from a large number of species. Methods: We present VESPA, software capable of automating a selective pressure analysis using codeML in addition to the preparatory analyses and summary statistics. VESPA is written in python and Perl and is designed to run within a UNIX environment. Results: We have benchmarked VESPA and our results show that the method is consistent, performs well on both large scale and smaller scale datasets, and produces results in line with previously published datasets. Discussion: Large-scale gene family identification, sequence alignment, and phylogeny reconstruction are all important aspects of large-scale molecular evolutionary analyses. VESPA provides flexible software for simplifying these processes along with downstream selective pressure variation analyses. The software automatically interprets results from codeML and produces simplified summary files to assist the user in better understanding the results

Cloud adjustment and its role in CO 2 radiative forcing and climate sensitivity: a review

Understanding the role of clouds in climate change remains a considerable challenge. Traditionally, this challenge has been framed in terms of understanding cloud feedback. However, recent work suggests that under increasing levels of atmospheric carbon dioxide, clouds not only amplify or dampen climate change through global feedback processes, but also through rapid (days to weeks) tropospheric temperature and land surface adjustments. In this article, we use the Met Office Hadley Centre climate model HadGSM1 to review these recent developments and assess their impact on radiative forcing and equilibrium climate sensitivity. We estimate that cloud adjustment contributes ~0.8 K to the 4.4 K equilibrium climate sensitivity of this particular model. We discuss the methods used to evaluate cloud adjustments, highlight the mechanisms and processes involved and identify low level cloudiness as a key cloud type. Looking forward, we discuss the outstanding issues, such as the application to transient forcing scenarios. We suggest that the upcoming CMIP5 multi-model database will allow a comprehensive assessment of the significance of cloud adjustments in fully coupled atmosphere-ocean-general-circulation models for the first time, and that future research should exploit this opportunity to understand cloud adjustments/feedbacks in non-idealised transient climate change scenarios

Hollow Fiber Bioreactors for In Vivo-like Mammalian Tissue Culture

Tissue culture has been used for over 100 years to study cells and responses ex vivo. The convention of this technique is the growth of anchorage dependent cells on the 2-dimensional surface of tissue culture plastic. More recently, there is a growing body of data demonstrating more in vivo-like behaviors of cells grown in 3-dimensional culture systems. This manuscript describes in detail the set-up and operation of a hollow fiber bioreactor system for the in vivo-like culture of mammalian cells. The hollow fiber bioreactor system delivers media to the cells in a manner akin to the delivery of blood through the capillary networks in vivo. The system is designed to fit onto the shelf of a standard CO2 incubator and is simple enough to be set-up by any competent cell biologist with a good understanding of aseptic technique. The systems utility is demonstrated by culturing the hepatocarcinoma cell line HepG2/C3A for 7 days. Further to this and in line with other published reports on the functionality of cells grown in 3-dimensional culture systems the cells are shown to possess increased albumin production (an important hepatic function) when compared to standard 2-dimensional tissue culture

Adaptive Evolution as a Predictor of Species-Specific Innate Immune Response

It has been proposed that positive selection may be associated with protein functional change. For example, human and macaque have different outcomes to HIV infection and it has been shown that residues under positive selection in the macaque TRIM5α receptor locate to the region known to influence species-specific response to HIV. In general, however, the relationship between sequence and function has proven difficult to fully elucidate, and it is the role of large-scale studies to help bridge this gap in our understanding by revealing major patterns in the data that correlate genotype with function or phenotype. In this study, we investigate the level of species-specific positive selection in innate immune genes from human and mouse. In total, we analyzed 456 innate immune genes using codon-based models of evolution, comparing human, mouse, and 19 other vertebrate species to identify putative species-specific positive selection. Then we used population genomic data from the recently completed Neanderthal genome project, the 1000 human genomes project, and the 17 laboratory mouse genomes project to determine whether the residues that were putatively positively selected are fixed or variable in these populations. We find evidence of species-specific positive selection on both the human and the mouse branches and we show that the classes of genes under positive selection cluster by function and by interaction. Data from this study provide us with targets to test the relationship between positive selection and protein function and ultimately to test the relationship between positive selection and discordant phenotypes

Self-harm in a primary care cohort of older people: incidence, clinical management, and risk of suicide and other causes of death

BACKGROUND: Self-harm is a major risk factor for suicide, with older adults (older than 65 years) having reportedly greater suicidal intent than any other age group. With the aging population rising and paucity of research focus in this age group, the extent of the problem of self-harm needs to be established. In a primary care cohort of older adults we aimed to investigate the incidence of self-harm, subsequent clinical management, prevalence of mental and physical diagnoses, and unnatural-cause mortality risk, including suicide. METHODS: The UK Clinical Practice Research Datalink contains anonymised patient records from general practice that routinely capture clinical information pertaining to both primary and secondary care services. We identified 4124 adults aged 65 years and older with a self-harm episode ascertained from Read codes recorded during 2001-14. We calculated standardised incidence and in 2854 adults with at least 12 months follow-up examined the frequency of psychiatric referrals and prescription of psychotropic medication after self-harm. We estimated prevalence of mental and physical illness diagnoses before and after self-harm and, using Cox regression in a matched cohort, we examined cause-specific mortality risks. FINDINGS: Overall incidence of self-harm in older adults aged 65 years and older was 4·1 per 10 000 person-years with stable gender-specific rates observed over the 13-year period. After self-harm, 335 (11·7%) of 2854 adults were referred to mental health services, 1692 (59·3%) were prescribed an antidepressant, and 336 (11·8%) were prescribed a tricyclic antidepressant (TCA). Having a diagnosed previous mental illness was twice as prevalent in the self-harm cohort as in the comparison cohort (prevalence ratio 2·10 [95% CI 2·03-2·17]) and with a previous physical health condition prevalence was 20% higher in the self-harm cohort compared to the comparison cohort (1·20 [1·17-1·23]). Adults from the self-harm cohort (n=2454) died from unnatural causes an estimated 20 times more frequently than the comparison cohort (n=48 921) during the first year. A markedly elevated risk of suicide (hazard ratio 145·4 [95% CI 53·9-392·3]) was observed in the self-harm cohort. INTERPRETATION: Within primary care, we have identified a group of older adults at high risk from unnatural death, particularly within the first year of self-harm. We have highlighted a high frequency of prescription of TCAs, known to be potentially fatally toxic in overdose. We emphasise the need for early intervention, careful alternative prescribing, and increased support when older adults consult after an episode of self-harm and with other health conditions. FUNDING: National Institute for Health Research Greater Manchester Patient Safety Translational Research Centre

Interactions between hydrological sensitivity, radiative cooling, stability, and low-level cloud amount feedback

This is the author accepted manuscript. The final version is available from American Meteorological Society via the DOI in this record.Low-level cloud feedbacks vary in magnitude but are positive in most climate models, due to reductions in low-level cloud fraction. This study explores the impact of surface evaporation on low-level cloud fraction feedback by performing climate change experiments with the aquaplanet configuration of the HadGEM2-A climate model, forcing surface evaporation to increase at different rates in two ways. Forcing the evaporation diagnosed in the surface scheme to increase at 7% K -1 with warming (more than doubling the hydrological sensitivity) results in an increase in global mean low-level cloud fraction and a negative global cloud feedback, reversing the signs of these responses compared to the standard experiments. The estimated inversion strength (EIS) increases more rapidly in these surface evaporation forced experiments, which is attributed to additional latent heat release and enhanced warming of the free troposphere. Stimulating a 7% K -1 increase in surface evaporation via enhanced atmospheric radiative cooling, however, results in a weaker EIS increase compared to the standard experiments and a slightly stronger low-level cloud reduction. The low-level cloud fraction response is predicted better by EIS than surface evaporation across all experiments. This suggests that surface-forced increases in evaporation increase low-level cloud fraction mainly by increasing EIS. Additionally, the results herein show that increases in surface evaporation can have a very substantial impact on the rate of increase in radiative cooling with warming, by modifying the temperature and humidity structure of the atmosphere. This has implications for understanding the factors controlling hydrological sensitivity.Mark Webb was supported by the Joint UK BEIS/Defra Met Office Hadley Centre Climate Programme 726 (GA01101)

Behavioural responses of reptile predators to invasive cane toads in tropical Australia

The ecological impact of an invasive species can depend on the behavioural responses of native fauna to the invader. For example, the greatest risk posed by invasive cane toads (Rhinella marinaBufonidae) in tropical Australia is lethal poisoning of predators that attempt to eat a toad; and thus, a predator's response to a toad determines its vulnerability. We conducted standardized laboratory trials on recently captured (toad-naïve) predatory snakes and lizards, in advance of the toad invasion front as it progressed through tropical Australia. Responses to a live edible-sized toad differed strongly among squamate species. We recorded attacks (and hence, predator mortality) in scincid, agamid and varanid lizards, and in elapid, colubrid and pythonid snakes. Larger-bodied predators were at greater risk, and some groups (elapid snakes and varanid lizards) were especially vulnerable. However, feeding responses differed among species within families and within genera. Some taxa (notably, many scincid and agamid lizards) do not attack toads; and many colubrid snakes either do not consume toads, or are physiologically resistant to the toad's toxins. Intraspecific variation in responses means that even in taxa that apparently are unaffected by toad invasion at the population level, some individual predators nonetheless may be fatally poisoned by invasive cane toads. © 2013 Ecological Society of Australia

Hollow Fiber Bioreactors for In Vivo-like Mammalian Tissue Culture

Tissue culture has been used for over 100 years to study cells and responses ex vivo. The convention of this technique is the growth of anchorage dependent cells on the 2-dimensional surface of tissue culture plastic. More recently, there is a growing body of data demonstrating more in vivo-like behaviors of cells grown in 3-dimensional culture systems. This manuscript describes in detail the set-up and operation of a hollow fiber bioreactor system for the in vivo-like culture of mammalian cells. The hollow fiber bioreactor system delivers media to the cells in a manner akin to the delivery of blood through the capillary networks in vivo. The system is designed to fit onto the shelf of a standard CO2 incubator and is simple enough to be set-up by any competent cell biologist with a good understanding of aseptic technique. The systems utility is demonstrated by culturing the hepatocarcinoma cell line HepG2/C3A for 7 days. Further to this and in line with other published reports on the functionality of cells grown in 3-dimensional culture systems the cells are shown to possess increased albumin production (an important hepatic function) when compared to standard 2-dimensional tissue culture